During the first phase of the COVID-19 epidemic, New York City experienced high prevalence compared to other U.S. cities, yet little is known about the circulation of SARS-CoV-2 within and among its boroughs. A study published in PLOS Pathogens by Simon Dellicour at Université Libre de Bruxelles, Belgium, Ralf Duerr and Adriana Heguy at New York University, USA, and colleagues describe the dispersal dynamics of COVID-19 viral lineages at the state and city levels, illustrating the relatively important role of the borough of Queens as a SARS-CoV-2 transmission hub.
To better understand how the virus dispersed throughout New York City during the first few months of the pandemic, the authors constructed a phylogenetic tree to illustrate the evolutionary relationships of all virus samples. The authors were able to recreate how the virus spread across the city, replicated, and mutated, including which areas of New York City transmitted the virus to other locations with greater frequency. The researchers also identified key mutations and tracked their dispersal.
The authors found that the borough of Queens played a significant role of COVID-19 transmission in the early phases of the pandemic due to the relatively higher local circulation of viral lineages. While the study provides important new insights into genomic surveillance, the lack of additional samples collected outside the city may have led to an underestimation of the viral circulation in neighboring areas.
According to the authors, “As in many other cities around the world, important commuting activity radiating out of central city areas likely played an important role in disseminating viral lineages throughout the state. However, commuting workers are likely not the only drivers of SARS-CoV-2 dissemination across the city.”
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Citation: Dellicour S, Hong SL, Vrancken B, Chaillon A, Gill MS, Maurano MT, et al. (2021) Dispersal dynamics of SARS-CoV-2 lineages during the first epidemic wave in New York City. PLoS Pathog 17(5): e1009571.
Image 1 Caption: Spatio-temporal analysis of viral genomes that help determine when and where SARS-CoV-2 dispersal occurred during spring of 2020 in the greater New York City area. It shows that most peripheral samples are directly connected to the NYC area rather than clustered together, indicating that samples collected outside NYC likely correspond to distinct dispersal events originating from the city area.
Image 1 Credit: Dellicour S et al., 2021, PLOS Pathogens, CC-BY 4.0 ()
Image 2 Caption: Representative reconstruction of the dispersal dynamics of SARS-CoV-2 in New York City in the spring of 2020 indicates that Queens, and to a smaller extent Brooklyn, acted as the main transmission hubs, with higher local circulation of the virus enabling spill into the other boroughs.
Image 2 Credit: Dellicour S et al., 2021, PLOS Pathogens, CC-BY 4.0 ()
Funding: SD is supported by the Fonds National de la Recherche Scientifique (FNRS, Belgium). SLH acknowledges support from the Research Foundation - Flanders (Fonds voor Wetenschappelijk Onderzoek - Vlaanderen, G0D5117N). BV is supported by a post-doctoral research fellowship (grant nr. 12U7121N) of the Research Foundation - Flanders (Fonds voor Wetenschappelijk Onderzoek). AC was supported by grants from the NIH (San Diego Center for AIDS Research, CFAR, AI306214 and AI100665), and the James B. Pendleton Charitable Trust. MTM is supported by a NIH Grant (R35GM119703). GWH is jointly funded by the South African Medical Research Council and the National Institutes of Health, USA grant 1U01Al152151-01. GB acknowledges support from the Research Foundation - Flanders (Fonds voor Wetenschappelijk Onderzoek - Vlaanderen, G0E1420N, G098321N) and from the Interne Fondsen KU Leuven/Internal Funds KU Leuven under grant agreement C14/18/094. RD was partially supported by the NIH grant 1R01AI122953. AH, SR, CM, and PZ are supported by the Genome Technology Center, which is in part by the Cancer Center Support Grant P30CA016087 at the Laura and Isaac Perlmutter Cancer Center. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Competing interests: The authors have declared that no competing interests exist.
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