You should read the following discussion and analysis of financial condition and results of operations together with the section entitled "Selected Consolidated Financial Data" and our consolidated financial statements and related notes included elsewhere in this Annual Report on Form 10-K. This discussion and other parts of this Annual Report on Form 10-K contain forward-looking statements that involve risks and uncertainties, such as statements regarding our plans, objectives, expectations, intentions, and projections. Our actual results could differ materially from those discussed in these forward-looking statements. Factors that could cause or contribute to such differences include, but are not limited to, those discussed in the "Risk Factors" section of this Annual Report on Form 10-K.

Overview

We are a biotechnology company that uses our robust, chemistry-driven approach and drug discovery capabilities to become a leader in the discovery and development of small molecule drugs for the treatment of viral infections and liver diseases. We discovered glecaprevir, the second of two protease inhibitors discovered and developed through our collaboration with AbbVie for the treatment of chronic hepatitis C virus, or HCV. Glecaprevir is co-formulated as part of AbbVie's leading brand of direct-acting antiviral, or DAA, combination treatment for HCV, which is marketed under the tradenames MAVYRET® (U.S.) and MAVIRET® (ex-U.S.) (glecaprevir/pibrentasvir). Our royalties from our AbbVie collaboration provide us funding to support our wholly-owned research and development programs, which are primarily focused on the following disease targets:



    •   Respiratory syncytial virus, or RSV, the most common cause of
        bronchiolitis and pneumonia in young children and a significant cause of
        respiratory illness in older adults, with estimates suggesting that
        approximately 200,000 hospitalizations in the U.S. and EU occur each year
        in children under the age of two and approximately 170,000
        hospitalizations in these regions occur each year in adults over the age
        of 65;


    •   Hepatitis B virus, or HBV, the most prevalent chronic hepatitis, which is
        estimated by the World Health Organization to affect more than 250 million
        individuals worldwide;


  • SARS-CoV-2, the virus that causes COVID-19;


    •   Human metapneumovirus, or hMPV, a virus that causes respiratory infection
        with symptoms similar to RSV; and


    •   Non-alcoholic steatohepatitis, or NASH, a liver disease estimated to
        affect approximately 1.5% to 6.5% of the population in the developed world
        (which translates to approximately 5 to 20 million individuals in the U.S.
        alone).

We had $419.3 million in cash and marketable securities at September 30, 2020. In fiscal 2020, we earned $122.5 million in product royalties on AbbVie's net sales of its HCV regimens. We expect cash flows from our continuing HCV royalties and our existing financial resources will allow us to continue to fund our wholly-owned research and development programs for the foreseeable future.

Our Wholly-Owned Programs

Our wholly-owned research and development programs are in virology, namely RSV, HBV, SARS-CoV-2 and hMPV, and in NASH, a non-viral liver disease:



    •   RSV: We have a clinical stage program for RSV, for which the lead asset is
        EDP-938.


        o   In June 2019, we announced positive topline results from our Phase 2a
            human challenge study of EDP-938 in healthy adults infected with a
            specific strain of RSV.


        o   Based on the results of the challenge study, we now have an ongoing
            Phase 2b study of EDP-938, which is in adult outpatients with
            community-acquired RSV infection. This study, named RSVP, is designed
            to help us better understand the feasibility of this direct-acting
            antiviral therapy. While many of the sites for the Northern Hemisphere
            missed an unusually early RSV season in 2019-2020 and COVID-19 delayed
            or prevented activation of some trial sites in the Southern
            Hemisphere, the mitigation steps to manage the COVID-19 pandemic
            significantly reduced the incidence of respiratory illnesses (other
            than COVID-19) at the activated sites in that region's RSV season. We
            are reactivating sites in North America and are adding sites in
            several countries in Europe in preparation for the 2020-2021 winter
            RSV season, and also plan to add sites in Asian countries in 2021.
            While it is too early to know the extent of any impact of COVID-19 on
            the levels of RSV infection in this season and our RSVP timelines,
            assuming full study enrollment in the Northern Hemisphere for the
            2020-2021 season, we would expect to have data in the third calendar
            quarter of 2021.


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        o   Concurrent with the RSVP study, we plan to initiate two additional
            Phase 2 RSV studies during the 2020-2021 Northern Hemisphere RSV
            season, one in adult transplant patients who are immune-compromised
            and one in pediatric patients. The adult transplant patient study,
            named RSVTx, is a Phase 2b randomized, double-blind,
            placebo-controlled study of EDP-938 to evaluate the effect of EDP-938
            in adult hematopoietic cell transplant recipients with acute RSV
            infection of the upper respiratory tract.


        o   The pediatric trial, named RSVPEDs, is a randomized, double-blind,
            placebo-controlled Phase 2 dose ranging study of EDP-938 to evaluate
            EDP-938 regimens in hospitalized or non-hospitalized infants and
            children aged 28 days to 24 months, who test positive for RSV based on
            an approved diagnostic assay.


        o   It is too early to know what impact, if any, COVID-19 may have on the
            timelines for the RSVTx or RSVPEDs studies.


