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Document And Entity Information - shares	9 Months Ended
Document And Entity Information - shares	Sep. 30, 2016	Oct. 31, 2016
Document And Entity Information [Abstract]
Document Type	10-Q
Amendment Flag	false
Document Period End Date	Sep. 30, 2016
Document Fiscal Year Focus	2016
Document Fiscal Period Focus	Q3
Entity Registrant Name	CHIMERIX INC
Entity Central Index Key	0001117480
Current Fiscal Year End Date	--12-31
Entity Filer Category	Large Accelerated Filer
Entity Common Stock, Shares Outstanding (in shares)		46,315,425

Consolidated Balance Sheets - USD ($) $ in Thousands	Sep. 30, 2016	Dec. 31, 2015
Current assets:
Cash and cash equivalents	$ 49,358	$ 20,605
Short-term investments, available-for-sale	200,315	199,729
Accounts receivable	379	2,432
Prepaid expenses and other current assets	4,318	6,071
Total current assets	254,370	228,837
Long-term investments	39,801	124,040
Property and equipment, net of accumulated depreciation	3,048	3,045
Other long-term assets	34	70
Total assets	297,253	355,992
Current liabilities:
Accounts payable	3,280	10,458
Accrued liabilities	6,338	9,721
Total current liabilities	9,618	20,179
Deferred rent	285	354
Total liabilities	9,903	20,533
Stockholders’ equity:
Preferred stock, $0.001 par value, 10,000,000 shares authorized at September 30, 2016 and December 31, 2015; no shares issued and outstanding as of September 30, 2016 and December 31, 2015	0	0
Common stock, $0.001 par value, 200,000,000 shares authorized at September 30, 2016 and December 31, 2015; 46,315,425 and 46,162,525 shares issued and outstanding as of September 30, 2016 and December 31, 2015, respectively	46	46
Additional paid-in capital	688,518	675,591
Accumulated other comprehensive loss, net	(366)	(764)
Accumulated deficit	(400,848)	(339,414)
Total stockholders’ equity	287,350	335,459
Total liabilities and stockholders’ equity	$ 297,253	$ 355,992

Consolidated Balance Sheets (Parenthetical) - $ / shares	Sep. 30, 2016	Dec. 31, 2015
Statement of Financial Position [Abstract]
Preferred stock, par value (in dollars per share)	$ 0.001	$ 0.001
Preferred stock, shares authorized (in shares)	10,000,000	10,000,000
Preferred stock shares issued (in shares)	0	0
Preferred stock, shares outstanding (in shares)	0	0
Common stock, par value (in dollars per share)	$ 0.001	$ 0.001
Common stock, shares authorized (in shares)	200,000,000	200,000,000
Common stock, shares issued (in shares)	46,315,425	46,162,525
Common stock, shares outstanding (in shares)	46,315,425	46,162,525

Consolidated Statements of Operations and Comprehensive Loss - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2016	Sep. 30, 2015	Sep. 30, 2016	Sep. 30, 2015
Revenues:
Contract revenue	$ 653	$ 2,271	$ 3,722	$ 6,104
Collaboration and licensing revenue	0	0	0	1,548
Total revenues	653	2,271	3,722	7,652
Operating expenses:
Research and development	12,247	26,495	46,942	65,867
General and administrative	5,827	8,524	19,359	21,812
Total operating expenses	18,074	35,019	66,301	87,679
Loss from operations	(17,421)	(32,748)	(62,579)	(80,027)
Interest income, net	396	299	1,146	498
Net loss	(17,025)	(32,449)	(61,433)	(79,529)
Other comprehensive loss:
Unrealized (loss) gain on investments, net	(98)	(1,448)	398	321
Comprehensive loss	$ (17,123)	$ (33,897)	$ (61,035)	$ (79,208)
Per share information:
Net loss, basic and diluted (in dollars per share)	$ (0.37)	$ (0.70)	$ (1.33)	$ (1.84)
Weighted-average shares outstanding, basic and diluted (in shares)	46,236,749	46,059,112	46,211,748	43,112,314

Consolidated Statements of Cash Flows - USD ($) $ in Thousands	9 Months Ended
	Sep. 30, 2016	Sep. 30, 2015
Cash flows from operating activities:
Net loss	$ (61,433)	$ (79,529)
Adjustments to reconcile net loss to net cash used in operating activities:
Depreciation of property and equipment	781	444
Amortization of debt costs	0	64
Amortization of premium/discount on investments	1,010	1,186
Share-based compensation	12,334	8,882
Amortization of deferred lease obligations	(51)	4
Loss on disposition of assets	4	0
Changes in operating assets and liabilities:
Accounts receivable	2,080	(419)
Prepaid expenses and other assets	1,737	(5,354)
Accounts payable and accrued liabilities	(10,580)	7,931
Net cash used in operating activities	(54,118)	(66,791)
Cash flows from investing activities:
Purchases of property and equipment	(763)	(1,574)
Purchases of short-term investments	(13,990)	(56,294)
Purchases of long-term investments	(50,867)	(212,766)
Proceeds from sales of short-term investments	0	1,003
Proceeds from maturities of short-term investments	147,899	90,822
Net cash provided by (used in) investing activities	82,279	(178,809)
Cash flows from financing activities:
Proceeds from exercise of stock options	152	1,967
Proceeds from employee stock purchase plan stock purchases	440	1,054
Proceeds from exercise of warrants	0	1,000
Proceeds from public offering, net of offering costs	0	161,880
Repayment of debt	0	(3,975)
Payments for deferred financing costs	0	(68)
Net cash provided by financing activities	592	161,858
Net increase (decrease) in cash and cash equivalents	28,753	(83,742)
Cash and cash equivalents:
Beginning of period	20,605	128,462
End of period	49,358	44,720
Supplemental disclosure of cash flow information:
Cash paid for interest	$ 0	$ 156

The Business and Summary of Significant Accounting Policies

9 Months Ended

Sep. 30, 2016

Accounting Policies [Abstract]

The Business and Summary of Significant Accounting Policies

Description of Business

Chimerix, Inc. (the Company) is a biopharmaceutical company dedicated to discovering, developing and commercializing novel antivirals to address areas of high unmet medical needs. The Company was founded in 2000 based on the promise of its proprietary lipid conjugate technology to unlock the potential of some of the most broad-spectrum antivirals by enhancing their antiviral activity and safety profiles in convenient dosing regimens. Based on the Company’s proprietary lipid conjugate technology, its lead compound, brincidofovir, is in clinical development for the treatment and prevention of adenovirus (AdV), cytomegalovirus (CMV) and smallpox. In addition, the Company has an active discovery program focusing on viral targets for which limited or no therapies are currently available, including most recently a clinical candidate for the prevention and treatment of norovirus infection.

Basis of Presentation

The accompanying unaudited consolidated financial statements include the accounts of the Company and its wholly owned subsidiary. The accompanying unaudited consolidated financial statements have been prepared in accordance with accounting principles generally accepted in the United States of America (GAAP) for interim financial information, the instructions to Form 10-Q and Article 10 of Regulation S-X. Accordingly, they do not include all of the information and footnotes required by GAAP for complete financial statements and should be read in conjunction with the Company’s audited financial statements and notes thereto included in its Annual Report on Form 10-K for the year ended December 31, 2015. In the opinion of the Company’s management, all adjustments, consisting of normal recurring adjustments, necessary for a fair presentation of its financial position, operating results and cash flows for the periods presented have been included. Operating results for the three and nine months ended September 30, 2016 are not necessarily indicative of the results that may be expected for the full year, for any other interim period or for any future year.

Fair Value of Financial Instruments

The carrying amounts of certain financial instruments, including accounts receivable, accounts payable and accrued expenses approximate their fair values due to the short-term nature of such instruments.

