My research focuses on the ecological, evolutionary, and behavioral drivers of respiratory virus epidemics, with aims to improve infectious disease surveillance and better understand and predict recurring and emerging outbreaks. I apply statistical and computational approaches to study respiratory virus transmission patterns and epidemiology, with a particular focus on influenza and SARS-CoV-2. I also produce operational forecasts and projections of respiratory virus outbreaks.
She/her/hers
United States
Tran-Kiem C, Perofsky AC, Lessler J, Bedford T. (2026). Characterizing the informativeness of pathogen genome sequence datasets about transmission between population groups. Proceedings. Biological sciences, 293(2067)
Bents SJ, Martin ET, Steven-Ayers T, Andrews C, Adler A, Perofsky A, Krantz EM, Blazevic R, Kimball L, Prentice R, Hansen C, Starita L, Han P, Englund JA, Wolter N, von Gottberg A, Maake L, Moyes J, Cohen C, Boeckh M, Hay JA, Waghmare A, Viboud C. (2025). Multiplex serology reveals age-specific immunodynamics of endemic respiratory pathogens in the wake of the COVID-19 pandemic. medRxiv : the preprint server for health sciences
Kostandova N, Corgel R, Bansal S, Bérubé S, Cleary E, Hansen C, Hitchings MDT, García-Carreras B, Gardner L, Kraemer MUG, Lai S, Li Y, Perofsky AC, Pullano G, Read JM, Ribeiro Dos Santos G, Salje H, Takahashi S, Viboud C, Wang J, Cummings DAT, Wesolowski A. (2025). Improving mobility data for infectious disease research. Nature human behaviour
Elias-Warren A, Bennett JC, Iwu CD, Starita LM, Stone J, Capodanno B, Prentice R, Han PD, Acker Z, Grindstaff SB, Reinhart D, Logue JK, Wolf CR, Boeckh M, Kong K, Xie H, Kim G, Greninger AL, Perofsky AC, Viboud C, Uyeki TM, Englund JA, Roychoudhury P, Chu HY. (2025). Epidemiology of Human Metapneumovirus Infection in a Community Setting, Seattle, Washington, USA. The Journal of infectious diseases, 232(Supplement_1)
Bents SJ, Martin ET, Stevens-Ayers T, Andrews C, Adler A, Perofsky AC, Krantz EM, Blazevic R, Kimball L, Prentice R, Hansen C, Starita L, Han P, Englund JA, Wolter N, von Gottberg A, Maake L, Moyes J, Cohen C, Boeckh M, Hay JA, Waghmare A, Viboud C. (2025). Multiplex serology reveals age-specific immunodynamics of respiratory pathogens in the wake of the COVID-19 pandemic. Nature communications, 16(1)
Tran-Kiem C, Paredes MI, Perofsky AC, Frisbie LA, Xie H, Kong K, Weixler A, Greninger AL, Roychoudhury P, Peterson JM, Delgado A, Halstead H, MacKellar D, Dykema P, Gamboa L, Frazar CD, Ryke E, Stone J, Reinhart D, Starita L, Thibodeau A, Yun C, Aragona F, Black A, Viboud C, Bedford T. (2025). Fine-scale patterns of SARS-CoV-2 spread from identical pathogen sequences. Nature
Hansen CL, Lee L, Bents SJ, Perofsky AC, Sun K, Starita LM, Adler A, Englund JA, Chow EJ, Chu HY, Viboud C. (2025). Scenario Projections of Respiratory Syncytial Virus Hospitalizations Averted Due to New Immunizations. JAMA network open, 8(6)
