10-Q

UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

WASHINGTON, D.C. 20549

FORM 10-Q

(Mark One)

xQUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934

For the quarterly period ended March 31, 2019

OR

oTRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934

For the transition period from                    to

Commission File Number: 000-30319

INNOVIVA, INC.

(Exact Name of Registrant as Specified in its Charter)

Delaware	94-3265960
(State or Other Jurisdiction of Incorporation or Organization)	(I.R.S. Employer Identification No.)

2000 Sierra Point Parkway, Suite 500

Brisbane, CA 94005

(Address of Principal Executive Offices)

(650) 238-9600

(Registrant’s Telephone Number, Including Area Code)

Indicate by check mark whether the registrant: (1) has filed all reports required to be filed by Section 13 or 15(d) of the Securities Exchange Act of 1934 during the preceding 12 months (or for such shorter period that the registrant was required to file such reports), and (2) has been subject to such filing requirements for the past 90 days.  Yes x  No o

Indicate by check mark whether the registrant has submitted electronically every Interactive Data File required to be submitted pursuant to Rule 405 of Regulation S-T (§ 232.405 of this chapter) during the preceding 12 months (or for such shorter period that the registrant was required to submit such files).  Yes x  No o

Indicate by check mark whether the registrant is a large accelerated filer, an accelerated filer, a non-accelerated filer, or a smaller reporting company. See the definitions of “large accelerated filer,” “accelerated filer” and “smaller reporting company” in Rule 12b-2 of the Exchange Act.

Large accelerated filer x	Accelerated filer o
Non-accelerated filer o	Smaller reporting company o
	Emerging growth company o

If an emerging growth company, indicate by check mark if the registrant has elected not to use the extended transition period for complying with any new or revised financial accounting standards provided pursuant to Section 13(a) of the Exchange Act. o

Indicate by check mark whether the registrant is a shell company (as defined in Rule 12b-2 of the Exchange Act).  Yes o  No x

The number of shares of registrant’s common stock outstanding on April 26, 2019 was 101,262,314.

TABLE OF CONTENTS

PART I — FINANCIAL INFORMATION
Item 1. Financial Statements
Condensed Consolidated Balance Sheets as of March 31, 2019 (Unaudited) and December 31, 2018	3
Unaudited Condensed Consolidated Statements of Operations for the Three Months Ended March 31, 2019 and 2018	4
Unaudited Condensed Consolidated Statements of Comprehensive Income for the Three Months Ended March 31, 2019 and 2018	5
Unaudited Condensed Consolidated Statements of Stockholders’ Equity (Deficit) for the Three Months Ended March 31, 2019 and 2018	6
Unaudited Condensed Consolidated Statements of Cash Flows for the Three Months Ended March 31, 2019 and 2018	7
Notes to Unaudited Condensed Consolidated Financial Statements	8
Item 2. Management’s Discussion and Analysis of Financial Condition and Results of Operations	15
Item 3. Quantitative and Qualitative Disclosures About Market Risk	21
Item 4. Controls and Procedures	21
PART II. OTHER INFORMATION
Item 1. Legal Proceedings	22
Item 1A. Risk Factors	22
Item 2. Unregistered Sales of Equity Securities and Use of Proceeds	22
Item 3. Defaults Upon Senior Securities	22
Item 4. Mine Safety Disclosure	22
Item 5. Other Information	22
Item 6. Exhibits	22
Signatures	23
Exhibits

2

PART I — FINANCIAL INFORMATION

Item 1. Financial Statements

INNOVIVA, INC.

CONDENSED CONSOLIDATED BALANCE SHEETS

(In thousands, except per share data)

	March 31,			December 31,
	2019			2018
	(unaudited)			*
Assets
Current assets:
Cash and cash equivalents	$	65,151		$	62,417
Short-term marketable securities	127,027			52,491
Related party receivables from collaborative arrangements	58,639			83,286
Prepaid expenses and other current assets	702			849
Total current assets	251,519			199,043
Property and equipment, net	148			160
Operating lease right-of-use asset	1,421			—
Capitalized fees paid to a related party, net	149,443			152,899
Deferred tax assets	187,546			196,054
Other assets	37			37
Total assets	$	590,114		$	548,193
Liabilities and Stockholders’ Equity
Current liabilities:
Accounts payable	$	144		$	11
Accrued personnel-related expenses	325			470
Accrued interest payable	1,775			4,264
Other accrued liabilities	1,258			955
Operating lease liability, current portion	308			—
Total current liabilities	3,810			5,700
Long-term debt, net of discount and issuance costs	384,744			382,855
Operating lease liability, net of current portion	1,238			—
Other long-term liabilities	379			586
Commitments and contingencies
Stockholders’ equity:
Preferred stock: $0.01 par value, 230 shares authorized, no shares issued and outstanding	—			—
Common stock: $0.01 par value, 200,000 shares authorized, 101,183 and 101,098 issued and outstanding as of March 31, 2019 and December 31, 2018, respectively	1,012			1,011
Additional paid-in capital	1,257,125			1,256,267
Accumulated other comprehensive income (loss)	10			(3		)
Accumulated deficit	(1,069,902		)	(1,103,692		)
Total Innoviva stockholders’ equity	188,245			153,583
Noncontrolling interest	11,698			5,469
Total stockholders’ equity	199,943			159,052
Total liabilities and stockholders’ equity	$	590,114		$	548,193

*Condensed consolidated balance sheet as of December 31, 2018 has been derived from audited consolidated financial statements.

See accompanying notes to condensed consolidated financial statements.

3

INNOVIVA, INC.

CONDENSED CONSOLIDATED STATEMENTS OF OPERATIONS

(In thousands, except per share data)

(Unaudited)

	Three Months Ended March 31,
	2019			2018
Royalty revenue from a related party, net of amortization of capitalized fees paid to a related party of $3,456 in the three months ended March 31, 2019 and 2018	$	55,183		$	52,380
Operating expenses:
General and administrative	3,015			8,985
General and administrative - related party	—			2,700
Total operating expenses	3,015			11,685
Income from operations	52,168			40,695
Other income (expense), net	1			(3,099		)
Interest income	975			391
Interest expense	(4,617		)	(7,657		)
Income before income taxes	48,527			30,330
Income tax expense, net	8,508			—
Net income	40,019			30,330
Net income attributable to noncontrolling interest	6,229			749
Net income attributable to Innoviva stockholders	$	33,790		$	29,581
Basic net income per share attributable to Innoviva stockholders	$	0.33		$	0.29
Diluted net income per share attributable to Innoviva stockholders	$	0.31		$	0.27
Shares used to compute Innoviva basic and diluted net income per share:
Shares used to compute basic net income per share	101,059			100,604
Shares used to compute diluted net income per share	113,376			113,566

See accompanying notes to condensed consolidated financial statements.

4

INNOVIVA, INC.

CONDENSED CONSOLIDATED STATEMENTS OF COMPREHENSIVE INCOME

(In thousands)

(Unaudited)

	Three Months Ended March 31,
	2019		2018
Net income	$	40,019	$	30,330
Unrealized gain (loss) on marketable securities, net	13		(4		)
Comprehensive income	40,032		30,326
Comprehensive income attributable to noncontrolling interest	6,229		749
Comprehensive income attributable to Innoviva stockholders	$	33,803	$	29,577

See accompanying notes to condensed consolidated financial statements.

5

INNOVIVA, INC.

CONDENSED CONSOLIDATED STATEMENTS OF STOCKHOLDERS’ EQUITY (DEFICIT)

(In thousands)

(Unaudited)

	Three months ended March 31, 2019
	Common Stock			Additional Paid-In		Accumulated Other Comprehensive			Accumulated			Noncontrolling		Total Stockholders’
	Shares	Amount		Capital		Income (Loss)			Deficit			Interest		Equity
Balance as of December 31, 2018	101,098	$	1,011	$	1,256,267	$	(3	)	$	(1,103,692	)	$	5,469	$	159,052
Exercise of stock options, and issuance of common stock units and stock awards, net of repurchase of shares to satisfy tax withholding	85	1		253		—			—			—		254
Stock-based compensation	—	—		605		—			—			—		605
Net income	—	—		—		—			33,790			6,229		40,019
Other comprehensive income	—	—		—		13			—			—		13
Balance as of March 31, 2019	101,183	$	1,012	$	1,257,125	$	10		$	(1,069,902	)	$	11,698	$	199,943

	Three months ended March 31, 2018
	Common Stock					Additional Paid-In			Accumulated Other Comprehensive			Accumulated			Treasury Stock					Noncontrolling			Total Stockholders’
	Shares		Amount			Capital			Loss			Deficit			Shares		Amount			Interest			Deficit
Balance as of December 31, 2017	102,046		$	1,019		$	1,258,151		$	(18	)	$	(1,498,748	)	(150	)	$	(3,263	)	$	152		$	(242,707	)
Distributions to noncontrolling interest	—		—			—			—			—			—		—			(90		)	(90		)
Exercise of stock options, and issuance of common stock units and stock awards, net of cancellation of stock awards and repurchase of shares to satisfy tax withholding	(571	)	(5		)	(2,492		)	—			—			—		—			—			(2,497		)
Stock-based compensation	—		—			2,169			—			—			—		—			—			2,169
Cash dividend forfeited	—		—			52			—			—			—		—			—			52
Net income	—		—			—			—			29,581			—		—			749			30,330
Other comprehensive loss	—		—			—			(4		)	—			—		—			—			(4		)
Balance as of March 31, 2018	101,475		$	1,014		$	1,257,880		$	(22	)	$	(1,469,167	)	(150	)	$	(3,263	)	$	811		$	(212,747	)

See accompanying notes to condensed consolidated financial statements.

6

INNOVIVA, INC.

CONDENSED CONSOLIDATED STATEMENTS OF CASH FLOWS

(In thousands)

(Unaudited)

	Three Months Ended March 31,
	2019			2018
Cash flows from operating activities
Net income	$	40,019		$	30,330
Adjustments to reconcile net income to net cash provided by operating activities:
Deferred income taxes	8,508			—
Depreciation and amortization	3,539			3,468
Stock-based compensation	605			2,169
Amortization of debt discount and issuance costs	1,889			2,092
Amortization of discount on short-term investments	(356		)	(100		)
Amortization of lease guarantee	(81		)	(81		)
Loss on extinguishment of debt	—			3,137
Changes in operating assets and liabilities:
Receivables from collaborative arrangements	24,647			14,705
Prepaid expenses and other current assets	147			(196		)
Accounts payable	133			(535		)
Accrued personnel-related expenses and other accrued liabilities	166			(1,702		)
Accrued interest payable	(2,489		)	(3,375		)
Operating lease liability	(72		)	—
Other long-term liabilities	—			2
Net cash provided by operating activities	76,655			49,914
Cash flows from investing activities
Maturities of marketable securities	27,875			31,875
Purchases of marketable securities	(102,042		)	(5,362		)
Net cash provided by (used in) investing activities	(74,167		)	26,513
Cash flows from financing activities
Repurchase of shares to satisfy tax withholding	(65		)	(2,611		)
Payments of principal on senior secured term loans	—			(120,000		)
Payments of cash dividends to stockholders	(8		)	(38		)
Proceeds from issuances of common stock, net	319			114
Distributions to noncontrolling interest	—			(90		)
Net cash provided by (used in) financing activities	246			(122,625		)
Net increase (decrease) in cash and cash equivalents	2,734			(46,198		)
Cash and cash equivalents at beginning of period	62,417			73,336
Cash and cash equivalents at end of period	$	65,151		$	27,138
Supplemental disclosure of cash flow information
Cash paid for interest	$	5,218		$	8,941

See accompanying notes to condensed consolidated financial statements.

7

INNOVIVA, INC.

NOTES TO CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

(Unaudited)

1. Description of Operations and Summary of Significant Accounting Policies

Description of Operations

Innoviva, Inc. (referred to as “Innoviva”, the “Company”, or “we” and other similar pronouns) is focused on royalty management. Innoviva’s portfolio includes the respiratory assets partnered with Glaxo Group Limited (“GSK”), including RELVAR®/BREO®ELLIPTA® (fluticasone furoate/ vilanterol, “FF/VI”), ANORO® ELLIPTA®(umeclidinium bromide/ vilanterol, “UMEC/VI”) and TRELEGY® ELLIPTA® (the combination FF/UMEC/VI). Under the Long-Acting Beta2 Agonist (“LABA”) Collaboration Agreement, Innoviva is entitled to receive royalties from GSK on sales of RELVAR®/BREO® ELLIPTA® as follows: 15% on the first $3.0 billion of annual global net sales and 5% for all annual global net sales above $3.0 billion; and royalties from the sales of and ANORO® ELLIPTA® which tier upward at a range from 6.5% to 10%  Innoviva is also entitled to 15% of royalty payments made by GSK under its agreements originally entered into with us, and since assigned to Theravance Respiratory Company, LLC (“TRC”), including TRELEGY® ELLIPTA® and any other product or combination of products that may be discovered or developed in the future under the LABA Collaboration Agreement and the Strategic Alliance Agreement with GSK (referred to herein as the “GSK Agreements”), which have been assigned to TRC other than RELVAR®/BREO® ELLIPTA® and ANORO® ELLIPTA®.

Basis of Presentation

The accompanying unaudited condensed consolidated financial statements have been prepared in accordance with accounting principles generally accepted in the United States of America (“US GAAP”) for interim financial information. Accordingly, they do not include all of the information and notes required by US GAAP for complete financial statements. In our opinion, the unaudited condensed consolidated financial statements have been prepared on the same basis as audited consolidated financial statements and include all adjustments, consisting of only normal recurring adjustments, necessary for the fair presentation of our financial position, results of operations, comprehensive income and cash flows. The interim results are not necessarily indicative of the results of operations to be expected for the year ending December 31, 2019 or any other period.

The accompanying unaudited condensed consolidated financial statements should be read in conjunction with the audited consolidated financial statements and notes thereto included in our Annual Report on Form 10-K for the year ended December 31, 2018 filed with the Securities and Exchange Commission (“SEC”) on February 19, 2019 (“2018 Form 10-K”).

Variable Interest Entity

We evaluate our ownership, contractual and other interest in entities to determine if they are variable interest entities (“VIE”), whether we have a variable interest in those entities and the nature and extent of those interests. Based on our evaluation, if we determine we are the primary beneficiary of a VIE, we consolidate the entity into our financial statements. We consolidate the financial results of TRC, which we have determined to be a VIE, because we have the power to direct the economically significant activities of TRC and the obligation to absorb losses of, or the right to receive benefits from, TRC. As of March 31, 2019 and December 31, 2018, $7.3 million and $6.4 million, respectively, of the related party receivables from collaborative arrangements were attributable to TRC. Total revenue for TRC related to TRELEGY® ELLIPTA® for the three months ended March 31, 2019 and 2018 was $7.3 million and $1.0 million, respectively.

Accounting Pronouncement Adopted by the Company

In February 2016, the Financial Accounting Standards Board (the “FASB”) issued Accounting Standards Update (“ASU”) 2016 02, Leases (Topic 842), which requires an entity to recognize right of use assets representing its right to use the underlying asset for the lease term and lease liabilities representing the present value of the future lease payments for both financing and operating leases on its consolidated balance sheets. For a lease with a term of 12 months or less, the standard allows an entity to elect not to recognize a right-of-use asset and a lease liability and recognize the lease expense on a straight-line basis. We adopted the standard on the effective date of January 1, 2019 using the alternative transition approach. This approach is similar to a prospective transition, which requires the application of ASC 842 at the effective date with a cumulative-effect adjustment recognized through retained earnings. Under this approach, we do not present the adjusted comparative periods. Our pro-rata share of common area expenses are recorded as lease expense when incurred since they are variable and considered nonlease components under the standard. The most significant impact of the adoption to us is that we recognized a right of use asset in the amount of $1.5 million and lease liabilities in

8

the total amount of $1.6 million at January 1, 2019 for the operating lease on our corporate headquarters. The adoption did not have a material impact on our retained earnings and consolidated statements of operations and cash flows.

