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

Our take —

This manuscript, available as a preprint and therefore not yet peer-reviewed, demonstrated how SARS-CoV-2 emerged in, and then spread throughout Louisiana at the beginning of 2020. The authors showed that SARS-CoV-2 was likely introduced domestically from a single source (likely Texas), that SARS-CoV-2 was likely circulating in New Orleans before the Mardi Gras festival in February 2020, and that Mardi Gras likely acted as a super-spreading event, greatly increasing the number of cases and deaths, and likely also seeding local outbreaks in nearby cities and states. Although sampling bias can affect our understanding of transmission patterns, the integration of genomic, epidemiological, and mobility data improves our confidence in these findings. Additionally, this paper contributes to the growing body of evidence that large events without precautions early in the pandemic likely contributed to the rapid rise of COVID-19 cases, and that these types of events should be approached with caution in the future.

Study design

Retrospective Cohort

Study population and setting

This study aimed to understand the early COVID-19 epidemic in New Orleans, Louisiana, and explored the connection between the annual Mardi Gras festival (which occurred, without precautions, in New Orleans in February 2020) and the subsequent rapid spread of SARS-CoV-2 in the Southern US and the rest of the country. The study used aggregated COVID-19 case data to analyze reported cases and deaths during the first wave of the epidemic in Louisiana, which lasted from the first detection of COVID-19 in the state on March 9, to May 15, 2020. The authors also analyzed 235 SARS-CoV-2 virus genomes collected from patients in New Orleans, Shreveport, and other parishes in Louisiana during this time period, alongside a representative sample of 1,263 publicly available global sequences. Finally, the authors used domestic and foreign air travel records to understand transmission into the state, as well as human mobility data collected from weekly cell phone records available as part of the SafeGraph database.

Summary of Main Findings

Using genomic and epidemiological data, the authors found that SARS-CoV-2 was likely introduced into Louisiana via domestic, not international, travel. Specifically, they found that there was very little genetic diversity within Louisiana sequences from the first wave (also suggesting that SARS-CoV-2 transmission within Louisiana was predominantly seeded from a single introduction), and that all lineages observed closely resembled sequences from other parts of the US. This matched airline data, which showed that the vast majority of airline travel during that period was from domestic locations. Using the genetic data, the authors also estimated the date of these introductions and found that SARS-CoV-2 likely emerged in the state prior to the Mardi Gras festival (around February 13, 2020, with a 95% posterior density interval of January 24 to February 27, 2020). Coupled with the rapid increase in cases in early March, this suggests that the Mardi Gras festival in late February likely acted as a super-spreader event for SARS-CoV-2 transmission. Finally, the authors used genetic, mobility, and epidemiological data to conclude that SARS-CoV-2 in Louisiana likely came from Texas, and that the Mardi Gras-related outbreak in Louisiana likely caused localized outbreaks in nearby states.

Study Strengths

Combining genomic, epidemiological, and human mobility data allowed the authors to draw conclusions from one dataset and support those findings with additional data. This significantly improves our confidence in understanding the early transmission patterns of the epidemic in Louisiana.

Limitations

Phylogeographic analyses are inherently limited by sampling bias. While confirmation from other datasets helps, conclusions involving pinpointing the source of a particular SARS-CoV-2 lineage are particularly difficult to make with certainty. For example, export risk from New Orleans is likely biased towards states with larger populations, as these states will have more sequence data as well as more mobility records. Additionally, the limited genetic data observed in Louisiana makes it difficult to pinpoint an exact time of introduction.

Value added

This manuscript improves our understanding of how COVID-19 spread in Louisiana at the beginning of the outbreak. Identification of Mardi Gras as a super-spreading event also highlights the contribution of large events to increases in COVID-19 cases, which both aids our understanding of observed cases and deaths in New Orleans, while acting as a cautionary tale for other large gatherings without appropriate precautions.

This review was posted on: 12 March 2021