Publications – Center for Communicable Disease Dynamics

Phylogenetic analysis of SARS-CoV-2 in the Boston area highlights the role of recurrent importation and superspreading events.

Author(s): Lemieux J, Siddle KJ, Shaw BM, Loreth C, Schaffner S, Gladden-Young A, Adams G, Fink T, Tomkins-Tinch CH, Krasilnikova LA, Deruff KC, Rudy M, Bauer MR, Lagerborg KA, Normandin E, Chapman SB, Reilly SK, Anahtar MN, Lin AE, Carter A, Myhrvold C, Kemball M, Chaluvadi S, Cusick C, Flowers K, Neumann A, Cerrato F, Farhat M, Slater D, Harris JB, Branda J, Hooper D, Gaeta JM, Baggett TP, O'Connell J, Gnirke A, Lieberman TD, Philippakis A, Burns M, Brown C, Luban J, Ryan ET, Turbett SE, LaRocque RC, Hanage WP, Gallagher G, Madoff LC, Smole S, Pierce VM, Rosenberg ES, Sabeti P, Park DJ, MacInnis BLJournal: medRxivPMID: 32869040 August 2020

SARS-CoV-2 has caused a severe, ongoing outbreak of COVID-19 in Massachusetts with 111,070 confirmed cases and 8,433 deaths as of…

Making Sense of Mutation: What D614G Means for the COVID-19 Pandemic Remains Unclear.

Author(s): Grubaugh ND, Hanage WP, Rasmussen ALJournal: CellPMID: 32697970 July 2020

In this issue of Cell, Korber et al. found that a SARS-CoV-2 variant in the spike protein D614G rapidly became dominant…

SARS-CoV-2 titers in wastewater foreshadow dynamics and clinical presentation of new COVID-19 cases.

Author(s): Wu F, Xiao A, Zhang J, Moniz K, Endo N, Armas F, Bonneau R, Brown MA, Bushman M, Chai PR, Duvallet C, Erickson TB, Foppe K, Ghaeli N, Gu X, Hanage WP, Huang KH, Lee WL, Matus M, McElroy KA, Nagler J, Rhode SF, Santillana M, Tucker JA, Wuertz S, Zhao S, Thompson J, Alm EJJournal: medRxivPMID: 32607521 June 2020

Current estimates of COVID-19 prevalence are largely based on symptomatic, clinically diagnosed cases. The existence of a large number of…

Reproducibility in science: important or incremental?

Author(s): Lee RS, Hanage WPJournal: Lancet MicrobePMID: 32835329 June 2020

In 2016, a survey was published in Nature in which more than 50% of researchers agreed that there was a…

Horizontal gene transfer rate is not the primary determinant of observed antibiotic resistance frequencies in Streptococcus pneumoniae.

Author(s): Lehtinen S, Chewapreecha C, Lees J, Hanage WP, Lipsitch M, Croucher NJ, Bentley SD, Turner P, Fraser C, Mostowy RJJournal: Sci AdvPMID: 32671212 May 2020

The extent to which evolution is constrained by the rate at which horizontal gene transfer (HGT) allows DNA to move…

Phylogenetic interpretation during outbreaks requires caution.

Author(s): Villabona-Arenas CJ, Hanage WPJournal: Nat MicrobiolPMID: 32427978 May 2020

How viruses are related, and how they have evolved and spread over time, can be investigated using phylogenetics. Here, we…

Leveraging Africa’s preparedness towards the next phase of the COVID-19 pandemic.

Author(s): Senghore M, Savi MK, Gnangnon B, Hanage WPJournal: Lancet Glob HealthPMID: 32416768 May 2020

The coronavirus disease 2019 (COVID-19) response in many African countries has been swift, progressive, and adaptable, despite resource limitations.1 As…

Structure and Dynamics of Bacterial Populations: Pangenome Ecology

Author(s): Azarian T, Huang IT, Hanage WP, Tettelin H, Medini DJournal: The PangenomePMID: 32633912 May 2020

Prokaryotes demonstrate tremendous variation in gene content, even within individual bacterial clones or lineages. This diversity is made possible by…

The risk of SARS-CoV-2 transmission in the healthcare setting and potential impact of cohorting strategies.

Author(s): Miller JC, Qiu X, Hanage WPJournal: medRxivPMID: 32511644 April 2020

The threat of the COVID-19 pandemic of SARS-CoV-2 virus has grown since its start late last year. A customary response…

The effect of human mobility and control measures on the COVID-19 epidemic in China.

Author(s): Kraemer MUG, Yang CH, Gutierrez B, Wu CH, Klein B, Pigott DM, Open COVID-19 Data Working Group., du Plessis L, Faria NR, Li R, Hanage WP, Brownstein JS, Layan M, Vespignani A, Tian H, Dye C, Pybus OG, Scarpino SVJournal: SciencePMID: 32213647 March 2020

The ongoing COVID-19 outbreak expanded rapidly throughout China. Major behavioral, clinical, and state interventions have been undertaken to mitigate the…