Cryptic transmission of SARS-CoV-2 in Washington state

Abstract

After its emergence in Wuhan, China, in late November or early December 2019, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus rapidly spread globally. Genome sequencing of SARS-CoV-2 allows the reconstruction of its transmission history, although this is contingent on sampling. We analyzed 453 SARS-CoV-2 genomes collected between 20 February and 15 March 2020 from infected patients in Washington state in the United States. We find that most SARS-CoV-2 infections sampled during this time derive from a single introduction in late January or early February 2020, which subsequently spread locally before active community surveillance was implemented.

Fig. 1. Maximum-likelihood phylogeny of 455 SARS-CoV-2 viruses collected from Washington state on a background of 493 globally collected viruses.

Viruses collected from Washington state are shown as red circles. Tips and branches are colored on the basis of location, branch lengths are proportional to the number of mutations along a branch, and the x axis is labeled with the number of substitutions relative to the root of the phylogeny—here equivalent to basal Wuhan outbreak viruses. The clustering of related viruses indicates community transmission after an introduction event. Branch locations are estimated on the basis of a discrete traits model. We observe a single introduction leading to a large outbreak clade of 384 sampled viruses from Washington state (marked by the larger arrow), and we observe a second introduction leading to a smaller outbreak clade of 39 viruses (marked by the smaller arrow). An interactive version of this figure is available at https://nextstrain.org/community/blab/ncov-cryptic-transmission/introductions.

Fig. 2. Maximum-likelihood phylogeny of the Washington state outbreak clade and immediately ancestral variants containing 448 SARS-CoV-2 viruses and Bayesian estimates of the date of the outbreak common ancestor and outbreak doubling time.

(A) Maximum-likelihood phylogeny. Tips are colored on the basis of location, branch lengths are proportional to the number of mutations between viruses, and the x axis is labeled with the number of substitutions relative to the root of the phylogeny—here equivalent to the WA1 haplotype. This comb-like phylogenetic structure of the Washington state outbreak clade is consistent with rapid exponential growth of the virus population. An interactive version of this figure is available at https://nextstrain.org/community/blab/ncov-cryptic-transmission/wa-clade. (B) Highest posterior density estimates for the date of the common ancestor of viruses from the Washington state outbreak clade (top) as well as the doubling time in days of the growth of this clade (bottom).

Fig. 3. Acute respiratory samples tested for SARS-CoV-2 collected as part of the Seattle Flu Study between 1 January and 15 March 2020.

(A) Total samples tested per day. In total, 10,382 samples collected between 1 January and 15 March were tested. (B) Number of samples testing positive per day. (C) Estimated proportion positive using a sequential Monte Carlo model to provide day-to-day smoothing. The solid red line is the mean estimate of proportion positive, and the gray shaded region is the 95% credible interval. All dates are those of sample collection, not dates of testing.