Publications – Center for Communicable Disease Dynamics

Evaluating reduced effectiveness after repeat influenza vaccination while accounting for confounding by recent infection and within-season waning.

Author(s): Bi Q, Dickerman BA, McLean HQ, Martin ET, Gaglani M, Wernli KJ, Goundappa B, Flannery B, Lipsitch M, Cobey S, US Flu Vaccine Effectiveness Network InvestigatorsJournal: medRxivPMID: 37016669 March 2023

Studies have reported that prior-season influenza vaccination is associated with higher risk of clinical influenza infection among vaccinees in a…

Correction: Practical considerations for measuring the effective reproductive number, Rt.

Author(s): 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 SJournal: PLoS Comput BiolPMID: 34879070 December 2021

[This corrects the article DOI: 10.1371/journal.pcbi.1008409.].

Investigate the origins of COVID-19.

Author(s): Bloom JD, Chan YA, Baric RS, Bjorkman PJ, Cobey S, Deverman BE, Fisman DN, Gupta R, Iwasaki A, Lipsitch M, Medzhitov R, Neher RA, Nielsen R, Patterson N, Stearns T, van Nimwegen E, Worobey M, Relman DAJournal: SciencePMID: 33986172 May 2021

Concerns about SARS-CoV-2 evolution should not hold back efforts to expand vaccination.

Author(s): Cobey S, Larremore DB, Grad YH, Lipsitch MJournal: Nat Rev ImmunolPMID: 33795856 April 2021

When vaccines are in limited supply, expanding the number of people who receive some vaccine, such as by halving doses…

Model-informed COVID-19 vaccine prioritization strategies by age and serostatus.

Author(s): Bubar KM, Reinholt K, Kissler SM, Lipsitch M, Cobey S, Grad YH, Larremore DBJournal: SciencePMID: 33479118 January 2021

Limited initial supply of SARS-CoV-2 vaccine raises the question of how to prioritize available doses. Here, we used a mathematical…

Practical considerations for measuring the effective reproductive number, Rt.

Author(s): 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 SJournal: PLoS Comput BiolPMID: 33301457 December 2020

Estimation of the effective reproductive number Rt is important for detecting changes in disease transmission over time. During the Coronavirus…

Use of an individual-based model of pneumococcal carriage for planning a randomized trial of a whole-cell vaccine.

Author(s): Cai FY, Fussell T, Cobey S, Lipsitch MJournal: PLoS Comput BiolPMID: 30273332 October 2018

For encapsulated bacteria such as Streptococcus pneumoniae, asymptomatic carriage is more common and longer in duration than disease, and hence…

Host population structure and treatment frequency maintain balancing selection on drug resistance.

Author(s): Cobey S, Baskerville EB, Colijn C, Hanage W, Fraser C, Lipsitch MJournal: J R Soc InterfacePMID: 28835542 August 2017

It is a truism that antimicrobial drugs select for resistance, but explaining pathogen- and population-specific variation in patterns of resistance…

Viral factors in influenza pandemic risk assessment.

Author(s): Lipsitch M, Barclay W, Raman R, Russell CJ, Belser JA, Cobey S, Kasson PM, Lloyd-Smith JO, Maurer-Stroh S, Riley S, Beauchemin CA, Bedford T, Friedrich TC, Handel A, Herfst S, Murcia PR, Roche B, Wilke CO, Russell CAJournal: ElifePMID: 27834632 November 2016

The threat of an influenza A virus pandemic stems from continual virus spillovers from reservoir species, a tiny fraction of…

Pathogen diversity and hidden regimes of apparent competition.

Author(s): Cobey S, Lipsitch MJournal: Am NatPMID: 23234842 January 2013

Competition through cross-reacting host immune responses, a form of apparent competition, is a major driver of pathogen evolution and diversity.…