Dataset Information

Emergence of an early SARS-CoV-2 epidemic in the United States.

ABSTRACT: The emergence of the early COVID-19 epidemic in the United States (U.S.) went largely undetected, due to a lack of adequate testing and mitigation efforts. The city of New Orleans, Louisiana experienced one of the earliest and fastest accelerating outbreaks, coinciding with the annual Mardi Gras festival, which went ahead without precautions. To gain insight into the emergence of SARS-CoV-2 in the U.S. and how large, crowded events may have accelerated early transmission, we sequenced SARS-CoV-2 genomes during the first wave of the COVID-19 epidemic in Louisiana. We show that SARS-CoV-2 in Louisiana initially had limited sequence diversity compared to other U.S. states, and that one successful introduction of SARS-CoV-2 led to almost all of the early SARS-CoV-2 transmission in Louisiana. By analyzing mobility and genomic data, we show that SARS-CoV-2 was already present in New Orleans before Mardi Gras and that the festival dramatically accelerated transmission, eventually leading to secondary localized COVID-19 epidemics throughout the Southern U.S.. Our study provides an understanding of how superspreading during large-scale events played a key role during the early outbreak in the U.S. and can greatly accelerate COVID-19 epidemics on a local and regional scale.

SUBMITTER: Zeller M

PROVIDER: S-EPMC7872376 | biostudies-literature | 2021 Feb

REPOSITORIES: biostudies-literature

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Emergence of an early SARS-CoV-2 epidemic in the United States.

Zeller Mark M Gangavarapu Karthik K Anderson Catelyn C Smither Allison R AR Vanchiere John A JA Rose Rebecca R Snyder Daniel J DJ Dudas Gytis G Watts Alexander A Matteson Nathaniel L NL Robles-Sikisaka Refugio R Marshall Maximilian M Feehan Amy K AK Sabino-Santos Gilberto G Bell-Kareem Antoinette R AR Hughes Laura D LD Alkuzweny Manar M Snarski Patricia P Garcia-Diaz Julia J Scott Rona S RS Melnik Lilia I LI Klitting Raphaälle R McGraw Michelle M Belda-Ferre Pedro P DeHoff Peter P Sathe Shashank S Marotz Clarisse C Grubaugh Nathan N Nolan David J DJ Drouin Arnaud C AC Genemaras Kaylynn J KJ Chao Karissa K Topol Sarah S Spencer Emily E Nicholson Laura L Aigner Stefan S Yeo Gene W GW Farnaes Lauge L Hobbs Charlotte A CA Laurent Louise C LC Knight Rob R Hodcroft Emma B EB Khan Kamran K Fusco Dahlene N DN Cooper Vaughn S VS Lemey Phillipe P Gardner Lauren L Lamers Susanna L SL Kamil Jeremy P JP Garry Robert F RF Suchard Marc A MA Andersen Kristian G KG

medRxiv : the preprint server for health sciences 20210208

The emergence of the early COVID-19 epidemic in the United States (U.S.) went largely undetected, due to a lack of adequate testing and mitigation efforts. The city of New Orleans, Louisiana experienced one of the earliest and fastest accelerating outbreaks, coinciding with the annual Mardi Gras festival, which went ahead without precautions. To gain insight into the emergence of SARS-CoV-2 in the U.S. and how large, crowded events may have accelerated early transmission, we sequenced SARS-CoV-2 ...[more]

PMID: 33564781

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Project description:Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a viral pathogen that quickly became a global pandemic in the winter of 2020-2021. In response, governments issued social distancing orders to minimize transmission by reducing community contacts. We tested the efficacy of this social distancing at the state level during the first 2 months of the pandemic in the United States. We utilized data on daily SARS-CoV-2 case numbers and human community mobility (anonymized, aggregated cell phone location data stratified into six categories used as an index of social distancing), the date of government-issued social distancing orders, demographics, urbanization and public transportation. We implemented cross-correlation to identify lag times between declines in mobility and SARS-CoV-2 cases. Incorporating state-specific lag times, we tested for associations between case counts and mobility metrics using Bayesian multilevel models. Decreased mobility around grocery stores/pharmacies, retail/recreation locations, transit stations and workplaces was correlated with decreases in SARS-CoV-2 cases with significant lag times of ≥21 days. Social distancing orders were associated with fewer cumulative SARS-CoV-2 cases when they were put in place earlier. Community mobility had already started declining prior to most social distancing orders, especially the more restrictive orders implemented later in the pandemic. Social distancing is an important tool that has been implemented throughout the pandemic to decrease SARS-CoV-2 transmission, although with significant social and economic impacts. Our results suggest that declines in cases were observed several weeks subsequent to implementation of social distancing measures, and that implementing social distancing earlier could potentially minimize the duration of time these policies need to be in effect. Our findings can inform ongoing management of this pandemic and other emerging infectious disease outbreaks by identifying areas where reductions in mobility are associated with reduced disease transmission, and the expected time frame between behavioural changes and measurable population outcomes.

Dataset Information

Emergence of an early SARS-CoV-2 epidemic in the United States.

Publications

Emergence of an early SARS-CoV-2 epidemic in the United States.

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