    •   HBV: Our lead candidate for the treatment of chronic infection with
        hepatitis B virus, or HBV, is EDP-514, a novel core inhibitor that
        displays potent anti-HBV activity in vitro at multiple points in the HBV
        lifecycle. We have initiated clinical development of EDP-514 and have
        ongoing studies of it in patients with chronic HBV.


        o   Our initial study was a randomized, double-blind, placebo-controlled
            Phase 1a/1b study designed in two parts. Part 1 of the study was
            completed successfully. Overall, EDP-514 demonstrated a favorable
            safety profile in healthy subjects. Based on these results, we
            initiated Part 2 of the study to evaluate EDP-514 in nuc-suppressed
            patients, and subject to any future adverse impact of the COVID-19
            pandemic, we expect to have topline results in the second calendar
            quarter of 2021.


        o   In addition, in July 2020, we initiated a separate Phase 1b study in
            patients with chronic HBV infection who are not on HBV therapy and
            have high levels of virus in their blood whom we refer to as viremic
            HBV patients. Subject to any future adverse impact of the COVID-19
            pandemic, we expect to have preliminary data from this study in the
            second quarter of calendar 2021.


    •   COVID-19: Since we announced our newest discovery program for the
        treatment of COVID-19, we have been leveraging our expertise in
        direct-acting antiviral mechanisms to discover new compounds to treat
        COVID-19, using a combination of screening and targeted drug design.


    •   hMPV: Since announcing our new drug discovery effort for hMPV in January
        2020, we have been optimizing nanomolar inhibitor leads against this virus
        and are working toward identifying our first clinical candidate for this
        indication.


    •   NASH: We currently have two compounds in clinical development for NASH,
        EDP-305 and EDP-297, referred to as FXR agonists. These compounds, which
        selectively bind to and activate the Farnesoid X receptor, or FXR,
        represent a class of FXR agonists designed to take advantage of increased
        binding interactions with this receptor.


        o   In July 2020 we initiated ARGON-2, a 72-week, Phase 2b, randomized,
            double-blind, placebo-controlled study, with histological endpoints,
            including fibrosis in 340 biopsy-confirmed NASH patients treated with
            EDP-305 or placebo. We are using EDP-305 doses of 1.5 mg and 2.0 mg,
            which we believe will favorably balance strong, efficacious target
            engagement with tolerability.


        o   In September 2020, we initiated a Phase 1 clinical study of EDP-297, a
            highly potent and targeted follow-on FXR agonist, being developed for
            the treatment of NASH. The Phase 1, randomized, double-blind,
            placebo-controlled, first-in-human study is designed to assess the
            safety, tolerability, and pharmacokinetics, including the effect of
            food intake, of orally administered EDP-297 in approximately 74
            healthy adult subjects. Two phases are planned: a single ascending
            dose phase enrolling six cohorts, including a two-part food effect
            cohort, and a multiple ascending dose phase enrolling three cohorts.
            Subject to any future adverse impact of the COVID-19 pandemic, we
            expect to have preliminary data from this study in the second calendar
            quarter of 2021.


        o   At approximately the same time that we expect to have data from the
            EDP-297 study, we expect that ARGON-2 will provide us an interim
            analysis at 12 weeks of treatment on a subset of patients to enhance
            our ability to prioritize our FXR agonist compounds and seek
            opportunities more quickly for development of one or both of them in
            combinations with other mechanisms for NASH with fibrosis.


        o   In addition, we have been pursuing research in other mechanisms that
            may provide therapeutic benefit in NASH, any of which might be used in
            combination with an FXR agonist or other therapies for NASH.

We have utilized our internal chemistry and drug discovery capabilities to generate all of our development-stage programs. We continue to invest substantial resources in research programs to discover back-up compounds as well as new compounds targeting different mechanisms of action, both in our disease areas of focus as well as potentially in other disease areas.



