Publications – Center for Communicable Disease Dynamics

Quantitatively assessing early detection strategies for mitigating COVID-19 and future pandemics.

Author(s): Liu AB, Lee D, Jalihal AP, Hanage WP, Springer MJournal: Nat CommunPMID: 38123536 December 2023

Researchers and policymakers have proposed systems to detect novel pathogens earlier than existing surveillance systems by monitoring samples from hospital…

Inferring bacterial transmission dynamics using deep sequencing genomic surveillance data.

Author(s): Senghore M, Read H, Oza P, Johnson S, Passarelli-Araujo H, Taylor BP, Ashley S, Grey A, Callendrello A, Lee R, Goddard MR, Lumley T, Hanage WP, Wiles SJournal: Nat CommunPMID: 37907520 October 2023

Identifying and interrupting transmission chains is important for controlling infectious diseases. One way to identify transmission pairs - two hosts…

Viral kinetics of sequential SARS-CoV-2 infections.

Author(s): Kissler SM, Hay JA, Fauver JR, Mack C, Tai CG, Anderson DJ, Ho DD, Grubaugh ND, Grad YHJournal: Nat CommunPMID: 37798265 October 2023

The impact of a prior SARS-CoV-2 infection on the progression of subsequent infections has been unclear. Using a convenience sample…

Increased vaccine sensitivity of an emerging SARS-CoV-2 variant.

Author(s): Lewnard JA, Hong V, Kim JS, Shaw SF, Lewin B, Takhar H, Lipsitch M, Tartof SYJournal: Nat CommunPMID: 37386005 June 2023

Host immune responses are a key source of selective pressure driving pathogen evolution. Emergence of many SARS-CoV-2 lineages has been…

An omics-based framework for assessing the health risk of antimicrobial resistance genes.

Author(s): Zhang AN, Gaston JM, Dai CL, Zhao S, Poyet M, Groussin M, Yin X, Li LG, van Loosdrecht MCM, Topp E, Gillings MR, Hanage WP, Tiedje JM, Moniz K, Alm EJ, Zhang TJournal: Nat CommunPMID: 34362925 August 2021

Antibiotic resistance genes (ARGs) are widespread among bacteria. However, not all ARGs pose serious threats to public health, highlighting the…

Reconstructing unseen transmission events to infer dengue dynamics from viral sequences

Author(s): Salje H, Wesolowski A, Brown TS, Kiang MV, Berry IM, Lefrancq N, Fernandez S, Jarman RG, Ruchusatsawat K, Iamsirithaworn S, Vandepitte WP, Suntarattiwong P, Read JM, Klungthong C, Thaisomboonsuk B, Engø-Monsen K, Buckee C, Cauchemez S, Cummings DATJournal: Nat CommunPMID: 33753725 March 2021

For most pathogens, transmission is driven by interactions between the behaviours of infectious individuals, the behaviours of the wider population,…

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…

Increased power from conditional bacterial genome-wide association identifies macrolide resistance mutations in Neisseria gonorrhoeae.

Author(s): Ma KC, Mortimer TD, Duckett MA, Hicks AL, Wheeler NE, Sánchez-Busó L, Grad YHJournal: Nat CommunPMID: 33097713 October 2020

The emergence of resistance to azithromycin complicates treatment of Neisseria gonorrhoeae, the etiologic agent of gonorrhea. Substantial azithromycin resistance remains…

The use of mobile phone data to inform analysis of COVID-19 pandemic epidemiology.

Author(s): Grantz KH, Meredith HR, Cummings DAT, Metcalf CJE, Grenfell BT, Giles JR, Mehta S, Solomon S, Labrique A, Kishore N, Buckee CO, Wesolowski AJournal: Nat CommunPMID: 32999287 September 2020

The ongoing coronavirus disease 2019 (COVID-19) pandemic has heightened discussion of the use of mobile phone data in outbreak response.…

Reductions in commuting mobility correlate with geographic differences in SARS-CoV-2 prevalence in New York City.

Author(s): Kissler SM, Kishore N, Prabhu M, Goffman D, Beilin Y, Landau R, Gyamfi-Bannerman C, Bateman BT, Snyder J, Razavi AS, Katz D, Gal J, Bianco A, Stone J, Larremore D, Buckee CO, Grad YHJournal: Nat CommunPMID: 32938924 September 2020

SARS-CoV-2-related mortality and hospitalizations differ substantially between New York City neighborhoods. Mitigation efforts require knowing the extent to which these…