For assets and liabilities recorded at fair value, it is the Company’s policy to maximize the use of observable inputs and minimize the use of unobservable inputs when developing fair value measurements, in accordance with the fair value hierarchy. Fair value measurements for assets and liabilities where there exists limited or no observable market data are based primarily upon estimates and are often calculated based on the economic and competitive environment, the characteristics of the asset or liability and other factors. Therefore, fair value measurements cannot be determined with precision and may not be realized in an actual sale or immediate settlement of the asset or liability. Additionally, there may be inherent weaknesses in any calculation technique and changes in the underlying assumptions used, including discount rates and estimates of future cash flows, could significantly affect the calculated current or future fair values. The Company utilizes fair value measurements to record fair value adjustments to certain assets and liabilities and to determine fair value disclosures.

The Company groups assets and liabilities at fair value in three levels, based on the markets in which the assets and liabilities are traded and the reliability of the assumptions used to determine fair value. An adjustment to the pricing method used within either Level 1 or Level 2 inputs could generate a fair value measurement that effectively falls in a lower level in the hierarchy. These levels are:


•	Level 1 — Valuations based on unadjusted quoted prices in active markets for identical assets or liabilities that the Company has the ability to access.


•	Level 2 — Valuations based on quoted prices for similar assets or liabilities in active markets, quoted prices for identical or similar assets or liabilities in markets that are not active, and models for which all significant inputs are observable, either directly or indirectly.


•	Level 3 — Valuations based on inputs that are unobservable and significant to the overall fair value measurement.

The determination of where an asset or liability falls in the hierarchy requires significant judgment. The Company evaluates hierarchy disclosures and, based on various factors, it is possible that an asset or liability may be classified differently from period to period. However, the Company expects that changes in classification between levels will be rare. In June 2016, the Company's preferred stock investment in ContraVir Pharmaceuticals (NASDAQ: CTRV) (ContraVir) was transferred from Level 3 to Level 2. In September 2016, the Company's investment in ContraVir was transferred from Level 2 to Level 1. See below for further discussion.

At September 30, 2016 and December 31, 2015, the Company had cash equivalents, consisting of money market accounts, and short-term and long-term investments consisting of U.S. Treasury securities, whose value is based on using quoted market prices. Accordingly, these securities are classified as Level 1.

At September 30, 2016 the Company had cash equivalents consisting of commercial paper, at September 30, 2016 and December 31, 2015, the Company had short-term investments consisting of brokered certificates of deposit, and at December 31, 2015, the Company had long-term investments consisting of brokered certificates of deposit. As quoted prices are not available for these securities, they are valued using independent pricing models or other model-based valuation techniques such as the present value of future cash flows, adjusted for the security’s credit rating, prepayment assumptions and other factors such as credit loss assumptions. Accordingly, these securities are classified as Level 2.

In December 2014, the Company entered into a license agreement with ContraVir for the development and commercialization of CMX157 for certain antiviral indications. Under the terms of the agreement, ContraVir has sole responsibility with respect to the control of the development and commercialization of CMX157. In exchange for the license to CMX157 rights, the Company received an upfront payment consisting of ContraVir Series B Convertible Preferred Stock. At December 31, 2015, the Company’s preferred stock investment in ContraVir was categorized as Level 3 as there were significant unobservable inputs. The valuation of the investment at December 31, 2015 was calculated on an as if converted to common share basis with a discount for lack of marketability applied due to the 18 month restriction from the date of the investment on selling the converted common shares, which ended on June 17, 2016. An option pricing model was used to determine the discount for lack of marketability of 10% at December 31, 2015. The key unobservable inputs used in the option pricing model at December 31, 2015 were (i) exercise price - $1.54, (ii) dividend yield - 0%, (iii) expected holding period - 0.46 years, (iv) risk-free rate - 0.44%, and (v) volatility - 75%. The valuation at June 30, 2016 was calculated on an as if converted to common share basis based on the common share price of ContraVir. At June 30, 2016, the Company's preferred stock investment in ContraVir was categorized as Level 2 as it was based on quoted prices for similar assets. On September 30, 2016, the Company converted its preferred stock investment in ContraVir into 1,071,429 shares of ContraVir common stock, which was categorized as a Level 1 asset and valued based on ContraVir's common stock value at September 30, 2016. The Company evaluates, among other things, the duration and extent to which the fair value of a security is less than its cost; the financial condition of the issuer and any changes thereto; and the Company’s intent to sell, or whether it will more likely than not be required to sell, the security before recovery of its market value. The Company does not currently intend to sell, and is not more likely than not to be required to sell, its investment in ContraVir before recovery of its market value. The change in valuation for the three and nine months ended September 30, 2016, primarily based on changes in the fair value of ContraVir common shares, was recorded to unrealized (loss) gain on investments, net in the Consolidated Statements of Operations and Comprehensive Loss.

There was no material re-measurement to fair value of financial assets and liabilities that are not measured at fair value on a recurring basis. For additional information regarding the Company's investments, please refer to Note 2, "Investments."

Below is a table that presents information about certain assets measured at fair value on a recurring basis (in thousands):



	Fair Value Measurements
	September 30, 2016
	Total		Quoted Prices in Active Markets for Identical Assets (Level 1)		Significant Other Observable Inputs (Level 2)		Significant Unobservable Inputs (Level 3)
Cash equivalents
Money market funds	$	24,276	$	24,276	$	—	$	—
Commercial paper	23,840		—		23,840		—
Total cash equivalents	48,116		24,276		23,840		—
Short-term investments
Certificates of deposit	16,342		—		16,342		—
U.S. Treasury securities	182,827		182,827		—		—
Common stock of U.S. corporation	1,146		1,146		—		—
Total short-term investments	200,315		183,973		16,342		—
Long-term investments
U.S. Treasury securities	39,801		39,801		—		—
Total long-term investments	39,801		39,801		—		—
Total assets	$	288,232	$	248,050	$	40,182	$	—

	Fair Value Measurements
	December 31, 2015
	Total		Quoted Prices in Active Markets for Identical Assets (Level 1)		Significant Other Observable Inputs (Level 2)		Significant Unobservable Inputs (Level 3)
Cash equivalents
Money market funds	$	19,795	$	19,795	$	—	$	—
Total cash equivalents	19,795		19,795		—		—
Short-term investments
Certificates of deposit	23,030		—		23,030		—
U.S. Treasury securities	175,214		175,214		—		—
Preferred stock of U.S. corporation	1,485		—		—		1,485
Total short-term investments	199,729		175,214		23,030		1,485
Long-term investments
Certificates of deposit	7,668		—		7,668		—
U.S. Treasury securities	116,372		116,372		—		—
Total long-term investments	124,040		116,372		7,668		—
Total assets	$	343,564	$	311,381	$	30,698	$	1,485

Below is a table that presents a reconciliation of the beginning and ending balances of assets and liabilities measured at fair value on a recurring basis using significant unobservable inputs (Level 3) at the beginning of the period (in thousands):



	Fair Value Measurements (Level 3)
Preferred stock of U.S. corporation:
Fair value at December 31, 2015	$	1,485
Fair value decrease recorded in other comprehensive loss	(371		)
Fair value transferred to Level 2	(1,114		)
Fair value at September 30, 2016	$	—

Accrued Liabilities

Accrued liabilities consisted of the following (in thousands):



	September 30, 2016		December 31, 2015
Accrued research and development expenses	$	3,236	$	3,596
Accrued compensation	2,090		2,939
Other accrued liabilities	1,012		3,186
Total accrued liabilities	$	6,338	$	9,721

Revenue Recognition

The Company’s revenues generally consist of (i) contract revenue – revenue generated under federal contracts, and (ii) collaboration and licensing revenue – revenue related to non-refundable upfront fees, royalties and milestone payments earned under license agreements. Revenue is recognized in accordance with the criteria outlined in the Securities and Exchange Commission (SEC)’s Topic 13 and Accounting Standards Codification (ASC) 605-25 issued by the Financial Accounting Standards Board (FASB). Following these accounting pronouncements, revenue is recognized when all four of the following criteria are met: (1) persuasive evidence of an arrangement exists; (2) delivery of the products and/or services has occurred and risk of loss has passed; (3) the selling price is fixed or determinable; and (4) collectability is reasonably assured. The Company recognizes revenue under government contracts as qualifying research activities are conducted based on invoices received.

