Though most trace the coronavirus outbreak to China, a new analysis finds most of the cases in New York seem to have originated in Europe.
Officially, the first case of coronavirus disease 2019 (COVID-19) was reported in New York City on February 29, but a new report based on genomic analysis suggests the disease was introduced as early as January, and that most cases were linked to Europe, rather than Asia.
The report, published in the journal Science, helps paint a picture of the early days of the spread of SARS-CoV-2 in what would become the major COVID-19 hotspot in the US.
Corresponding author Harm van Bakel, PhD, of the Icahn School of Medicine at Mount Sinai, explained that the medical school has a multidisciplinary pathogen analysis program called the Pathogen Surveillance Program. When COVID-19 hit, the lab was able to use that existing infrastructure to evaluate 90 SARS-CoV-2 isolates from 84 patients who visited the health system between February 29 and March 18.
Those isolates tell a considerable amount about how the virus arrived and spread in New York, according to van Bakel and co-authors.
“Based on genetic similarity and phylogenetic analysis of full-length viral genome sequences, most cases diagnosed during the 18 days after the first-reported COVID-19 case in New York State appear to be associated with untracked transmission and potential travel-related exposure,” the authors write.
However, van Bakel and colleagues said it does not appear that most cases originated in Asia. Instead, the majority of introductions of the virus seem to have come from Europe and from elsewhere in the United States.
As for community transmission, the authors report that 21 cases of COVID-19 appeared to be closely related, which is evidence that they are the result of community spread.
In their analysis, the authors assigned each SARS-CoV-2 isolate to a main monophyletic clade based on amino acid and nucleotide substitutions and statistical information using the maximum-likelihood and Bayesian methods.
The first two isolates came from patients with recent travel to the Middle East and Europe and thus were excluded from inferences made based on phylogenetic analysis.
Of the remaining isolates, the vast majority (87%) clustered with clade A2a, and the majority of isolates in that clade (72%) are cases of patients with COVID-19 in Europe, suggesting that Europe was the major origin of COVID-19 cases in New York in march, the authors write.
The investigators say it is likely these cases began in New York between late January and mid-February. Another 6% of isolates fit in clase A1a, which is also made up largely of isolates originating in Europe.
The remaining clades (B, B1, and B4) are cases believed to have been introduced in New York between February and early March. Two of the introductions appear to have come from Washington State. A majority of the sequences in the B clade originated in Asia, though the authors report that the closest relatives of the New York isolates originated in Europe and North America.
“We find clear evidence for multiple independent introductions into the NYC metropolitan area from different regions globally, as well as from other parts of the United States,” investigators wrote.
Notably, investigators said cases that were identified based on travel histories resulted in quick quarantine and hospitalization and do not appear to be linked to significant community spread.
“We find that New York City, as an international hub, provides not only a snapshot of the diversity of disease-causing SARS-CoV-2, at the global level, but also informs on the dynamics of the pandemic at the local level,” investigators concluded.