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Our Out-Licensed Products

Through our Collaborative Development and License Agreement with AbbVie, we have discovered and out-licensed to AbbVie two protease inhibitor compounds that have been clinically tested, manufactured, and commercialized by AbbVie as part of its combination regimens for HCV. We have earned all $330.0 million milestone payments under the agreement related to clinical development and commercialization regulatory approvals of these regimens in major markets. Glecaprevir is the protease inhibitor we discovered that was developed by AbbVie in a fixed-dose combination with its NS5A inhibitor, pibrentasvir, for the treatment of HCV. This patented combination, currently marketed under the brand names MAVYRET® (U.S.) and MAVIRET® (ex-U.S.), is referred to in this report as MAVYRET/MAVIRET. This regimen is a once-daily, all-oral, fixed-dose, ribavirin-free treatment for HCV genotypes 1-6, or GT1-6, which is referred to as being pan-genotypic. In the U.S., EU and Japan it is approved as an 8-week treatment for patients with and without compensated cirrhosis and new to treatment. Today, these patients are estimated to represent the majority of HCV patients in over 50 countries where MAVYRET/MAVIRET is sold by AbbVie and where MAVYRET/MAVIRET remains the only 8-week pan-genotypic HCV treatment.

Since August 2017, substantially all of our royalty revenue has been derived from AbbVie's net sales of MAVYRET/MAVIRET. Our ongoing royalty revenues from this regimen consist of annually tiered, double-digit, per-product royalties on 50% of the calendar year net sales of the 2-DAA glecaprevir/pibrentasvir combination in MAVYRET/MAVIRET. These royalties are calculated separately from the royalties on AbbVie's paritaprevir-containing regimens, AbbVie's initial HCV treatment now replaced by MAVYRET/MAVIRET in most markets worldwide. The annual royalty tiers for each of these royalty-bearing products return to the lowest tier for sales on and after each January 1.

Financial Operations Overview

We are currently funding all research and development for our wholly-owned programs, which are targeted toward the discovery and development of novel compounds for the treatment of viral infections and liver diseases. In 2020, we had two Phase 2 studies ongoing for our wholly-owned programs in RSV and NASH and two Phase 1 studies in our HBV and NASH programs. We are also progressing other compounds into preclinical development in our RSV, HBV and NASH programs as well as pursuing drug discovery efforts in hMPV and COVID-19.

During 2020, we experienced disruptions in our business due to the spread of COVID-19. Specifically, we paused recruitment of our Phase 2 ARGON-2 study in NASH and Part 2 of our Phase 1a/1b study in nuc-suppressed HBV patients in March 2020 but were able to resume recruitment in both of these studies in July 2020. Further, COVID-19 resulted in a delay or prevention in site activation in the Southern Hemisphere for our Phase 2 RSVP trial in RSV for that region's RSV season. However, we are reactivating sites in North America and are adding sites in several countries in Europe in preparation for the 2020-2021 winter RSV season, and also plan to add sites in Asian countries in 2021.

As a result of our clinical development programs, as well as efforts to advance other compounds into preclinical development, we expect to incur greater expenses in fiscal 2021 than in 2020 as we continue to advance our RSV, NASH, HBV, hMPV, and SARS CoV-2 programs. However, if the COVID-19 pandemic slows down our research and development programs, it will reduce our spending in those areas in the near term.

We are funding our operations primarily through royalty payments received under our collaboration agreement with AbbVie and our existing cash, cash equivalents, and short-term and long-term marketable securities. Our revenue is currently dependent on royalty payments we receive from AbbVie on its sales of MAVYRET/MAVIRET. During 2020, royalty revenues declined as compared to the prior year due primarily to the worldwide impact of COVID-19 on treated patient volumes as well as competitive pricing pressures in select markets. Given the uncertainty regarding the level of AbbVie's future MAVYRET/MAVIRET sales that will generate our royalty revenue as well as increases in our future expenditures for the advancement of our internally developed compounds, we expect our expenses will exceed our revenues in fiscal 2021.

Revenue

Our revenue is derived from our collaboration agreement with AbbVie. Substantially all our royalty revenues are now derived from the sales of MAVYRET/MAVIRET, an 8-week treatment regimen that is pan-genotypic.

Under the terms of our AbbVie agreement, we earn annually tiered, double-digit royalties on the 50% of AbbVie's net sales of MAVYRET/MAVIRET allocated to glecaprevir, the protease inhibitor we discovered. Beginning with each January 1, the cumulative net sales of each royalty-bearing product start at zero for purposes of calculating the tiered royalties on a product-by-product basis.