For arrangements that involve the delivery of more than one element, each product, service and/or right to use assets is evaluated to determine whether it qualifies as a separate unit of accounting. This determination is based on whether the deliverable has “stand-alone value” to the customer. The consideration that is fixed or determinable is then allocated to each separate unit of accounting based on the relative selling prices of each deliverable. The consideration allocated to each unit of accounting is recognized as the related goods and services are delivered, limited to the consideration that is not contingent upon future deliverables. If the arrangement constitutes a single unit of accounting, the revenue recognition policy must be determined for the entire arrangement and the consideration received is recognized over the period of inception through the date the last deliverable within the single unit of accounting is expected to be delivered. Revisions to the estimated period of recognition are reflected in revenue prospectively.

Non-refundable upfront fees are recorded as deferred revenue and recognized into revenue as license fees from collaborations on a straight-line basis over the estimated period of the Company’s substantive performance obligations. If the Company does not have substantive performance obligations, the Company recognizes non-refundable upfront fees into revenue through the date the deliverable is satisfied. Analyzing the arrangement to identify deliverables requires the use of judgment and each deliverable may be an obligation to deliver services, a right or license to use an asset, or another performance obligation.

Milestone payments are recognized when earned, provided that (i) the milestone event is substantive; (ii) there is no ongoing performance obligation related to the achievement of the milestone earned; and (iii) it would result in additional payments. Milestone payments are considered substantive if all of the following conditions are met: the milestone payment is non-refundable; achievement of the milestone was not reasonably assured at the inception of the arrangement; substantive effort is involved to achieve the milestone; and the amount of the milestone appears reasonable in relation to the effort expended and the other milestones in the arrangement; and the related risk associated with the achievement of the milestone. Contingent based event payments the Company may receive under a license or collaboration agreement will be recognized when received.

Research and Development Prepaids and Accruals

As part of the process of preparing financial statements, the Company is required to estimate its expenses resulting from its obligation under contracts with vendors and consultants and clinical site agreements in connection with its research and development efforts. The financial terms of these contracts are subject to negotiations which vary contract to contract and may result in payment flows that do not match the periods over which materials or services are provided to the Company under such contracts.

The Company’s objective is to reflect the appropriate research and development expenses in its financial statements by matching those expenses with the period in which services and efforts are expended. The Company accounts for these expenses according to the progress of its research and development efforts. The Company determines prepaid and accrual estimates through discussion with applicable personnel and outside service providers as to the progress or state of communication of clinical trials, or other services completed. The Company adjusts its rate of research and development expense recognition if actual results differ from its estimates. The Company makes estimates of its prepaid and accrued expenses as of each balance sheet date in its financial statements based on facts and circumstances known at that time. Although the Company does not expect its estimates to be materially different from amounts actually incurred, its understanding of status and timing of services performed relative to the actual status and timing of services performed may vary and may result in the Company reporting amounts that are too high or too low for any particular period. Through September 30, 2016, there had been no material adjustments to the Company’s prior period estimates of prepaid and accruals for research and development expenses. The Company’s research and development prepaids and accruals are dependent upon the timely and accurate reporting of contract research organizations and other third-party vendors.

Basic and Diluted Net Loss Per Share of Common Stock

Basic net loss per share of common stock is computed by dividing net loss by the weighted-average number of shares of common stock outstanding during the period, excluding the dilutive effects of warrants to purchase common stock, employee stock purchase plan purchase rights, options to purchase common stock and restricted stock units. Diluted net loss per share of common stock is computed by dividing net loss by the sum of the weighted-average number of shares of common stock outstanding during the period and the potential dilutive effects of warrants and options to purchase common stock outstanding during the period calculated in accordance with the treasury stock method, and employee stock purchase plan purchase rights unless the effects of these potentially dilutive items are anti-dilutive. Because the effects of these potentially dilutive items are anti-dilutive during periods of net loss, there was no difference between basic and diluted loss per share of common stock for the three and nine months ended September 30, 2016 and 2015.

The calculation of weighted-average diluted shares outstanding excludes the dilutive effect of warrants to purchase common stock, employee stock purchase plan purchase rights and options to purchase common stock as the impacts of such items are anti-dilutive during periods of net loss. Potential common shares excluded from the calculations were 1.4 million and 1.1 million for the three months ended September 30, 2016 and 2015, respectively, and 0.9 million and 1.3 million for the nine months ended September 30, 2016 and 2015, respectively.

Impact of Recently Issued Accounting Standards

In May 2014, the FASB issued Accounting Standards Update (ASU) No. 2014-09, “Revenue from Contracts with Customers (Topic 606).” The ASU establishes a principles-based approach for accounting for revenue arising from contracts with customers and supersedes existing revenue recognition guidance. The ASU provides that an entity should apply a five-step approach for recognizing revenue, including (1) identify the contract with a customer; (2) identify the performance obligations in the contract; (3) determine the transaction price; (4) allocate the transaction price to the performance obligations in the contract; and (5) recognize revenue when, or as, the entity satisfies a performance obligation. Also, the entity must provide various disclosures concerning the nature, amount and timing of revenue and cash flows arising from contracts with customers. The FASB has issued several updates to the standard which (1) defer the original effective date to annual periods and interim periods within those annual periods beginning after December 15, 2017, while allowing for early adoption as of January 1, 2017 (ASU 2015-14); (2) clarify the application of the principal versus agent guidance (ASU 2016-08); and (3) clarify the guidance on inconsequential and perfunctory promises and licensing (ASU 2016-10). The Company is currently analyzing the impact of the adoption of ASU No. 2014-09 on its consolidated financial statements.

In January 2016, the FASB issued ASU No. 2016-01, “Financial Instruments-Overall (Subtopic 825-10)-Recognition and Measurement of Financial Assets and Financial Liabilities.” The new standard enhances reporting for financial instruments. The ASU is effective for financial statements issued for annual periods and interim periods within those annual periods beginning after December 15, 2017. Earlier adoption is permitted for interim and annual reporting periods as of the beginning of the fiscal year of adoption. The Company does not expect the adoption of ASU 2016-01 to have a material impact on its consolidated financial statements.

In February 2016, the FASB issued ASU No. 2016-02, “Leases (Topic 842)”, which increases transparency and comparability among companies accounting for lease transactions. The most significant change of this update will require the recognition of lease assets and liabilities on the balance sheet for lessees for operating lease arrangements with lease terms greater than 12 months. This update will require a modified retrospective application which includes a number of optional practical expedients related to the identification and classification of leases commenced before the effective date. This ASU is effective for financial statements issued for annual periods and interim periods within those annual periods, beginning after December 18, 2018. The Company is currently analyzing the impact of the adoption of ASU No. 2016-02 on its consolidated financial statements.

In March 2016, the FASB issued ASU No. 2016-09, "Improvements to Employee Share-Based Payment Accounting", which simplifies several aspects of accounting for share-based payment transactions, including the income tax consequences, classification of awards as either equity or liabilities, and classification on the statement of cash flows. The ASU is effective for financial statements issued for annual periods and interim periods within those annual periods, beginning after December 15, 2016, with early adoption permitted. The Company is currently analyzing the impact of the adoption of ASU No. 2016-09 on its consolidated financial statements.

Impact of Recently Adopted Accounting Standards

In June 2015, the FASB issued ASU 2015-10, “Technical Corrections and Improvements.” The amendments in ASU 2015-10 clarify and correct some of the differences that arose between original guidance from FASB, EITF and other sources, and the translation into the new Codification. ASU 2015-10 is effective for annual periods and interim periods within those annual periods beginning after December 15, 2015. ASU 2015-10 became effective for the Company beginning in the first quarter of 2016. The Company's adoption of ASU 2015-10 did not have a material impact on its consolidated financial statements.

