Dispersal dynamics of SARS-CoV-2 lineages during the first epidemic wave in New York City.

Dellicour, Simon; Hong, Samuel L.; Vrancken, Bram; Chaillon, Antoine; Gill, Mandev S.; Maurano, Matthew T.; Ramaswami, Sitharam; Zappile, Paul; Marier, Christian; Harkins, Gordon W.; Baele, Guy; Duerr, Ralf; Heguy, Adriana

During the first phase of the COVID-19 epidemic, New York City rapidly became the epicenter of the pandemic in the United States. While molecular phylogenetic analyses have previously highlighted multiple introductions and a period of cryptic community transmission within New York City, little is known about the circulation of SARS-CoV-2 within and among its boroughs. We here perform phylogeographic investigations to gain insights into the circulation of viral lineages during the first months of the New York City outbreak. Our analyses describe the dispersal dynamics of viral lineages at the state and city levels, illustrating that peripheral samples likely correspond to distinct dispersal events originating from the main metropolitan city areas. In line with the high prevalence recorded in this area, our results highlight the relatively important role of the borough of Queens as a transmission hub associated with higher local circulation and dispersal of viral lineages toward the surrounding boroughs. Author summary: In the context of epidemics, analyses of viral genomes can be used to link infectious cases in space and time. When the sampling is dense enough, phylogeographic investigations can be performed to obtain estimates of the dispersal history and dynamics of viral lineages. In our study, we take advantage of a comprehensive data set of SARS-CoV-2 genomes sampled from New York State to analyze the circulation of the virus during spring 2020. In particular, we focus on New York City, then the epicenter of the United States epidemic, to unravel the dispersal of viral lineages among its five boroughs, which tends to confirm the relative importance of the Queens area in the overall transmission chain. From a methodological point of view, our study illustrates how fine-scale phylogeographic analyses can be exploited to gain insight into the epidemiological dynamic of local viral epidemics, which constitute timely but also complementary tool to standard epidemiological approaches.

NEW York (N.Y.); SARS-CoV-2; COVID-19 pandemic; INFECTIOUS disease transmission; VIRAL genomes; EPIDEMICS; PANDEMICS

PLoS Pathogens, 2021, Vol 17, Issue 5, p1

1553-7366

Academic Journal

10.1371/journal.ppat.1009571