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The following table is a summary of revenue recognized for the years ended September 30, 2020, 2019, and 2018:





                          Years Ended September 30,
                      2020          2019          2018
                               (in thousands)
AbbVie agreement:
Royalties           $ 122,473     $ 205,197     $ 191,625
Milestones                  -             -        15,000
Total revenue       $ 122,473     $ 205,197     $ 206,625




AbbVie Agreement

We currently receive annually tiered, double-digit royalties per protease inhibitor product on AbbVie's net sales allocable to either of our collaboration's protease inhibitor products. Under the terms of our AbbVie agreement, as amended in October 2014, 50% of AbbVie's net sales of MAVYRET/MAVIRET are allocated to glecaprevir. In the case of regimens containing paritaprevir, 30% of net sales of 3-DAA regimens containing paritaprevir and 45% of net sales of 2-DAA regimens containing paritaprevir are allocated to paritaprevir for purposes of calculating our annually tiered royalties. Beginning with each January 1, the cumulative net sales of each royalty-bearing product start at zero for purposes of calculating the tiered royalties on a product-by-product basis. For detail regarding the royalty tiers under our AbbVie agreement, see Note 7 in Notes to Consolidated Financial Statements of this report which is incorporated herein by this reference.

Since all of our research performance obligations under the AbbVie agreement were concluded by June 30, 2011, all milestone payments received since then have been recognized as revenue upon achievement of each milestone by AbbVie. During the fiscal year ended September 30, 2018, we earned and recognized as revenue the last milestone payment for glecaprevir, which was a $15.0 million milestone payment upon AbbVie's achievement of commercialization regulatory approval of MAVIRET® in Japan.

We expect all of our revenue in 2021 to be generated from our collaboration agreement with AbbVie.

Internal Programs

As our internal product candidates are currently in Phase 1 or Phase 2 clinical development, we have not generated any revenue from our own product sales and do not expect to generate any revenue from product sales derived from these product candidates for at least the next several years.

Operating Expenses

The following table summarizes our operating expenses for the years ended September 30, 2020, 2019, and 2018:





                                   Years Ended September 30,
                               2020          2019          2018
                                        (in thousands)
Research and development     $ 136,756     $ 142,213     $  94,856
General and administrative      27,356        26,246        23,441
Total operating expenses     $ 164,112     $ 168,459     $ 118,297

Research and Development Expenses

Research and development expenses consist of costs incurred to conduct basic research, such as the discovery and development of novel small molecules as therapeutics, as well as any external expenses of preclinical and clinical development activities. We expense all costs of research and development as incurred. These expenses consist primarily of:



    •   personnel costs, including salaries, related benefits and stock-based
        compensation for employees engaged in scientific research and development
        functions;


    •   third-party contract costs relating to research, formulation,
        manufacturing, preclinical study and clinical trial activities;


  • laboratory consumables;


  • allocated facility-related costs; and


  • third-party license fees.


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Project-specific expenses reflect costs directly attributable to our clinical development candidates and preclinical candidates nominated and selected for further development. Remaining research and development expenses are reflected in research and drug discovery, which represents early-stage drug discovery programs. At any given time, we typically have several active early stage research and drug discovery projects. Our internal resources, employees and infrastructure are not directly tied to any individual research or drug discovery project and are typically deployed across multiple projects. As such, we do not report information regarding costs incurred for our early-stage research and drug discovery programs on a project-specific basis. We expect that our research and development expenses will continue to increase in the future as we advance our research and development programs.

Our research and drug discovery programs are at early stages; therefore, the successful development of our product candidates is highly uncertain and may not result in approved products. Completion dates and completion costs can vary significantly for each product candidate and are difficult to predict. Given the uncertainty associated with clinical trial enrollments, particularly in the context of the COVID-19 pandemic, and the risks inherent in the development process, we are unable to determine the duration and completion costs of the current or future clinical trials of our product candidates or if, or to what extent, we will generate revenue from the commercialization and sale of any of our product candidates. We anticipate that we will make determinations as to which development programs to pursue and how much funding to direct to each program on an ongoing basis in response to the preclinical and clinical success and prospects of each product candidate, as well as ongoing assessments of the commercial potential of each product candidate.

General and Administrative Expenses

General and administrative expenses consist primarily of personnel costs, which include salaries, related benefits and stock-based compensation, of our executive, finance, business and corporate development and other administrative functions. General and administrative expenses also include travel expenses, allocated facility-related costs not otherwise included in research and development expenses, directors and officers liability insurance premiums, and professional fees for auditing, tax, and legal services and patent expenses.

We expect that general and administrative expenses will increase in the future primarily due to the ongoing expansion of our operating activities in support of our own research and development programs, as well as potential additional costs associated with operating a growing publicly traded company.

Other Income (Expense), Net

Other income (expense), net consists of interest and investment income and the change in fair value of our outstanding Series 1 nonconvertible preferred stock. Interest income consists of interest earned on our cash equivalents and short-term and long-term marketable securities balances as well as interest earned for any refunds received from tax authorities. Investment income consists of the amortization or accretion of any purchased premium or discount on our short-term and long-term marketable securities. The change in fair value of our Series 1 nonconvertible preferred stock relates to the remeasurement of these financial instruments from period to period as these instruments may require a transfer of assets because of the liquidation preference features of the underlying instrument.