Investments

9 Months Ended

Sep. 30, 2016

Investments, Debt and Equity Securities [Abstract]

Investments

The following tables summarize the Company's short-term and long-term investments (in thousands):



	September 30, 2016
	Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Estimated Fair Value
Certificates of deposit	$	16,325	$	17	$	—		$	16,342
U.S. Treasury securities	222,612		69		(53		)	222,628
Common stock of U.S. corporation	1,545		—		(399		)	1,146
Total investments	$	240,482	$	86	$	(452	)	$	240,116

	December 31, 2015
	Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Estimated Fair Value
Certificates of deposit	$	30,724	$	2	$	(28	)	$	30,698
U.S. Treasury securities	292,264		—		(678		)	291,586
Preferred stock of U.S. corporation	1,545		—		(60		)	1,485
Total investments	$	324,533	$	2	$	(766	)	$	323,769

The following tables summarize the Company's investments with unrealized losses, aggregated by investment type and the length of time that individual investments have been in a continuous unrealized loss position (in thousands, except number of securities):



	September 30, 2016
	Less than 12 Months					Greater than 12 Months				Total
	Fair Value		Unrealized Loss			Fair Value		Unrealized Loss		Fair Value		Unrealized Loss
U.S. Treasury securities	$	51,063	$	(53	)	$	—	$	—	$	51,063	$	(53	)
Common stock of U.S. corporation	1,146		(399		)	—		—		1,146		(399		)
Total	$	52,209	$	(452	)	$	—	$	—	$	52,209	$	(452	)
Number of securities with unrealized losses			12					—				12

	December 31, 2015
	Less than 12 Months					Greater than 12 Months				Total
	Fair Value		Unrealized Loss			Fair Value		Unrealized Loss		Fair Value		Unrealized Loss
Certificates of deposit	$	24,450	$	(28	)	$	—	$	—	$	24,450	$	(28	)
U.S. Treasury securities	291,586		(678		)	—		—		291,586		(678		)
Preferred stock of U.S. corporation	1,485		(60		)	—		—		1,485		(60		)
Total	$	317,521	$	(766	)	$	—	$	—	$	317,521	$	(766	)
Number of securities with unrealized losses			180					—				180

The Company periodically reviews available-for-sale securities for other-than-temporary declines in fair value below the cost basis and whenever events or changes in circumstances indicate that the carrying amount of an asset may not be recoverable. The Company evaluates, among other things, the duration and extent to which the fair value of a security is less than its cost; the financial condition of the issuer and any changes thereto; and the Company’s intent to sell, or whether it will more likely than not be required to sell, the security before recovery of its amortized cost basis. The Company does not currently intend to sell, and is not more likely than not to be required to sell, the available-for-sale securities in an unrealized loss position before recovery of the amortized cost bases of the securities, which may be maturity. Any such declines in value judged to be other-than-temporary on available-for-sale securities are reported in interest income or expense, net. There were no such declines in value for the three and nine months ended September 30, 2016 and 2015. The Company recognizes interest income on an accrual basis in interest income, net in the Consolidated Statements of Operations and Comprehensive Loss.

The following table summarizes the scheduled maturity for the Company's debt investments at September 30, 2016 (in thousands):



Maturing in one year or less	$	199,169
Maturing after one year through two years	39,801
Total debt investments	238,970
Common stock of U.S. corporation	1,146
Total investments	$	240,116

- Definition

The entire disclosure for investments in certain debt and equity securities.

+ References + Details

Equity Transactions and Share-based Compensation

9 Months Ended

Sep. 30, 2016

Disclosure of Compensation Related Costs, Share-based Payments [Abstract]

Equity Transactions and Share-based Compensation

Warrants

For the three and nine months ended September 30, 2016, there were no exercises of warrants for the purchase of shares of the Company's common stock.

Stock Options

In connection with the Company’s IPO, the Company adopted the 2013 Equity Incentive Plan (the 2013 Plan). The 2013 Plan provides for the grant of incentive stock options (ISOs), non-statutory stock options (NSOs), stock appreciation rights, restricted stock awards, restricted stock unit (RSU) awards, performance-based stock awards, and other forms of equity compensation (collectively, stock awards), all of which may be granted to employees, including officers, non-employee directors and consultants of the Company and its affiliates. Additionally, the 2013 Plan provides for the grant of performance cash awards. The number of shares of common stock reserved for future issuance automatically increases on January 1 of each calendar year by 4% of the total number of shares of capital stock outstanding on December 31 of the preceding calendar year, or a lesser number of shares determined by the Company’s board of directors. On January 1, 2016, the common stock reserved for issuance under the 2013 Plan was automatically increased by 1.8 million shares. As of September 30, 2016, there was a total of 0.6 million shares reserved for future issuance under the 2013 Plan. The Company issued approximately 45,000 shares of common stock pursuant to the exercise of stock options for the nine months ended September 30, 2016. There were no shares of common stock issued pursuant to the exercise of stock options for the three months ended September 30, 2016

Employee Stock Purchase Plan

In February 2013, the Company’s board of directors adopted the 2013 Employee Stock Purchase Plan (ESPP), which was subsequently ratified by stockholders and became effective in April 2013. Initially, the ESPP authorized the issuance of 704,225 shares of common stock pursuant to purchase rights granted to the Company’s employees or to employees of any of its designated affiliates. The number of shares of common stock reserved for issuance automatically increases on January 1 of each calendar year, from January 1, 2014 through January 1, 2023 by the lesser of (a) 1% of the total number of shares of common stock outstanding on December 31 of the preceding calendar year, (b) 422,535 shares, or (c) a number determined by the Company’s board of directors that is less than (a) and (b). On January 1, 2016, the common stock reserved for issuance under the ESPP was automatically increased by an additional 0.4 million shares bringing the total number of shares of common stock that may be purchased under the ESPP to 1.8 million.

The Company has reserved a total of 1.8 million shares of common stock to be purchased under the ESPP, of which 1.6 million shares remained available for purchase as of September 30, 2016. The ESPP provides for an automatic reset feature to start participants on a new twenty-four month participation period in the event that the common stock market value on a purchase date is less than the common stock value on the first day of the twenty-four month offering period. Eligible employees may authorize an amount up to 15% of their salary to purchase common stock at the lower of a 15% discount to the beginning price of their offering period or a 15% discount to the ending price of each six-month purchase interval. The Company issued approximately 100,000 shares of common stock pursuant to the ESPP for the three months ended September 30, 2016. The Company issued approximately 108,000 shares of common stock pursuant to the ESPP for the nine months ended September 30, 2016. Compensation expense for shares purchased under the ESPP related to the purchase discount and the “look-back” option and were determined using a Black-Scholes option pricing model.

Restricted Stock Units

In May 2016, the Company issued restricted stock units (RSUs) to certain employees which vest based on service criteria. When vested, the RSU represents the right to be issued the number of shares of the Company's common stock that is equal to the number of RSUs granted. The grant date fair value for RSUs is based upon the market price of the Company's common stock on the date of the grant. The fair value is then amortized to compensation expense over the requisite service period or vesting term. The Company issued no shares of common stock pursuant to the vesting of RSUs for the three and nine months ended September 30, 2016.

For awards with only service conditions and graded-vesting features, the Company recognizes compensation expense on a straight-line basis over the requisite service period. For the three and nine months ended September 30, 2016 and 2015, there was no non-employee share-based compensation expense. Employee share-based compensation expense recognized related to stock options, the ESPP and RSUs was as follows (in thousands):



	Three Months Ended September 30,				Nine Months Ended September 30,
	2016		2015		2016		2015
Research and development expense	$	1,942	$	1,594	$	5,373	$	3,820
General and administrative expense	2,153		2,085		6,961		5,062
Total share-based compensation expense	$	4,095	$	3,679	$	12,334	$	8,882

- Definition

The entire disclosure for compensation-related costs for equity-based compensation, which may include disclosure of policies, compensation plan details, allocation of equity compensation, incentive distributions, equity-based arrangements to obtain goods and services, deferred compensation arrangements, employee stock ownership plan details and employee stock purchase plan details.

