Amanda C. Perofsky, PhD

Fogarty International Center, U.S. National Institutes of Health
amanda.perofsky@nih.gov

Education

2018 Ph.D., Ecology, Evolution, and Behavior, University of Texas at Austin, Austin, TX, USA

2009 B.Sc., Biology, B.Sc., Ecology, University of Georgia, Athens, GA, USA
Summa cum laude with Highest Honors

Research Experience

Apr 2021–present Guest Researcher
Fogarty International Center, U.S. National Institutes of Health
Division of International Epidemiology and Population Studies
Supervisor: Cécile Viboud

Apr 2021–Jan 2025 Epidemiological Data Scientist (Research Scientist/Engineer 3)
Seattle Flu Study, Brotman Baty Institute for Precision Medicine, University of Washington
Supervisors: Cécile Viboud (NIH) and Robin Prentice (UW)

Sep 2018–Apr 2021 Postdoctoral Research Fellow
Fogarty International Center, U.S. National Institutes of Health
Division of International Epidemiology and Population Studies
Advisor: Cécile Viboud

Aug 2011–Aug 2018 Doctoral Research
Department of Integrative Biology, University of Texas at Austin
Dissertation: “Ecological, Evolutionary, and Behavioral Determinants of Gut Microbiomes in Malagasy Mammals”
Advisor: Lauren Ancel Meyers

Jan 2010–Aug 2011 Postbaccalaureate IRTA Fellow
National Institute of Dental and Craniofacial Research, U.S. National Institutes of Health
Adeno-Associated Virus Biology Section
Supervisor: John Chiorini

Aug 2009–Dec 2009 Research Assistant
Odum School of Ecology, University of Georgia
Supervisor: Andrew Park

Publications

Publication list also available in Google Scholar. † = shared first authorship.

Preprints and submitted manuscripts

Bents, S. J., E. T. Martin, … A. Perofsky, … A. Waghmare, C. Viboud. (2025) Multiplex serology reveals age-specific immunodynamics of endemic respiratory pathogens in the wake of the COVID-19 pandemic. medRxiv 2025.03.26.25324738. doi: 10.1101/2025.03.26.25324738. (Submitted, Nature Communications)

Elias-Warren, A., J.C. Bennett, … A.C. Perofsky, … H.Y. Chu. (2025) Epidemiology of Human Metapneumovirus Infection in a Community Setting, Seattle, WA, USA. (Submitted, The Journal of Infectious Diseases)

Srinivas Duddu, A.†, I. Elgamal†, J. Camacho-Mateu†, O. Holubowska†, S.A. Rella†, S.J. Bents, C. Viboud, C.L. Hansen, G. Pullano, & A.C. Perofsky. (2024) Modeling the effects of COVID-19 mobility disruptions on RSV transmission in Seattle, Washington. medRxiv 2024.09.13.24313667. doi: 10.1101/2024.09.13.24313667. (Complexity 72h report, in prep for submission)

Journal articles

Hansen, C. L., L. Lee, S.J. Bents, A.C. Perofsky, K. Sun, L.M. Starita, A. Adler, J.A. Englund, E.J. Chow, H.Y. Chu, & C. Viboud. (2025) Scenario Projections of Respiratory Syncytial Virus Hospitalizations Averted Due to New Immunizations. JAMA Network Open 8(6):e2514622. doi: 10.1001/jamanetworkopen.2025.14622.

Kostandova, N., R. Corgel, … A.C. Perofsky, … D.A.T. Cummings, & A. Wesolowski. (2025) Improving mobility data for infectious disease research. Nature Human Behaviour. doi: 10.1038/s41562-025-02151-3.

Tran-Kiem, C., M.I. Paredes, A.C. Perofsky, … C. Viboud, & T. Bedford. (2025) Fine-scale patterns of SARS-CoV-2 spread from identical pathogen sequences. Nature 640, 176-185. doi: 10.1038/s41586-025-08637-4.

Perofsky, A.C., J. Huddleston, … S.G. Sullivan, I.G. Barr, K. Subbarao, F. Krammer, T. Bedford, & C. Viboud. (2024) Antigenic drift and subtype interference shape A(H3N2) epidemic dynamics in the United States. eLife 13:RP91849. doi: 10.7554/eLife.91849.