In August 2018, the U.S. Securities and Exchange Commission (the “SEC”) adopted the final rule under SEC Release No. 33-10532, Disclosure Update and Simplification, amending certain disclosure requirements that were redundant, duplicative, overlapping, outdated or superseded. In addition, the amendments expanded the disclosure requirements relating to the analysis of stockholders’ equity for interim financial statements. Under the amendments, an analysis of changes in each caption of stockholders’ equity presented in the balance sheet must be provided in a note or separate statement. The analysis should present a reconciliation of the beginning balance to the ending balance of each period for which a statement of income is required to be filed. This final rule is effective on November 5, 2018. Effective January 1, 2019, the Company adopted SEC Release No. 33-10532. In accordance with the new guidance, the Company has added a Condensed Consolidated Statement of Changes in Stockholders’ Equity (Deficit) in its Form 10-Q and elected to present a reconciliation in a single statement that shows the changes in stockholders equity for each interim period, as well as each comparable period.

2. Net Income Per Share

Basic net income per share attributable to Innoviva stockholders is computed by dividing net income attributable to Innoviva stockholders by the weighted-average number of shares of common stock outstanding. Diluted net income per share attributable to Innoviva stockholders is computed by dividing net income attributable to Innoviva stockholders by the weighted-average number of shares of common stock and dilutive potential common stock equivalents then outstanding. Dilutive potential common stock equivalents include the assumed exercise, vesting and issuance of employee stock awards using the treasury stock method, as well as common stock issuable upon assumed conversion of our convertible subordinated notes due 2023 (the “2023 Notes”) using the if-converted method.

Our convertible senior notes due 2025 (the “2025 Notes”) are convertible, based on the applicable conversion rate, into cash, shares of our common stock or a combination thereof, at our election. Our current intent is to settle the principal amount of the 2025 Notes in cash upon conversion. The impact of the assumed conversion premium to diluted net income per share is computed using the treasury stock method. As the average market price per share of our common stock as reported on The Nasdaq Global Select Market during the relevant periods was lower than the initial conversion price of $17.26 per share, there was no dilutive effect of the assumed conversion premium for the three months ended March 31, 2019.

The following table shows the computation of basic and diluted net income per share for the three months ended March 31, 2019 and 2018:

	Three Months Ended March 31,
(In thousands except per share data)	2019		2018
Numerator:
Net income attributable to Innoviva stockholders, basic	$	33,790	$	29,581
Add: interest expense on 2023 Notes	1,415		1,412
Net income attributable to Innoviva stockholders, diluted	$	35,205	$	30,993
Denominator:
Weighted-average shares used to compute basic net income per share attributable to Innoviva stockholders	101,059		100,604
Dilutive effect of 2023 Notes	12,189		12,189
Dilutive effect of options and awards granted under equity incentive plan and employee stock purchase plan	128		773
Weighted-average shares used to compute diluted net income per share attributable to Innoviva stockholders	113,376		113,566
Net income per share attributable to Innoviva stockholders
Basic	$	0.33	$	0.29
Diluted	$	0.31	$	0.27

9

Anti-Dilutive Securities

The following common stock equivalents were not included in the computation of diluted net income per share because their effect was anti-dilutive:

	Three Months Ended March 31,
(In thousands)	2019	2018
Outstanding options and awards granted under equity incentive plan and employee stock purchase plan	1,053	1,492

3. Revenue Recognition and Collaborative Arrangements

Revenue is recognized when our customer obtains control of promised goods or services, in an amount that reflects the consideration which we expect to receive in exchange for those goods or services. Revenue is recognized through a five-step process: (i) identify the contract with a customer; (ii) identify the performance obligations in the contract; (iii) determine the transaction price for the contract; (iv) allocate the transaction price to the performance obligations in the contract; and (v) recognize revenue when (or as) a performance obligation is satisfied. We recognize the royalty revenue on licensee net sales of products with respect to which we have contractual royalty rights in the period in which the royalties are earned and reported to us. Royalties are recognized net of amortization of capitalized fees associated with any approval and launch milestone payments made to GSK.

Net Revenue from Collaborative Arrangements

Net revenue recognized under our GSK Agreements was as follows:

	Three Months Ended March 31,
(In thousands)	2019			2018
Royalties from a related party - RELVAR/BREO	$	42,740		$	46,160
Royalties from a related party - ANORO	8,570			8,724
Royalties from a related party - TRELEGY	7,329			952
Total royalties from a related party	58,639			55,836
Less: amortization of capitalized fees paid to a related party	(3,456		)	(3,456		)
Royalty revenue from GSK	$	55,183		$	52,380

4. Available-for-Sale Securities and Fair Value Measurements

Available-for-Sale Securities

The estimated fair value of available-for-sale securities is based on quoted market prices for these or similar investments that were based on prices obtained from a commercial pricing service. Available-for-sale securities are summarized below:

	March 31, 2019
(In thousands)	Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses		Estimated Fair Value
U.S. government securities	$	68,691	$	9	$	—	$	68,700
U.S. government agencies	24,768		1		—		24,769
U.S. commercial paper	41,550		—		—		41,550
Money market funds	45,253		—		—		45,253
Total	$	180,262	$	10	$	—	$	180,272

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	December 31, 2018
(In thousands)	Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Estimated Fair Value
U.S. government securities	$	29,736	$	—	$	(3	)	$	29,733
U.S. government agencies	4,971		—		—			4,971
U.S. corporate notes	2,875		—		—			2,875
U.S. commercial paper	22,037		—		—			22,037
Money market funds	49,358		—		—			49,358
Total	$	108,977	$	—	$	(3	)	$	108,974

As of March 31, 2019, all of the available-for-sale securities had contractual maturities within one year and the weighted average maturity of marketable securities was approximately four months.

Fair Value Measurements

Our available-for-sale securities are measured at fair value on a recurring basis and our debt is carried at amortized cost basis. The estimated fair values were as follows:

	Estimated Fair Value Measurements as of March 31, 2019 Using:
Types of Instruments	Quoted Price in Active Markets for Identical Assets		Significant Other Observable Inputs		Significant Unobservable Inputs
(In thousands)	Level 1		Level 2		Level 3		Total
Assets
U.S. government securities	$	—	$	68,700	$	—	$	68,700
U.S. government agencies	—		24,769		—		24,769
U.S. commercial paper	—		41,550		—		41,550
Money market funds	45,253		—		—		45,253
Total assets measured at estimated fair value	$	45,253	$	135,019	$	—	$	180,272
Debt
Term B Loan	$	—	$	13,750	$	—	$	13,750
2023 Notes	—		245,353		—		245,353
2025 Notes	—		205,911		—		205,911
Total fair value of debt	$	—	$	465,014	$	—	$	465,014

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	Estimated Fair Value Measurements as of December 31, 2018 Using:
Types of Instruments	Quoted Price in Active Markets for Identical Assets		Significant Other Observable Inputs		Significant Unobservable Inputs
(In thousands)	Level 1		Level 2		Level 3		Total
Assets
U.S. government securities	$	—	$	29,733	$	—	$	29,733
U.S. government agencies	—		4,971		—		4,971
U.S. corporate notes	—		2,875		—		2,875
U.S. commercial paper	—		22,037		—		22,037
Money market funds	49,358		—		—		49,358
Total assets measured at estimated fair value	$	49,358	$	59,616	$	—	$	108,974
Debt
Term B Loan	$	—	$	13,750	$	—	$	13,750
2023 Notes	—		258,918		—		258,918
2025 Notes	—		230,692		—		230,692
Total fair value of debt	$	—	$	503,360	$	—	$	503,360

The fair value of our marketable securities classified within Level 2 is based upon observable inputs that may include benchmark yields, reported trades, broker/dealer quotes, issuer spreads, two-sided markets, benchmark securities, bids, offers and reference data, including market research publications.

The fair value of our 2023 Notes and of our 2025 Notes is based on recent trading prices of the instruments. The carrying amount of our initial senior secured term loan (the “Term B Loan”) before deducting debt issuance costs approximates fair value as the loan carries a variable interest rate that is tied to the LIBOR rate plus an applicable spread.

5. Stock-Based Compensation

Market-Based RSAs and RSUs

2016 Market-Based RSAs and RSUs

On January 14, 2016, the Compensation Committee approved and granted 282,394 RSAs and 46,294 RSUs to senior management. These awards include a market condition based on Total Shareholder Return (“TSR”) and a service condition that requires continued employment.

In February 2018, the Compensation Committee certified the maximum achievement of the TSR as of the first measurement date, January 12, 2018. RSAs totaling 69,440 and RSUs totaling 30,862 representing two-thirds of the amounts were released on February 20, 2018. In connection with the separation of certain members of senior management from the Company in early February 2018, the Board of Directors agreed to accelerate the vesting and distribution of an aggregate of 118,821 RSAs to these members of senior management. The remaining 59,411 RSAs for these members of senior management were forfeited. As a net result of the vesting acceleration of the RSAs and the forfeiture of those unvested RSAs, an additional $0.7 million compensation expense was recognized during the three months ended March 31, 2018.

In August and September 2018, the remaining 34,722 RSAs and 15,432 RSUs were forfeited due to the additional separation of senior management members, and $0.2 million of previously recognized compensation expense was reversed.

2017 Market-Based RSAs and RSUs

On January 17, 2017, the Compensation Committee approved and granted 353,508 RSAs and 53,360 RSUs to senior management. These awards include a market condition based on the TSR of Innoviva’s common stock as compared to the TSR of NASDAQ Biotechnology Index (“Index”) and a service condition that requires continued employment.

In connection with the separation of certain members of senior management from the Company in February 2018, an aggregate of 233,448 RSAs were forfeited, and $0.8 million of previously recognized compensation expense was reversed during the three months ended March 31, 2018.

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In August and September 2018, the remaining 120,060 RSAs and 53,360 RSUs were forfeited due to the additional separation of senior management members, and $0.9 million of previously recognized compensation expense was reversed.

2018 Market-Based RSAs and RSUs

On March 2, 2018, the Compensation Committee approved and granted 111,668 RSAs and 49,630 RSUs to senior management. These awards include a market condition based on the TSR of Innoviva’s common stock over a three-year performance period from the date of grant for the RSAs and from the date of grant until September 30, 2020 for RSUs, and a service condition that requires continued employment. The grant date fair value of these awards was determined using a Monte Carlo valuation model. The aggregate value of $1.7 million was to be recognized as compensation expense over the implied service period and would not be reversed if the market condition was not met, but with the exception of such person’s continued employment with the Company.

In August and September 2018, all of 111,668 RSAs and 49,630 RSUs were forfeited, and $0.2 million of previously recognized compensation expense was reversed due to the separation of these senior management members.

Stock-Based Compensation Expense

Stock-based compensation expense is included in the condensed consolidated statements of operations as follows:

	Three Months Ended March 31,
(In thousands)	2019		2018
General and administrative	$	605	$	2,169

As of March 31, 2019, unrecognized stock-based compensation cost was as follows:

(In thousands)	Unrecognized Compensation Cost
RSUs	$	327
RSAs	1,317
Total unrecognized compensation cost	$	1,644

6. Debt

Our debt consists of:

	March 31,			December 31,
(In thousands)	2019			2018
Term B Loan	$	13,750		$	13,750
2023 Notes	240,984			240,984
2025 Notes	192,500			192,500
Total debt	447,234			447,234
Unamortized debt discount and issuance costs	(62,490		)	(64,379		)
Net long-term debt	$	384,744		$	382,855

Prepayments of Senior Secured Term Loans

On February 28 and August 1, 2018, we prepaid the principal balance of the Term B Loan by $120.0 million and $110.0 million, respectively. With the prepayments, we incurred a loss on the extinguishment of debt of $3.1 million and $2.6 million, respectively, representing unamortized debt issuance costs. The loss on the extinguishment of debt is presented as part of other expense, net in our consolidated statements of operations. As of March 31, 2019, the outstanding principal balance of the Term B Loan was $13.8 million.

Convertible Senior Notes Due 2025

In accordance with accounting guidance for debt with conversion and other options, we separately account for the liability and equity components of the 2025 Notes by allocating the proceeds between the liability component and the embedded conversion

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option (“equity component”) due to our ability to settle the conversion obligation of the 2025 Notes in cash, common stock or a combination of cash and common stock, at our option. The carrying amount of the liability component was calculated by measuring the fair value of a similar liability that does not have an associated convertible feature using the income approach. The allocation was performed in a manner that reflected our non-convertible debt borrowing rate for similar debt. The equity component of the 2025 Notes was recognized as a debt discount and represents the difference between the proceeds from the issuance of the 2025 Notes and the fair value of the liability of the 2025 Notes on the date of issuance. The excess of the principal amount of the liability component over its carrying amount (“debt discount”) is amortized to interest expense using the effective interest method over the term of the 2025 Notes. The equity component is not remeasured as long as it continues to meet the conditions for equity classification.

Our outstanding 2025 Notes balances consisted of the following:

	March 31,			December 31,
(In thousands)	2019			2018
Liability component
Principal	$	192,500		$	192,500
Debt discount and issuance costs, net	(60,032		)	(61,766		)
Net carrying amount	$	132,468		$	130,734
Equity component, net	$	65,361		$	65,361

The following table sets forth total interest expense recognized related to the 2025 Notes for the three months ended March 31, 2019 and 2018:

	Three Months Ended March 31,
(In thousands)	2019		2018
Contractual interest expense	$	1,203	$	1,190
Amortization of debt issuance costs	133		123
Amortization of debt discount	1,601		1,479
Total interest and amortization expense	$	2,937	$	2,792

Debt Maturities

The aggregate scheduled maturities of our long-term debt as of March 31, 2019, are as follows:

(In thousands)
Years ending December 31:
2019 to 2021	$	—
2022	13,750
2023	240,984
Thereafter	192,500
Total	$	447,234

7. Related Party Transaction

On February 12, 2018, the Company entered into an agreement with Sarissa Capital Management LP, and certain of its affiliates (collectively, the “Sarissa Group”) related to the Company’s 2018 Annual Meeting of Stockholders (the “2018 Annual Meeting”). The agreement provided for, among other things, the concurrent appointment of three designees of the Sarissa Group as members of the Company’s Board of Directors and an agreement to recommend and nominate a five-person slate of directors for election at the 2018 Annual Meeting composed of the three new directors and two current directors of the Company and partially reimburse the Sarissa Group $2.7 million for expenses, which reimbursement obligation relating to the 2018 Annual Meeting arose upon execution of the agreement. The Sarissa Group is considered to be a related party due to its representation on the Board of Directors.

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8. Income Taxes

Provisional income tax expense for the three months ended March 31, 2019 was $8.5 million, compared to a minimal amount for the same period in 2018 as a full valuation allowance was maintained on the Company’s gross deferred taxes. The difference between the Company’s effective income tax rate of 17.5% for the three months ended March 31, 2019 and the U.S. federal statutory rate of 21% is primarily attributable to state income tax, non-deductible expenses and noncontrolling interest.