+ References + Details

Significant Agreements	9 Months Ended
Significant Agreements	Sep. 30, 2016
Revenue Recognition [Abstract]
Significant Agreements	Significant Agreements The Regents of the University of California In May 2002, the Company entered into a license agreement with The Regents of the University of California (UC) under which the Company obtained an exclusive, worldwide license to UC’s patent rights in certain inventions (the UC Patent Rights) related to lipid-conjugated antiviral compounds and their use, including certain patents relating to brincidofovir. The license agreement was amended in September 2002 in order to expand the scope of the license and again in December 2010 in order to modify certain financial terms. The agreement was amended a third time in September 2011 to add additional patents related to certain metabolically stable lipid-conjugate compounds. A fourth amendment was executed in July 2012 to alter the rights and obligations of the parties in light of the Company’s then current business plans. As partial consideration for the rights granted to the Company under the license agreement, the Company is required to pay certain cash milestone payments in connection with the development and commercialization of compounds that are covered by the UC Patent Rights. In connection with the development and commercialization of brincidofovir and CMX157, the Company could be required to pay UC up to an aggregate of $3.4 million in milestone payments, assuming the achievement of all applicable milestone events under the license agreement. Under the license agreement, the Company is permitted to research, develop, manufacture and commercialize products utilizing the UC Patent Rights for all human and veterinary uses, and to sublicense such rights. UC retained the right, on behalf of itself and other non-profit institutions, to use the UC Patent Rights for educational and research purposes and to publish information about the UC Patent Rights. In consideration for the rights granted under the license agreement, the Company has issued UC an aggregate of 64,788 shares of common stock. As additional consideration, the Company is required to pay certain cash milestone payments in connection with the development and commercialization of compounds that are covered by the UC Patent Rights, plus certain annual fees to maintain such patents until the Company commercializes a product utilizing UC Patent Rights. In addition, upon commercialization of any product utilizing the UC Patent Rights (which would include the commercialization of brincidofovir), the Company will be required to pay low single digit royalties on net sales of such product. In the event the Company sublicenses a UC Patent Right (including UC Patent Rights relating to brincidofovir or CMX157) the Company is obligated to pay to UC a fee, which amount will vary depending upon the amount of any payments the Company receives and the clinical development stage of the compound being sublicensed, but which could be up to approximately 50% of the sublicense fee in certain circumstances. With respect to brincidofovir, the fee payable to UC will not exceed 5% of the sublicense fee. In addition, the Company will also be required to pay to UC a low single digit sublicense royalty on net sales of products that use the sublicensed UC Patent Rights, but in no event will the Company be required to pay more than 50% of the royalties it receives in connection with the relevant sublicense. Any such royalty payment will be reduced by other payments the Company is required to make to third parties until a minimum royalty has been reached. The Company did not recognize expenses under this agreement for the three and nine months ended September 30, 2016 and 2015. Biomedical Advanced Research and Development Authority In February 2011, the Company entered into a contract with BARDA for the advanced development of brincidofovir as a medical countermeasure in the event of a smallpox release. The contract has been amended numerous times. In August 2016, the contract was amended to extend the period of performance for the second option segment through June 30, 2017. In September 2015, the third option segment of the contract to provide approximately $13 million through October 31, 2016 was executed and in October 2016 was amended to extend the period of performance for the third option segment through January 31, 2017. Under the contract, BARDA will reimburse the Company, plus pay a fixed fee, for the research and development of brincidofovir as a broad-spectrum therapeutic antiviral for the treatment of smallpox infections. The contract consists of an initial performance period, referred to as the base performance segment, plus up to four extension periods, referred to as option segments, each of which may be exercised at BARDA’s sole discretion. The Company must complete the agreed upon milestones and deliverables in each discrete work segment before the next option segment is eligible to be exercised. Under the contract as currently in effect, the Company may cumulatively receive up to $75.8 million in expense reimbursement and $5.3 million in fees if all remaining option segments are exercised. As of September 30, 2016, the Company had recognized revenue in aggregate of $49.7 million with respect to the base performance segment and the first three extension periods. The Company is currently performing under the second and third option segments of the contract during which the Company may receive up to a total of $17.5 million in expense reimbursement and fees and $13 million in expense reimbursement and fees, respectively. The second option segment is scheduled to end on June 30, 2017 and the third option segment is scheduled to end on January 31, 2017. For the three months ended September 30, 2016 and 2015, the Company recognized revenue under this contract of $0.7 million and $2.3 million, respectively, and for the nine months ended September 30, 2016 and 2015, the Company recognized revenue under this contract of $3.7 million and $6.1 million, respectively. ContraVir Pharmaceuticals In December 2014, the Company entered into a license agreement with ContraVir for the development and commercialization of CMX157 for certain antiviral indications. Under the terms of the agreement, ContraVir has sole responsibility with respect to the control of the development and commercialization of CMX157. In exchange for the license to CMX157 rights, the Company received an upfront payment consisting of 120,000 shares of ContraVir Series B Convertible Preferred Stock with a stated value of $1.2 million. In addition, the Company is eligible to receive up to approximately $20 million in clinical, regulatory and initial commercial milestones in the United States and Europe, as well as royalties and additional milestones based on commercial sales in those territories. Either party may terminate the license agreement upon the occurrence of a material breach by the other party (subject to standard cure periods), or upon certain events involving the bankruptcy or insolvency of the other party. ContraVir may also terminate the license agreement without cause on a country-by-country basis upon sixty (60) days’ prior written notice. The upfront payment of 120,000 shares of ContraVir Series B Convertible Preferred Stock was valued at $1.5 million at the time of the agreement. The Company recorded this amount as a long-term investment and deferred revenue, which was included in accrued liabilities in the Consolidated Balance Sheets. Upon completion of the transfer of the investigational new drug and technical know-how related to CMX157, the Company recognized the upfront payment as revenue during the three months ended June 30, 2015. In September 2016, the Company converted its shares of ContraVir Series B Convertible Preferred Stock into 1,071,429 shares of ContraVir common stock. As of September 30, 2016 and December 31, 2015, the fair value of the investment was recorded as a short-term investment of $1.1 million and $1.5 million, respectively.

The Business and Summary of Significant Accounting Policies (Policy)

9 Months Ended

Sep. 30, 2016

Accounting Policies [Abstract]

Fair Value of Financial Instruments


•	Level 1 — Valuations based on unadjusted quoted prices in active markets for identical assets or liabilities that the Company has the ability to access.


•	Level 2 — Valuations based on quoted prices for similar assets or liabilities in active markets, quoted prices for identical or similar assets or liabilities in markets that are not active, and models for which all significant inputs are observable, either directly or indirectly.


•	Level 3 — Valuations based on inputs that are unobservable and significant to the overall fair value measurement.

Revenue Recognition

Research and Development Prepaids and Accruals

Basic and Diluted Net Loss Per Share of Common Stock

Impact of Recently Issued Accounting Standards and Impact of Recently Adopted Accounting Standards

Impact of Recently Issued Accounting Standards

Impact of Recently Adopted Accounting Standards

Investments (Tables)

9 Months Ended

Sep. 30, 2016

Investments, Debt and Equity Securities [Abstract]

Summary of Short-term and Long-term investments

The following tables summarize the Company's short-term and long-term investments (in thousands):



	September 30, 2016
	Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Estimated Fair Value
Certificates of deposit	$	16,325	$	17	$	—		$	16,342
U.S. Treasury securities	222,612		69		(53		)	222,628
Common stock of U.S. corporation	1,545		—		(399		)	1,146
Total investments	$	240,482	$	86	$	(452	)	$	240,116

	December 31, 2015
	Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Estimated Fair Value
Certificates of deposit	$	30,724	$	2	$	(28	)	$	30,698
U.S. Treasury securities	292,264		—		(678		)	291,586
Preferred stock of U.S. corporation	1,545		—		(60		)	1,485
Total investments	$	324,533	$	2	$	(766	)	$	323,769

Summary of Investments with Unrealized Losses, Aggregated by Investment Type and the Length of Time



	September 30, 2016
	Less than 12 Months					Greater than 12 Months				Total
	Fair Value		Unrealized Loss			Fair Value		Unrealized Loss		Fair Value		Unrealized Loss
U.S. Treasury securities	$	51,063	$	(53	)	$	—	$	—	$	51,063	$	(53	)
Common stock of U.S. corporation	1,146		(399		)	—		—		1,146		(399		)
Total	$	52,209	$	(452	)	$	—	$	—	$	52,209	$	(452	)
Number of securities with unrealized losses			12					—				12

