Publications – Center for Communicable Disease Dynamics

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…

Adaptation to the cervical environment is associated with increased antibiotic susceptibility in Neisseria gonorrhoeae.

Author(s): Ma KC, Mortimer TD, Hicks AL, Wheeler NE, Sánchez-Busó L, Golparian D, Taiaroa G, Rubin DHF, Wang Y, Williamson DA, Unemo M, Harris SR, Grad YHJournal: Nat CommunPMID: 32807804 August 2020

Neisseria gonorrhoeae is an urgent public health threat due to rapidly increasing incidence and antibiotic resistance. In contrast with the…

Resolving the cause of recurrent Plasmodium vivax malaria probabilistically.

Author(s): Taylor AR, Watson JA, Chu CS, Puaprasert K, Duanguppama J, Day NPJ, Nosten F, Neafsey DE, Buckee CO, Imwong M, White NJJournal: Nat CommunPMID: 31811128 December 2019

Relapses arising from dormant liver-stage Plasmodium vivax parasites (hypnozoites) are a major cause of vivax malaria. However, in endemic areas,…

Estimating sources and sinks of malaria parasites in Madagascar.

Author(s): Ihantamalala FA, Herbreteau V, Rakotoarimanana FMJ, Rakotondramanga JM, Cauchemez S, Rahoilijaona B, Pennober G, Buckee CO, Rogier C, Metcalf CJE, Wesolowski AJournal: Nat CommunPMID: 30254280 September 2018

In areas where malaria epidemiology is spatially and temporally heterogeneous, human-mediated parasite importation can result in non-locally acquired clinical cases…