Income Tax (Expense) Benefit

Income tax (expense) benefit for the years ended September 30, 2020, 2019, and 2018 is the result of federal and state taxes generated from our domestic operations. Income tax (expense) benefit is based on our best estimate of applicable income tax rates, net research and development tax credits, net operating loss carryforwards and carrybacks, changes in valuation allowance estimates and deferred income taxes, for the entire fiscal year applied to pre-tax profit or loss reported for the year-to-date period, except when a reliable estimate of the annual effective tax rate cannot be made and we instead use the year-to-date effective tax rate.

Critical Accounting Policies

Our consolidated financial statements are prepared in accordance with accounting principles generally accepted in the United States of America. The preparation of our consolidated financial statements and related disclosures requires us to make estimates and assumptions that affect the reported amount of assets, liabilities, equity, revenue, costs and expenses, and related disclosures. We believe that the estimates and assumptions involved in the accounting policies described below may have the greatest potential impact on our consolidated financial statements and, therefore, consider these to be our critical accounting policies. We evaluate our estimates and assumptions on an ongoing basis. Actual results may differ from these estimates under different assumptions and conditions. See also Note 2 to the consolidated financial statements included elsewhere in this Annual Report on Form 10-K for information about these critical accounting policies as well as a description of our other significant accounting policies.



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Research and Development and Pharmaceutical Drug Manufacturing Accruals

We have entered into various contracts with third parties to perform research and development and pharmaceutical drug manufacturing. These include contracts with contract research organizations ("CROs"), clinical manufacturing organizations ("CMOs"), testing laboratories, research hospitals and not-for-profit organizations and other entities to support our research and development activities. We expense the cost of each contract as the work is performed. When billing terms under these contracts do not coincide with the timing of when the work is performed, we are required to make estimates of our outstanding obligation as of period end to those third parties. Our accrual estimates are based on a number of factors, including our knowledge of the research and development programs and pharmaceutical drug manufacturing activities associated with timelines, invoicing to date, and the provisions in the contract. Significant judgments and estimates are made in determining the accrued balances at the end of any reporting period. Actual results could differ from our estimates.

Income Taxes

Income taxes are provided for tax effects of transactions reported in the consolidated financial statements and consist of income taxes currently due plus deferred income taxes related to timing differences between the basis of certain assets and liabilities for financial statement reporting purposes and the basis for income tax reporting purposes. Deferred taxes are determined based on the difference between the financial reporting and tax basis of assets and liabilities using enacted tax rates in effect in the years in which the differences are expected to reverse. Changes in deferred tax assets and liabilities are recorded in income tax expense.

A valuation allowance is provided if, based upon the weight of available evidence, it is more likely than not that some or all of the deferred tax assets will not be realized. At each balance sheet date, we assess the likelihood that deferred tax assets will be realized and recognize a valuation allowance if it is more likely than not that all or some portion of the deferred tax assets will not be realized. The realization of deferred tax assets is dependent upon the ability to generate future taxable income during the periods in which those temporary differences become deductible. Assessment of a potential recovery of deferred tax assets requires significant judgment and is evaluated by estimating the future taxable income expected and considering prudent and feasible tax planning strategies. As of September 30, 2020, we recorded a valuation allowance against the majority of our deferred tax assets because we do not expect to have sufficient taxable income in the future to realize the majority of our existing deferred tax assets.

Uncertain tax positions represent tax positions for which reserves have been established. We account for uncertainty in income taxes recognized in the consolidated financial statements by applying a two-step process to determine the amount to be recognized. First, the tax position must be evaluated to determine the likelihood that it will be sustained upon external examination by the taxing authorities. If the tax position is deemed more likely than not to be sustained, the tax position is then assessed to determine the amount to be recognized in the financial statements. The amount that may be recognized is the largest amount that has a greater than 50% likelihood of being realized upon ultimate settlement. Income tax expense includes the effects of any resulting tax reserves, or unrecognized tax benefits, that are considered appropriate as well as the related net interest and penalties.

Results of Operations

Comparison of Years Ended September 30, 2020, 2019, and 2018





                                                       Years Ended September 30,
                                                   2020           2019           2018
                                                             (in thousands)
Revenue                                         $  122,473     $  205,197     $  206,625
Research and development                           136,756        142,213         94,856
General and administrative                          27,356         26,246         23,441
Other income (expense):
Interest and investment income, net                  6,471          8,819          4,852
Change in fair value of Series 1
nonconvertible preferred stock                         149              -            (59 )
Income tax (expense) benefit                        (1,149 )          826        (21,165 )
Net income (loss)                                  (36,168 )       46,383         71,956



Revenue. We recognized revenue of $122.5 million during the year ended September 30, 2020, as compared to $205.2 million during the year ended September 30, 2019. The decrease in revenue of $82.7 million year-over-year was due to lower numbers of treated HCV patients as a result of the worldwide COVID-19 pandemic as well as competitive pricing pressures in select markets.



