Spatiotemporal Analyses of 2 Co-Circulating SARS-CoV-2 Variants, New York State, USA

Russell, Alexis; O’Connor, Collin; Lasek‐Nesselquist, Erica; Plitnick, Jonathan; Kelly, John P.; Lamson, Daryl M.; George, Kirsten St.

doi:10.3201/eid2803.211972

Cited by 7 publications

(10 citation statements)

References 22 publications

(29 reference statements)

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“…Our comparison of the introduction patterns confirms that Iota likely emerged within or in close proximity to the NY state area [18,37], and reveals that Delta had the lowest tendency to establish large transmission chains in the NYC area. Iota is characterised by a main cluster corresponding to its initial emergence, as well as a series of smaller ones that emerged towards the end of its circulation period corresponding to re-introduction events in the NYC area.…”

Section: Discussionsupporting

confidence: 65%

“…In late 2020/early 2021, the first VOIs/VOCs started circulating in New York City/ State (see Fig 1 for the evolution of the estimated relative abundance of the main VOI/VOCs across New York State). VOI Iota apparently arose in NYC and caused a regional epidemic, which also coincided with the global spread and introduction of VOC Alpha into the NYC area [15][16][17][18]. In early 2021, VOC Gamma was also introduced into the NYC area [19], but its circulation remained relatively limited compared to the other variants (Fig 1).…”

Section: Introductionmentioning

confidence: 97%

See 1 more Smart Citation

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

et al. 2023

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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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Section: Discussionsupporting

confidence: 65%

Section: Introductionmentioning

confidence: 97%

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

et al. 2023

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“…It is possible that this dynamic may have contributed to increased transmission during the initial phase of vaccination before the local population reached a 50% vaccination rate. Our findings are concordant with the epidemiological scenario in the United States 34 , 41 , 48 .…”

Section: Discussionsupporting

confidence: 90%

“…The resulting sequence reads were screened for quality, trimmed, and assembled into complete consensus SARS-CoV-2 genomes using the Genome Detective Virus Tool v1.136 32 ( https://www.genomedetective.com ) and assembly confirmed with iVar 33 . The Pangolin COVID-19 Lineage Assigner tool was used for lineage assignment 34 ( https://pangolin.cog-uk.io ). A total of 753 samples were sequenced with more than 95% genome coverage at a minimum of 10x sequence depth.…”

Section: Methodsmentioning

confidence: 99%

Genomic surveillance of SARS-CoV-2 in Puerto Rico enabled early detection and tracking of variants

et al. 2022

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Background Puerto Rico has experienced the full impact of the COVID-19 pandemic. Since SARS-CoV-2, the virus that causes COVID-19, was first detected on the island in March of 2020, it spread rapidly though the island’s population and became a critical threat to public health. Methods We conducted a genomic surveillance study through a partnership with health agencies and academic institutions to understand the emergence and molecular epidemiology of the virus on the island. We sampled COVID-19 cases monthly over 19 months and sequenced a total of 753 SARS-CoV-2 genomes between March 2020 and September 2021 to reconstruct the local epidemic in a regional context using phylogenetic inference. Results Our analyses reveal that multiple importation events propelled the emergence and spread of the virus throughout the study period, including the introduction and spread of most SARS-CoV-2 variants detected world-wide. Lineage turnover cycles through various phases of the local epidemic were observed, where the predominant lineage was replaced by the next competing lineage or variant after ~4 months of circulation locally. We also identified the emergence of lineage B.1.588, an autochthonous lineage that predominated in Puerto Rico from September to December 2020 and subsequently spread to the United States. Conclusions The results of this collaborative approach highlight the importance of timely collection and analysis of SARS-CoV-2 genomic surveillance data to inform public health responses.

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“…United States has experienced one of the world's highest COVID-19 burdens during the pandemic, with a total of 86.4M confirmed cases and 1.01M deaths as of May 31, 2022. While some reports are available detailing the evolution of the COVID-19 pandemic in select cities and states[43,44], there are few comprehensive reports at the national level. To demonstrate the capabilities of ViralVar, we downloaded all high quality whole genome sequence data available in GISAID on specimens collected in the USA between January 1, 2020 and May 15, 2022 (n = 1,739,797 SARS-CoV-2 sequences total).…”

mentioning

confidence: 99%

ViralVar: A Web Tool for Multilevel Visualization of SARS-CoV-2 Genomes

Alisoltani¹,

Jaroszewski²,

Godzik³

et al. 2022

Preprint

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The unprecedented growth of publicly available SARS-CoV-2 genome sequence data has increased demand for effective and accessible SARS-CoV-2 data analysis and visualization tools. A majority of the currently available tools either require computational expertise to deploy or limit user input to pre-selected subsets of SARS-CoV-2 genomes. To address these limitations, we developed ViralVar, a publicly available, point-and-click webtool that gives users the freedom to investigate and visualize user-selected subsets of SARS-CoV-2 genomes obtained from the GISAID public database. ViralVar has two primary features that enable: 1) visualization of spatiotemporal dynamics of SARS-CoV-2 lineages, and 2) structural/functional analysis of genomic mutations. As proof-of-principle, ViralVar was used to explore the evolution of the SARS-CoV-2 pandemic in the USA in the pediatric, adult, and elderly population (n > 1.7 million genomes). While the spatiotemporal dynamics of variants did not differ between these age groups, several USA-specific sublineages arose relative to the rest of the world. Our development and utilization of ViralVar to provide insights on the evolution of SARS-CoV-2 in the USA demonstrates the importance of developing accessible tools to facilitate and accelerate large-scale surveillance of circulating pathogens. The ViralVar webserver is freely available at http://viralvar.org/.

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Spatiotemporal Analyses of 2 Co-Circulating SARS-CoV-2 Variants, New York State, USA

Cited by 7 publications

References 22 publications

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

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

Genomic surveillance of SARS-CoV-2 in Puerto Rico enabled early detection and tracking of variants

ViralVar: A Web Tool for Multilevel Visualization of SARS-CoV-2 Genomes

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