Mathis, S.M., A.E. Webber, … A.C. Perofsky, … M. Biggerstaff, & R.K. Borchering (110 authors). (2024) Evaluation of FluSight influenza forecasting in the 2021–22 and 2022–23 seasons with a new target laboratory-confirmed influenza hospitalizations. Nature Communications 15, 6289. doi: 10.1038/s41467-024-50601-9.

Perofsky, A.C., C.L. Hansen, … M. Famulare, J. Shendure, T. Bedford, H.Y. Chu, J.A. Englund, L.M. Starita, & C. Viboud. (2024) Impacts of human mobility on the citywide transmission dynamics of 18 respiratory viruses in pre- and post-COVID-19 pandemic years. Nature Communications 15, 4164. doi: 10.1038/s41467-024-48528-2.

Paredes, M.I., A.C. Perofsky, … C. Viboud, H.Y. Chu, N.F. Müller, & T. Bedford. (2024) Local-scale phylodynamics reveal differential community impact of SARS-CoV-2 in a metropolitan US county. PLOS Pathogens 20(3):e1012117. doi: 10.1371/journal.ppat.1012117.

Hansen, C.L., A.C. Perofsky, … J.A. Englund, J. Shendure, T. Bedford, H.Y. Chu, L.M. Starita, & C. Viboud. (2022) Trends in risk factors and symptoms associated with SARS-CoV-2 and Rhinovirus test positivity in King County, Washington: A Test-Negative Design Study of the Greater Seattle Coronavirus Assessment Network. JAMA Network Open 5(12):e2245861. doi: 10.1001/jamanetworkopen.2022.45861.

Perofsky, A.C., S. Tempia, J. Bingham, C. Maslo, M. Toubkin, A. Laubscher, S. Walaza, J.R.C. Pulliam, C. Viboud, & C. Cohen. (2022) The direct and indirect effects of the COVID-19 pandemic on private healthcare utilization in South Africa. Clinical Infectious Diseases 75(1):e1000-e1010. doi: 10.1093/cid/ciac055.

Perofsky, A.C., L.A. Meyers, L.A. Abondano, A. Di Fiore, & R.J. Lewis. (2021) Social groups constrain the spatiotemporal dynamics of wild sifaka gut microbiomes. Molecular Ecology 30:6759–6775. doi: 10.1111/mec.16193.

McBride, D.S.†, A.C. Perofsky†, J.M. Nolting, M.I. Nelson, & A.S. Bowman. (2021) Tracing the source of influenza A virus zoonoses in interconnected circuits of swine exhibitions. The Journal of Infectious Diseases jiab122. doi: 10.1093/infdis/jiab122.

Perofsky, A.C., & M.I. Nelson. (2020) Seasonal influenza: The challenges of vaccine strain selection. eLife 9:e62955. doi: 10.7554/eLife.62955. (Invited Insight article)

Nelson, M.I., A. Perofsky, D.S. McBride, B.L. Rambo-Martin, M.M. Wilson, J.R. Barnes, H. van Bakel, J.M. Nolting, & A.S. Bowman. (2020) A heterogenous swine show circuit drives zoonotic transmission of influenza A viruses in the United States. Journal of Virology 94(24):e01453-20. doi: 10.1128/JVI.01453-20.

Viboud, C., K. Gostic, M.I. Nelson, G.E. Price, A. Perofsky, K. Sun, N. Sequeira Trovão, B. Cowling, S. Epstein, & D.J. Spiro. (2020) Beyond Clinical Trials: Evolutionary and Epidemiological Considerations for Development of a Universal Flu Vaccine. PLOS Pathogens 16(9):e1008583. doi: 10.1371/journal.ppat.1008583.

Perofsky, A.C., R.J. Lewis, & L.A. Meyers. (2018) Terrestriality and bacterial transfer: A comparative study of gut microbiomes in sympatric Malagasy mammals. The ISME Journal 13:50–63. doi: 10.1038/s41396-018-0251-5.

Perofsky, A.C., R.J. Lewis, L. Abondano, A. Di Fiore, & L.A. Meyers. (2017) Hierarchical social networks shape gut microbial composition in wild Verreaux’s sifaka. Proceedings of the Royal Society B 284:20172274. doi: 10.1098/rspb.2017.2274.