	December 31, 2015
	Less than 12 Months					Greater than 12 Months				Total
	Fair Value		Unrealized Loss			Fair Value		Unrealized Loss		Fair Value		Unrealized Loss
Certificates of deposit	$	24,450	$	(28	)	$	—	$	—	$	24,450	$	(28	)
U.S. Treasury securities	291,586		(678		)	—		—		291,586		(678		)
Preferred stock of U.S. corporation	1,485		(60		)	—		—		1,485		(60		)
Total	$	317,521	$	(766	)	$	—	$	—	$	317,521	$	(766	)
Number of securities with unrealized losses			180					—				180

Summary of the scheduled maturity of Company investments

The following table summarizes the scheduled maturity for the Company's debt investments at September 30, 2016 (in thousands):



Maturing in one year or less	$	199,169
Maturing after one year through two years	39,801
Total debt investments	238,970
Common stock of U.S. corporation	1,146
Total investments	$	240,116

- Definition

Tabular disclosure of available-for-sale securities which includes, but is not limited to, changes in the cost basis and fair value, fair value and gross unrealized gain (loss), fair values by type of security, contractual maturity and classification, amortized cost basis, contracts to acquire securities to be accounted for as available-for-sale, debt maturities, transfers to trading, change in net unrealized holding gain (loss) net of tax, continuous unrealized loss position fair value, aggregate losses qualitative disclosures, other than temporary impairment (OTTI) losses or other disclosures related to available for sale securities.

+ References + Details

The Business and Summary of Significant Accounting Policies (Narrative) (Details) - $ / shares		3 Months Ended		9 Months Ended
	Dec. 31, 2015	Sep. 30, 2016	Sep. 30, 2015	Sep. 30, 2016	Sep. 30, 2015
Schedule of Fair Value of Separate Accounts by Major Category of Investment [Line Items]
Fair value, investments, redemption restriction period	18 months
Fair value inputs, discount for lack of marketability	10.00%
Fair value assumptions, exercise price (in dollars per share)	$ 1.54
Fair value assumptions, expected divided rate	0.00%
Fair value assumptions, expected term	169 days
Fair value assumptions, risk free interest rate	0.44%
Fair value assumptions, expected volatility rate	75.00%
Anti-dilutive securities excluded from the calculation loss per share (in shares)		1,400,000	1,100,000	900,000	1,300,000
Common stock of U.S. corporation \| Quoted Prices in Active Markets for Identical Assets (Level 1)
Schedule of Fair Value of Separate Accounts by Major Category of Investment [Line Items]
Convertible preferred stock, shares issued upon conversion (in shares)		1,071,429		1,071,429

The Business and Summary of Significant Accounting Policies (Assets and Liabilities Measured at Fair Value on a Recurring Basis) (Details) - USD ($) $ in Thousands	9 Months Ended
	Sep. 30, 2016	Dec. 31, 2015
Schedule of Fair Value of Separate Accounts by Major Category of Investment [Line Items]
Short-term investments	$ 200,315	$ 199,729
Long-term investments	39,801	124,040
Fair Value, Assets Measured on Recurring Basis, Unobservable Input Reconciliation, Calculation [Roll Forward]
Fair value transferred to Level 2	(1,114)
Fair value, measurements, recurring
Schedule of Fair Value of Separate Accounts by Major Category of Investment [Line Items]
Cash equivalents	48,116	19,795
Short-term investments	200,315	199,729
Long-term investments	39,801	124,040
Total assets	288,232	343,564
Fair value, measurements, recurring \| Quoted Prices in Active Markets for Identical Assets (Level 1)
Schedule of Fair Value of Separate Accounts by Major Category of Investment [Line Items]
Cash equivalents	24,276	19,795
Short-term investments	183,973	175,214
Long-term investments	39,801	116,372
Total assets	248,050	311,381
Fair value, measurements, recurring \| Significant Other Observable Inputs (Level 2)
Schedule of Fair Value of Separate Accounts by Major Category of Investment [Line Items]
Cash equivalents	23,840	0
Short-term investments	16,342	23,030
Long-term investments	0	7,668
Total assets	40,182	30,698
Fair value, measurements, recurring \| Significant Unobservable Inputs (Level 3)
Schedule of Fair Value of Separate Accounts by Major Category of Investment [Line Items]
Cash equivalents	0	0
Short-term investments	0	1,485
Long-term investments	0	0
Total assets	0	1,485
Money market funds \| Fair value, measurements, recurring
Schedule of Fair Value of Separate Accounts by Major Category of Investment [Line Items]
Cash equivalents	24,276	19,795
Money market funds \| Fair value, measurements, recurring \| Quoted Prices in Active Markets for Identical Assets (Level 1)
Schedule of Fair Value of Separate Accounts by Major Category of Investment [Line Items]
Cash equivalents	24,276	19,795
Money market funds \| Fair value, measurements, recurring \| Significant Other Observable Inputs (Level 2)
Schedule of Fair Value of Separate Accounts by Major Category of Investment [Line Items]
Cash equivalents	0	0
Money market funds \| Fair value, measurements, recurring \| Significant Unobservable Inputs (Level 3)
Schedule of Fair Value of Separate Accounts by Major Category of Investment [Line Items]
Cash equivalents	0	0
Commercial paper \| Fair value, measurements, recurring
Schedule of Fair Value of Separate Accounts by Major Category of Investment [Line Items]
Cash equivalents	23,840
Commercial paper \| Fair value, measurements, recurring \| Quoted Prices in Active Markets for Identical Assets (Level 1)
Schedule of Fair Value of Separate Accounts by Major Category of Investment [Line Items]
Cash equivalents	0
Commercial paper \| Fair value, measurements, recurring \| Significant Other Observable Inputs (Level 2)
Schedule of Fair Value of Separate Accounts by Major Category of Investment [Line Items]
Cash equivalents	23,840
Commercial paper \| Fair value, measurements, recurring \| Significant Unobservable Inputs (Level 3)
Schedule of Fair Value of Separate Accounts by Major Category of Investment [Line Items]
Cash equivalents	0
Certificates of deposit \| Fair value, measurements, recurring
Schedule of Fair Value of Separate Accounts by Major Category of Investment [Line Items]
Short-term investments	16,342	23,030
Long-term investments		7,668
Certificates of deposit \| Fair value, measurements, recurring \| Quoted Prices in Active Markets for Identical Assets (Level 1)
Schedule of Fair Value of Separate Accounts by Major Category of Investment [Line Items]
Short-term investments	0	0
Long-term investments		0
Certificates of deposit \| Fair value, measurements, recurring \| Significant Other Observable Inputs (Level 2)
Schedule of Fair Value of Separate Accounts by Major Category of Investment [Line Items]
Short-term investments	16,342	23,030
Long-term investments		7,668
Certificates of deposit \| Fair value, measurements, recurring \| Significant Unobservable Inputs (Level 3)
Schedule of Fair Value of Separate Accounts by Major Category of Investment [Line Items]
Short-term investments	0	0
Long-term investments		0
U.S. Treasury securities \| Fair value, measurements, recurring
Schedule of Fair Value of Separate Accounts by Major Category of Investment [Line Items]
Short-term investments	182,827	175,214
Long-term investments	39,801	116,372
U.S. Treasury securities \| Fair value, measurements, recurring \| Quoted Prices in Active Markets for Identical Assets (Level 1)
Schedule of Fair Value of Separate Accounts by Major Category of Investment [Line Items]
Short-term investments	182,827	175,214
Long-term investments	39,801	116,372
U.S. Treasury securities \| Fair value, measurements, recurring \| Significant Other Observable Inputs (Level 2)
Schedule of Fair Value of Separate Accounts by Major Category of Investment [Line Items]
Short-term investments	0	0
Long-term investments	0	0
U.S. Treasury securities \| Fair value, measurements, recurring \| Significant Unobservable Inputs (Level 3)
Schedule of Fair Value of Separate Accounts by Major Category of Investment [Line Items]
Short-term investments	0	0
Long-term investments	0	0
Common stock of U.S. corporation \| Fair value, measurements, recurring
Schedule of Fair Value of Separate Accounts by Major Category of Investment [Line Items]
Short-term investments	1,146
Common stock of U.S. corporation \| Fair value, measurements, recurring \| Quoted Prices in Active Markets for Identical Assets (Level 1)
Schedule of Fair Value of Separate Accounts by Major Category of Investment [Line Items]
Short-term investments	1,146
Common stock of U.S. corporation \| Fair value, measurements, recurring \| Significant Other Observable Inputs (Level 2)
Schedule of Fair Value of Separate Accounts by Major Category of Investment [Line Items]
Short-term investments	0
Common stock of U.S. corporation \| Fair value, measurements, recurring \| Significant Unobservable Inputs (Level 3)
Schedule of Fair Value of Separate Accounts by Major Category of Investment [Line Items]
Short-term investments	0
Preferred stock of U.S. corporation
Fair Value, Assets Measured on Recurring Basis, Unobservable Input Reconciliation, Calculation [Roll Forward]
Fair value at December 31, 2015	1,485
Fair value decrease recorded in other comprehensive loss	(371)
Fair value at September 30, 2016	$ 0
Preferred stock of U.S. corporation \| Fair value, measurements, recurring
Schedule of Fair Value of Separate Accounts by Major Category of Investment [Line Items]
Short-term investments		1,485
Preferred stock of U.S. corporation \| Fair value, measurements, recurring \| Quoted Prices in Active Markets for Identical Assets (Level 1)
Schedule of Fair Value of Separate Accounts by Major Category of Investment [Line Items]
Short-term investments		0
Preferred stock of U.S. corporation \| Fair value, measurements, recurring \| Significant Other Observable Inputs (Level 2)
Schedule of Fair Value of Separate Accounts by Major Category of Investment [Line Items]
Short-term investments		0
Preferred stock of U.S. corporation \| Fair value, measurements, recurring \| Significant Unobservable Inputs (Level 3)
Schedule of Fair Value of Separate Accounts by Major Category of Investment [Line Items]
Short-term investments		$ 1,485