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We recognized revenue of $205.2 million during the year ended September 30, 2019 compared to $206.6 million during the year ended September 30, 2018. The decrease in revenue of $1.4 million year-over-year was due to the fact that in fiscal 2018 we received the final milestone payment of $15.0 million earned under our AbbVie agreement related to reimbursement approval for MAVIRET®, in Japan. This decrease was offset by an increase of $13.6 million in royalties earned under our AbbVie agreement which were driven by the launch of MAVYRET/MAVIRET in late calendar 2017.

Our weighted average royalty rate on the portion of AbbVie's sales allocable to our protease inhibitor products was approximately 13%, 13% and 12% during the years ended September 30, 2020, September 30, 2019 and 2018, respectively.

Our royalty revenues eligible to be earned in the future will depend on AbbVie's HCV market share, the pricing of the MAVYRET/MAVIRET regimen, the impact of the COVID-19 pandemic on treated patient volumes and the number of patients treated. In addition, at the beginning of each calendar year (the second quarter of our fiscal year), our royalty rate resets to the lowest tier for each of our royalty-bearing products licensed to AbbVie. (See Note 7 to our consolidated financial statements for further details on our royalty rate tier.)

Research and development expenses.





                                               Years Ended September 30,
                                            2020          2019          2018
                                                     (in thousands)
R&D programs:
Virology                                  $  85,856     $  75,087     $ 40,047
Liver disease                                45,001        66,892       54,691
Other                                         5,899           234          118

Total research and development expenses $ 136,756 $ 142,213 $ 94,856

Research and development expense decreased by $5.5 million for the year ended September 30, 2020 as compared to the same period in 2019. The decrease year-over-year was primarily due to timing of our clinical studies in our virology and liver disease programs as well as the impact of the COVID-19 pandemic. In fiscal 2020, we initiated a Phase 2 study in our RSV program (RSVP), continued our Phase 1a/1b study of EDP-514 (HBV program) in nuc-suppressed patients, and initiated a separate Phase 1b study in patients with chronic HBV infection in our virology program. We also initiated our ARGON-2 study in our liver disease program. However, in March 2020, we paused enrollment of the ARGON-2 and HBV nuc-suppressed studies and experienced a delay or prevention of site activation of some trial sites in the Southern Hemisphere in our RSVP study due to mitigation steps to manage the pandemic in that region. However, we were able to resume recruitment of the ARGON-2 and HBV nuc-suppressed studies in July 2020 and are reactivating sites in North America and are adding sites in Europe in preparation for the 2020-2021 winter RSV season for our RSVP study. In comparison, in fiscal 2019, we had initiated and completed part 1 of a Phase 2a human challenge study of EDP-938 and initiated a Phase 1a/1b clinical study of EDP-514, both of which are part of our virology programs. In our liver disease program, we had two Phase 2 studies of EDP-305 ongoing, one in NASH patients and one in PBC patients.

Research and development expense increased by $47.4 million for the year ended September 30, 2019 as compared to the same period in 2018. The increase was primarily due to progression of clinical activities in our virology and liver disease programs. In fiscal 2018 we initiated two Phase 2 studies of EDP-305 which continued into 2019 and advanced other compounds in preclinical development in our liver disease programs. In addition to these ongoing studies in our liver disease programs, in fiscal 2019 we initiated and completed part 1 of a Phase 2a human challenge study of EDP-938 and initiated a Phase 1a/1b clinical study of EDP-514, both of which are part of our virology programs. Increases in our research and development expenses were driven by an increase in headcount to support our programs and an increase in external costs for clinical activities.

We expect that our research and development expenses will continue to increase in the future as we conduct more clinical development activities.

General and administrative expenses. General and administrative expenses increased by $1.1 million for the year ended September 30, 2020 as compared to the same comparable period in 2019. The increase was primarily due to an increase in patent costs to support our broadening patent portfolio and premiums on directors and officers insurance.

General and administrative expenses increased by $2.8 million for the year ended September 30, 2019 as compared to the same period in 2018. The increase was primarily due to an increase in compensation expense due to increased headcount as well as an increase in patent costs to support our broadening patent portfolio.

We expect our general and administrative expenses will continue to increase in the future as our operations grow to support further research and development.



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Other income (expense), net. Changes in components of other income (expense), net were as follows:

Interest and investment income, net. Interest and investment income, net, decreased by $2.3 million for the year ended September 30, 2020 compared to the same period in 2019, primarily due to more purchases of our debt securities at a premium in fiscal 2020.