9. Lease

We have an operating lease for our corporate headquarters with a remaining lease term of approximately 4.2 years. The lease includes a five-year renewal option at our sole discretion. The total operating lease expense for this lease was $0.1 million for the three months ended March 31, 2019 and 2018, respectively. Cash paid for amount included in the measurement of operating lease liabilities was $0.1 million for the three months ended March 31, 2019. The lease liabilities were measured using a discount rate of 7.15% based on the most recent borrowing rate for our senior secured Term B Loan.

Future minimum lease payments on our corporate headquarters as of March 31, 2019 are as follows:

(In thousands)
Years ending December 31:
Remainder of 2019	$	304
2020	416
2021	428
2022	441
2023	201
Total future minimum lease payments	1,790
Imputed interest	(244		)
Total	$	1,546
Reported as of March 31, 2019
Operating lease liability, current portion	$	308
Operating lease liability, net of current portion	1,238
Total	$	1,546

Item 2. Management’s Discussion and Analysis of Financial Condition and Results of Operations

Forward-Looking Statements

The information in this Quarterly Report on Form 10-Q contains forward-looking statements within the meaning of Section 27A of the Securities Act of 1933, as amended (“Securities Act”), and Section 21E of the Securities Exchange Act of 1934, as amended. Such forward-looking statements involve substantial risks, uncertainties and assumptions. All statements contained herein that are not of historical fact, including, without limitation, statements regarding our strategy, future operations, future financial position, future revenue, projected costs, prospects, plans, intentions, expectations, goals and objectives, may be forward-looking statements. The words “anticipates,” “believes,” “could,” “designed,” “estimates,” “expects,” “goal,” “intends,” “may,” “objective,” “plans,” “projects,” “pursue,” “will,” “would” and similar expressions (including the negatives thereof) are intended to identify forward-looking statements, although not all forward-looking statements contain these identifying words. We may not actually achieve the plans, intentions, expectations or objectives disclosed in our forward-looking statements and the assumptions underlying our forward-looking statements may prove incorrect. Therefore, you should not place undue reliance on our forward-looking statements. Actual results or events could differ materially from the plans, intentions, expectations and objectives disclosed in the forward-looking statements that we make. All written and verbal forward-looking statements attributable to us or any person acting on our behalf are expressly qualified in their entirety by the cautionary statements contained or referred to in this section. Important factors that we believe could cause actual results or events to differ materially from our forward-looking statements include, but are not limited to, risks related to: lower than expected future royalty revenue from respiratory products partnered with GSK; the commercialization of RELVAR®/BREO® ELLIPTA®, ANORO® ELLIPTA® and TRELEGY® ELLIPTA® in the jurisdictions in which these products have been approved; the strategies, plans and objectives of the Company (including the Company’s growth strategy and corporate development initiatives beyond the existing respiratory portfolio); the timing, manner and amount of potential

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capital returns to stockholders; the status and timing of clinical studies, data analysis and communication of results; the potential benefits and mechanisms of action of product candidates; expectations for product candidates through development and commercialization; the timing of regulatory approval of product candidates; projections of revenue, expenses and other financial items; and risks discussed in “Risk Factors” in Item 1A of Part I of our Annual Report on Form 10-K for the year ended December 31, 2018 filed with the Securities and Exchange Commission (“SEC”) on February 19, 2019 (“2018 Form 10-K”) and Item 1A of Part II of our Quarterly Reports on Form 10-Q and below in “Management’s Discussion and Analysis of Financial Condition and Results of Operations” in this Item 2 of Part I. All forward-looking statements in this Quarterly Report on Form 10-Q are based on current expectations as of the date hereof and we do not assume any obligation to update any forward-looking statements on account of new information, future events or otherwise, except as required by law.

We encourage you to read our consolidated financial statements contained in this Quarterly Report on Form 10-Q. We also encourage you to read Item 1A of Part I of our 2018 Form 10-K and Item 1A of Part II of our Quarterly Reports on Form 10-Q entitled “Risk Factors,” which contain a more complete discussion of the risks and uncertainties associated with our business. In addition to the risks described above and in Item 1A of Part I of our 2018 Form 10-K and Item 1A of Part II of this report, other unknown or unpredictable factors also could affect our results. Therefore, the information in this report should be read together with other reports and documents that we file with the SEC from time to time, including on Form 10-K, Form 10-Q and Form 8-K, which may supplement, modify, supersede or update those risk factors. As a result of these factors, we cannot assure you that the forward-looking statements in this report will prove to be accurate. Furthermore, if our forward-looking statements prove to be inaccurate, the inaccuracy may be material. In light of the significant uncertainties in these forward-looking statements, you should not regard these statements as a representation or warranty by us or any other person that we will achieve our objectives and plans in any specified time frame, or at all.

OVERVIEW

Executive Summary

Innoviva, Inc. (“Innoviva”, the “Company” or “we”) is focused on royalty management. Innoviva’s portfolio includes the respiratory assets partnered with Glaxo Group Limited (“GSK”), including RELVAR®/BREO® ELLIPTA® (fluticasone furoate/ vilanterol, “FF/VI”), ANORO® ELLIPTA® (umeclidinium bromide/ vilanterol, “UMEC/VI”) and TRELEGY® ELLIPTA® (the combination FF/UMEC/VI). Under the Long-Acting Beta2 Agonist (“LABA”) Collaboration Agreement, Innoviva is entitled to receive royalties from GSK on sales of RELVAR®/BREO® ELLIPTA® as follows: 15% on the first $3.0 billion of annual global net sales and 5% for all annual global net sales above $3.0 billion; and royalties from the sales of ANORO® ELLIPTA®, which tier upward at a range from 6.5% to 10%. Innoviva is also entitled to 15% of royalty payments made by GSK under its agreements originally entered into with us, and since assigned to Theravance Respiratory Company, LLC (“TRC”), including TRELEGY® ELLIPTA® and any other product or combination of products that may be discovered or developed in the future under the LABA Collaboration Agreement and the Strategic Alliance Agreement with GSK (referred to herein as the “GSK Agreements”), which have been assigned to TRC other than RELVAR®/BREO® ELLIPTA® and ANORO® ELLIPTA®.

Our company structure and organization are tailored to our focused activities of managing our respiratory assets with GSK, the commercial and developmental obligations associated with the GSK Agreements, intellectual property, licensing operations, business development activities and providing for certain essential reporting and management functions of a public company. As of March 31, 2019, we had six employees. Our revenues consist of royalties from our respiratory partnership agreements with GSK.

Recent Highlights

·GSK Net Sales:

·First quarter 2019 net sales of RELVAR®/BREO® ELLIPTA® by GSK were $284.9 million, down 7% from $307.7 million in the first quarter of 2018, with $100.1 million in net sales from the U.S. market and $184.8 million from non-U.S. markets.

·First quarter 2019 net sales of ANORO® ELLIPTA® by GSK were $131.8 million, down 2% from $134.2 million in the first quarter of 2018, with $75.7 million net sales from the U.S. market and $56.1 million from non-U.S. markets.

·First quarter 2019 net sales of TRELEGY® ELLIPTA® by GSK were $112.7 million, up significantly from $14.6 million in the first quarter of 2018, with $85.1 million in net sales from the U.S. market and $27.6 million in net sales from non-U.S. markets.

·Product Updates:

·The Pharmaceuticals and Medical Devices Agency of Japan approved TRELEGY® ELLIPTA® (fluticasone furoate/umeclidinium/vilanterol ‘FF/UMEC/VI’) for the treatment of chronic obstructive pulmonary disease (COPD).  TRELEGY® ELLIPTA® is the first triple therapy in a single inhaler approved in Japan.

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Collaborative Arrangements with GSK

LABA Collaboration

In November 2002, we entered into our LABA Collaboration Agreement with GSK to develop and commercialize once-daily LABA products for the treatment of chronic obstructive pulmonary disease (“COPD”) and asthma. The collaboration has developed three combination products: (1) RELVAR®/BREO® ELLIPTA® (FF/VI) (BREO® ELLIPTA® is the proprietary name in the U.S. and Canada and RELVAR® ELLIPTA® is the proprietary name outside the U.S. and Canada), a once-daily combination medicine consisting of a LABA, vilanterol (VI), and an inhaled corticosteroid (ICS), fluticasone furoate (FF), (2) ANORO® ELLIPTA® (UMEC/VI), a once-daily medicine combining a long-acting muscarinic antagonist (“LAMA”), umeclidinium bromide (UMEC), with a LABA, VI and (3) TRELEGY® ELLIPTA®, fluticasone furoate/umeclidinium/vilanterol (FF/UMEC/VI), a once-daily combination medicine consisting of an ICS, LAMA and LABA.

As a result of the launch and approval of RELVAR®/BREO® ELLIPTA® and ANORO® ELLIPTA® in the U.S., Japan and Europe, in accordance with the LABA Collaboration Agreement, we paid milestone fees to GSK totaling $220.0 million during the year ended December 31, 2014. The milestone fees paid to GSK were recognized as capitalized fees paid to a related party, which are being amortized over their estimated useful lives commencing upon the commercial launch of the products.

2004 Strategic Alliance

In March 2004, we entered into the Strategic Alliance Agreement with GSK where GSK received an option to license exclusive development and commercialization rights to product candidates from certain of our discovery programs on pre-determined terms and on an exclusive, worldwide basis. In 2005, GSK licensed our MABA program for the treatment of COPD, and in October 2011, we and GSK expanded the MABA program by adding six additional Innoviva-discovered preclinical MABA compounds (the “Additional MABAs”). The development program has been funded in full by GSK. GSK is in the process of determining next steps for the program. For a detailed discussion of our alliance with GSK, see Management’s Discussion and Analysis of Financial Condition and Results of Operations contained in Part II, Item 7 of our 2018 Form 10-K.

Critical Accounting Policies and Estimates

Our management’s discussion and analysis of our financial condition and results of operations is based on our financial statements, which have been prepared in accordance with accounting principles generally accepted in the United States of America (“US GAAP”). The preparation of these financial statements requires us to make estimates and assumptions that affect the reported amounts of assets and liabilities and the disclosure of contingent assets and liabilities as of the date of the financial statements, as well as the reported revenue generated and expenses incurred during the reporting periods. Our estimates are based on our historical experience and on various other factors that we believe are reasonable under the circumstances, the results of which form the basis for making judgments about the carrying value of assets and liabilities that are not readily apparent from other sources. Actual results may differ from these estimates under different assumptions or conditions.

In February 2016, the Financial Accounting Standards Board (the “FASB”) issued Accounting Standards Update (“ASU”) 2016 02, Leases (Topic 842), which requires an entity to recognize right of use assets representing its right to use the underlying asset for the lease term and lease liabilities representing the present value of the future lease payments for both financing and operating leases on its consolidated balance sheets. For a lease with a term of 12 months or less, the standard allows an entity to elect not to recognize a right-of-use asset and a lease liability and recognize the lease expense on a straight-line basis. We adopted the standard on the effective date of January 1, 2019 using the alternative transition approach. This approach is similar to a prospective transition, which requires the application of ASC 842 at the effective date with a cumulative-effect adjustment recognized through retained earnings. Under this approach, we do not present the adjusted comparative periods. Our pro-rata share of common area expenses are recorded as lease expense when incurred since they are variable and considered nonlease components under the standard. The most significant impact of the adoption to us is that we recognized a right of use asset in the amount of $1.5 million and lease liabilities in the total amount of $1.6 million at January 1, 2019 for the operating lease on our corporate headquarters. The adoption did not have a material impact on our retained earnings and consolidated statements of operations and cash flows.

There were no other significant changes to our critical accounting policies and estimates. Management’s Discussion and Analysis of Financial Condition and Results of Operations contained in Part II, Item 7 of our Annual Report on Form 10-K for the year ended December 31, 2018 filed with the SEC on February 19, 2019 provides a more complete discussion of our critical accounting policies and estimates.

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Results of Operations

Net Revenue

Total net revenue, as compared to the prior year period, was as follows:

	Three Months Ended March 31,						Change
(In thousands)	2019			2018			$			%
Royalties from a related party - RELVAR/BREO	$	42,740		$	46,160		$	(3,420	)	(7	)%
Royalties from a related party - ANORO	8,570			8,724			(154		)	(2	)%
Royalties from a related party - TRELEGY	7,329			952			6,377			*
Total royalties from a related party	58,639			55,836			2,803			5	%
Less: amortization of capitalized fees paid to a related party	(3,456		)	(3,456		)	—			—
Royalty revenue from GSK	$	55,183		$	52,380		$	2,803		5	%

*Not meaningful

Total net revenue increased to $55.2 million for the three months ended March 31, 2019, compared to $52.4 million for the same period a year ago primarily due to the growth in prescriptions and market share quarter over quarter for TRELEGY® ELLIPTA®, offset with the lower royalties for RELVAR®/BREO® ELLIPTA® and ANORO® ELLIPTA® primarily due to increasing pricing pressure in the U.S.

General & Administrative

General and administrative expenses, as compared to the prior year period, were as follows:

	Three Months Ended March 31,				Change
(In thousands)	2019		2018		$			%
General and administrative expenses	$	3,015	$	8,985	$	(5,970	)	(66	)%
General and administrative expenses - related party	—		2,700		(2,700		)	—

General and administrative expenses for the three months ended March 31, 2019 were $3.0 million compared with $11.7 million in the three months ended March 31, 2018, a decrease of $8.7 million. The amount for the three months ended March 31, 2018 included $3.2 million cash severance payments in connection with certain members of senior management’s separation from the Company and payment of $2.7 million to Sarissa to partially reimburse expenses pursuant to a settlement agreement in February 2018.  The rest of the decrease in general and administrative expenses in the three months ended March 31, 2019 is mainly attributable to lower personnel-related expenses as a result of lower headcount.

Other Income (Expense), net and Interest Income

Other income (expense), net and interest income, as compared to the prior year period, were as follows:

	Three Months Ended March 31,					Change
(In thousands)	2019		2018			$		%
Other income (expense), net	$	1	$	(3,099	)	$	3,100	*
Interest income	975		391			584		149	%

*Not meaningful

Other income (expense), net for the three months ended March 31, 2018, mainly consists of the loss on the extinguishment of debt of $3.1 million in relation to the $120.0 million prepayment of our Term B Loan.

Interest income increased for the three months ended March 31, 2019, as compared to the same period a year ago primarily due to higher interest generated from our investments in marketable securities.

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Interest Expense

Interest expense, as compared to the prior year period, was as follows:

	Three Months Ended March 31,				Change
(In thousands)	2019		2018		$			%
Interest expense	$	4,617	$	7,657	$	(3,040	)	(40	)%

Interest expense decreased for the three months ended March 31, 2019, compared to the same period a year ago primarily due to the lower average outstanding debt balance. See “Liquidity” section below for further information.

Provision for Income Taxes

The provisional income tax expense for the three months ended March 31, 2019 was $8.5 million with an effective income tax rate of 17.5%, compared to an immaterial amount in the same period a year ago as a full valuation allowance was maintained on our gross deferred taxes.

Net Income Attributable to Noncontrolling Interest

Net income attributable to noncontrolling interest, as compared to the prior period, was as follows:

	Three Months Ended March 31,				Change
(In thousands)	2019		2018		$		%
Net income attributable to noncontrolling interest	$	6,229	$	749	$	5,480	732	%

This represents the 85% share of net income in Theravance Respiratory Company, LLC for Theravance Biopharma for the three months ended March 31, 2019 and 2018. The increase was primarily due to the increase in the growth in prescriptions and market share for TRELEGY® ELLIPTA®.

