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

Reduced effectiveness of repeat influenza vaccination: distinguishing among within-season waning, recent clinical infection, and subclinical infection.
Reduced effectiveness of repeat influenza vaccination: distinguishing among within-season waning, recent clinical infection, and subclinical infection. medRxiv. 2023 Sep 27.
PMID: 37016669

Germline-encoded specificities and the predictability of the B cell response.
Germline-encoded specificities and the predictability of the B cell response. PLoS Pathog. 2023 08; 19(8):e1011603.
PMID: 37624867

Investigation of the Impact of Childhood Immune Imprinting on Birth Year-Specific Risk of Clinical Infection During Influenza A Virus Epidemics in Hong Kong.
Investigation of the Impact of Childhood Immune Imprinting on Birth Year-Specific Risk of Clinical Infection During Influenza A Virus Epidemics in Hong Kong. J Infect Dis. 2023 Jul 14; 228(2):169-172.
PMID: 36637115

Antigen-driven colonic inflammation is associated with development of dysplasia in primary sclerosing cholangitis.
Antigen-driven colonic inflammation is associated with development of dysplasia in primary sclerosing cholangitis. Nat Med. 2023 Jun; 29(6):1520-1529.
PMID: 37322120

Tracking changes in SARS-CoV-2 transmission with a novel outpatient sentinel surveillance system in Chicago, USA.
Tracking changes in SARS-CoV-2 transmission with a novel outpatient sentinel surveillance system in Chicago, USA. Nat Commun. 2022 09 22; 13(1):5547.
PMID: 36138039

COVID-19 and children.
COVID-19 and children. Science. 2022 09 09; 377(6611):1144-1149.
PMID: 36074833

PARIS and SPARTA: Finding the Achilles' Heel of SARS-CoV-2.
PARIS and SPARTA: Finding the Achilles' Heel of SARS-CoV-2. mSphere. 2022 06 29; 7(3):e0017922.
PMID: 35586986

SARS-CoV-2 Infection Among Pregnant People at Labor and Delivery and Changes in Infection Rates in the General Population: Lessons Learned From Illinois.
SARS-CoV-2 Infection Among Pregnant People at Labor and Delivery and Changes in Infection Rates in the General Population: Lessons Learned From Illinois. Public Health Rep. 2022 Jul-Aug; 137(4):672-678.
PMID: 35510756

Improvements in Severe Acute Respiratory Syndrome Coronavirus 2 Testing Cascade in the United States: Data From Serial Cross-sectional Assessments.
Improvements in Severe Acute Respiratory Syndrome Coronavirus 2 Testing Cascade in the United States: Data From Serial Cross-sectional Assessments. Clin Infect Dis. 2022 05 03; 74(9):1534-1542.
PMID: 34374758

Incorporating temporal distribution of population-level viral load enables real-time estimation of COVID-19 transmission.
Incorporating temporal distribution of population-level viral load enables real-time estimation of COVID-19 transmission. Nat Commun. 2022 03 03; 13(1):1155.
PMID: 35241662

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