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.

Emergence in late 2020 of multiple lineages of SARS-CoV-2 Spike protein variants affecting amino acid position 677

“…Despite accounting for roughly 25% of globally recorded COVID-19 cases, and approximately 20% of the available SARS-CoV-2 genome data, relatively few studies have detailed the introduction and emergence of SARS-CoV-2 lineages in the United States (Rochman et al, 2020;Worobey et al, 2020;Washington et al, 2021;Zeller et al, 2021). Furthermore, seroprevalence surveys indicate that between 1 in 10 and 1 in 3 people in the USA have already been infected with SARS-CoV-2, potentially high enough that selection for immune evasion may be present (Angulo, Finelli and Swerdlow, 2021;Bubar et al, 2021).…”

Early and ongoing importations of SARS-CoV-2 in Canada

“…Phylogeographic methods to infer ancestral states of sampled viruses have been applied widely to quantify the timing and geographic origins of SARS-CoV-2 introductions into the United Kingdom (UK) 5 , United States of America (USA) [1][2][3]22 , Brazil 23,24 , New Zealand (NZ) 4,25 , and Europe 1,26 , among others. Drastically different epidemic dynamics have been elucidated globally.…”

“…An analysis of early epidemic dynamics in the state of Louisiana, USA, revealed starkly contrasting importation dynamics, wherein the first wave of SARS-CoV-2 was almost entirely attributable to a single domestic introduction. This introduction likely originated from Texas, which occurred several weeks prior to the annual Mardi Gras festival, during which superspreader events likely gave rise to a large number of cases within Louisiana and neighbouring Southern states 22 . Furthermore, in NZ, where border closures and stringent lockdown measures were enacted early in the pandemic 4 , reductions in international introductions and in reproductive numbers following lockdown were proportional to the reduction in mobility nationwide 4 .…”

Unrecognized introductions of SARS-CoV-2 into the state of Georgia shaped the early epidemic

“…Sequences in this clade canonically harbor substitutions C14408T, A23403G (responsible for the widely reported D614G amino acid substitution in the spike protein 12 ), G28881A, and G28882A relative to Wuhan/Hu-1 (EPI_ISL_402125 13 ). Clade 20B was prominent throughout Europe 14 and a number of U.S. states 15 throughout early 2020. Despite being the first identified clade in GA, local transmission of 20B appears to have been limited and it was only sporadically (N=6/107) identified throughout March 2020.…”