Dataset Information

Introductions and early spread of SARS-CoV-2 in the New York City area.

ABSTRACT: New York City (NYC) has emerged as one of the epicenters of the current SARS-CoV-2 pandemic. To identify the early transmission events underlying the rapid spread of the virus in the NYC metropolitan area, we sequenced the virus causing COVID-19 in patients seeking care at the Mount Sinai Health System. Phylogenetic analysis of 84 distinct SARS-CoV2 genomes indicates multiple, independent but isolated introductions mainly from Europe and other parts of the United States. Moreover, we find evidence for community transmission of SARS-CoV-2 as suggested by clusters of related viruses found in patients living in different neighborhoods of the city.

SUBMITTER: Gonzalez-Reiche AS

PROVIDER: S-EPMC7259823 | biostudies-literature | 2020 May

REPOSITORIES: biostudies-literature

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Introductions and early spread of SARS-CoV-2 in the New York City area.

Gonzalez-Reiche Ana S AS Hernandez Matthew M MM Sullivan Mitchell J MJ Ciferri Brianne B Alshammary Hala H Obla Ajay A Fabre Shelcie S Kleiner Giulio G Polanco Jose J Khan Zenab Z Alburquerque Bremy B van de Guchte Adriana A Dutta Jayeeta J Francoeur Nancy N Melo Betsaida Salom BS Oussenko Irina I Deikus Gintaras G Soto Juan J Sridhar Shwetha Hara SH Wang Ying-Chih YC Twyman Kathryn K Kasarskis Andrew A Altman Deena R DR Smith Melissa M Sebra Robert R Aberg Judith J Krammer Florian F García-Sastre Adolfo A Luksza Marta M Patel Gopi G Paniz-Mondolfi Alberto A Gitman Melissa M Sordillo Emilia Mia EM Simon Viviana V van Bakel Harm H

Science (New York, N.Y.) 20200529 6501

New York City (NYC) has emerged as one of the epicenters of the current severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic. To identify the early transmission events underlying the rapid spread of the virus in the NYC metropolitan area, we sequenced the virus that causes coronavirus disease 2019 (COVID-19) in patients seeking care at the Mount Sinai Health System. Phylogenetic analysis of 84 distinct SARS-CoV-2 genomes indicates multiple, independent, but isolated introduction ...[more]

PMID: 32471856

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Project description:Millions of Norway rats (Rattus norvegicus) inhabit New York City (NYC), presenting the potential for transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from humans to rats. We evaluated SARS-CoV-2 exposure among 79 rats captured from NYC during the fall of 2021. Our results showed that 13 of the 79 rats (16.5%) tested IgG- or IgM-positive, and partial SARS-CoV-2 genomes were recovered from all 4 rats that were qRT-PCR (reverse transcription-quantitative PCR)-positive. Genomic analyses suggest these viruses were associated with genetic lineage B, which was predominant in NYC in the spring of 2020 during the early pandemic period. To further investigate rat susceptibility to SARS-CoV-2 variants, we conducted a virus challenge study and showed that Alpha, Delta, and Omicron variants can cause infections in wild-type Sprague Dawley (SD) rats, including high replication levels in the upper and lower respiratory tracts and induction of both innate and adaptive immune responses. Additionally, the Delta variant resulted in the highest infectivity. In summary, our results indicate that rats are susceptible to infection with Alpha, Delta, and Omicron variants, and wild Norway rats in the NYC municipal sewer systems have been exposed to SARS-CoV-2. Our findings highlight the need for further monitoring of SARS-CoV-2 in urban rat populations and for evaluating the potential risk of secondary zoonotic transmission from these rat populations back to humans. IMPORTANCE The host tropism expansion of SARS-CoV-2 raises concern for the potential risk of reverse-zoonotic transmission of emerging variants into rodent species, including wild rat species. In this study, we present both genetic and serological evidence for SARS-CoV-2 exposure to the New York City wild rat population, and these viruses may be linked to the viruses that were circulating during the early stages of the pandemic. We also demonstrated that rats are susceptible to additional variants (i.e., Alpha, Delta, and Omicron) that have been predominant in humans and that susceptibility to infection varies by variant. Our findings highlight the reverse zoonosis of SARS-CoV-2 to urban rats and the need for further monitoring of SARS-CoV-2 in rat populations for potential secondary zoonotic transmission to humans.

Dataset Information

Introductions and early spread of SARS-CoV-2 in the New York City area.

Publications

Introductions and early spread of SARS-CoV-2 in the New York City area.

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