Interest and investment income, net, increased by $4.0 million for the year ended September 30, 2019 compared to the same period in 2018, primarily due to higher average marketable securities balances in 2019 as a result of receipt of significant royalties in 2019 under our AbbVie agreement.

Change in fair value of Series 1 nonconvertible preferred stock. We recognized other income for the year ended September 30, 2020 of $0.1 million due to a decrease in the fair value of outstanding Series 1 nonconvertible preferred stock year over year. In fiscal 2019, we determined that no fair value adjustment was required for our outstanding Series 1 nonconvertible preferred stock. In fiscal 2018, we recognized expense due to the increase in fair value of outstanding Series 1 nonconvertible preferred stock year over year, offset by the expiration of unexercised warrants outstanding as of October 4, 2017.

Income tax (expense) benefit. We recorded income tax expense of $(1.1) million and an income tax benefit of $0.8 million for the years ended September 30, 2020 and 2019, respectively. The effective tax rate for the year ended September 30, 2020 was 3.3% and for the year ended September 30, 2019 it was an effective tax rate of (1.8%). The increase in income tax expense in fiscal year 2020 was primarily due to a valuation allowance charge recorded against the majority of our deferred tax assets of $18.3 million, partially offset by a federal net operating loss carryback as permitted under the Coronavirus Aid, Relief and Economic Security Act ("CARES Act"), research and development tax credits generated during the year and release of an uncertain tax position reserve related to the close of a tax audit. A valuation allowance was recorded against our deferred tax assets because it was more likely than not that we will not have sufficient taxable income in the future that will allow us to realize the majority of our existing deferred tax assets. In 2019, although we reported higher income before taxes, we recorded an income tax benefit due to federal income tax benefits associated with foreign-derived royalty income, higher federal research and development tax credits and higher tax deductions from employee stock-award related activity during 2019.

We recorded an income tax benefit of $0.8 million and expense of $(21.2) million for the years ended September 30, 2019 and 2018, respectively. The effective tax rate for the year ended September 30, 2019 was (1.8%) and the effective tax rate for the year ended September 30, 2018 was 22.7%. The decrease in income tax expense was primarily due to a decrease in income before taxes year over year, a federal income tax benefit associated with foreign-derived royalty income recognized in 2019, an increase in federal research and development tax credits due to increased research and development expenses and an increase in tax deductions from employee stock-award related activity during 2019. The 2018 effective tax rate was driven by higher income before taxes as well as a non-cash revaluation charge against deferred tax assets due to the reduced federal corporate income tax rate in the U.S. Tax Cuts and Jobs Act (the "Tax Act") enacted in December 2017.

Income tax benefit (expense) for all periods presented was attributable to the tax provision on earnings of our operations, all of which are domestic.

Liquidity and Capital Resources

During fiscal 2020, 2019 and 2018, we funded our operations with cash flows generated from operations. At September 30, 2020, our principal sources of liquidity were cash and cash equivalents and short-term and long-term marketable securities of $419 million.

The following table shows a summary of our cash flows for each of the years ended September 30, 2020, 2019, and 2018:





                                                       Years Ended September 30,
                                                   2020           2019           2018
                                                             (in thousands)
Cash provided by (used in):
Operating activities                            $    7,088     $   71,418     $   29,220
Investing activities                                19,830        (86,664 )      (35,402 )
Financing activities                                 8,983          2,574          4,409
Net increase (decrease) in cash and cash
equivalents                                     $   35,901     $  (12,672 )   $   (1,773 )

Net cash provided by operating activities

Cash provided by operating activities was $7.1 million for the year ended September 30, 2020 as compared to $71.4 million for the same period in 2019. The decrease in cash provided by operating activities was primarily driven by a decrease in royalty payments received under our collaboration with AbbVie and an increase in research and development costs incurred year-over-year, which were partially offset by a decrease in cash taxes paid. For the foreseeable future, we expect to incur substantial additional costs associated with research and development for our internally developed programs.



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Cash provided by operating activities was $71.4 million for the year ended September 30, 2019 as compared to $29.2 million for the same period in 2018. The increase in cash provided by operating activities was primarily driven by an increase in royalty payments received under our collaboration with AbbVie as well as a decrease in cash taxes paid, partially offset by increased research and development costs incurred year-over-year.

Net cash provided by (used in) investing activities

The increase of $106.5 million in cash provided by investing activities for the year ended September 30, 2020 as compared to the same period in 2019 was driven by timing of purchases, sales and maturities of marketable securities.

The increase of $51.3 million in cash used in investing activities for the year ended September 30, 2019 as compared to the same period in 2018 was driven by timing of purchases, sales and maturities of marketable securities.

