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Variant-specific introduction and dispersal dynamics of SARS-CoV-2 in New York City – from Alpha to Omicron

Since the latter part of 2020, SARS-CoV-2 evolution has been characterised by the emergence of viral variants associated with distinct biological characteristics. While the main research focus has centred on the ability of new variants to increase in frequency and impact the effective reproductive n...

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Autores principales: Dellicour, Simon, Hong, Samuel L., Hill, Verity, Dimartino, Dacia, Marier, Christian, Zappile, Paul, Harkins, Gordon W., Lemey, Philippe, Baele, Guy, Duerr, Ralf, Heguy, Adriana
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10180688/
https://www.ncbi.nlm.nih.gov/pubmed/37071654
http://dx.doi.org/10.1371/journal.ppat.1011348
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author Dellicour, Simon
Hong, Samuel L.
Hill, Verity
Dimartino, Dacia
Marier, Christian
Zappile, Paul
Harkins, Gordon W.
Lemey, Philippe
Baele, Guy
Duerr, Ralf
Heguy, Adriana
author_facet Dellicour, Simon
Hong, Samuel L.
Hill, Verity
Dimartino, Dacia
Marier, Christian
Zappile, Paul
Harkins, Gordon W.
Lemey, Philippe
Baele, Guy
Duerr, Ralf
Heguy, Adriana
author_sort Dellicour, Simon
collection PubMed
description Since the latter part of 2020, SARS-CoV-2 evolution has been characterised by the emergence of viral variants associated with distinct biological characteristics. While the main research focus has centred on the ability of new variants to increase in frequency and impact the effective reproductive number of the virus, less attention has been placed on their relative ability to establish transmission chains and to spread through a geographic area. Here, we describe a phylogeographic approach to estimate and compare the introduction and dispersal dynamics of the main SARS-CoV-2 variants – Alpha, Iota, Delta, and Omicron – that circulated in the New York City area between 2020 and 2022. Notably, our results indicate that Delta had a lower ability to establish sustained transmission chains in the NYC area and that Omicron (BA.1) was the variant fastest to disseminate across the study area. The analytical approach presented here complements non-spatially-explicit analytical approaches that seek a better understanding of the epidemiological differences that exist among successive SARS-CoV-2 variants of concern.
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spelling pubmed-101806882023-05-13 Variant-specific introduction and dispersal dynamics of SARS-CoV-2 in New York City – from Alpha to Omicron Dellicour, Simon Hong, Samuel L. Hill, Verity Dimartino, Dacia Marier, Christian Zappile, Paul Harkins, Gordon W. Lemey, Philippe Baele, Guy Duerr, Ralf Heguy, Adriana PLoS Pathog Research Article Since the latter part of 2020, SARS-CoV-2 evolution has been characterised by the emergence of viral variants associated with distinct biological characteristics. While the main research focus has centred on the ability of new variants to increase in frequency and impact the effective reproductive number of the virus, less attention has been placed on their relative ability to establish transmission chains and to spread through a geographic area. Here, we describe a phylogeographic approach to estimate and compare the introduction and dispersal dynamics of the main SARS-CoV-2 variants – Alpha, Iota, Delta, and Omicron – that circulated in the New York City area between 2020 and 2022. Notably, our results indicate that Delta had a lower ability to establish sustained transmission chains in the NYC area and that Omicron (BA.1) was the variant fastest to disseminate across the study area. The analytical approach presented here complements non-spatially-explicit analytical approaches that seek a better understanding of the epidemiological differences that exist among successive SARS-CoV-2 variants of concern. Public Library of Science 2023-04-18 /pmc/articles/PMC10180688/ /pubmed/37071654 http://dx.doi.org/10.1371/journal.ppat.1011348 Text en © 2023 Dellicour et al https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Dellicour, Simon
Hong, Samuel L.
Hill, Verity
Dimartino, Dacia
Marier, Christian
Zappile, Paul
Harkins, Gordon W.
Lemey, Philippe
Baele, Guy
Duerr, Ralf
Heguy, Adriana
Variant-specific introduction and dispersal dynamics of SARS-CoV-2 in New York City – from Alpha to Omicron
title Variant-specific introduction and dispersal dynamics of SARS-CoV-2 in New York City – from Alpha to Omicron
title_full Variant-specific introduction and dispersal dynamics of SARS-CoV-2 in New York City – from Alpha to Omicron
title_fullStr Variant-specific introduction and dispersal dynamics of SARS-CoV-2 in New York City – from Alpha to Omicron
title_full_unstemmed Variant-specific introduction and dispersal dynamics of SARS-CoV-2 in New York City – from Alpha to Omicron
title_short Variant-specific introduction and dispersal dynamics of SARS-CoV-2 in New York City – from Alpha to Omicron
title_sort variant-specific introduction and dispersal dynamics of sars-cov-2 in new york city – from alpha to omicron
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10180688/
https://www.ncbi.nlm.nih.gov/pubmed/37071654
http://dx.doi.org/10.1371/journal.ppat.1011348
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