Liquidity and Capital Resources

Liquidity

Since our inception, we have financed our operations primarily through private placements and public offerings of equity and debt securities and payments received under collaborative arrangements. For the three months ended March 31, 2019, we generated gross royalty revenues from GSK of $58.6 million. Net cash and cash equivalents, short term investments and marketable securities totaled $192.2 million, and royalties receivable from GSK totaled $58.6 million as of March 31, 2019.

On August 18, 2017, we entered into a Credit Agreement and completed a financing of the $250.0 million Term B Loan. The Term B Loan will mature on August 18, 2022. Two and a half percent (2.5%) of the initial principal amount was originally due quarterly beginning December 31, 2017. The remaining outstanding balance is due at maturity. Prepayments, in whole or in part, can be made at any time without a penalty. The Credit Agreement also provides us the ability to request one or more additional tranches of term loans (or increase an existing term loan) at any time prior to maturity. In December 2017, February 2018 and August 2018, we repaid the principal balance of the Term B Loan by $6.3 million, $120.0 million and $110.0 million, respectively. The outstanding principal balance of the Term B Loan as of March 31, 2019 was $13.8 million.

Adequacy of Cash Resources to Meet Future Needs

We believe that cash from projected future royalty revenues and our cash, cash equivalents and marketable securities will be sufficient to meet our anticipated debt service and operating needs for at least the next 12 months based upon current operating plans and financial forecasts. If our current operating plans and financial forecasts change, we may require additional funding sooner in the form of public or private equity offerings or debt financings. Furthermore, if in our view favorable financing opportunities arise, we may seek additional funding at any time. However, future financing may not be available in amounts or on terms acceptable to us, if at all. This could leave us without adequate financial resources to fund our operations as currently planned. In addition, from time to time we may restructure or reduce our debt, including through tender offers, redemptions, amendments, repurchases or otherwise, all consistent with the terms of our debt agreements.

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Cash Flows

Cash flows, as compared to the prior year period, were as follows:

	Three Months Ended March 31,
(In thousands)	2019			2018			Change
Net cash provided by operating activities	$	76,655		$	49,914		$	26,741
Net cash provided by (used in) investing activities	(74,167		)	26,513			(100,680		)
Net cash provided by (used in) financing activities	246			(122,625		)	122,871

Cash Flows from Operating Activities

Cash provided by operating activities for the three months ended March 31, 2019 was $76.7 million, consisting primarily of our net income of $40.0 million, adjusted for non-cash items such as $8.5 million of deferred income taxes, $3.5 million of depreciation and amortization and $1.9 million amortization of debt discount and issuance costs, as well as decrease in receivables from collaborative arrangements of $24.6 million, partially offset by a reduction in accrued interest payable of $2.5 million.

Cash provided by operating activities for the three months ended March 31, 2018 was $49.9 million, consisting primarily of our net income of $30.3 million, adjusted for non-cash items such as $3.5 million of depreciation and amortization, $3.1 million of loss on extinguishment of debt and $2.2 million of stock-based compensation expense, as well as changes in operating assets and liabilities, including a decrease in receivables from collaborative arrangements of $14.7 million, partially offset by a reduction in accrued interest payable of $3.4 million.

Cash Flows from Investing Activities

Net cash flows used in investing activities for the three months ended March 31, 2019 of $74.2 million was primarily due to $102.0 million in purchases of marketable securities partially offset by $27.9 million proceeds received from maturities of marketable securities.

Net cash flows from investing activities for the three months ended March 31, 2018 of $26.5 million was primarily due to $31.9 million proceeds received from maturities of marketable securities, partially offset by $5.4 million in purchases of marketable securities.

Cash Flows from Financing Activities

Net cash provided by financing activities for the three months ended March 31, 2019 of $0.2 million was primarily due to $0.3 million net proceeds from issuance of common stock.

Net cash used in financing activities for the three months ended March 31, 2018 of $122.6 million was primarily due to $120.0 million prepayment on our Term B Loan and $2.6 million paid for the repurchase of shares to satisfy tax withholding.

Off-Balance Sheet Arrangements

In June 2014, our facility leases in South San Francisco, California were assigned to Theravance Biopharma, Inc. (“Theravance Biopharma”) in connection with the spin-off of Theravance Biopharma. However, if Theravance Biopharma were to default on its lease obligations, we would be held liable by the landlord and thus, we have in substance guaranteed the lease payments for these facilities. We would also be responsible for lease-related payments including utilities, property taxes, and common area maintenance, which may be as much as the actual lease payments. As of March 31, 2019, the total remaining lease payments for the duration of the lease, which runs through May 2020, were $7.7 million. The carrying value of this lease guarantee was $0.4 million as of March 31, 2019 and is reflected in other long-term liabilities in our condensed consolidated balance sheet.

Contractual Obligations and Commercial Commitments

In the table below, we set forth our significant enforceable and legally binding obligations and future commitments as of March 31, 2019.

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			Payment Due by Period
			Less Than						More Than
(In thousands)	Total		1 Year		1 - 3 Years		3 - 5 Years		5 Years
2023 Notes	$	261,468	$	5,121	$	10,242	$	246,105	$	—
2025 Notes	223,781		4,813		9,625		9,625		199,718
Term B Loan*	13,750		—		—		13,750		—
Facility lease	1,790		406		850		534		—
Total	$	500,789	$	10,340	$	20,717	$	270,014	$	199,718

* The Term B Loan balances reflect the principal repayment obligations and do not include the interest payments as the loan bears interest at a varying rate of three-month LIBOR plus 4.5% margin.

Item 3. Quantitative and Qualitative Disclosure about Market Risk

There have been no significant changes in our market risk or how our market risk is managed compared to those disclosed in our Annual Report on Form 10-K for the year ended December 31, 2018.

Item 4. Controls and Procedures

Evaluation of Disclosure Controls and Procedures.

We conducted an evaluation as of March 31, 2019, under the supervision and with the participation of our management, of the effectiveness of the design and operation of our disclosure controls and procedures, which are defined under SEC rules as controls and other procedures of a company that are designed to ensure that information required to be disclosed by a company in the reports that it files under the Securities Exchange Act of 1934 (“Exchange Act”) is recorded, processed, summarized and reported within required time periods. Based upon that evaluation, our Interim Principal Executive Officer and Chief Accounting Officer, concluded that, as of such date, our disclosure controls and procedures were effective at the reasonable assurance levels.

Limitations on the Effectiveness of Controls

Our management does not expect that our disclosure controls and procedures or our internal control over financial reporting will prevent all errors and all frauds. A control system, no matter how well conceived and operated, can provide only reasonable, not absolute, assurance that the objectives of the control system are met. Further, the design of a control system must reflect the fact that there are resource constraints, and the benefit of controls must be considered relative to their costs. Because of the inherent limitations in all control systems, no evaluation of controls can provide absolute assurance that all control issues and instances of fraud, if any, within Innoviva have been detected. Also, projections of any evaluation of effectiveness to future periods are subject to the risk that controls may become inadequate because of changes in conditions, or that the degree of compliance with the policies or procedures may deteriorate.

Changes in Internal Control over Financial Reporting

There were no material changes in our internal control over financial reporting (as defined in Rule 13a-15(f) of the Exchange Act) that occurred during the quarter ended March 31, 2019 that have materially affected, or are reasonably likely to materially affect, our internal control over financial reporting.

21

PART II. OTHER INFORMATION

Item 1. Legal Proceedings

We are not a party to any material legal proceedings.

Item 1A. Risk Factors

Our business is subject to a number of risks, including those identified in Item 1A of Part I of our 2018 Form 10-K. There have been no material changes to the risk factors described in our 2018 Form 10-K, which is incorporated by reference herein.

Item 2. Unregistered Sales of Equity Securities and Use of Proceeds

None.

Item 3: Defaults Upon Senior Securities

None.

Item 4: Mine Safety Disclosures

None.

Item 5: Other Information

None.

Item 6. Exhibits

(a) Index to Exhibits

Exhibit Number	Description	Form	Exhibit	Incorporated by Reference Filing Date/Period End Date
31.1	Certification of Principal Executive Officer pursuant to Rules 13a-14 pursuant to the Securities Exchange Act of 1934
31.2	Certification of Principal Financial Officer pursuant to Rules 13a-14 pursuant to the Securities Exchange Act of 1934
32	Certifications Pursuant to 18 U.S.C. Section 1350
101	Interactive Data File (Quarterly Report on Form 10-Q, for the quarterly period ended March 31, 2019)

22

SIGNATURES

Pursuant to the requirements of the Securities Exchange Act of 1934, the registrant has duly caused this report to be signed on its behalf by the undersigned thereunto duly authorized.

	Innoviva, Inc.
Date: May 1, 2019	/s/ Geoffrey Hulme
	Geoffrey Hulme
	Interim Principal Executive Officer
	(Principal Executive Officer)
Date: May 1, 2019	/s/ Marianne Zhen
	Marianne Zhen
	Chief Accounting Officer
	(Principal Financial Officer)

23

EX-31.1

Exhibit 31.1

Certification of Principal Executive Officer

Pursuant to Section 302 of the Sarbanes-Oxley Act of 2002

I, Geoffrey Hulme, certify that:

1. I have reviewed this quarterly report on Form 10-Q of Innoviva, Inc.;

2. Based on my knowledge, this report does not contain any untrue statement of a material fact or omit to state a material fact necessary to make the statements made, in light of the circumstances under which such statements were made, not misleading with respect to the period covered by this report;

3. Based on my knowledge, the financial statements, and other financial information included in this report, fairly present in all material respects the financial condition, results of operations and cash flows of the registrant as of, and for, the periods presented in this report;

4. The registrant’s other certifying officer(s) and I are responsible for establishing and maintaining disclosure controls and procedures (as defined in Exchange Act Rules 13a-15(e) and 15d-15(e)) and internal control over financial reporting (as defined in Exchange Act Rules 13a-15(f) and 15(d)-15(f)) for the registrant and have:

a) Designed such disclosure controls and procedures, or caused such disclosure controls and procedures to be designed under our supervision, to ensure that material information relating to the registrant, including its consolidated subsidiaries, is made known to us by others within those entities, particularly during the period in which this report is being prepared;

b) Designed such internal control over financial reporting, or caused such internal control over financial reporting to be designed under our supervision, to provide reasonable assurance regarding the reliability of financial reporting and the preparation of financial statements for external purposes in accordance with generally accepted accounting principles;

c) Evaluated the effectiveness of the registrant’s disclosure controls and procedures and presented in this report our conclusions about the effectiveness of the disclosure controls and procedures, as of the end of the period covered by this report based on such evaluation; and

d) Disclosed in this report any change in the registrant’s internal control over financial reporting that occurred during the registrant’s most recent fiscal quarter (the registrant’s fourth fiscal quarter in the case of an annual report) that has materially affected, or is reasonably likely to materially affect, the registrant’s internal control over financial reporting; and

5. The registrant’s other certifying officer(s) and I have disclosed, based on our most recent evaluation of internal control over financial reporting, to the registrant’s auditors and the audit committee of the registrant’s board of directors (or persons performing the equivalent functions):

a) All significant deficiencies and material weaknesses in the design or operation of internal control over financial reporting which are reasonably likely to adversely affect the registrant’s ability to record, process, summarize and report financial information; and

b) Any fraud, whether or not material, that involves management or other employees who have a significant role in the registrant’s internal control over financial reporting.

Date: May 1, 2019	/s/ Geoffrey Hulme
	Geoffrey Hulme
	Interim Principal Executive Officer
	(Principal Executive Officer)

EX-31.2

Exhibit 31.2

Certification of Principal Financial Officer

Pursuant to Section 302 of the Sarbanes-Oxley Act of 2002

I, Marianne Zhen, certify that:

1. I have reviewed this quarterly report on Form 10-Q of Innoviva, Inc.;

2. Based on my knowledge, this report does not contain any untrue statement of a material fact or omit to state a material fact necessary to make the statements made, in light of the circumstances under which such statements were made, not misleading with respect to the period covered by this report;

3. Based on my knowledge, the financial statements, and other financial information included in this report, fairly present in all material respects the financial condition, results of operations and cash flows of the registrant as of, and for, the periods presented in this report;

4. The registrant’s other certifying officer(s) and I are responsible for establishing and maintaining disclosure controls and procedures (as defined in Exchange Act Rules 13a-15(e) and 15d-15(e)) and internal control over financial reporting (as defined in Exchange Act Rules 13a-15(f) and 15(d)-15(f)) for the registrant and have:

a) Designed such disclosure controls and procedures, or caused such disclosure controls and procedures to be designed under our supervision, to ensure that material information relating to the registrant, including its consolidated subsidiaries, is made known to us by others within those entities, particularly during the period in which this report is being prepared;

b) Designed such internal control over financial reporting, or caused such internal control over financial reporting to be designed under our supervision, to provide reasonable assurance regarding the reliability of financial reporting and the preparation of financial statements for external purposes in accordance with generally accepted accounting principles;

c) Evaluated the effectiveness of the registrant’s disclosure controls and procedures and presented in this report our conclusions about the effectiveness of the disclosure controls and procedures, as of the end of the period covered by this report based on such evaluation; and

d) Disclosed in this report any change in the registrant’s internal control over financial reporting that occurred during the registrant’s most recent fiscal quarter (the registrant’s fourth fiscal quarter in the case of an annual report) that has materially affected, or is reasonably likely to materially affect, the registrant’s internal control over financial reporting; and

5. The registrant’s other certifying officer(s) and I have disclosed, based on our most recent evaluation of internal control over financial reporting, to the registrant’s auditors and the audit committee of the registrant’s board of directors (or persons performing the equivalent functions):

a) All significant deficiencies and material weaknesses in the design or operation of internal control over financial reporting which are reasonably likely to adversely affect the registrant’s ability to record, process, summarize and report financial information; and

b) Any fraud, whether or not material, that involves management or other employees who have a significant role in the registrant’s internal control over financial reporting.

Date: May 1, 2019	/s/ Marianne Zhen
	Marianne Zhen
	Chief Accounting Officer
	(Principal Financial Officer)

EX-32

Exhibit 32

CERTIFICATION OF PRINCIPAL EXECUTIVE OFFICER

PURSUANT TO

18 U.S.C. SECTION 1350,

AS ADOPTED PURSUANT TO

SECTION 906 OF THE SARBANES-OXLEY ACT OF 2002

I, Geoffrey Hulme, certify, pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002, that the Quarterly Report of Innoviva, Inc. on Form 10-Q for the period ended March 31, 2019 fully complies with the requirements of Section 13(a) or 15(d) of the Securities Exchange Act of 1934, as amended and that information contained in such Quarterly Report on Form 10-Q fairly presents in all material respects the financial condition of Innoviva, Inc. at the end of the periods covered by such Quarterly Report on Form 10-Q and results of operations of Innoviva, Inc. for the periods covered by such Quarterly Report on Form 10-Q.

