Atea Pharmaceuticals : First Quarter 2023 Financial Results Conference Call Presentation

First Quarter 2023

Financial and Business Update

May 8, 2023

June 2020

DISCLAIMERS

Forward-Looking Statements

This presentation contains "forward-looking statements" within the meaning of the Private Securities Litigation Reform Act of 1995. Forward-looking statements are neither historical facts nor assurances of future performance. Instead, they are based on our current beliefs, expectations and assumptions regarding the future of our business, future plans and strategies, our clinical results and other future conditions including without limitation the future of the COVID-19 and HCV landscapes and related commercial market opportunities. All statements other than statements of historical facts contained in this presentation are forward-looking statements, including statements by Atea Pharmaceuticals, Inc. (the "Company") regarding future results of operations and financial position, including our anticipated cash runway; business strategy; current and prospective product candidates; anticipated milestone events; potential benefits of our product candidates and market opportunity; planned clinical trials, including, without limitation, anticipated initiation, enrollment, regulatory submission and data readout timelines; preclinical activities; product approvals; manufacturing availability; degree of market acceptance of any products that may be approved; research and development costs; current and prospective collaborations; and prospects and opportunities for investors. In some cases, you can identify forward-looking statements by terms such as "may," "will," "should," "expects," "plans," "anticipates," "could," "intends," "targets," "projects," "contemplates," "believes," "estimates," "predicts," "potential" or "continue" or the negative of these terms or other similar expressions.

The information in this presentation, including without limitation the forward-looking statements contained herein, represent our views as of the date of this presentation. These statements are neither promises nor guarantees, but involve known and unknown risks, uncertainties and other important factors that may cause our actual results, performance or achievements to be materially different from any anticipated results, performance or achievements expressed or implied by the forward-looking statements. Risks and uncertainties that may cause actual results to differ materially include uncertainties inherent in the drug discovery and development process and the regulatory approval process, in particular for bemnifosbuvir, our reliance on third parties over which we may not always have full control, competition from authorized and approved treatments for COVID-19 and hepatitis C, risks related to the continued evolution of the COVID-19 pandemic, and other important risks and uncertainties that are described in our Annual Report on Form 10-K filed for the year ended December 31, 2022 and our most recent quarterly report on Form 10-Q filed with the Securities and Exchange Commission ("SEC") and our other filings with the SEC. New risk factors and uncertainties may emerge from time to time, and it is not possible to predict all risk factors and uncertainties. Accordingly, you are cautioned not to place undue reliance on these forward-looking statements.

Except as required by applicable law, we do not plan to publicly update or revise any forward-looking statements contained herein, whether as a result of any new information, future events, changed circumstances or otherwise. No representations or warranties (expressed or implied) are made about the accuracy of any such forward-looking statements.

Industry Information

Market data and industry information used throughout this presentation are based on management's knowledge of the industry and the good faith estimates of management. We also relied, to the extent available, upon management's review of independent industry surveys and publications and other publicly available information prepared by a number of third-party sources. All of the market data and industry information used in this presentation involves a number of assumptions and limitations, and you are cautioned not to give undue weight to such estimates. Although we believe that these sources are reliable, we cannot guarantee the accuracy or completeness of this information, and we have not independently verified this information. While we believe the estimated market position, market opportunity and market size information included in this presentation are generally reliable, such information, which is derived in part from management's estimates and beliefs, is inherently uncertain and imprecise. No representations or warranties are made by the Company or any of its affiliates as to the accuracy of any such statements or projections. Projections, assumptions and estimates of our future performance and the future performance of the industry in which we operate are necessarily subject to a high degree of uncertainty and risk due to a variety of factors, including those described above. These and other factors could cause results to differ materially from those expressed in our estimates and beliefs and in the estimates prepared by independent parties.

