Publications

† denotes equal contribution. Full list available on Google Scholar .

Preprints and Submitted Manuscripts

• Characterizing the informativeness of pathogen genome sequence datasets about transmission between population groups (medRxiv, 2025)
  Tran-Kiem C, Perofsky AC, Lessler J, Bedford T.
  → In press, Proc R Soc B

• Clinical and genomic epidemiology of influenza viruses before and during the COVID-19 pandemic, Seattle, Washington USA. (In review)
  Iwu CD, Elias-Warren A, Bennett JC, … Perofsky AC, … Chu HY.

• RSV Molecular Epidemiology Pre- and Post-COVID-19 Pandemic Periods in Seattle, Washington, USA. (In review)
  Bennett JC, Elias-Warren A, Wetzler E, … Perofsky AC, … Chu HY.

• Modeling the effects of COVID-19 mobility disruptions on RSV transmission in Seattle, Washington (medRxiv, 2024)
  Srinivas Duddu A†, Elgamal I†, Camacho-Mateu J†, … Perofsky AC.
  → Complexity 72h report · Manuscript in prep

Publications

• Multiplex serology reveals age-specific immunodynamics of respiratory pathogens in the wake of the COVID-19 pandemic (Nat Commun, 2025)
  Bents SJ, Martin ET, Stevens-Ayers T, … Perofsky AC, … Viboud C.

• Epidemiology of Human Metapneumovirus Infection in a Community Setting, Seattle, Washington, USA (J Infect Dis, 2025)
  Elias-Warren A, Bennett JC, Iwu CD, … Perofsky AC, … Chu HY.

• Scenario Projections of Respiratory Syncytial Virus Hospitalizations Averted Due to New Immunizations (JAMA Netw Open, 2025)
  Hansen CL, Lee L, Bents SJ, Perofsky AC, … Viboud C.

• Improving mobility data for infectious disease research (Nat Hum Behav, 2025)
  Kostandova N, Corgel R, Bansal S, … Perofsky AC, … Wesolowski A.

• Fine-scale patterns of SARS-CoV-2 spread from identical pathogen sequences (Nature, 2025)
  Tran-Kiem C, Paredes MI, Perofsky AC, … Bedford T.

• Antigenic drift and subtype interference shape A(H3N2) epidemic dynamics in the United States (eLife, 2024)
  Perofsky AC, Huddleston J, Hansen CL, … Viboud C.
  → eLife podcast · Press release

• Evaluation of FluSight influenza forecasting in the 2021–22 and 2022–23 seasons with a new target laboratory-confirmed influenza hospitalizations (Nat Commun, 2024)
  Mathis SM, Webber AE, … Perofsky AC, … Borchering RK.

• Impacts of human mobility on the citywide transmission dynamics of 18 respiratory viruses in pre- and post-COVID-19 pandemic years (Nat Commun, 2024)
  Perofsky AC, Hansen CL, Burstein R, … Viboud C.
  → UW Medicine news · Editors’ Highlights for “Public Health”

• Local-scale phylodynamics reveal differential community impact of SARS-CoV-2 in a metropolitan US county (PLOS Pathog, 2024)
  Paredes MI, Perofsky AC, Frisbie L, … Bedford T.

• Trends in risk factors and symptoms associated with SARS-CoV-2 and Rhinovirus test positivity in King County, Washington (JAMA Netw Open, 2022)
  Hansen CL, Perofsky AC, Burstein R, … Viboud C.

• The direct and indirect effects of the COVID-19 pandemic on private healthcare utilization in South Africa (Clin Infect Dis, 2022)
  Perofsky AC, Tempia S, Bingham J, … Cohen C.

• Social groups constrain the spatiotemporal dynamics of wild sifaka gut microbiomes (Mol Ecol, 2021)
  Perofsky AC, Meyers LA, Abondano LA, Di Fiore A, Lewis RJ.

• Tracing the source of influenza A virus zoonoses in interconnected circuits of swine exhibitions (J Infect Dis, 2021)
  McBride DS†, Perofsky AC†, Nolting JM, Nelson MI, Bowman AS.
  → Cover article

• Seasonal influenza: The challenges of vaccine strain selection (eLife, 2020)
  Perofsky AC, Nelson MI.

• A heterogeneous swine show circuit drives zoonotic transmission of influenza A viruses in the United States (J Virol, 2020)
  Nelson MI, Perofsky A, McBride DS, … Bowman AS.

• Beyond clinical trials: Evolutionary and epidemiological considerations for development of a universal influenza vaccine (PLOS Pathog, 2020)
  Viboud C, Gostic K, Nelson MI, … Perofsky AC, … Spiro DJ.

• Terrestriality and bacterial transfer: A comparative study of gut microbiomes in sympatric Malagasy mammals (ISME J, 2018)
  Perofsky AC, Lewis RJ, Meyers LA.

• Characterization of the tree holes used by Lepilemur ruficaudatus in the dry, deciduous forest of Kirindy Mitea National Park (Folia Primatol, 2017)
  Rakotomalala EJ, Rakotondraparany F, Perofsky AC, Lewis RJ.

• Hierarchical social networks shape gut microbial composition in wild Verreaux’s sifaka (Proc R Soc B, 2017)
  Perofsky AC, Lewis RJ, Abondano LA, Di Fiore A, Meyers LA.

• Wetland cover dynamics drive hemorrhagic disease patterns in white-tailed deer in the United States (J Wildl Dis, 2013)
  Berry BS†, Magori K†, Perofsky AC, Stallknecht DE, Park AW.