Date: May 1, 2019	By:	/s/ Geoffrey Hulme
		Geoffrey Hulme
		Interim Principal Executive Officer
		(Principal Executive Officer)

CERTIFICATION OF

PRINCIPAL FINANCIAL OFFICER

PURSUANT TO

18 U.S.C. SECTION 1350,

AS ADOPTED PURSUANT TO

SECTION 906 OF THE SARBANES-OXLEY ACT OF 2002

I, Marianne Zhen, certify, pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002, that the Quarterly Report of Innoviva, Inc. on Form 10-Q for the period ended March 31, 2019 fully complies with the requirements of Section 13(a) or 15(d) of the Securities Exchange Act of 1934, as amended and that information contained in such Quarterly Report on Form 10-Q fairly presents in all material respects the financial condition of Innoviva, Inc. at the end of the periods covered by such Quarterly Report on Form 10-Q and results of operations of Innoviva, Inc. for the periods covered by such Quarterly Report on Form 10-Q.

Date: May 1, 2019	By:	/s/ Marianne Zhen
		Marianne Zhen
		Chief Accounting Officer
		(Principal Financial Officer)

XML

Document and Entity Information - shares	3 Months Ended
	Mar. 31, 2019	Apr. 26, 2019
Document and Entity Information
Entity Registrant Name	Innoviva, Inc.
Entity Central Index Key	0001080014
Document Type	10-Q
Document Period End Date	Mar. 31, 2019
Amendment Flag	false
Current Fiscal Year End Date	--12-31
Entity Current Reporting Status	Yes
Entity Filer Category	Large Accelerated Filer
Entity Small Business	false
Entity Emerging Growth Company	false
Entity Common Stock, Shares Outstanding		101,262,314
Document Fiscal Year Focus	2019
Document Fiscal Period Focus	Q1

XML

CONDENSED CONSOLIDATED BALANCE SHEETS - USD ($) $ in Thousands	Mar. 31, 2019	Dec. 31, 2018	[1]
Current assets:
Cash and cash equivalents	$ 65,151	$ 62,417
Short-term marketable securities	127,027	52,491
Related party receivables from collaborative arrangements	58,639	83,286
Prepaid expenses and other current assets	702	849
Total current assets	251,519	199,043
Property and equipment, net	148	160
Operating lease right-of-use asset	1,421	0
Capitalized fees paid to a related party, net	149,443	152,899
Deferred tax assets	187,546	196,054
Other assets	37	37
Total assets	590,114	548,193
Current liabilities:
Accounts payable	144	11
Accrued personnel-related expenses	325	470
Accrued interest payable	1,775	4,264
Other accrued liabilities	1,258	955
Operating lease liability, current portion	308	0
Total current liabilities	3,810	5,700
Long-term debt, net of discount and issuance costs	384,744	382,855
Operating lease liability, net of current portion	1,238	0
Other long-term liabilities	379	586
Commitments and contingencies
Stockholders' equity
Preferred stock: $0.01 par value, 230 shares authorized, no shares issued and outstanding	0	0
Common stock: $0.01 par value, 200,000 shares authorized, 101,183 and 101,098 issued and outstanding as of March 31, 2019 and December 31, 2018, respectively	1,012	1,011
Additional paid-in capital	1,257,125	1,256,267
Accumulated other comprehensive income (loss)	10	(3)
Accumulated deficit	(1,069,902)	(1,103,692)
Total Innoviva stockholders' equity	188,245	153,583
Noncontrolling interest	11,698	5,469
Total stockholders' equity	199,943	159,052
Total liabilities and stockholders' equity	$ 590,114	$ 548,193

[1] Condensed consolidated balance sheet as of December 31, 2018 has been derived from audited consolidated financial statements.

XML

CONDENSED CONSOLIDATED BALANCE SHEETS (Parenthetical) - $ / shares shares in Thousands	Mar. 31, 2019	Dec. 31, 2018
CONDENSED CONSOLIDATED BALANCE SHEETS
Preferred stock, par value (in dollars per share)	$ 0.01	$ 0.01
Preferred stock, shares authorized	230	230
Preferred stock, shares issued	0	0
Preferred stock, shares outstanding	0	0
Common stock, par value (in dollars per share)	$ 0.01	$ 0.01
Common stock, shares authorized	200,000	200,000
Common stock, shares issued	101,183	101,098
Common stock, shares outstanding	101,183	101,098

XML

CONDENSED CONSOLIDATED STATEMENTS OF OPERATIONS - USD ($) shares in Thousands, $ in Thousands	3 Months Ended
	Mar. 31, 2019	Mar. 31, 2018
Revenue:
Royalty revenue from a related party, net of amortization of capitalized fees paid to a related party of $3,456 in the three months ended March 31, 2019 and 2018	$ 55,183	$ 52,380
Operating expenses:
General and administrative	3,015	8,985
General and administrative - related party	0	2,700
Total operating expenses	3,015	11,685
Income from operations	52,168	40,695
Other income (expense), net	1	(3,099)
Interest income	975	391
Interest expense	(4,617)	(7,657)
Income before income taxes	48,527	30,330
Income tax expense, net	8,508	0
Net income	40,019	30,330
Net income attributable to noncontrolling interest	6,229	749
Net income attributable to Innoviva stockholders	$ 33,790	$ 29,581
Basic net income per share attributable to Innoviva stockholders	$ 0.33	$ 0.29
Diluted net income per share attributable to Innoviva stockholders	$ 0.31	$ 0.27
Shares used to compute Innoviva basic and diluted net income per share:
Shares used to compute basic net income per share	101,059	100,604
Shares used to compute diluted net income per share	113,376	113,566

XML

CONDENSED CONSOLIDATED STATEMENTS OF OPERATIONS (Parenthetical) - USD ($) $ in Thousands	3 Months Ended
	Mar. 31, 2019	Mar. 31, 2018
Royalty revenue from a related party | GSK
Amortization of capitalized fees paid to a related party	$ 3,456	$ 3,456

XML

CONDENSED CONSOLIDATED STATEMENTS OF COMPREHENSIVE INCOME - USD ($) $ in Thousands	3 Months Ended
	Mar. 31, 2019	Mar. 31, 2018
CONDENSED CONSOLIDATED STATEMENTS OF COMPREHENSIVE INCOME
Net income	$ 40,019	$ 30,330
Unrealized gain (loss) on marketable securities, net	13	(4)
Comprehensive income	40,032	30,326
Comprehensive income attributable to noncontrolling interest	6,229	749
Comprehensive income attributable to Innoviva stockholders	$ 33,803	$ 29,577

XML

CONDENSED CONSOLIDATED STATEMENTS OF STOCKHOLDERS' EQUITY (DEFICIT) - USD ($) shares in Thousands, $ in Thousands	Common Stock	Additional Paid-In Capital	Accumulated Other Comprehensive Income (loss)	Accumulated Deficit	Treasury Stock	Noncontrolling Interest	Total
Balance at Dec. 31, 2017	$ 1,019	$ 1,258,151	$ (18)	$ (1,498,748)	$ (3,263)	$ 152	$ (242,707)
Balance (in shares) at Dec. 31, 2017	102,046				(150)
Increase (Decrease) in Stockholders' Equity
Distributions to noncontrolling interest	$ 0	0	0	0	$ 0	(90)	(90)
Exercise of stock options, and issuance of common stock units and stock awards, net of cancellation of stock awards and repurchase of shares to satisfy tax withholding	$ (5)	(2,492)	0	0	0	0	(2,497)
Exercise of stock options, and issuance of common stock units and stock awards, net of cancellation of stock awards and repurchase of shares to satisfy tax withholding (in shares)	(571)
Stock-based compensation	$ 0	2,169	0	0	0	0	2,169
Cash dividend forfeited	0	52	0	0	0	0	52
Net income	0	0	0	29,581	0	749	30,330
Other comprehensive income (loss)	0	0	(4)	0	0	0	(4)
Balance at Mar. 31, 2018	$ 1,014	1,257,880	(22)	(1,469,167)	$ (3,263)	811	(212,747)
Balance (in shares) at Mar. 31, 2018	101,475				(150)
Balance at Dec. 31, 2018	$ 1,011	1,256,267	(3)	(1,103,692)		5,469	$ 159,052	[1]
Balance (in shares) at Dec. 31, 2018	101,098						101,098
Increase (Decrease) in Stockholders' Equity
Exercise of stock options, and issuance of common stock units and stock awards, net of cancellation of stock awards and repurchase of shares to satisfy tax withholding	$ 1	253	0	0		0	$ 254
Exercise of stock options, and issuance of common stock units and stock awards, net of cancellation of stock awards and repurchase of shares to satisfy tax withholding (in shares)	85
Stock-based compensation	$ 0	605	0	0		0	605
Net income	0	0	0	33,790		6,229	40,019
Other comprehensive income (loss)	0	0	13	0		0	13
Balance at Mar. 31, 2019	$ 1,012	$ 1,257,125	$ 10	$ (1,069,902)		$ 11,698	$ 199,943
Balance (in shares) at Mar. 31, 2019	101,183						101,183

[1] Condensed consolidated balance sheet as of December 31, 2018 has been derived from audited consolidated financial statements.

XML

CONDENSED CONSOLIDATED STATEMENTS OF CASH FLOWS - USD ($) $ in Thousands	3 Months Ended
	Mar. 31, 2019	Mar. 31, 2018
Cash flows from operating activities
Net income	$ 40,019	$ 30,330
Adjustments to reconcile net income to net cash provided by operating activities:
Deferred income taxes	8,508	0
Depreciation and amortization	3,539	3,468
Stock-based compensation	605	2,169
Amortization of debt discount and issuance costs	1,889	2,092
Amortization of discount on short-term investments	(356)	(100)
Amortization of lease guarantee	(81)	(81)
Loss on extinguishment of debt	0	3,137
Changes in operating assets and liabilities:
Receivables from collaborative arrangements	24,647	14,705
Prepaid expenses and other current assets	147	(196)
Accounts payable	133	(535)
Accrued personnel-related expenses and other accrued liabilities	166	(1,702)
Accrued interest payable	(2,489)	(3,375)
Operating lease liability	(72)	0
Other long-term liabilities	0	2
Net cash provided by operating activities	76,655	49,914
Cash flows from investing activities
Maturities of marketable securities	27,875	31,875
Purchases of marketable securities	(102,042)	(5,362)
Net cash provided by (used in) investing activities	(74,167)	26,513
Cash flows from financing activities
Repurchase of shares to satisfy tax withholding	(65)	(2,611)
Payments of principal on senior secured term loans	0	(120,000)
Payments of cash dividends to stockholders	(8)	(38)
Proceeds from issuances of common stock, net	319	114
Distributions to noncontrolling interest	0	(90)
Net cash provided by (used in) financing activities	246	(122,625)
Net increase (decrease) in cash and cash equivalents	2,734	(46,198)
Cash and cash equivalents at beginning of period	62,417	73,336
Cash and cash equivalents at end of period	65,151	27,138
Supplemental disclosure of cash flow information
Cash paid for interest	$ 5,218	$ 8,941

XML

Description of Operations and Summary of Significant Accounting Policies

3 Months Ended

Mar. 31, 2019

Description of Operations and Summary of Significant Accounting Policies

Description of Operations and Summary of Significant Accounting Policies

1. Description of Operations and Summary of Significant Accounting Policies

Description of Operations

Innoviva, Inc. (referred to as “Innoviva”, the “Company”, or “we” and other similar pronouns) is focused on royalty management. Innoviva’s portfolio includes the respiratory assets partnered with Glaxo Group Limited (“GSK”), including RELVAR®/BREO®ELLIPTA® (fluticasone furoate/ vilanterol, “FF/VI”), ANORO® ELLIPTA®(umeclidinium bromide/ vilanterol, “UMEC/VI”) and TRELEGY® ELLIPTA® (the combination FF/UMEC/VI). Under the Long-Acting Beta2 Agonist (“LABA”) Collaboration Agreement, Innoviva is entitled to receive royalties from GSK on sales of RELVAR®/BREO® ELLIPTA® as follows: 15% on the first $3.0 billion of annual global net sales and 5% for all annual global net sales above $3.0 billion; and royalties from the sales of and ANORO® ELLIPTA® which tier upward at a range from 6.5% to 10% Innoviva is also entitled to 15% of royalty payments made by GSK under its agreements originally entered into with us, and since assigned to Theravance Respiratory Company, LLC (“TRC”), including TRELEGY® ELLIPTA® and any other product or combination of products that may be discovered or developed in the future under the LABA Collaboration Agreement and the Strategic Alliance Agreement with GSK (referred to herein as the “GSK Agreements”), which have been assigned to TRC other than RELVAR®/BREO® ELLIPTA® and ANORO® ELLIPTA®.

Basis of Presentation

The accompanying unaudited condensed consolidated financial statements have been prepared in accordance with accounting principles generally accepted in the United States of America ("US GAAP”) for interim financial information. Accordingly, they do not include all of the information and notes required by US GAAP for complete financial statements. In our opinion, the unaudited condensed consolidated financial statements have been prepared on the same basis as audited consolidated financial statements and include all adjustments, consisting of only normal recurring adjustments, necessary for the fair presentation of our financial position, results of operations, comprehensive income and cash flows. The interim results are not necessarily indicative of the results of operations to be expected for the year ending December 31, 2019 or any other period.

The accompanying unaudited condensed consolidated financial statements should be read in conjunction with the audited consolidated financial statements and notes thereto included in our Annual Report on Form 10-K for the year ended December 31, 2018 filed with the Securities and Exchange Commission (“SEC”) on February 19, 2019 (“2018 Form 10-K”).

Variable Interest Entity

We evaluate our ownership, contractual and other interest in entities to determine if they are variable interest entities (“VIE”), whether we have a variable interest in those entities and the nature and extent of those interests. Based on our evaluation, if we determine we are the primary beneficiary of a VIE, we consolidate the entity into our financial statements. We consolidate the financial results of TRC, which we have determined to be a VIE, because we have the power to direct the economically significant activities of TRC and the obligation to absorb losses of, or the right to receive benefits from, TRC. As of March 31, 2019 and December 31, 2018, $7.3 million and $6.4 million, respectively, of the related party receivables from collaborative arrangements were attributable to TRC. Total revenue for TRC related to TRELEGY® ELLIPTA® for the three months ended March 31, 2019 and 2018 was $7.3 million and $1.0 million, respectively.

Accounting Pronouncement Adopted by the Company

In February 2016, the Financial Accounting Standards Board (the “FASB”) issued Accounting Standards Update (“ASU”) 2016 02, Leases (Topic 842), which requires an entity to recognize right of use assets representing its right to use the underlying asset for the lease term and lease liabilities representing the present value of the future lease payments for both financing and operating leases on its consolidated balance sheets. For a lease with a term of 12 months or less, the standard allows an entity to elect not to recognize a right-of-use asset and a lease liability and recognize the lease expense on a straight-line basis. We adopted the standard on the effective date of January 1, 2019 using the alternative transition approach. This approach is similar to a prospective transition, which requires the application of ASC 842 at the effective date with a cumulative-effect adjustment recognized through retained earnings. Under this approach, we do not present the adjusted comparative periods. Our pro-rata share of common area expenses are recorded as lease expense when incurred since they are variable and considered nonlease components under the standard. The most significant impact of the adoption to us is that we recognized a right of use asset in the amount of $1.5 million and lease liabilities in the total amount of $1.6 million at January 1, 2019 for the operating lease on our corporate headquarters. The adoption did not have a material impact on our retained earnings and consolidated statements of operations and cash flows.