2

Q1 2023 and Recent Highlights

COVID-19

Bemnifosbuvir for COVID-19

• Fast Track designation for COVID-19 granted by
  US FDA
• Execution on global SUNRISE-3 geographic footprint with regulatory approvals in >50% of targeted countries
• Multiple data presentations at CROI, ICAR and ECCMID detailing bemnifosbuvir's clinical efficacy and favorable safety and drug interaction profile
• Fully active against Omicron subvariants tested, including XBB
• Second-generationprotease inhibitor advancing

Hepatitis C virus (HCV)

Bemnifosbuvir + Ruzasvir combination for HCV

• Phase 2 combination HCV trial
• • Ongoing regulatory submissions and approvals
  • On target for first patient dosed in Q2 2023
  • Initial results 4Q'23 from cohort of 60 patients
• Data presentation at ICAR supports combination profile
• New in vitro results of combination indicate highly compelling antiviral profile

3

Q1 2023 and Recent Presentations at Scientific Meetings

	Bemnifosbuvir for COVID-19 Data Presentations
CROI	No Dose Adjustments for CYP3A4 Substrates When Co-Administered with
2023	Bemnifosbuvir
CROI	Bemnifosbuvir Has Low Potential to Inhibit P-gp, BCRP, and OATP1B1
2023	Mediated Transport
ICAR	Low Risk of Drug-Drug Interactions (DDIs) for Bemnifosbuvir (BEM) Based
2023	Upon In Vitro Metabolism and Transporter Interaction Studies
ICAR	Pharmacokinetics and Metabolism of [14C]-Bemnifosbuvir in Healthy Male
2023	Participants
ICAR	Bemnifosbuvir (BEM, AT-527) a Potent Inhibitor of SARS-CoV-2 Variants of
2023	Concern (VOC), and a Promising Oral Antiviral with a High Resistance
	Barrier for Treatment of COVID-19 and other Coronaviruses Infections
ICAR	Five Cellular Enzymes in the Activation Pathway of Bemnifosbuvir, a Drug-
2023	Candidate Against SARS-CoV-2 Infections
ECCMID	Bemnifosbuvir (AT-527) Treatment of Non-Hospitalized Individuals with
2023	Mild to Moderate COVID-19: Results from a Truncated Phase 3,
	Randomized, Double-Blind,Placebo-Controlled Trial (MORNINGSKY)

Bemnifosbuvir Data Highlights:

• No dose adjustments for CYP3A4 substrates when co-administered
• Low risk of drug-drug interactions with medicines commonly prescribed to HCV patients and patients at high risk for severe COVID-19
• High barrier to resistance to COVID variants due to MOA
• MORNINGSKY results showed 71% reduction in risk of hospitalizations with bemnifosbuvir vs placebo (secondary endpoint); in exploratory analysis 82% reduction in risk in patients >40 years old

Q1 2023 and Recent Presentations at Scientific Meetings

	Bemnifosbuvir + Ruzasvir for HCV
	Data Presentations
ICAR 2023	The Combination of Bemnifosbuvir (BEM) and Ruzasvir (RZR), the
	HCV NS5B and NS5A Inhibitors, Demonstrates Potent In
	Vitro Synergistic Antiviral Activity and In Vivo Preclinical Safety
	Without Adverse Interactions

	AT-752 for Dengue Data Presentations
ICAR 2023 &	AT-752 Targets Multiple Sites and Activities on the Dengue Virus
Antiviral Research	Replication Enzyme NS5
April 2023
ECCMID 2023	AT-752, A Novel Nucleotide Prodrug With Pan-Serotype Activity
	Against Dengue Virus, Does Not Affect Cardiac Repolarization:
	Results From a Robust QT/QTc Evaluation in Healthy Participants

• In February 2023, Atea made business decision to deprioritize further clinical development of AT-752 for dengue due to anticipated long clinical timelines and associated costs

Data Highlights

Bemnifosbuvir+Ruzasvir for HCV

AT-752 for Dengue*:

• Combination of bemnifosbuvir + ruzasvir for HCV demonstrated potent in vitro synergistic antiviral activity and in vivo preclinical safety without adverse interactions
• AT-752'smechanism inhibited the essential DENV NS5 enzyme
• AT-752is well tolerated; no clinically relevant effects on cardiac repolarization, heart rate, PR or QRS intervals

5