Rakotomalala, E.J., F. Rakotondraparany, A.C. Perofsky, & R.J. Lewis. (2017) Characterization of the tree holes used by Lepilemur ruficaudatus in the dry, deciduous forest of Kirindy Mitea National Park. Folia Primatologica 88:28-41. doi: 10.1159/000464406.

Berry, B.S.†, K. Magori†, A.C. Perofsky, D.E. Stallknecht, & A.W. Park. (2013) Wetland cover dynamics drive hemorrhagic disease patterns in white-tailed deer in the United States. Journal of Wildlife Diseases 49(3):501-509. doi: 10.7589/2012-11-283.

Research Funding

Fellowships

2012-2017 National Science Foundation Graduate Research Fellowship, $125,000 (three years of funding over five years)

2011 Graduate Recruitment Fellowship, Department of Integrative Biology, University of Texas at Austin, $33,000

2010-2011 Postbaccalaureate Intramural Research Training Award (IRTA) Fellowship, National Institutes of Health, $56,000

Grants

2018 Research Exchange Grant, NSF Infectious Disease Evolution Across Scales Research Coordination Network, $2800

2015 Research Grant DBI-0939454, BEACON: An NSF Science and Technology Center for the Study of Evolution in Action, $16,000
Co-PI with Lauren Ancel Meyers and Rebecca Lewis

2015 Dissertation Improvement Grant, Ecology, Evolution, & Behavior Graduate Program, University of Texas at Austin, $8000

2012 Small Research Grant, American Society of Primatologists, $2000

2012 Small Research Grant, International Primatological Society, $1500

2011 Startup Grant, Ecology, Evolution, & Behavior Graduate Program, University of Texas at Austin, $2000

2008 NSF Research Experiences for Undergraduates (REU) Award, NSF Coweeta Long Term Ecological Research Program, $3600

Contributions to other grants (non PI-status)

2022-2024 BAA Contract 75D30122C14368, U.S. CDC Advanced Molecular Detection Program, $2M
“Collaborative technology development, and analyses to support genetic epidemiology in Washington State”
PIs: Lea Starita and Trevor Bedford
Role: Epidemiology Lead

2021-2022 Seattle Flu Study and Seattle Coronavirus Assessment Network, Gates Ventures, $11.6M
PIs: Trevor Bedford, Michael Boeckh, Helen Chu, Janet Englund, Tina Lockwood, Barry Lutz, Jay Shendure, Lea Starita, Cécile Viboud, Alpana Waghmare.
Role: Staff Scientist

Honors and Awards

2023 Director’s Individual Merit Award, Fogarty International Center, National Institutes of Health. “For excellence in scientific research in epidemiological modeling with a focus on influenza antigenic evolution and the role of human mobility in COVID-19 disease dynamics.”

2020, 2021 Director’s Group Merit Award, Fogarty International Center, National Institutes of Health. “For outstanding modeling work to support the COVID-19 pandemic response domestically and internationally.”

2020 Young Scientist Award, European Scientific Working group on Influenza (ESWI) Conference

2019 Director’s Individual Merit Award, Fogarty International Center, National Institutes of Health. “For outstanding efforts to forecast weekly influenza-like illness activity in 27 U.S. military facilities in collaboration with DoD.”

2017, 2018 Graduate School Summer Semester Continuing Fellowship, University of Texas at Austin

2017 Course Fellowship, Network Modeling for Epidemics, University of Washington, Seattle, WA

2017 Graduate Student Professional Development Award, College of Natural Sciences, University of Texas at Austin

2014, 2015 Scholarship and Travel Award, Summer Institute in Statistics and Modeling in Infectious Diseases (SISMID), University of Washington, Seattle, WA

2011 Scholarship and Travel Award, Meaningful Modeling of Epidemiological Data (MMED) Clinic, African Institute for Mathematical Sciences, Cape Town, South Africa

2010, 2011 Scholarship and Travel Award, Ecology and Evolution of Infectious Diseases (EEID) Conference Workshop. Cornell University, Ithaca, NY (2010) and University of California, Santa Barbara, Isla Vista, CA (2011)

2009 Center for Undergraduate Research (CURO) Scholar distinction, University of Georgia

2008 Inducted, Phi Beta Kappa

2007 Honors International Scholarship, University of Georgia Honors Program

2005–2009 Georgia Governor’s Scholarship
Awarded to high school valedictorians attending in-state universities. Annual $900 stipend.