In August 2018, the U.S. Securities and Exchange Commission (the “SEC”) adopted the final rule under SEC Release No. 33-10532, Disclosure Update and Simplification, amending certain disclosure requirements that were redundant, duplicative, overlapping, outdated or superseded. In addition, the amendments expanded the disclosure requirements relating to the analysis of stockholders’ equity for interim financial statements. Under the amendments, an analysis of changes in each caption of stockholders’ equity presented in the balance sheet must be provided in a note or separate statement. The analysis should present a reconciliation of the beginning balance to the ending balance of each period for which a statement of income is required to be filed. This final rule is effective on November 5, 2018. Effective January 1, 2019, the Company adopted SEC Release No. 33-10532. In accordance with the new guidance, the Company has added a Condensed Consolidated Statement of Changes in Stockholders’ Equity (Deficit) in its Form 10-Q and elected to present a reconciliation in a single statement that shows the changes in stockholders equity for each interim period, as well as each comparable period.

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Net Income Per Share

3 Months Ended

Mar. 31, 2019

Net Income Per Share

Net Income Per Share

2. Net Income Per Share

Basic net income per share attributable to Innoviva stockholders is computed by dividing net income attributable to Innoviva stockholders by the weighted-average number of shares of common stock outstanding. Diluted net income per share attributable to Innoviva stockholders is computed by dividing net income attributable to Innoviva stockholders by the weighted-average number of shares of common stock and dilutive potential common stock equivalents then outstanding. Dilutive potential common stock equivalents include the assumed exercise, vesting and issuance of employee stock awards using the treasury stock method, as well as common stock issuable upon assumed conversion of our convertible subordinated notes due 2023 (the “2023 Notes”) using the if-converted method.

Our convertible senior notes due 2025 (the “2025 Notes”) are convertible, based on the applicable conversion rate, into cash, shares of our common stock or a combination thereof, at our election. Our current intent is to settle the principal amount of the 2025 Notes in cash upon conversion. The impact of the assumed conversion premium to diluted net income per share is computed using the treasury stock method. As the average market price per share of our common stock as reported on The Nasdaq Global Select Market during the relevant periods was lower than the initial conversion price of $17.26 per share, there was no dilutive effect of the assumed conversion premium for the three months ended March 31, 2019.

The following table shows the computation of basic and diluted net income per share for the three months ended March 31, 2019 and 2018:

	Three Months Ended March 31,
(In thousands except per share data)	2019		2018
Numerator:
Net income attributable to Innoviva stockholders, basic	$	33,790	$	29,581
Add: interest expense on 2023 Notes		1,415		1,412
Net income attributable to Innoviva stockholders, diluted	$	35,205	$	30,993
Denominator:
Weighted-average shares used to compute basic net income per share attributable to Innoviva stockholders		101,059		100,604
Dilutive effect of  2023 Notes		12,189		12,189
Dilutive effect of options and awards granted under equity incentive plan and employee stock purchase plan		128		773
Weighted-average shares used to compute diluted net income per share attributable to Innoviva stockholders		113,376		113,566
Net income per share attributable to Innoviva stockholders
Basic	$	0.33	$	0.29
Diluted	$	0.31	$	0.27

Anti-Dilutive Securities

The following common stock equivalents were not included in the computation of diluted net income per share because their effect was anti-dilutive:

	Three Months Ended March 31,
(In thousands)	2019	2018
Outstanding options and awards granted under equity incentive plan and employee stock purchase plan	1,053	1,492

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Revenue Recognition and Collaborative Arrangements

3 Months Ended

Mar. 31, 2019

Revenue Recognition and Collaborative Arrangements

Revenue Recognition and Collaborative Arrangements

3. Revenue Recognition and Collaborative Arrangements

Revenue is recognized when our customer obtains control of promised goods or services, in an amount that reflects the consideration which we expect to receive in exchange for those goods or services. Revenue is recognized through a five-step process: (i) identify the contract with a customer; (ii) identify the performance obligations in the contract; (iii) determine the transaction price for the contract; (iv) allocate the transaction price to the performance obligations in the contract; and (v) recognize revenue when (or as) a performance obligation is satisfied. We recognize the royalty revenue on licensee net sales of products with respect to which we have contractual royalty rights in the period in which the royalties are earned and reported to us. Royalties are recognized net of amortization of capitalized fees associated with any approval and launch milestone payments made to GSK.

Net Revenue from Collaborative Arrangements

Net revenue recognized under our GSK Agreements was as follows:

	Three Months Ended March 31,
(In thousands)	2019		2018
Royalties from a related party - RELVAR/BREO	$	42,740	$	46,160
Royalties from a related party - ANORO		8,570		8,724
Royalties from a related party - TRELEGY		7,329		952
Total royalties from a related party		58,639		55,836
Less: amortization of capitalized fees paid to a related party		(3,456)		(3,456)
Royalty revenue from GSK	$	55,183	$	52,380

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Available-for-Sale Securities and Fair Value Measurements

3 Months Ended

Mar. 31, 2019

Available-for-Sale Securities and Fair Value Measurements

Available-for-Sale Securities and Fair Value Measurements

4. Available-for-Sale Securities and Fair Value Measurements

Available-for-Sale Securities

The estimated fair value of available-for-sale securities is based on quoted market prices for these or similar investments that were based on prices obtained from a commercial pricing service. Available-for-sale securities are summarized below:

	March 31, 2019
			Gross		Gross
			Unrealized		Unrealized		Estimated
(In thousands)	Amortized Cost		Gains		Losses		Fair Value
U.S. government securities	$	68,691	$	9	$	—	$	68,700
U.S. government agencies		24,768		1		—		24,769
U.S. commercial paper		41,550		—		—		41,550
Money market funds		45,253		—		—		45,253
Total	$	180,262	$	10	$	—	$	180,272

	December 31, 2018
			Gross		Gross
			Unrealized		Unrealized		Estimated
(In thousands)	Amortized Cost		Gains		Losses		Fair Value
U.S. government securities	$	29,736	$	—	$	(3)	$	29,733
U.S. government agencies		4,971		—		—		4,971
U.S. corporate notes		2,875		—		—		2,875
U.S. commercial paper		22,037		—		—		22,037
Money market funds		49,358		—		—		49,358
Total	$	108,977	$	—	$	(3)	$	108,974

As of March 31, 2019, all of the available-for-sale securities had contractual maturities within one year and the weighted average maturity of marketable securities was approximately four months.  

Fair Value Measurements

Our available-for-sale securities are measured at fair value on a recurring basis and our debt is carried at amortized cost basis. The estimated fair values were as follows:

	Estimated Fair Value Measurements as of March 31, 2019 Using:
	Quoted Price in
	Active Markets		Significant Other		Significant
	for Identical		Observable		Unobservable
Types of Instruments	Assets		Inputs		Inputs
(In thousands)	Level 1		Level 2		Level 3		Total
Assets
U.S. government securities	$	—	$	68,700	$	—	$	68,700
U.S. government agencies		—		24,769		—		24,769
U.S. commercial paper		—		41,550		—		41,550
Money market funds		45,253		—		—		45,253
Total assets measured at estimated fair value	$	45,253	$	135,019	$	—	$	180,272
Debt
Term B Loan	$	—	$	13,750	$	—	$	13,750
2023 Notes		—		245,353		—		245,353
2025 Notes		—		205,911		—		205,911
Total fair value of debt	$	—	$	465,014	$	—	$	465,014

	Estimated Fair Value Measurements as of December 31, 2018 Using:
Types of Instruments	Quoted Price in Active Markets for Identical Assets		Significant Other Observable Inputs		Significant Unobservable Inputs
(In thousands)	Level 1		Level 2		Level 3		Total
Assets
U.S. government securities	$	—	$	29,733	$	—	$	29,733
U.S. government agencies		—		4,971		—		4,971
U.S. corporate notes		—		2,875		—		2,875
U.S. commercial paper		—		22,037		—		22,037
Money market funds		49,358		—		—		49,358
Total assets measured at estimated fair value	$	49,358	$	59,616	$	—	$	108,974
Debt
Term B Loan	$	—	$	13,750	$	—	$	13,750
2023 Notes		—		258,918		—		258,918
2025 Notes		—		230,692		—		230,692
Total fair value of debt	$	—	$	503,360	$	—	$	503,360

The fair value of our marketable securities classified within Level 2 is based upon observable inputs that may include benchmark yields, reported trades, broker/dealer quotes, issuer spreads, two-sided markets, benchmark securities, bids, offers and reference data, including market research publications.

The fair value of our 2023 Notes and of our 2025 Notes is based on recent trading prices of the instruments. The carrying amount of our initial senior secured term loan (the “Term B Loan”) before deducting debt issuance costs approximates fair value as the loan carries a variable interest rate that is tied to the LIBOR rate plus an applicable spread.

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Stock-Based Compensation

3 Months Ended

Mar. 31, 2019

Stock-Based Compensation

Stock-Based Compensation

5. Stock-Based Compensation

Market-Based RSAs and RSUs

2016 Market-Based RSAs and RSUs

On January 14, 2016, the Compensation Committee approved and granted 282,394 RSAs and 46,294 RSUs to senior management. These awards include a market condition based on Total Shareholder Return (“TSR”) and a service condition that requires continued employment.

In February 2018, the Compensation Committee certified the maximum achievement of the TSR as of the first measurement date, January 12, 2018. RSAs totaling 69,440 and RSUs totaling 30,862 representing two-thirds of the amounts were released on February 20, 2018. In connection with the separation of certain members of senior management from the Company in early February 2018, the Board of Directors agreed to accelerate the vesting and distribution of an aggregate of 118,821 RSAs to these members of senior management. The remaining 59,411 RSAs for these members of senior management were forfeited. As a net result of the vesting acceleration of the RSAs and the forfeiture of those unvested RSAs, an additional $0.7 million compensation expense was recognized during the three months ended March 31, 2018.

In August and September 2018, the remaining 34,722 RSAs and 15,432 RSUs were forfeited due to the additional separation of senior management members, and $0.2 million of previously recognized compensation expense was reversed.

2017 Market-Based RSAs and RSUs

On January 17, 2017, the Compensation Committee approved and granted 353,508 RSAs and 53,360 RSUs to senior management. These awards include a market condition based on the TSR of Innoviva’s common stock as compared to the TSR of NASDAQ Biotechnology Index (“Index”) and a service condition that requires continued employment.

In connection with the separation of certain members of senior management from the Company in February 2018, an aggregate of 233,448 RSAs were forfeited, and $0.8 million of previously recognized compensation expense was reversed during the three months ended March 31, 2018.

In August and September 2018, the remaining 120,060 RSAs and 53,360 RSUs were forfeited due to the additional separation of senior management members, and $0.9 million of previously recognized compensation expense was reversed.

2018 Market-Based RSAs and RSUs

On March 2, 2018, the Compensation Committee approved and granted 111,668 RSAs and 49,630 RSUs to senior management. These awards include a market condition based on the TSR of Innoviva’s common stock over a three-year performance period from the date of grant for the RSAs and from the date of grant until September 30, 2020 for RSUs, and  a service condition that requires continued employment. The grant date fair value of these awards was determined using a Monte Carlo valuation model. The aggregate value of $1.7 million was to be recognized as compensation expense over the implied service period and would not be reversed if the market condition was not met, but with the exception of such person’s continued employment with the Company.

In August and September 2018, all of 111,668 RSAs and 49,630 RSUs were forfeited, and $0.2 million of previously recognized compensation expense was reversed due to the separation of these senior management members.

Stock-Based Compensation Expense

Stock-based compensation expense is included in the condensed consolidated statements of operations as follows:

	Three Months Ended March 31,
(In thousands)	2019		2018
General and administrative	$	605	$	2,169

As of March 31, 2019, unrecognized stock-based compensation cost was as follows:

	Unrecognized
	Compensation
(In thousands)	Cost
RSUs	$	327
RSAs		1,317
Total unrecognized compensation cost	$	1,644

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Debt

3 Months Ended

Mar. 31, 2019

Debt

Debt

6. Debt

Our debt consists of:

	March 31,		December 31,
(In thousands)	2019		2018
Term B Loan	$	13,750	$	13,750
2023 Notes		240,984		240,984
2025 Notes		192,500		192,500
Total debt		447,234		447,234
Unamortized debt discount and issuance costs		(62,490)		(64,379)
Net long-term debt	$	384,744	$	382,855

Prepayments of Senior Secured Term Loans

On February 28 and August 1, 2018, we prepaid the principal balance of the Term B Loan by $120.0 million and $110.0 million, respectively. With the prepayments, we incurred a loss on the extinguishment of debt of $3.1 million and $2.6 million, respectively, representing unamortized debt issuance costs. The loss on the extinguishment of debt is  presented as part of other expense, net in our consolidated statements of operations. As of March 31, 2019, the outstanding principal balance of the Term B Loan was $13.8 million.

Convertible Senior Notes Due 2025

In accordance with accounting guidance for debt with conversion and other options, we separately account for the liability and equity components of the 2025 Notes by allocating the proceeds between the liability component and the embedded conversion option (“equity component”) due to our ability to settle the conversion obligation of the 2025 Notes in cash, common stock or a combination of cash and common stock, at our option. The carrying amount of the liability component was calculated by measuring the fair value of a similar liability that does not have an associated convertible feature using the income approach. The allocation was performed in a manner that reflected our non-convertible debt borrowing rate for similar debt. The equity component of the 2025 Notes was recognized as a debt discount and represents the difference between the proceeds from the issuance of the 2025 Notes and the fair value of the liability of the 2025 Notes on the date of issuance. The excess of the principal amount of the liability component over its carrying amount (“debt discount”) is amortized to interest expense using the effective interest method over the term of the 2025 Notes. The equity component is not remeasured as long as it continues to meet the conditions for equity classification.

Our outstanding 2025 Notes balances consisted of the following:

	March 31,		December 31,
(In thousands)	2019		2018
Liability component
Principal	$	192,500	$	192,500
Debt discount and issuance costs, net		(60,032)		(61,766)
Net carrying amount	$	132,468	$	130,734
Equity component, net	$	65,361	$	65,361

The following table sets forth total interest expense recognized related to the 2025 Notes for the three months ended March 31, 2019 and 2018:

	Three Months Ended March 31,
(In thousands)	2019		2018
Contractual interest expense	$	1,203	$	1,190
Amortization of debt issuance costs		133		123
Amortization of debt discount		1,601		1,479
Total interest and amortization expense	$	2,937	$	2,792

Debt Maturities

The aggregate scheduled maturities of our long-term debt as of March 31, 2019, are as follows:

(In thousands)
Years ending December 31:
2019 to 2021	$	—
2022		13,750
2023		240,984
Thereafter		192,500
Total	$	447,234

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Related Party Transaction

3 Months Ended

Mar. 31, 2019

Related Party Transaction

Related Party Transaction

7. Related Party Transaction

On February 12, 2018, the Company entered into an agreement with Sarissa Capital Management LP, and certain of its affiliates (collectively, the “Sarissa Group”) related to the Company’s 2018 Annual Meeting of Stockholders (the “2018 Annual Meeting”). The agreement provided for, among other things, the concurrent appointment of three designees of the Sarissa Group as members of the Company’s Board of Directors and an agreement to recommend and nominate a five-person slate of directors for election at the 2018 Annual Meeting composed of the three new directors and two current directors of the Company and partially reimburse the Sarissa Group $2.7 million for expenses, which reimbursement obligation relating to the 2018 Annual Meeting arose upon execution of the agreement. The Sarissa Group is considered to be a related party due to its representation on the Board of Directors.

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Income Taxes

3 Months Ended

Mar. 31, 2019

Income Taxes

Income Taxes

8. Income Taxes

Provisional income tax expense for the three months ended March 31, 2019 was $8.5 million, compared to a minimal amount for the same period in 2018 as a full valuation allowance was maintained on the Company's gross deferred taxes. The difference between the Company’s effective income tax rate of 17.5% for the three months ended March 31, 2019 and the U.S. federal statutory rate of 21% is primarily attributable to state income tax, non-deductible expenses and noncontrolling interest.