Net cash provided by financing activities

The increase in cash provided by financing activities of $6.4 million for the year ended September 30, 2020 as compared to the same period in 2019 was driven by an increase in proceeds from stock option exercises in 2020 as compared to 2019 as well as a decrease in withholding tax payments for the settlement of share-based awards of $2.7 million driven by a decrease in the amount of awards settled as well as a decline in our stock price year-over-year at the time of vesting of certain share-based awards.

The decrease in cash provided by financing activities of $1.8 million for the year ended September 30, 2019 as compared to the same period in 2018 was driven by an increase in tax withholding payments for the vesting of performance-based stock unit awards in 2019.

Funding Requirements

As of September 30, 2020, we had $419 million in cash, cash equivalents and short-term and long-term marketable securities. We believe that our existing cash, cash equivalents and marketable securities as of September 30, 2020 will be sufficient to meet our anticipated cash requirements for the foreseeable future. However, our forecast of the period of time through which our financial resources will be adequate to support our operations is a forward-looking statement that involves risks and uncertainties, and actual results could vary materially.

Our future capital requirements are difficult to forecast and will depend on many factors, including:



    •   the amount of royalties generated from MAVYRET/MAVIRET sales under our
        existing collaboration with AbbVie;


    •   any continuing impact of the COVID-19 pandemic on the numbers of treated
        HCV patients;


  • the number and characteristics of our research and development programs;


    •   the scope, progress, results and costs of researching and developing any
        of our product candidates on our own, including conducting advanced
        clinical trials;


    •   delays and additional expense in our clinical trials as a result of the
        COVID-19 pandemic;


    •   the cost of manufacturing our product candidates for clinical development
        and any products we successfully commercialize independently;


    •   opportunities to in-license or otherwise acquire new technologies,
        therapeutic candidates and therapies;


    •   the timing of, and the costs involved in, obtaining regulatory approvals
        for any product candidates we develop independently;


    •   the cost of commercialization activities, if any, of any product
        candidates we develop independently that are approved for sale, including
        marketing, sales and distribution costs;


    •   the timing and amount of any sales of our product candidates, if any, or
        royalties thereon;


    •   our ability to establish new collaborations, licensing or other
        arrangements, if any, and the financial terms of such arrangements;


    •   the costs involved in preparing, filing, prosecuting, maintaining,
        defending and enforcing patents, including any litigation costs and the
        outcomes of any such litigation; and


  • potential fluctuations in foreign currency exchange rates.


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We do not believe that inflation had a material effect on our business, financial condition or results of operations in the last three fiscal years. If our costs were to become subject to significant inflationary pressures, we could not offset such higher costs through revenue increases because our revenues are substantially outside of our control. Our inability to do so could harm our business, financial condition and results of operations.

Off-Balance Sheet Arrangements

We do not engage in any off-balance sheet financing activities. We do not have any interest in entities referred to as variable interest entities, which include special purpose entities and other structured finance entities.

Recently Issued Accounting Pronouncements

A description of recently issued accounting pronouncements that may potentially impact our financial position and results of operations is set forth in Note 2 to the consolidated financial statements included in this Annual Report on Form 10-K.

Contractual Obligations and Commitments

We lease space in Watertown, Massachusetts under two separate lease agreements.

The first lease, located at 500 Arsenal Street, commenced on October 1, 2011 and was amended in 2015 to expand the rented space and extend the lease term through September 2022. This lease is for office and laboratory space. In conjunction with the amendment of the lease, the Company entered into a capital lease agreement to fund certain leasehold improvements and the purchase of lab equipment.

The second lease, located at 400 Talcott Avenue, commenced on September 24, 2018 for office space and extends through August 1, 2024.



The following table summarizes our contractual obligations at September 30, 2020
and the effect such obligations are expected to have on our liquidity and cash
flow in future periods:



                                        Payments Due by Period
                                                               2026 and
                    2021        2022-2023       2024-2025        later        Total
                                            (in thousands)
Operating leases   $ 4,654     $     3,544     $       519     $       -     $ 8,717

As of September 30, 2020, we had 1.9 million outstanding shares of Series 1 nonconvertible preferred stock, all of which we classified as long-term liabilities on our consolidated balance sheet and recorded at fair value of $1.5 million. The fair value of the preferred stock was measured based on significant inputs not observable in the market, which represented a Level 3 measurement within the fair value hierarchy. The fair value of these instruments represents less than 10% of liabilities measured at fair value as of September 30, 2020. The Series 1 nonconvertible preferred stock issued would require the payment of $2.0 million in the event of a qualifying merger or sale of the company. The table above does not include this liability because we are unable to estimate the timing of this required payment, or if it will ever be required.

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