Mathis SM, Webber AE, León TM, Murray EL, Sun M, White LA, Brooks LC, Green A, Hu AJ, Rosenfeld R, Shemetov D, Tibshirani RJ, McDonald DJ, Kandula S, Pei S, Yaari R, Yamana TK, Shaman J, Agarwal P, Balusu S, Gururajan G, Kamarthi H, Prakash BA, Raman R, Zhao Z, Rodríguez A, Meiyappan A, Omar S, Baccam P, Gurung HL, Suchoski BT, Stage SA, Ajelli M, Kummer AG, Litvinova M, Ventura PC, Wadsworth S, Niemi J, Carcelen E, Hill AL, Loo SL, McKee CD, Sato K, Smith C, Truelove S, Jung SM, Lemaitre JC, Lessler J, McAndrew T, Ye W, Bosse N, Hlavacek WS, Lin YT, Mallela A, Gibson GC, Chen Y, Lamm SM, Lee J, Posner RG, Perofsky AC, Viboud C, Clemente L, Lu F, Meyer AG, Santillana M, Chinazzi M, Davis JT, Mu K, Pastore Y Piontti A, Vespignani A, Xiong X, Ben-Nun M, Riley P, Turtle J, Hulme-Lowe C, Jessa S, Nagraj VP, Turner SD, Williams D, Basu A, Drake JM, Fox SJ, Suez E, Cojocaru MG, Thommes EW, Cramer EY, Gerding A, Stark A, Ray EL, Reich NG, Shandross L, Wattanachit N, Wang Y, Zorn MW, Aawar MA, Srivastava A, Meyers LA, Adiga A, Hurt B, Kaur G, Lewis BL, Marathe M, Venkatramanan S, Butler P, Farabow A, Ramakrishnan N, Muralidhar N, Reed C, Biggerstaff M, Borchering RK. (2024). Title evaluation of FluSight influenza forecasting in the 2021-22 and 2022-23 seasons with a new target laboratory-confirmed influenza hospitalizations. Nature communications, 15(1)
Paredes MI, Perofsky AC, Frisbie L, Moncla LH, Roychoudhury P, Xie H, Bakhash SAM, Kong K, Arnould I, Nguyen TV, Wendm ST, Hajian P, Ellis S, Mathias PC, Greninger AL, Starita LM, Frazar CD, Ryke E, Zhong W, Gamboa L, Threlkeld M, Lee J, Stone J, McDermot E, Truong M, Shendure J, Oltean HN, Viboud C, Chu H, Müller NF, Bedford T. (2024). Local-scale phylodynamics reveal differential community impact of SARS-CoV-2 in a metropolitan US county. PLoS pathogens, 20(3)
Tran-Kiem C, Paredes MI, Perofsky AC, Frisbie LA, Xie H, Kong K, Weixler A, Greninger AL, Roychoudhury P, Peterson JM, Delgado A, Halstead H, MacKellar D, Dykema P, Gamboa L, Frazar CD, Ryke E, Stone J, Reinhart D, Starita L, Thibodeau A, Yun C, Aragona F, Black A, Viboud C, Bedford T. (2024). Fine-scale spatial and social patterns of SARS-CoV-2 transmission from identical pathogen sequences. medRxiv : the preprint server for health sciences
Perofsky AC, Huddleston J, Hansen CL, Barnes JR, Rowe T, Xu X, Kondor R, Wentworth DE, Lewis N, Whittaker L, Ermetal B, Harvey R, Galiano M, Daniels RS, McCauley JW, Fujisaki S, Nakamura K, Kishida N, Watanabe S, Hasegawa H, Sullivan SG, Barr IG, Subbarao K, Krammer F, Bedford T, Viboud C. (2024). Antigenic drift and subtype interference shape A(H3N2) epidemic dynamics in the United States. eLife, (13)
Perofsky AC, Hansen CL, Burstein R, Boyle S, Prentice R, Marshall C, Reinhart D, Capodanno B, Truong M, Schwabe-Fry K, Kuchta K, Pfau B, Acker Z, Lee J, Sibley TR, McDermot E, Rodriguez-Salas L, Stone J, Gamboa L, Han PD, Adler A, Waghmare A, Jackson ML, Famulare M, Shendure J, Bedford T, Chu HY, Englund JA, Starita LM, Viboud C. (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(1)
Mathis SM, Webber AE, León TM, Murray EL, Sun M, White LA, Brooks LC, Green A, Hu AJ, McDonald DJ, Rosenfeld R, Shemetov D, Tibshirani RJ, Kandula S, Pei S, Shaman J, Yaari R, Yamana TK, Agarwal P, Balusu S, Gururajan G, Kamarthi H, Prakash BA, Raman R, Rodríguez A, Zhao Z, Meiyappan A, Omar S, Baccam P, Gurung HL, Stage SA, Suchoski BT, Ajelli M, Kummer AG, Litvinova M, Ventura PC, Wadsworth S, Niemi J, Carcelen E, Hill AL, Jung SM, Lemaitre JC, Lessler J, Loo SL, McKee CD, Sato K, Smith C, Truelove S, McAndrew T, Ye W, Bosse N, Hlavacek WS, Lin YT, Mallela A, Chen Y, Lamm SM, Lee J, Posner RG, Perofsky AC, Viboud C, Clemente L, Lu F, Meyer AG, Santillana M, Chinazzi M, Davis JT, Mu K, Piontti APY, Vespignani A, Xiong X, Ben-Nun M, Riley P, Turtle J, Hulme-Lowe C, Jessa S, Nagraj VP, Turner SD, Williams D, Basu A, Drake JM, Fox SJ, Gibson GC, Suez E, Thommes EW, Cojocaru MG, Cramer EY, Gerding A, Stark A, Ray EL, Reich NG, Shandross L, Wattanachit N, Wang Y, Zorn MW, Al Aawar M, Srivastava A, Meyers LA, Adiga A, Hurt B, Kaur G, Lewis BL, Marathe M, Venkatramanan S, Butler P, Farabow A, Muralidhar N, Ramakrishnan N, Reed C, Biggerstaff M, Borchering RK. (2023). Evaluation of FluSight influenza forecasting in the 2021-22 and 2022-23 seasons with a new target laboratory-confirmed influenza hospitalizations. medRxiv : the preprint server for health sciences
