Publications – Center for Communicable Disease Dynamics

SARS-CoV-2 Attack Rate and Population Immunity in Southern New England, March 2020 to May 2021.

Author(s): Tran TN, Wikle NB, Yang F, Inam H, Leighow S, Gentilesco B, Chan P, Albert E, Strong ER, Pritchard JR, Hanage WP, Hanks EM, Crawford FW, Boni MFJournal: JAMA Netw OpenPMID: 35616938 May 2022

In emergency epidemic and pandemic settings, public health agencies need to be able to measure the population-level attack rate, defined…

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Sequence Characteristics of Coronavirus Disease 2019 (COVID-19) Persistence and Reinfection.

Author(s): Choudhary MC, Crain CR, Qiu X, Hanage W, Li JZJournal: Clin Infect DisPMID: 33906227 January 2022

Both severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) reinfection and persistent infection have been reported, but sequence characteristics in these…

SARS-CoV-2 epidemic after social and economic reopening in three U.S. states reveals shifts in age structure and clinical characteristics.

Author(s): Wikle NB, Tran TN, Gentilesco B, Leighow SM, Albert E, Strong ER, Břinda K, Inam H, Yang F, Hossain S, Chan P, Hanage WP, Messick M, Pritchard JR, Hanks EM, Boni MFJournal: Sci AdvPMID: 35080987 January 2022

State-level reopenings in late spring 2020 facilitated the resurgence of severe acute respiratory syndrome coronavirus 2 transmission. Here, we analyze…

Rise in the prevalence of resistance to extended-spectrum cephalosporins in the USA, nursing homes and antibiotic prescribing in outpatient and inpatient settings.

Author(s): Goldstein EJournal: J Antimicrob ChemotherPMID: 34297821 December 2021

The prevalence of resistance to extended-spectrum (ES) cephalosporins for multiple types of infections treated in US hospitals and the incidence…

Variant abundance estimation for SARS-CoV-2 in wastewater using RNA-Seq quantification.

Author(s): Baaijens JA, Zulli A, Ott IM, Petrone ME, Alpert T, Fauver JR, Kalinich CC, Vogels CBF, Breban MI, Duvallet C, McElroy K, Ghaeli N, Imakaev M, Mckenzie-Bennett M, Robison K, Plocik A, Schilling R, Pierson M, Littlefield R, Spencer M, Simen BB, Yale SARS-CoV-2 Genomic Surveillance Initiative., Hanage WP, Grubaugh ND, Peccia J, Baym MJournal: medRxivPMID: 34494031 September 2021

Effectively monitoring the spread of SARS-CoV-2 variants is essential to efforts to counter the ongoing pandemic. Wastewater monitoring of SARS-CoV-2…

Reporting practices for genomic epidemiology of tuberculosis: a systematic review of the literature using STROME-ID guidelines as a benchmark.

Author(s): Cheng B, Behr MA, Howden BP, Cohen T, Lee RSJournal: Lancet MicrobePMID: 33842904 August 2021

Pathogen genomics have become increasingly important in infectious disease epidemiology and public health. The Strengthening the Reporting of Molecular Epidemiology…

When intuition falters: repeated testing accuracy during an epidemic.

Author(s): Hay JA, Hellewell J, Qiu XJournal: Eur J EpidemiolPMID: 34322830 July 2021

Widespread, repeated testing using rapid antigen tests to proactively detect asymptomatic SARS-CoV-2 infections has been a promising yet controversial topic…

Estimating internationally imported cases during the early COVID-19 pandemic.

Author(s): Menkir TF, Chin T, Hay JA, Surface ED, De Salazar PM, Buckee CO, Watts A, Khan K, Sherbo R, Yan AWC, Mina MJ, Lipsitch M, Niehus RJournal: Nat CommunPMID: 33436574 January 2021

Early in the COVID-19 pandemic, predictions of international outbreaks were largely based on imported cases from Wuhan, China, potentially missing…

Individual quarantine versus active monitoring of contacts for the mitigation of COVID-19: a modelling study.

Author(s): Peak CM, Kahn R, Grad YH, Childs LM, Lipsitch M, Buckee COJournal: Lancet Infect DisPMID: 32445710 May 2020

Voluntary individual quarantine and voluntary active monitoring of contacts are core disease control strategies for emerging infectious diseases such as…

Combining genomics and epidemiology to track mumps virus transmission in the United States.

Author(s): Wohl S, Metsky HC, Schaffner SF, Piantadosi A, Burns M, Lewnard JA, Chak B, Krasilnikova LA, Siddle KJ, Matranga CB, Bankamp B, Hennigan S, Sabina B, Byrne EH, McNall RJ, Shah RR, Qu J, Park DJ, Gharib S, Fitzgerald S, Barreira P, Fleming S, Lett S, Rota PA, Madoff LC, Yozwiak NL, MacInnis BL, Smole S, Grad YH, Sabeti PCJournal: PLoS BiolPMID: 32045407 February 2020

Unusually large outbreaks of mumps across the United States in 2016 and 2017 raised questions about the extent of mumps…