Investments - Summary of Investments with Unrealized Losses, Aggregated by Investment Type and the Length of Time (Details)	3 Months Ended		9 Months Ended
	Sep. 30, 2016 USD ($) securities	Sep. 30, 2015 USD ($)	Sep. 30, 2016 USD ($) securities	Sep. 30, 2015 USD ($)	Dec. 31, 2015 USD ($) securities
Schedule of Available-for-sale Securities [Line Items]
Fair Value, Less than 12 Months	$ 52,209,000		$ 52,209,000		$ 317,521,000
Unrealized Loss, Less than 12 Months	(452,000)		(452,000)		(766,000)
Fair Value, Greater than 12 Months	0		0		0
Unrealized Loss, Greater than 12 Months	0		0		0
Fair Value, Total	52,209,000		52,209,000		317,521,000
Unrealized Loss, Total	$ (452,000)		$ (452,000)		$ (766,000)
Number of securities with unrealized losses, Less than 12 Months \| securities	12		12		180
Number of securities with unrealized losses, Greater than 12 Months \| securities	0		0		0
Number of securities with unrealized losses, Total \| securities	12		12		180
Other than temporary impairment, investments, available-for-sale	$ 0	$ 0	$ 0	$ 0
Certificates of deposit
Schedule of Available-for-sale Securities [Line Items]
Fair Value, Less than 12 Months					$ 24,450,000
Unrealized Loss, Less than 12 Months					(28,000)
Fair Value, Greater than 12 Months					0
Unrealized Loss, Greater than 12 Months					0
Fair Value, Total					24,450,000
Unrealized Loss, Total					(28,000)
U.S. Treasury securities
Schedule of Available-for-sale Securities [Line Items]
Fair Value, Less than 12 Months	51,063,000		51,063,000		291,586,000
Unrealized Loss, Less than 12 Months	(53,000)		(53,000)		(678,000)
Fair Value, Greater than 12 Months	0		0		0
Unrealized Loss, Greater than 12 Months	0		0		0
Fair Value, Total	51,063,000		51,063,000		291,586,000
Unrealized Loss, Total	(53,000)		(53,000)		(678,000)
Common stock of U.S. corporation
Schedule of Available-for-sale Securities [Line Items]
Fair Value, Less than 12 Months	1,146,000		1,146,000
Unrealized Loss, Less than 12 Months	(399,000)		(399,000)
Fair Value, Greater than 12 Months	0		0
Unrealized Loss, Greater than 12 Months	0		0
Fair Value, Total	1,146,000		1,146,000
Unrealized Loss, Total	$ (399,000)		$ (399,000)
Preferred stock of U.S. corporation
Schedule of Available-for-sale Securities [Line Items]
Fair Value, Less than 12 Months					1,485,000
Unrealized Loss, Less than 12 Months					(60,000)
Fair Value, Greater than 12 Months					0
Unrealized Loss, Greater than 12 Months					0
Fair Value, Total					1,485,000
Unrealized Loss, Total					$ (60,000)

Equity Transactions and Share-based Compensation - Stock-based Compensation (Narrative) (Details) - USD ($)		3 Months Ended		9 Months Ended
	Jan. 01, 2016	Sep. 30, 2016	Sep. 30, 2015	Sep. 30, 2016	Sep. 30, 2015	Feb. 28, 2013
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Allocated share-based compensation expense		$ 4,095,000	$ 3,679,000	$ 12,334,000	$ 8,882,000
The 2013 Plan
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Share-based compensation, evergreen option provision, equity increase				4.00%
Additional shares authorized (in shares)	1,800,000.0
Share-based compensation arrangement by share-based payment award, number of shares available for grant (in shares)		600,000.0		600,000.0
Share-based compensation arrangement by share-based payment award, options, exercises in period (in shares)		0		45,000
The 2013 Employee Stock Purchase Plan
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Share-based compensation, evergreen option provision, equity increase				1.00%
Number of shares reserved for issuance, annual increase (in shares)				422,535
Additional shares authorized (in shares)	400,000.0
Share-based compensation arrangement by share-based payment award, number of shares available for grant (in shares)		1,600,000.0		1,600,000.0
Number of shares authorized to be granted (in shares)	1,800,000.0	1,800,000.0		1,800,000.0		704,225
Percentage of pay that employee can contribute, maximum		15.00%		15.00%
Discounted purchase price from market price, offering date				15.00%
Discounted purchase price from market price, purchase date				15.00%
Non-employee
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Allocated share-based compensation expense		$ 0	$ 0	$ 0	$ 0