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Lease

3 Months Ended

Mar. 31, 2019

Lease

Lease

9. Lease

We have an operating lease for our corporate headquarters with a remaining lease term of approximately 4.2 years. The lease includes a five-year renewal option at our sole discretion. The total operating lease expense for this lease was $0.1 million for the three months ended March 31, 2019 and 2018, respectively. Cash paid for amount included in the measurement of operating lease liabilities was $0.1  million for the three months ended March 31, 2019. The lease liabilities were measured using a discount rate of 7.15% based on the most recent borrowing rate for our senior secured Term B Loan.

Future minimum lease payments on our corporate headquarters as of March 31, 2019 are as follows:

(In thousands)
Years ending December 31:
Remainder of 2019	$	304
2020		416
2021		428
2022		441
2023		201
Total future minimum lease payments		1,790
Imputed interest		(244)
Total	$	1,546
Reported as of March 31, 2019
Operating lease liability, current portion	$	308
Operating lease liability, net of current portion		1,238
Total	$	1,546

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Description of Operations and Summary of Significant Accounting Policies (Policies)

3 Months Ended

Mar. 31, 2019

Description of Operations and Summary of Significant Accounting Policies

Basis of Presentation

Basis of Presentation

The accompanying unaudited condensed consolidated financial statements have been prepared in accordance with accounting principles generally accepted in the United States of America ("US GAAP”) for interim financial information. Accordingly, they do not include all of the information and notes required by US GAAP for complete financial statements. In our opinion, the unaudited condensed consolidated financial statements have been prepared on the same basis as audited consolidated financial statements and include all adjustments, consisting of only normal recurring adjustments, necessary for the fair presentation of our financial position, results of operations, comprehensive income and cash flows. The interim results are not necessarily indicative of the results of operations to be expected for the year ending December 31, 2019 or any other period.

The accompanying unaudited condensed consolidated financial statements should be read in conjunction with the audited consolidated financial statements and notes thereto included in our Annual Report on Form 10-K for the year ended December 31, 2018 filed with the Securities and Exchange Commission (“SEC”) on February 19, 2019 (“2018 Form 10-K”).

Variable Interest Entity

Variable Interest Entity

We evaluate our ownership, contractual and other interest in entities to determine if they are variable interest entities (“VIE”), whether we have a variable interest in those entities and the nature and extent of those interests. Based on our evaluation, if we determine we are the primary beneficiary of a VIE, we consolidate the entity into our financial statements. We consolidate the financial results of TRC, which we have determined to be a VIE, because we have the power to direct the economically significant activities of TRC and the obligation to absorb losses of, or the right to receive benefits from, TRC. As of March 31, 2019 and December 31, 2018, $7.3 million and $6.4 million, respectively, of the related party receivables from collaborative arrangements were attributable to TRC. Total revenue for TRC related to TRELEGY® ELLIPTA® for the three months ended March 31, 2019 and 2018 was $7.3 million and $1.0 million, respectively.

Accounting Pronouncement Adopted by the Company

Accounting Pronouncement Adopted by the Company

In February 2016, the Financial Accounting Standards Board (the “FASB”) issued Accounting Standards Update (“ASU”) 2016 02, Leases (Topic 842), which requires an entity to recognize right of use assets representing its right to use the underlying asset for the lease term and lease liabilities representing the present value of the future lease payments for both financing and operating leases on its consolidated balance sheets. For a lease with a term of 12 months or less, the standard allows an entity to elect not to recognize a right-of-use asset and a lease liability and recognize the lease expense on a straight-line basis. We adopted the standard on the effective date of January 1, 2019 using the alternative transition approach. This approach is similar to a prospective transition, which requires the application of ASC 842 at the effective date with a cumulative-effect adjustment recognized through retained earnings. Under this approach, we do not present the adjusted comparative periods. Our pro-rata share of common area expenses are recorded as lease expense when incurred since they are variable and considered nonlease components under the standard. The most significant impact of the adoption to us is that we recognized a right of use asset in the amount of $1.5 million and lease liabilities in the total amount of $1.6 million at January 1, 2019 for the operating lease on our corporate headquarters. The adoption did not have a material impact on our retained earnings and consolidated statements of operations and cash flows.

In August 2018, the U.S. Securities and Exchange Commission (the “SEC”) adopted the final rule under SEC Release No. 33-10532, Disclosure Update and Simplification, amending certain disclosure requirements that were redundant, duplicative, overlapping, outdated or superseded. In addition, the amendments expanded the disclosure requirements relating to the analysis of stockholders’ equity for interim financial statements. Under the amendments, an analysis of changes in each caption of stockholders’ equity presented in the balance sheet must be provided in a note or separate statement. The analysis should present a reconciliation of the beginning balance to the ending balance of each period for which a statement of income is required to be filed. This final rule is effective on November 5, 2018. Effective January 1, 2019, the Company adopted SEC Release No. 33-10532. In accordance with the new guidance, the Company has added a Condensed Consolidated Statement of Changes in Stockholders’ Equity (Deficit) in its Form 10-Q and elected to present a reconciliation in a single statement that shows the changes in stockholders equity for each interim period, as well as each comparable period.

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Net Income Per Share (Tables)

3 Months Ended

Mar. 31, 2019

Net Income Per Share

Schedule of computation of basic and diluted net income per share

	Three Months Ended March 31,
(In thousands except per share data)	2019		2018
Numerator:
Net income attributable to Innoviva stockholders, basic	$	33,790	$	29,581
Add: interest expense on 2023 Notes		1,415		1,412
Net income attributable to Innoviva stockholders, diluted	$	35,205	$	30,993
Denominator:
Weighted-average shares used to compute basic net income per share attributable to Innoviva stockholders		101,059		100,604
Dilutive effect of  2023 Notes		12,189		12,189
Dilutive effect of options and awards granted under equity incentive plan and employee stock purchase plan		128		773
Weighted-average shares used to compute diluted net income per share attributable to Innoviva stockholders		113,376		113,566
Net income per share attributable to Innoviva stockholders
Basic	$	0.33	$	0.29
Diluted	$	0.31	$	0.27

Schedule of anti-dilutive securities

	Three Months Ended March 31,
(In thousands)	2019	2018
Outstanding options and awards granted under equity incentive plan and employee stock purchase plan	1,053	1,492

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Revenue Recognition and Collaborative Arrangements (Tables)

3 Months Ended

Mar. 31, 2019

Revenue Recognition and Collaborative Arrangements

Schedule of net revenue from collaborative arrangements

	Three Months Ended March 31,
(In thousands)	2019		2018
Royalties from a related party - RELVAR/BREO	$	42,740	$	46,160
Royalties from a related party - ANORO		8,570		8,724
Royalties from a related party - TRELEGY		7,329		952
Total royalties from a related party		58,639		55,836
Less: amortization of capitalized fees paid to a related party		(3,456)		(3,456)
Royalty revenue from GSK	$	55,183	$	52,380

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Available-for-Sale Securities and Fair Value Measurements (Tables)

3 Months Ended

Mar. 31, 2019

Available-for-Sale Securities and Fair Value Measurements

Schedule of amortized cost and estimated fair values for available-for-sale securities

	March 31, 2019
			Gross		Gross
			Unrealized		Unrealized		Estimated
(In thousands)	Amortized Cost		Gains		Losses		Fair Value
U.S. government securities	$	68,691	$	9	$	—	$	68,700
U.S. government agencies		24,768		1		—		24,769
U.S. commercial paper		41,550		—		—		41,550
Money market funds		45,253		—		—		45,253
Total	$	180,262	$	10	$	—	$	180,272

	December 31, 2018
			Gross		Gross
			Unrealized		Unrealized		Estimated
(In thousands)	Amortized Cost		Gains		Losses		Fair Value
U.S. government securities	$	29,736	$	—	$	(3)	$	29,733
U.S. government agencies		4,971		—		—		4,971
U.S. corporate notes		2,875		—		—		2,875
U.S. commercial paper		22,037		—		—		22,037
Money market funds		49,358		—		—		49,358
Total	$	108,977	$	—	$	(3)	$	108,974

Schedule of available-for-sale securities measured at fair value on a recurring basis

	Estimated Fair Value Measurements as of March 31, 2019 Using:
	Quoted Price in
	Active Markets		Significant Other		Significant
	for Identical		Observable		Unobservable
Types of Instruments	Assets		Inputs		Inputs
(In thousands)	Level 1		Level 2		Level 3		Total
Assets
U.S. government securities	$	—	$	68,700	$	—	$	68,700
U.S. government agencies		—		24,769		—		24,769
U.S. commercial paper		—		41,550		—		41,550
Money market funds		45,253		—		—		45,253
Total assets measured at estimated fair value	$	45,253	$	135,019	$	—	$	180,272
Debt
Term B Loan	$	—	$	13,750	$	—	$	13,750
2023 Notes		—		245,353		—		245,353
2025 Notes		—		205,911		—		205,911
Total fair value of debt	$	—	$	465,014	$	—	$	465,014

	Estimated Fair Value Measurements as of December 31, 2018 Using:
Types of Instruments	Quoted Price in Active Markets for Identical Assets		Significant Other Observable Inputs		Significant Unobservable Inputs
(In thousands)	Level 1		Level 2		Level 3		Total
Assets
U.S. government securities	$	—	$	29,733	$	—	$	29,733
U.S. government agencies		—		4,971		—		4,971
U.S. corporate notes		—		2,875		—		2,875
U.S. commercial paper		—		22,037		—		22,037
Money market funds		49,358		—		—		49,358
Total assets measured at estimated fair value	$	49,358	$	59,616	$	—	$	108,974
Debt
Term B Loan	$	—	$	13,750	$	—	$	13,750
2023 Notes		—		258,918		—		258,918
2025 Notes		—		230,692		—		230,692
Total fair value of debt	$	—	$	503,360	$	—	$	503,360

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Stock-Based Compensation (Tables)

3 Months Ended

Mar. 31, 2019

Stock-Based Compensation

Schedule of stock-based compensation expense

	Three Months Ended March 31,
(In thousands)	2019		2018
General and administrative	$	605	$	2,169

Schedule of unrecognized stock-based compensation cost

As of March 31, 2019, unrecognized stock-based compensation cost was as follows:

	Unrecognized
	Compensation
(In thousands)	Cost
RSUs	$	327
RSAs		1,317
Total unrecognized compensation cost	$	1,644

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Debt (Tables)

3 Months Ended

Mar. 31, 2019

Debt

Schedule of debt

	March 31,		December 31,
(In thousands)	2019		2018
Term B Loan	$	13,750	$	13,750
2023 Notes		240,984		240,984
2025 Notes		192,500		192,500
Total debt		447,234		447,234
Unamortized debt discount and issuance costs		(62,490)		(64,379)
Net long-term debt	$	384,744	$	382,855

Aggregate scheduled maturities of long-term debt

The aggregate scheduled maturities of our long-term debt as of March 31, 2019, are as follows:

(In thousands)
Years ending December 31:
2019 to 2021	$	—
2022		13,750
2023		240,984
Thereafter		192,500
Total	$	447,234

2025 Notes

Debt

Summary of liability and equity components of convertible notes

Our outstanding 2025 Notes balances consisted of the following:

	March 31,		December 31,
(In thousands)	2019		2018
Liability component
Principal	$	192,500	$	192,500
Debt discount and issuance costs, net		(60,032)		(61,766)
Net carrying amount	$	132,468	$	130,734
Equity component, net	$	65,361	$	65,361

Schedule of components of interest expense

	Three Months Ended March 31,
(In thousands)	2019		2018
Contractual interest expense	$	1,203	$	1,190
Amortization of debt issuance costs		133		123
Amortization of debt discount		1,601		1,479
Total interest and amortization expense	$	2,937	$	2,792

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Lease (Tables)

3 Months Ended

Mar. 31, 2019

Lease

Schedule of future minimum lease payments

Future minimum lease payments on our corporate headquarters as of March 31, 2019 are as follows:

(In thousands)
Years ending December 31:
Remainder of 2019	$	304
2020		416
2021		428
2022		441
2023		201
Total future minimum lease payments		1,790
Imputed interest		(244)
Total	$	1,546
Reported as of March 31, 2019
Operating lease liability, current portion	$	308
Operating lease liability, net of current portion		1,238
Total	$	1,546

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Description of Operations and Summary of Significant Accounting Policies - Description of Operations and Variable Interest Entity (Details) - USD ($) $ in Thousands	3 Months Ended
	Mar. 31, 2019	Mar. 31, 2018	Dec. 31, 2018
Description of Operations and Summary of Significant Accounting Policies
Net revenue	$ 55,183	$ 52,380
GSK
Description of Operations and Summary of Significant Accounting Policies
Net revenue	$ 55,183	52,380
Long-Acting Beta2 Agonist (LABA) Collaboration | GSK
Description of Operations and Summary of Significant Accounting Policies
Percentage of economic interest in any future payments made under the agreements	15.00%
Long-Acting Beta2 Agonist (LABA) Collaboration | GSK | RELVAR/BREO
Description of Operations and Summary of Significant Accounting Policies
Royalty rate for first level of annual global net sales (as a percent)	15.00%
Annual global sales level used to determine royalty rate	$ 3,000,000
Royalty rate for sales above first level of annual global net sales (as a percent)	5.00%
Long-Acting Beta2 Agonist (LABA) Collaboration | GSK | ANORO | Minimum
Description of Operations and Summary of Significant Accounting Policies
Royalty rate for combination products (as a percent)	6.50%
Long-Acting Beta2 Agonist (LABA) Collaboration | GSK | ANORO | Maximum
Description of Operations and Summary of Significant Accounting Policies
Royalty rate for combination products (as a percent)	10.00%
TRC | TRELEGY
Description of Operations and Summary of Significant Accounting Policies
Net revenue	$ 7,300	$ 1,000
TRC | Collaborative arrangement
Description of Operations and Summary of Significant Accounting Policies
Related-party receivables	$ 7,300		$ 6,400

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Description of Operations and Summary of Significant Accounting Policies - Accounting Pronouncements (Details) - USD ($) $ in Thousands	Mar. 31, 2019	Jan. 01, 2019	Dec. 31, 2018	[1]
Recently Issued Accounting Pronouncement Not Yet Adopted
Operating lease right-of-use asset	$ 1,421		$ 0
Operating lease liability	$ 1,546
ASU 2016-02, Leases
Recently Issued Accounting Pronouncement Not Yet Adopted
Operating lease right-of-use asset		$ 1,500
Operating lease liability		$ 1,600

[1] Condensed consolidated balance sheet as of December 31, 2018 has been derived from audited consolidated financial statements.