Hansen C, Perofsky AC, Burstein R, Famulare M, Boyle S, Prentice R, Marshall C, McCormick BJJ, Reinhart D, Capodanno B, Truong M, Schwabe-Fry K, Kuchta K, Pfau B, Acker Z, Lee J, Sibley TR, McDermot E, Rodriguez-Salas L, Stone J, Gamboa L, Han PD, Duchin JS, Waghmare A, Englund JA, Shendure J, Bedford T, Chu HY, Starita LM, Viboud C. (2022). Trends in Risk Factors and Symptoms Associated With SARS-CoV-2 and Rhinovirus Test Positivity in King County, Washington, June 2020 to July 2022. JAMA network open, 5(12)
Perofsky AC, Tempia S, Bingham J, Maslo C, Toubkin M, Laubscher A, Walaza S, Pulliam JRC, Viboud C, Cohen C. (2022). The direct and indirect effects of the COVID-19 pandemic on private healthcare utilization in South Africa, March 2020 - September 2021. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America
Paredes MI, Perofsky AC, Frisbie L, Moncla LH, Roychoudhury P, Xie H, Mohamed Bakhash SA, Kong K, Arnould I, Nguyen TV, Wendm ST, Hajian P, Ellis S, Mathias PC, Greninger AL, Starita LM, Frazar CD, Ryke E, Zhong W, Gamboa L, Threlkeld M, Lee J, Stone J, McDermot E, Truong M, Shendure J, Oltean HN, Viboud C, Chu H, Müller NF, Bedford T. (2022). Local-Scale phylodynamics reveal differential community impact of SARS-CoV-2 in metropolitan US county. medRxiv : the preprint server for health sciences
Perofsky AC, Ancel Meyers L, Abondano LA, Di Fiore A, Lewis RJ. (2021). Social groups constrain the spatiotemporal dynamics of wild sifaka gut microbiomes. Molecular Ecology, 30(24)
McBride DS, Perofsky AC, Nolting JM, Nelson MI, Bowman AS. (2021). Tracing the Source of Influenza A Virus Zoonoses in Interconnected Circuits of Swine Exhibitions. The Journal of Infectious Diseases, 224(3)
Viboud C, Gostic K, Nelson MI, Price GE, Perofsky A, Sun K, Sequeira Trovão N, Cowling BJ, Epstein SL, Spiro DJ. (2020). Beyond clinical trials: Evolutionary and epidemiological considerations for development of a universal influenza vaccine. PLoS pathogens, 16(9)
Perofsky AC, Nelson MI. (2020). The challenges of vaccine strain selection. eLife, (9)
Nelson MI, Perofsky A, McBride DS, Rambo-Martin BL, Wilson MM, Barnes JR, van Bakel H, Khan Z, Dutta J, Nolting JM, Bowman AS. (2020). A Heterogeneous Swine Show Circuit Drives Zoonotic Transmission of Influenza A Viruses in the United States. Journal of Virology, 94(24)
Perofsky AC, Lewis RJ, Meyers LA. (2018). Terrestriality and bacterial transfer: a comparative study of gut microbiomes in sympatric Malagasy mammals. The ISME journal, 13(1)
Perofsky AC, Lewis RJ, Abondano LA, Di Fiore A, Meyers LA. (2017). Hierarchical social networks shape gut microbial composition in wild Verreaux's sifaka. Proceedings. Biological sciences, 284(1868)
Berry BS, Magori K, Perofsky AC, Stallknecht DE, Park AW. (2013). Wetland cover dynamics drive hemorrhagic disease patterns in white-tailed deer in the United States. Journal of wildlife diseases, 49(3)
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