Practical considerations for measuring the effective reproductive number, Rt. Author(s): Gostic KM, McGough L, Baskerville E, Abbott S, Joshi K, Tedijanto C, Kahn R, Niehus R, Hay JA, De Salazar PM, Hellewell J, Meakin S, Munday J, Bosse N, Sherratt K, Thompson RM, White LF, Huisman J, Scire J, Bonhoeffer S, Stadler T, Wallinga J, Funk S, Lipsitch M, Cobey S|Journal: medRxiv|PMID: 32607522| June 2020 Estimation of the effective reproductive number, R , is important for detecting changes in disease transmission over time. During the…
Age-specific differences in the dynamics of protective immunity to influenza. Author(s): Ranjeva S, Subramanian R, Fang VJ, Leung GM, Ip DKM, Perera RAPM, Peiris JSM, Cowling BJ, Cobey S|Journal: Nat Commun|PMID: 30971703| August 2019 Influenza A viruses evolve rapidly to escape host immunity, causing reinfection. The form and duration of protection after each influenza virus…
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 M|Journal: PLoS Comput Biol|PMID: 30273332| October 2018 For encapsulated bacteria such as Streptococcus pneumoniae, asymptomatic carriage is more common and longer in duration than disease, and hence…
Immune History and Influenza Vaccine Effectiveness. Author(s): Lewnard JA, Cobey S|Journal: Vaccines (Basel)|PMID: 29883414| May 2018 The imperfect effectiveness of seasonal influenza vaccines is often blamed on antigenic mismatch, but even when the match appears good,…
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 M|Journal: J R Soc Interface|PMID: 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 CA|Journal: Elife|PMID: 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 M|Journal: Am Nat|PMID: 23234842| January 2013 Competition through cross-reacting host immune responses, a form of apparent competition, is a major driver of pathogen evolution and diversity.…
Niche and neutral effects of acquired immunity permit coexistence of pneumococcal serotypes. Author(s): Cobey S, Lipsitch M|Journal: Science|PMID: 22383809| March 2012 Over 90 capsular serotypes of Streptococcus pneumoniae, a common nasopharyngeal colonizer and major cause of pneumonia, bacteremia, and meningitis, are…
Predicting the epidemic sizes of influenza A/H1N1, A/H3N2, and B: a statistical method. Author(s): Goldstein E, Cobey S, Takahashi S, Miller JC, Lipsitch M|Journal: PLoS Med|PMID: 21750666| July 2011 The epidemic sizes of influenza A/H3N2, A/H1N1, and B infections vary from year to year in the United States. We…
