Phylogenetic estimates of SARS-CoV-2 introductions into Washington State

Abstract

Background: The first confirmed case of SARS-CoV-2 in North America was identified in Washington state on January 21, 2020. We aimed to quantify the number and temporal trends of out-of-state introductions of SARS-CoV-2 into Washington. Methods: We conducted a phylogenetic analysis of 11,422 publicly available whole genome SARS-CoV-2 sequences from GISAID sampled between December 2019 and September 2020. We used maximum parsimony ancestral state reconstruction methods on time-calibrated phylogenies to enumerate introductions/exports, their likely geographic source (e.g. US, non-US, and between eastern and western Washington), and estimated date of introduction. To incorporate phylogenetic uncertainty into our estimates, we conducted 5,000 replicate analyses by generating 25 random time-stratified samples of non-Washington reference sequences, 20 random polytomy resolutions, and 10 random resolutions of the reconstructed ancestral state. Results: We estimated a minimum 287 separate introductions (median, range 244-320) into Washington and 204 exported lineages (range 188-227) of SARS-CoV-2 out of Washington. Introductions began in mid-January and peaked on March 29, 2020. Lineages with the Spike D614G variant accounted for the majority (88%) of introductions. Overall, 61% (range 55-65%) of introductions into Washington likely originated from a source elsewhere within the US, while the remaining 39% (range 35-45%) likely originated from outside of the US. Intra-state transmission accounted for 65% and 28% of introductions into eastern and western Washington, respectively. Conclusions: There is phylogenetic evidence that the SARS-CoV-2 epidemic in Washington is continually seeded by a large number of introductions, and that there was significant inter- and intra-state transmission. Due to incomplete sampling our data underestimate the true number of introductions.

Seroprevalence of SARS-CoV-2 antibodies in the general population of Oman: results from four successive nationwide sero-epidemiological surveys

“…We observed marked regional differences between the different governorates in Oman that generally match the surveillance data (Figure 2); this could partly be due to the different epidemic introduction times to the governorates as it started from the capital governorate (Muscat) and then spread to the adjacent governorates, this has also been shown from a study from Washington, USA (Tordoff et al, 2021). There was also earlier spread in the governorates on the borders of other countries.…”

COVID-19 epidemiology as emergent behavior on a dynamic transmission forest

“…5b is certainly an oversimplification, lacking for example the importations that would be needed to explain the variants of concern to come. But despite that, perhaps because importations are a minority of all events [23], the contact distributions p(T t ) seem to be generally consistent with other, more individualistic measures of the interactions driving trans-mission. That they can be calculated directly from the model trajectories, essentially by hand, is remarkable.…”

“…The yellow chain's finite lifetime motivates a high-level comparison to Washington's genetic sequencing data, arranged into a phylogenetic tree in Ref. 23. In that paper, the phylogenetic tree is separated into subclades, groups of ancestrally related sequences arranged over time, associated with a single SARS-CoV-2 importation and subsequent transmission.…”

“…Specifically, breaking the forest into its disconnected components, we can coarsely estimate a subclade size by sampling nodes to account for their probability of being reported (Fig. 3, again) and their probability of being se- quenced (roughly 6% [23]). Then, we can also calculate a subclade lifetime from the exposure dates of the first and last sequenced nodes.…”

Local-Scale phylodynamics reveal differential community impact of SARS-CoV-2 in metropolitan US county

“…Since initial detection of the virus, genomic epidemiology has played a crucial role in identifying and estimating new introductions and community transmission in WA (1-3) and throughout the US (4,5) and has motivated rapid public health interventions. While international introductions continue to seed new viral lineages into the US, the majority of transmission is driven by infections and movement at a local scale, wherein neighboring states, regions, counties, or even zip codes can have vastly different epidemic dynamics (3,6,7).…”