Sequencing identifies multiple early introductions of SARS-CoV-2 to the New York City Region

Abstract

Effective public response to a pandemic relies upon accurate measurement of the extent and dynamics of an outbreak. Viral genome sequencing has emerged as a powerful approach to link seemingly unrelated cases, and large-scale sequencing surveillance can inform on critical epidemiological parameters. Here, we report the analysis of 236 SARS-CoV2 sequences from cases in the New York City metropolitan area during the initial stages of the 2020 COVID-19 outbreak. The majority of cases throughout the region had no recent travel history or known exposure, and genetically linked cases were spread throughout the region. Comparison to global viral sequences showed that the majority were most related to cases from Europe. Our data are consistent with numerous seed transmissions from multiple sources and a prolonged period of unrecognized community spreading. This work highlights the complementary role of real-time genomic surveillance in addition to traditional epidemiological indicators.

The emergence of SARS-CoV-2 in Europe and the US

“…These findings again reveal that epidemiological linkages inferred from genetically similar SARS-CoV-2 viruses associated with outbreaks in different locations can be highly tenuous, given low levels of sampled viral genetic diversity and insufficient background data from key locations. f Interestingly, our approach is also able to infer that this major European clade, the same one that dominates in New York City (14,15) and Arizona (22), had an origin in Italy, as might be expected from the epidemiological evidence. This inference makes use of the recent travel history, where available, of various sequences in that cluster from people who had recently travelled to Italy.…”

“…The Markov jump estimates of the movement from Hubei to Italy were: Feb. 7 th , 2020 (95% HPD Jan. 31 st -Feb. 14 th ). This Italian/European cluster, in turn, was the source of multiple introductions to New York City (NYC) (14,15). Using the same approach, we date the introduction leading to the largest NYC transmission cluster to Feb. 20 th , 2020 (95% HPD Feb. 14 th -Feb. 26 th ).…”

“…Importantly, this lineage also spread to North America, establishing an early beachhead in New York City (14,15). Furthermore, the B.1 lineage harbors a D614G mutation in the Spike protein that has been controversially claimed to make the virus more contagious (16).…”

Ultrafast Sample Placement on Existing Trees (UShER) Empowers Real-Time Phylogenetics for the SARS-CoV-2 Pandemic

“…turnaround times are enabling a type of "genomic contact tracing" where genetic similarities (or dissimilarity) between viral genomes isolated for different hosts carries important information about the transmission dynamics of the virus. For example, these data can be used to infer the number of unique introductions of the viral genome in a given area [5][6][7][8][9][10][11] and to identify "transmission chains" among otherwise seemingly unrelated infections [12][13][14][15][16] .…”

The Covid-19 Global Pandemic: A Natural Experiment in the Making

“…Due to the rapid rate of mutation in RNA viruses such as SARS-CoV-2, viral genome sequencing will help to determine the origin of these outbreaks and their subsequent spread within a country [3]. Indeed, sequencing viral samples collected from patients in New York City during the early stages of the outbreak suggest that that majority of these cases were related to viral samples isolated from cases in Europe [4]. Even after strict travel restrictions were implemented, the virus spread rapidly across the USA and phylogenetic analyses have proved useful to clarify the importance of domestic transmission [5].…”