2005–2009 Charter Scholarship, University of Georgia Honors Program
Awarded to 200 new students for outstanding achievement in academics. Annual $2000 stipend.

2005–2009 National Merit Scholarship, University of Georgia

2005–2009 Georgia HOPE Scholarship
Merit-based full tuition scholarship awarded to Georgia residents attending in-state universities.

Conferences

Organization

2025 Co-organizer, EpiMob Satellite (“Epidemic control: from mobility data to public health”), NetSci International Conference on Network Science, Maastricht, the Netherlands. (upcoming, June 2025)

2024 Co-organizer, EpiMob Satellite (“Epidemic control: from mobility data to public health”), NetSci International Conference on Network Science, Québec City, Canada.

Panels

2022 Invited Panelist, “Reflections on COVID-19,” NIH Modeling of Infectious Disease Agent Study (MIDAS) Annual Meeting, Bethesda, MD.

Podium presentations

2025 NetSci International Conference on Network Science, Maastricht, the Netherlands. Modelling the effects of COVID-19 mobility disruptions on RSV transmission in Seattle, Washington.

2024 NetSci International Conference on Network Science, Québec City, Canada. Impacts of human mobility on the citywide transmission dynamics of respiratory viruses in pre- and post-COVID-19 pandemic years.

2023 Epidemics9 International Conference on Infectious Disease Dynamics, Bologna, Italy. Are changes in population mobility predictive of respiratory virus transmission? Insights from high resolution mobile phone data in the pre- and post-COVID-19 pandemic periods in Seattle, Washington.

2023 EpiMob Satellite (“Epidemic control: from mobility data to public health”), NetSci International Conference on Network Science, Vienna, Austria. Are changes in population mobility predictive of respiratory virus transmission? Insights from high resolution mobile phone data in the pre- and post-COVID-19 pandemic periods in Seattle, Washington. *Invited keynote speaker

2022 Options XI for the Control of Influenza, Belfast, Northern Ireland. Impact of antigenic drift on influenza A/H3N2 vaccine effectiveness in the United States.

2022 NIH/FDA COVID-19 Research Workshop (Virtual). The impact of COVID-19 restrictions and mobility behavior on respiratory pathogen transmission in Seattle, Washington.

2022 NIH Modeling of Infectious Disease Agent Study (MIDAS) Annual Meeting, Bethesda, MD. The impact of social distancing on respiratory pathogen transmission in Seattle, Washington.

2021 NIH Modeling of Infectious Disease Agent Study (MIDAS) Annual Meeting (Virtual). Impact of antigenic drift on influenza A/H3N2 vaccine effectiveness in the United States.

2021 NIH NIAID Centers of Excellence for Influenza Research and Surveillance (CEIRS) Annual Meeting (Virtual). Impact of antigenic drift on influenza A/H3N2 vaccine effectiveness in the United States.

2020 NIH/FDA COVID-19 Research Workshop (Virtual). Utilizing Respiratory Syndromic Surveillance Data to Monitor COVID-19 Activity in South Africa.

2019 Epidemics7 International Conference on Infectious Disease Dynamics, Charleston, SC. Impact of influenza antigenic evolution on disease dynamics in the United States.

2019 Options X for the Control of Influenza, Singapore. Impact of influenza antigenic evolution on disease dynamics in the United States.

2018 American Association of Physical Anthropologists (AAPA) Conference, Austin, TX. Gut microbiome diversity across sympatric mammal populations of Madagascar reflects diet, substrate use, and host phylogeny.

2016 NSF BEACON Annual Congress, Michigan State University, East Lansing, MI. Social network structure shapes gut microbial communities in wild Verreaux’s sifaka.

Poster presentations

2020 European Scientific Working group on Influenza (ESWI) Conference (Virtual). Impact of influenza antigenic evolution on disease dynamics in the United States.

2019 Ecology and Evolution of Infectious Diseases (EEID) Conference, Princeton, NJ. Impact of influenza antigenic evolution on disease dynamics in the United States.

2017 Society of Molecular Biology and Evolution (SMBE) Conference, Austin, TX. Hierarchical social networks shape gut microbial composition in wild Verreaux’s sifaka.

