People

Sarah E. Cobey, PhD

Broadly, my group investigates the coevolution of pathogens and hosts’ adaptive immunity. We use computational and mathematical tools to test hypotheses and to advance theory. Our earlier work focused on the evolutionary consequences of immune-mediated competition between different pathogen strains, including pneumococcus, human papillomavirus, and especially influenza. More recently, our focus has expanded to include the related dynamics of the host immune response. We are investigating the evolution of antibody repertoires within hosts over time, in particular to identify the roles of infection history, chance, vaccination, and host genetics in generating the diversity of B cell responses. This research involves linking epidemiological and immunological observations of B cells to the antigenic and genetic evolution of influenza viruses. Consequently, it makes extensive use of longitudinal dynamical models of individuals and birth cohorts as well as techniques from molecular evolution to investigate coevolution across scales.



Understanding the dynamics of vaccination is another area of focus. We have investigated the actual and expected impacts of vaccines against pneumococcus, human papillomavirus, and influenza. With influenza, we have been investigating the impact of the vaccine on viral transmission and local evolution and how immune history might reduce the vaccine’s effectiveness and alter selective pressures. Improving vaccination strategies given hosts’ diverse immune histories and the potential for rapid evolution by the pathogen is a long-term aim of our work. Ultimately, we want to explain coevolution sufficiently well to enable prediction, or at least to determine when prediction is not feasible.

Harvard School of Public Health
Postdoctoral - Infectious disease dynamics
2013

University of Michigan, Ann Arbor
PhD - Ecology & Evolution
2009

Princeton University
AB - Ecology & Evolution
2002

Practical considerations for measuring the effective reproductive number, Rt.
Gostic KM, McGough L, Baskerville EB, Abbott S, Joshi K, Tedijanto C, Kahn R, Niehus R, Hay JA, De Salazar PM, Hellewell J, Meakin S, Munday JD, Bosse NI, Sherrat K, Thompson RN, White LF, Huisman JS, Scire J, Bonhoeffer S, Stadler T, Wallinga J, Funk S, Lipsitch M, Cobey S. Practical considerations for measuring the effective reproductive number, Rt. PLoS Comput Biol. 2020 12; 16(12):e1008409.
PMID: 33301457

Preexisting immunity shapes distinct antibody landscapes after influenza virus infection and vaccination in humans.
Dugan HL, Guthmiller JJ, Arevalo P, Huang M, Chen YQ, Neu KE, Henry C, Zheng NY, Lan LY, Tepora ME, Stovicek O, Bitar D, Palm AE, Stamper CT, Changrob S, Utset HA, Coughlan L, Krammer F, Cobey S, Wilson PC. Preexisting immunity shapes distinct antibody landscapes after influenza virus infection and vaccination in humans. Sci Transl Med. 2020 Dec 09; 12(573).
PMID: 33298562

Model-informed COVID-19 vaccine prioritization strategies by age and serostatus.
Bubar KM, Reinholt K, Kissler SM, Lipsitch M, Cobey S, Grad YH, Larremore DB. Model-informed COVID-19 vaccine prioritization strategies by age and serostatus. medRxiv. 2020 Dec 07.
PMID: 33330882

Comparison of Human H3N2 Antibody Responses Elicited by Egg-Based, Cell-Based, and Recombinant Protein-Based Influenza Vaccines During the 2017-2018 Season.
Gouma S, Zost SJ, Parkhouse K, Branche A, Topham DJ, Cobey S, Hensley SE. Comparison of Human H3N2 Antibody Responses Elicited by Egg-Based, Cell-Based, and Recombinant Protein-Based Influenza Vaccines During the 2017-2018 Season. Clin Infect Dis. 2020 Sep 12; 71(6):1447-1453.
PMID: 31598646

Middle-aged individuals may be in a perpetual state of H3N2 influenza virus susceptibility.
Gouma S, Kim K, Weirick ME, Gumina ME, Branche A, Topham DJ, Martin ET, Monto AS, Cobey S, Hensley SE. Middle-aged individuals may be in a perpetual state of H3N2 influenza virus susceptibility. Nat Commun. 2020 09 11; 11(1):4566.
PMID: 32917903

Earliest infections predict the age distribution of seasonal influenza A cases.
Arevalo P, McLean HQ, Belongia EA, Cobey S. Earliest infections predict the age distribution of seasonal influenza A cases. Elife. 2020 07 07; 9.
PMID: 32633233

Practical considerations for measuring the effective reproductive number, Rt.
Gostic KM, McGough L, Baskerville EB, Abbott S, Joshi K, Tedijanto C, Kahn R, Niehus R, Hay J, De Salazar PM, Hellewell J, Meakin S, Munday J, Bosse NI, Sherrat K, Thompson RN, White LF, Huisman JS, Scire J, Bonhoeffer S, Stadler T, Wallinga J, Funk S, Lipsitch M, Cobey S. Practical considerations for measuring the effective reproductive number, Rt. medRxiv. 2020 Jun 20.
PMID: 32607522

Modeling infectious disease dynamics.
Cobey S. Modeling infectious disease dynamics. Science. 2020 May 15; 368(6492):713-714.
PMID: 32332062

CpG-creating mutations are costly in many human viruses.
Caudill VR, Qin S, Winstead R, Kaur J, Tisthammer K, Pineda EG, Solis C, Cobey S, Bedford T, Carja O, Eggo RM, Koelle K, Lythgoe K, Regoes R, Roy S, Allen N, Aviles M, Baker BA, Bauer W, Bermudez S, Carlson C, Castellanos E, Catalan FL, Chemel AK, Elliot J, Evans D, Fiutek N, Fryer E, Goodfellow SM, Hecht M, Hopp K, Hopson ED, Jaberi A, Kinney C, Lao D, Le A, Lo J, Lopez AG, López A, Lorenzo FG, Luu GT, Mahoney AR, Melton RL, Nascimento GD, Pradhananga A, Rodrigues NS, Shieh A, Sims J, Singh R, Sulaeman H, Thu R, Tran K, Tran L, Winters EJ, Wong A, Pennings PS. CpG-creating mutations are costly in many human viruses. Evol Ecol. 2020; 34(3):339-359.
PMID: 32508375

Comparison of human H3N2 antibody responses elicited by egg-based, cell-based, and recombinant protein-based influenza vaccines during the 2017-2018 season.
Gouma S, Zost SJ, Parkhouse K, Branche A, Topham DJ, Cobey S, Hensley SE. Comparison of human H3N2 antibody responses elicited by egg-based, cell-based, and recombinant protein-based influenza vaccines during the 2017-2018 season. Clin Infect Dis. 2019 Oct 09.
PMID: 31598646

View All Publications

Neubauer Faculty Development Fellowship
University of Chicago
2016

James S. McDonnell Foundation Complex Systems Scholar Award
University of Chicago
2014

NIH New Innovator Award
University of Chicago
2014

NIH Kirchstein National Research Service Award
Harvard School of Public Health
2011

NSF Graduate Research Fellowship
University of Michigan
2005

Sigma Xi Society
Princeton University
2002

Phi Beta Kappa
Princeton University
2002

Senior Book Prize, Ecology & Evolution
Princeton University
2002