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Net Income Per Share - Basic and Diluted EPS (Details) - USD ($) $ / shares in Units, shares in Thousands, $ in Thousands	3 Months Ended
	Mar. 31, 2019	Mar. 31, 2018
Numerator:
Net income attributable to Innoviva stockholders, basic	$ 33,790	$ 29,581
Add: interest expense on 2023 Notes	1,415	1,412
Net income attributable to Innoviva stockholders, diluted	$ 35,205	$ 30,993
Denominator:
Weighted-average shares used to compute basic net income per share attributable to Innoviva stockholders	101,059	100,604
Dilutive effect of 2023 Notes	12,189	12,189
Dilutive effect of options and awards granted under equity incentive plan and employee stock purchase plan	128	773
Weighted-average shares used to compute diluted net income per share attributable to Innoviva stockholders	113,376	113,566
Net income per share attributable to Innoviva stockholders
Basic net income per share	$ 0.33	$ 0.29
Diluted net income per share	$ 0.31	$ 0.27
Convertible senior notes | 2025 Notes
Net Income Per Share
Dilutive effect of 2025 Notes	0
Convertible senior notes | 2025 Notes | Common Stock
Net Income Per Share
Conversion price of convertible notes into common stock (in dollars per share)	$ 17.26

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Net Income Per Share - Anti-Dilutive Securities (Details) - shares shares in Thousands	3 Months Ended
	Mar. 31, 2019	Mar. 31, 2018
Equity incentive plans and ESPP
Anti-Dilutive Securities
Anti-dilutive securities (in shares)	1,053	1,492

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Revenue Recognition and Collaborative Arrangements (Details) - USD ($) $ in Thousands	3 Months Ended
	Mar. 31, 2019	Mar. 31, 2018
Revenue Recognition and Collaborative Arrangements
Total net revenue from GSK	$ 55,183	$ 52,380
GSK
Revenue Recognition and Collaborative Arrangements
Total net revenue from GSK	55,183	52,380
GSK | Royalty revenue from a related party
Revenue Recognition and Collaborative Arrangements
Royalties from a related party	58,639	55,836
Less: amortization of capitalized fees paid to a related party	(3,456)	(3,456)
GSK | RELVAR/BREO
Revenue Recognition and Collaborative Arrangements
Royalties from a related party	42,740	46,160
GSK | ANORO
Revenue Recognition and Collaborative Arrangements
Royalties from a related party	8,570	8,724
GSK | TRELEGY
Revenue Recognition and Collaborative Arrangements
Royalties from a related party	$ 7,329	$ 952

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Available-for-Sale Securities and Fair Value Measurements - Available-for-Sale Securities (Details) - USD ($) $ in Thousands	3 Months Ended
	Mar. 31, 2019	Dec. 31, 2018
Available-for-Sale Securities
Amortized Cost	$ 180,262	$ 108,977
Gross Unrealized Gains	10	0
Gross Unrealized Losses	0	(3)
Estimated Fair Value	$ 180,272	108,974
Maturity period for marketable securities
Maximum contractual maturity	1 year
Weighted average maturity	4 months
U.S. government securities
Available-for-Sale Securities
Amortized Cost	$ 68,691	29,736
Gross Unrealized Gains	9	0
Gross Unrealized Losses	0	(3)
Estimated Fair Value	68,700	29,733
U.S. government agencies
Available-for-Sale Securities
Amortized Cost	24,768	4,971
Gross Unrealized Gains	1	0
Gross Unrealized Losses	0	0
Estimated Fair Value	24,769	4,971
U.S. corporate notes
Available-for-Sale Securities
Amortized Cost		2,875
Gross Unrealized Gains		0
Gross Unrealized Losses		0
Estimated Fair Value		2,875
U.S. commercial paper
Available-for-Sale Securities
Amortized Cost	41,550	22,037
Gross Unrealized Gains	0	0
Gross Unrealized Losses	0	0
Estimated Fair Value	41,550	22,037
Money market funds
Available-for-Sale Securities
Amortized Cost	45,253	49,358
Gross Unrealized Gains	0	0
Gross Unrealized Losses	0	0
Estimated Fair Value	$ 45,253	$ 49,358

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Available-for-Sale Securities and Fair Value Measurements - Fair Value Measurements (Details) - USD ($) $ in Thousands	Mar. 31, 2019	Dec. 31, 2018
Recurring basis
Assets
Total assets measured at estimated fair value	$ 180,272	$ 108,974
Recurring basis | U.S. government securities
Assets
Total assets measured at estimated fair value	68,700	29,733
Recurring basis | U.S. government agencies
Assets
Total assets measured at estimated fair value	24,769	4,971
Recurring basis | U.S. corporate notes
Assets
Total assets measured at estimated fair value		2,875
Recurring basis | U.S. commercial paper
Assets
Total assets measured at estimated fair value	41,550	22,037
Recurring basis | Money market funds
Assets
Total assets measured at estimated fair value	45,253	49,358
Recurring basis | Quoted Price in Active Markets for Identical Assets, Level 1
Assets
Total assets measured at estimated fair value	45,253	49,358
Recurring basis | Quoted Price in Active Markets for Identical Assets, Level 1 | U.S. government securities
Assets
Total assets measured at estimated fair value	0	0
Recurring basis | Quoted Price in Active Markets for Identical Assets, Level 1 | U.S. government agencies
Assets
Total assets measured at estimated fair value	0	0
Recurring basis | Quoted Price in Active Markets for Identical Assets, Level 1 | U.S. corporate notes
Assets
Total assets measured at estimated fair value		0
Recurring basis | Quoted Price in Active Markets for Identical Assets, Level 1 | U.S. commercial paper
Assets
Total assets measured at estimated fair value	0	0
Recurring basis | Quoted Price in Active Markets for Identical Assets, Level 1 | Money market funds
Assets
Total assets measured at estimated fair value	45,253	49,358
Recurring basis | Significant Other Observable Inputs, Level 2
Assets
Total assets measured at estimated fair value	135,019	59,616
Recurring basis | Significant Other Observable Inputs, Level 2 | U.S. government securities
Assets
Total assets measured at estimated fair value	68,700	29,733
Recurring basis | Significant Other Observable Inputs, Level 2 | U.S. government agencies
Assets
Total assets measured at estimated fair value	24,769	4,971
Recurring basis | Significant Other Observable Inputs, Level 2 | U.S. corporate notes
Assets
Total assets measured at estimated fair value		2,875
Recurring basis | Significant Other Observable Inputs, Level 2 | U.S. commercial paper
Assets
Total assets measured at estimated fair value	41,550	22,037
Recurring basis | Significant Other Observable Inputs, Level 2 | Money market funds
Assets
Total assets measured at estimated fair value	0	0
Recurring basis | Significant Unobservable Inputs, Level 3
Assets
Total assets measured at estimated fair value	0	0
Recurring basis | Significant Unobservable Inputs, Level 3 | U.S. government securities
Assets
Total assets measured at estimated fair value	0	0
Recurring basis | Significant Unobservable Inputs, Level 3 | U.S. government agencies
Assets
Total assets measured at estimated fair value	0	0
Recurring basis | Significant Unobservable Inputs, Level 3 | U.S. corporate notes
Assets
Total assets measured at estimated fair value		0
Recurring basis | Significant Unobservable Inputs, Level 3 | U.S. commercial paper
Assets
Total assets measured at estimated fair value	0	0
Recurring basis | Significant Unobservable Inputs, Level 3 | Money market funds
Assets
Total assets measured at estimated fair value	0	0
Nonrecurring basis | Debt
Debt
Term B Loan	13,750	13,750
2023 Notes	245,353	258,918
2025 Notes	205,911	230,692
Total fair value of liabilities	465,014	503,360
Nonrecurring basis | Quoted Price in Active Markets for Identical Assets, Level 1 | Debt
Debt
Term B Loan	0	0
2023 Notes	0	0
2025 Notes	0	0
Total fair value of liabilities	0	0
Nonrecurring basis | Significant Other Observable Inputs, Level 2 | Debt
Debt
Term B Loan	13,750	13,750
2023 Notes	245,353	258,918
2025 Notes	205,911	230,692
Total fair value of liabilities	465,014	503,360
Nonrecurring basis | Significant Unobservable Inputs, Level 3 | Debt
Debt
Term B Loan	0	0
2023 Notes	0	0
2025 Notes	0	0
Total fair value of liabilities	$ 0	$ 0

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Stock-Based Compensation - 2016 Market-Based RSAs and RSUs (Details) - 2016 Market-Based RSAs and RSUs - USD ($) $ in Millions		1 Months Ended	2 Months Ended	3 Months Ended
	Jan. 14, 2016	Feb. 28, 2018	Sep. 30, 2018	Mar. 31, 2018
Market-Based RSAs and RSUs
Stock-based compensation
Reversal of previously recognized compensation expense			$ 0.2
Market-Based RSAs and RSUs | TSR and Performance Measures | Released on February 20, 2018
Stock-based compensation
Vesting percentage		66.70%
Market-Based RSAs
Stock-based compensation
Forfeited (in shares)			34,722
Market-Based RSAs | TSR and Performance Measures | Released on February 20, 2018
Stock-based compensation
Exercised (in shares)		69,440
Market-Based RSAs | TSR and Performance Measures | Senior Management
Stock-based compensation
Granted (in shares)	282,394
Vested (in shares)		118,821
Stock-based compensation, net				$ 0.7
Forfeited (in shares)		59,411
Market-Based RSUs
Stock-based compensation
Forfeited (in shares)			15,432
Market-Based RSUs | TSR and Performance Measures | Released on February 20, 2018
Stock-based compensation
Exercised (in shares)		30,862
Market-Based RSUs | TSR and Performance Measures | Senior Management
Stock-based compensation
Granted (in shares)	46,294

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Stock-Based Compensation - 2017 Market-Based RSAs and RSUs (Details) - 2017 Market-Based RSAs and RSUs - USD ($) $ in Millions		2 Months Ended	3 Months Ended
	Jan. 17, 2017	Sep. 30, 2018	Mar. 31, 2018
Market-Based RSAs and RSUs
Stock-based compensation
Reversal of previously recognized compensation expense		$ 0.9
Market-Based RSAs
Stock-based compensation
Forfeited (in shares)		120,060
Market-Based RSAs | TSR and Performance Measures | Senior Management
Stock-based compensation
Granted (in shares)	353,508
Forfeited (in shares)			233,448
Reversal of previously recognized compensation expense			$ 0.8
Market-Based RSUs
Stock-based compensation
Forfeited (in shares)		53,360
Market-Based RSUs | TSR and Performance Measures | Senior Management
Stock-based compensation
Granted (in shares)	53,360

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Stock-Based Compensation - 2018 Market-Based RSAs and RSUs (Details) - 2018 Market-Based RSAs and RSUs $ in Millions	Mar. 02, 2018 USD ($) shares
Market-Based RSAs and RSUs
Stock-based compensation
Reversal of previously recognized compensation expense | $	$ 0.2
Market-Based RSAs and RSUs | TSR and Performance Measures | Senior Management
Stock-based compensation
Timeframe for calculation of TSR	3 years
Aggregate value to be recognized as compensation expense | $	$ 1.7
Market-Based RSAs
Stock-based compensation
Forfeited (in shares)	111,668
Market-Based RSAs | TSR and Performance Measures | Senior Management
Stock-based compensation
Granted (in shares)	111,668
Market-Based RSUs
Stock-based compensation
Forfeited (in shares)	49,630
Market-Based RSUs | TSR and Performance Measures | Senior Management
Stock-based compensation
Granted (in shares)	49,630

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Stock-Based Compensation - Stock-Based Compensation Expense (Details) - USD ($) $ in Thousands	3 Months Ended
	Mar. 31, 2019	Mar. 31, 2018
Stock-based compensation
Unrecognized compensation cost	$ 1,644
RSUs
Stock-based compensation
Unrecognized compensation cost	327
RSAs
Stock-based compensation
Unrecognized compensation cost	1,317
General and administrative
Stock-based compensation
Total stock-based compensation expense	$ 605	$ 2,169

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Debt - Summary (Details) - USD ($) $ in Thousands	Mar. 31, 2019	Dec. 31, 2018
Debt
Total debt	$ 447,234	$ 447,234
Unamortized debt discount and issuance costs	(62,490)	(64,379)
Net long-term debt	384,744	382,855	[1]
Term B Loan | Senior secured term loans
Debt
Total debt	13,750	13,750
2023 Notes | Convertible subordinated notes
Debt
Total debt	240,984	240,984
2025 Notes | Convertible senior notes
Debt
Total debt	192,500	192,500
Unamortized debt discount and issuance costs	$ (60,032)	$ (61,766)

[1] Condensed consolidated balance sheet as of December 31, 2018 has been derived from audited consolidated financial statements.

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Debt - Prepayments of Senior Secured Term Loans (Details) - USD ($) $ in Thousands	Aug. 01, 2018	Feb. 28, 2018	Mar. 31, 2019	Dec. 31, 2018
Debt
Total debt			$ 447,234	$ 447,234
Senior secured term loans | Term B Loan
Debt
Prepayments of principal on senior secured term loans	$ 110,000	$ 120,000
Total debt			$ 13,750	$ 13,750
Senior secured term loans | Term B Loan | Other Expense
Debt
Write-off of debt issuance costs	$ 2,600	$ 3,100

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Debt - Convertible Senior Notes - Liability and Equity Components (Details) - USD ($) $ in Thousands	Mar. 31, 2019	Dec. 31, 2018
Liability component
Outstanding principal balance	$ 447,234	$ 447,234
Debt discount and issuance costs, net	(62,490)	(64,379)
Convertible senior notes | 2025 Notes
Liability component
Outstanding principal balance	192,500	192,500
Debt discount and issuance costs, net	(60,032)	(61,766)
Net carrying amount	132,468	130,734
Equity component, net	$ 65,361	$ 65,361

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Debt - Convertible Senior Notes - Interest and Amortization Expense (Details) - Convertible senior notes - 2025 Notes - USD ($) $ in Thousands	3 Months Ended
	Mar. 31, 2019	Mar. 31, 2018
Interest expense
Contractual interest expense	$ 1,203	$ 1,190
Amortization of debt issuance costs	133	123
Amortization of debt discount	1,601	1,479
Total interest and amortization expense	$ 2,937	$ 2,792

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Debt - Debt Maturities (Details) - USD ($) $ in Thousands	Mar. 31, 2019	Dec. 31, 2018
Long-term debt maturities
2019-2021	$ 0
2022	13,750
2023	240,984
Thereafter	192,500
Total	$ 447,234	$ 447,234

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Related Party Transaction (Details) - Sarissa Group $ in Millions	Feb. 12, 2018 USD ($) director
Related Parties
Appointment of designees as as members of the Company's Board of Directors	3
Total number of directors nominated for election	5
Number of new directors nominated for election	3
Number of current directors nominated for election	2
Payments for agreements with related parties | $	$ 2.7

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Income Taxes (Details) - USD ($) $ in Thousands	3 Months Ended
	Mar. 31, 2019	Mar. 31, 2018
Income Taxes
Effective tax rate (as a percent)	17.50%
Federal statutory tax rate (as a percent)	21.00%
Income tax expense, net	$ 8,508	$ 0

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Lease (Details) - USD ($) $ in Thousands	3 Months Ended
	Mar. 31, 2019	Mar. 31, 2018	Dec. 31, 2018	[1]
Lease
Operating lease, remaining lease term	4 years 2 months 12 days
Operating lease, renewal term	5 years
Operating lease, existence of option to extend	true
Operating lease expense	$ 100	$ 100
Cash paid for amount included in the measurement of operating lease liabilities	$ 100
Discount rate used to measure lease liability	7.15%
Future minimum lease payments
Remainder of 2019	$ 304
2020	416
2021	428
2022	441
2023	201
Total future minimum lease payments	1,790
Imputed interest	(244)
Total	1,546
Operating lease liability, current portion	308		$ 0
Operating lease liability, net of current portion	$ 1,238		$ 0

[1] Condensed consolidated balance sheet as of December 31, 2018 has been derived from audited consolidated financial statements.