Significant Agreements (Details)	1 Months Ended		3 Months Ended		9 Months Ended		17 Months Ended	68 Months Ended	77 Months Ended
Significant Agreements (Details)	Dec. 31, 2014 USD ($) shares	May 31, 2002 USD ($) shares	Sep. 30, 2016 USD ($) shares	Sep. 30, 2015 USD ($)	Sep. 30, 2016 USD ($) period extension shares	Sep. 30, 2015 USD ($)	Jan. 31, 2017 USD ($)	Sep. 30, 2016 USD ($) shares	Jun. 30, 2017 USD ($)	Dec. 31, 2015 USD ($)
Long-term Purchase Commitment [Line Items]
Operating expenses			$ 18,074,000	$ 35,019,000	$ 66,301,000	$ 87,679,000
Contract revenue			653,000	2,271,000	3,722,000	6,104,000
Estimated Fair Value			240,116,000		240,116,000			$ 240,116,000		$ 323,769,000
Preferred stock of U.S. corporation
Long-term Purchase Commitment [Line Items]
Estimated Fair Value										1,485,000
Common stock of U.S. corporation
Long-term Purchase Commitment [Line Items]
Estimated Fair Value			1,146,000		1,146,000			1,146,000
Regents of University of California
Long-term Purchase Commitment [Line Items]
Number of options outstanding, Granted (in shares) \| shares		64,788
Operating expenses			0	0	0	0
Regents of University of California \| Maximum
Long-term Purchase Commitment [Line Items]
Milestone payments		$ 3,400,000.0
Sublicense fee percentage		50.00%
Royalties percentage		50.00%
Regents of University of California \| Maximum \| Brincidofovir
Long-term Purchase Commitment [Line Items]
Sublicense fee amount, payable fee percentage		5.00%
BARDA
Long-term Purchase Commitment [Line Items]
Contract revenue			700,000	$ 2,300,000	$ 3,700,000	$ 6,100,000		49,700,000
Number of extension periods \| extension					4
Number of extension periods through which revenue has been recognized \| period					3
BARDA \| Maximum \| Scenario, Forecast
Long-term Purchase Commitment [Line Items]
Reimbursement revenue									$ 75,800,000
Fees and commissions, other									5,300,000
BARDA Second Option Segment \| Maximum \| Scenario, Forecast
Long-term Purchase Commitment [Line Items]
Contract revenue									$ 17,500,000
ContraVir Pharmaceuticals
Long-term Purchase Commitment [Line Items]
License agreement, termination notice					60 days
ContraVir Pharmaceuticals \| Preferred stock of U.S. corporation
Long-term Purchase Commitment [Line Items]
Other significant noncash transaction, shares received as consideration (in shares) \| shares	120,000
Estimated Fair Value	$ 1,500,000									$ 1,500,000
ContraVir Pharmaceuticals \| Common stock of U.S. corporation
Long-term Purchase Commitment [Line Items]
Estimated Fair Value			$ 1,100,000		$ 1,100,000			$ 1,100,000
ContraVir Pharmaceuticals \| Stated Value \| Preferred stock of U.S. corporation
Long-term Purchase Commitment [Line Items]
Other significant noncash transaction, value of consideration received	$ 1,200,000
ContraVir Pharmaceuticals \| Maximum
Long-term Purchase Commitment [Line Items]
Collaboration and licensing revenue					$ 20,000,000
Subsequent Event \| BARDA Third Option Segment \| Maximum
Long-term Purchase Commitment [Line Items]
Contract revenue							$ 13,000,000
Quoted Prices in Active Markets for Identical Assets (Level 1) \| Common stock of U.S. corporation
Long-term Purchase Commitment [Line Items]
Convertible preferred stock, shares issued upon conversion (in shares) \| shares			1,071,429		1,071,429			1,071,429

Commitments and Contingencies	9 Months Ended
Commitments and Contingencies	Sep. 30, 2016
Commitments and Contingencies Disclosure [Abstract]
Commitments and Contingencies	Commitments and Contingencies Leases The Company leases its facilities and certain office equipment under long-term non-cancelable operating leases that expire at various dates through 2021. Rent expense under non-cancelable operating leases and other month-to-month equipment rental agreements, including common area maintenance fees, totaled approximately $0.2 million and $0.2 million for the three months ended September 30, 2016 and 2015, respectively, and $0.6 million and $0.5 million for the nine months ended September 30, 2016 and 2015, respectively. Significance of Revenue Source The Company is the recipient of federal research contract funds from the Biomedical Advanced Research and Development Authority (BARDA), the sole source of the Company's contract revenue. Periodic audits are required under the Company’s BARDA agreement and certain costs may be questioned as appropriate under the BARDA agreement. Management believes that such amounts in the current year, if any, are not significant. Accordingly, no provision for refundable amounts under the BARDA agreement had been made as of September 30, 2016 and December 31, 2015.

Income Taxes	9 Months Ended
Income Taxes	Sep. 30, 2016
Income Tax Disclosure [Abstract]
Income Taxes	Income Taxes The Company estimates an annual effective tax rate of 0% for the year ending December 31, 2016 as the Company incurred losses for the nine months ended September 30, 2016 and is forecasting additional losses through the 4th quarter, resulting in an estimated net loss for both financial statement and tax purposes for the year ending December 31, 2016. Therefore, no federal or state income taxes are expected and none have been recorded at this time. Income taxes have been accounted for using the liability method in accordance with FASB ASC 740. Due to the Company's history of losses since inception, there is not enough evidence at this time to support that the Company will generate future income of a sufficient amount and nature to utilize the benefits of its net deferred tax assets. Accordingly, the deferred tax assets have been reduced by a full valuation allowance, since the Company does not currently believe that realization of its deferred tax assets is more likely than not. As of September 30, 2016, the Company had no unrecognized tax benefits that would reduce the Company’s effective tax rate if recognized.

Subsequent Event	9 Months Ended
Subsequent Event	Sep. 30, 2016
Subsequent Events [Abstract]
Subsequent Events	Subsequent Events The Company has evaluated subsequent events through the issuance date of these financial statements to ensure that this filing includes appropriate disclosure of events both recognized in the financial statements as of September 30, 2016, and events which occurred subsequently but were not recognized in the financial statements.

The Business and Summary of Significant Accounting Policies (Schedule of Accrued Liabilities) (Details) - USD ($) $ in Thousands	Sep. 30, 2016	Dec. 31, 2015
Other Liabilities Disclosure [Abstract]
Accrued research and development expenses	$ 3,236	$ 3,596
Accrued compensation	2,090	2,939
Other accrued liabilities	1,012	3,186
Total accrued liabilities	$ 6,338	$ 9,721

Investments - Summary of Available-for-Sale securities (Details) - USD ($) $ in Thousands	Sep. 30, 2016	Dec. 31, 2015
Schedule of Investments [Line Items]
Amortized Cost	$ 240,482	$ 324,533
Gross Unrealized Gains	86	2
Gross Unrealized Losses	(452)	(766)
Estimated Fair Value	240,116	323,769
Certificates of deposit
Schedule of Investments [Line Items]
Amortized Cost	16,325	30,724
Gross Unrealized Gains	17	2
Gross Unrealized Losses	0	(28)
Estimated Fair Value	16,342	30,698
U.S. Treasury securities
Schedule of Investments [Line Items]
Amortized Cost	222,612	292,264
Gross Unrealized Gains	69	0
Gross Unrealized Losses	(53)	(678)
Estimated Fair Value	222,628	291,586
Common stock of U.S. corporation
Schedule of Investments [Line Items]
Amortized Cost	1,545
Gross Unrealized Gains	0
Gross Unrealized Losses	(399)
Estimated Fair Value	$ 1,146
Preferred stock of U.S. corporation
Schedule of Investments [Line Items]
Amortized Cost		1,545
Gross Unrealized Gains		0
Gross Unrealized Losses		(60)
Estimated Fair Value		$ 1,485

Investments - Schedule of Investment Maturity (Details) - USD ($) $ in Thousands	Sep. 30, 2016	Dec. 31, 2015
Schedule of Available-for-sale Securities [Line Items]
Maturing in one year or less	$ 199,169
Maturing after one year through two years	39,801
Total debt investments	238,970
Estimated fair value	240,116	$ 323,769
Common stock of U.S. corporation
Schedule of Available-for-sale Securities [Line Items]
Estimated fair value	$ 1,146

Equity Transactions and Share-based Compensation - Common Stock Narrative (Details) - shares	3 Months Ended	9 Months Ended
	Sep. 30, 2016	Sep. 30, 2016
Class of Stock [Line Items]
Stock issued during period, shares, restricted stock award, gross (in shares)	0	0
Common stock of U.S. corporation
Class of Stock [Line Items]
Shares issued for warrants exercised (in shares)	0	0
The 2013 Employee Stock Purchase Plan
Class of Stock [Line Items]
Stock issued during period, shares, employee stock purchase plans (in shares)	100,000	108,000

Income Taxes (Narrative) (Details) - USD ($)	3 Months Ended		9 Months Ended		12 Months Ended
Income Taxes (Narrative) (Details) - USD ($)	Sep. 30, 2016	Sep. 30, 2015	Sep. 30, 2016	Sep. 30, 2015	Dec. 31, 2016
Income Tax Contingency [Line Items]
Federal or state income taxes	$ 0	$ 0	$ 0	$ 0
Unrecognized tax benefits	$ 0		$ 0
Scenario, Forecast
Income Tax Contingency [Line Items]
Estimated annual effective tax rate					0.00%