2017 Ecology and Evolution of Infectious Diseases (EEID) Conference, Isla Vista, CA. Hierarchical social networks shape gut microbial composition in wild Verreaux’s sifaka.

2015 Epidemics5 International Conference on Infectious Disease Dynamics, Clearwater Beach, FL. Social network structure shapes gut microbial communities in wild Verreaux’s sifaka.

Seminar Presentations

Invited talks

2024 Yale School of Public Health, New Haven, CT. Impacts of human mobility on the citywide transmission dynamics of respiratory viruses: Insights from the Seattle Flu Study and high-resolution mobile phone data.

2024 Network Science Institute, Northeastern University, Boston, MA. Impacts of human mobility on the citywide transmission dynamics of respiratory viruses in pre- and post-COVID-19 pandemic years.

2023 U.S. CDC Technical Outreach and Assistance to States (TOAST) Office Hours (Virtual). Are changes in population mobility predictive of respiratory virus transmission? Insights from high resolution mobile phone data in the pre- and post-COVID-19 pandemic periods in Seattle, Washington.

2023 Pierre Louis Institute of Epidemiology and Public Health, French National Institute of Health and Medical Research (INSERM), Paris, France. Are changes in population mobility predictive of respiratory virus transmission? Insights from high resolution mobile phone data in the pre- and post-COVID-19 pandemic periods in Seattle, Washington.

2023 Infectious Disease Modeling Working Group, World Health Organization (Virtual). Antigenic drift and subtype interference shape A/H3N2 epidemic dynamics in the United States.

2023 California Department of Public Health COVID-19 Modeling Team Open House (Virtual). A time series approach for short-term forecasts and long-term scenario projections of influenza hospitalizations.

2023 NIH NIAID Centers of Excellence for Influenza Research and Response (CEIRR) Computational Modeling Core (Virtual). Antigenic drift and subtype interference shape A/H3N2 epidemic dynamics in the United States.

2023 U.S. CDC Infectious Disease Forecasting Call (Virtual). Impact of influenza antigenic evolution on A/H3N2 epidemics and vaccine effectiveness in the United States.

2023 Center for the Ecology of Infectious Diseases, University of Georgia (Virtual). The impact of physical distancing on respiratory pathogen transmission in Seattle, Washington.

2021 Influenza Research Group, National Animal Disease Center, U.S. Department of Agriculture (Virtual). Impact of influenza antigenic evolution on A/H3N2 vaccine effectiveness in the United States.

2018 Fogarty International Center, National Institutes of Health, Bethesda, MD. Drivers of gut microbial composition and transmission within and among wild lemur populations.

2016 Kirindy Mitea National Park headquarters, Belo Sur Mer, Madagascar. Bacteria transmission dynamics among wildlife in Kirindy Mitea National Park.

2012 Kirindy Mitea National Park headquarters, Morondava, Madagascar. Infectious disease transmission in a wild lemur population.

Internal seminars

2023 Respiratory Virus Interest Group, National Institutes of Health (Virtual). The impact of influenza antigenic drift on A/H3N2 vaccine effectiveness in the United States.

2019 Influenza Interest Group, National Institutes of Health, Bethesda, MD. Impact of influenza antigenic evolution on disease dynamics in the United States.

2017 NSF BEACON weekly seminar, University of Texas at Austin, Austin, TX. Gut microbiome diversity across sympatric mammal populations of Madagascar reflects diet, substrate use, and host phylogeny.

2016 NSF BEACON weekly seminar, University of Texas at Austin, Austin, TX. Social networks shape the gut microbial communities of wild Verreaux’s sifaka.

2015 Department of Integrative Biology, University of Texas at Austin, Austin, TX. Social networks shape the gut microbial communities of wild Verreaux’s sifaka.

Teaching and Mentoring Experience

Student mentoring

Jun 2024 Tutor, Complexity 72h: Interdisciplinary workshop for young researchers in complex systems, Carlos III University de Madrid, Spain. Led a team of 5 graduate students in carrying out a research project within 3 days (i.e., 72h). Project title: “Impacts of COVID-19 restrictions on mobility networks and the spread of endemic respiratory viruses.” medRxiv preprint

Summer 2012, 2016 Master’s student mentoring in primate field ecology, Department of Animal Biology, University of Antananarivo, Madagascar. Mentored and trained two Malagasy Masters’ students in field techniques, data collection, and specimen preservation at Kirindy Mitea National Park, Madagascar. Guided mentees in developing independent research projects and helped them connect their work to broader questions in primatology and animal behavior.
2012: Elvis Rakotomalala, Lepilemur tree hole characteristics; 2016: Safidy Rasolonjatovo, Verreaux’s sifaka scent marking behavior

Short courses

Sep 2019 Co-Instructor, Fogarty International Center-DIVERGE Training Workshop on RSV Genomics and Evolution, National Institutes of Health, Bethesda, MD.

Dec 2018 Co-Instructor, Fogarty International Center-NICD Training Workshop on Infectious Disease Dynamics and Evolution, National Institutes of Communicable Diseases, Johannesburg, South Africa.

Assistant teaching

Fall 2016, 2017 Scientific Inquiry Across Disciplines, University of Texas at Austin

Spring 2013 Social Networks and Infectious Diseases, University of Texas at Austin

Guest lectures

Nov 2015 Biological Networks and Social Network Analysis, Introduction to Biological Statistics Course, Center for Computational Biology and Bioinformatics, University of Texas at Austin.

Nov 2014 Introduction to Networks, Introduction to Biological Statistics Course, Center for Computational Biology and Bioinformatics, University of Texas at Austin.

Professional training

Spring 2020 Scientists Teaching Science, National Institutes of Health. Completed 9-week pedagogy course on best practices for teaching and learning in STEM subjects at the undergraduate level.

Professional Activities

Feb 2023 Working group on the use of human mobility data in infectious disease modeling, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD.

2022–2024 Coordinated and led monthly Seattle Flu Study Data Analysis meetings

2022, 2023, 2024 Abstract reviewer, NIH Modeling of Infectious Disease Agent Study (MIDAS) Annual Meetings

Feb 2020 Poster Judge, NIH Annual Graduate Student Research Symposium, Bethesda, MD.

2019–2021 Policy essay editor, Science Policy for All. Policy blog with contributors from the Washington, DC area.

Feb 2017 Invited Panelist, NSF BEACON Public Engagement Workshop, University of Texas at Austin, Austin, TX.

Ad-hoc peer review (select journals): American Journal of Epidemiology, American Journal of Primatology, Animal Behaviour, BMJ Global Health, Ecology and Evolution, Epidemics, The ISME Journal, Molecular Ecology, Nature Communications, Nature Physics, PLOS Computational Biology, PNAS Nexus

Science Outreach

Apr 2024 Elife podcast interview, Flu virus evolution: Combining antibody responses and genetic data can help gauge the threats posed by evolving flu strains.

Jun 2021 Science Policy for All blogpost, Can the United States achieve herd immunity? Vaccine mandates and other policies to increase COVID-19 vaccination.

May 2020 Science Policy for All blogpost, The Use of COVID-19 Prediction Models in Guiding Policy Decisions.

2019–2021 Member, NIH Science Policy Discussion Group. Biweekly seminar series for early-career scientists focused on the intersection of scientific research and legislative policy. Delivered science policy presentations, invited two guest speakers, and wrote and edited articles for the Science Policy for All blog.

Feb 2018 Selected speaker, American Association for the Advancement of Science (AAAS) Classroom Science Days, Austin, TX. Outreach lecture “Meet the Lemurs” to middle school students. AAAS coverage

2016–2017 Member, Austin Science Advocates, University of Texas at Austin. Student group aimed at improving communication between scientists, the public, and policymakers.

Nov 2016 Public outreach lecture “Meet the Lemurs”, Science Under the Stars, Brackenridge Field Laboratory, Austin, TX. Daily Texan coverage

Mar 2016 NSF BEACON “Researchers at Work” essay, How lemur social networks shape microbial transmission.

2011–2018 Radio DJ and Science Talk Show Co-host, They Blinded Me with Science on KVRX 91.7FM, University of Texas at Austin. Co-hosted weekly educational talk show that interviewed UT-based and visiting researchers and reviewed science publications and news. Recruited guests, conducted interviews, and produced podcasts.

2011–2017 Co-organizer and Volunteer, Science Under the Stars, Brackenridge Field Laboratory, Austin, TX. Monthly public outreach lecture series founded and organized by graduate students in the Department of Integrative Biology.