Phylogenetic analysis of SARS-CoV-2 in Boston highlights the impact of superspreading events.

Science
Jacob LemieuxBronwyn L MacInnis

Abstract

Analysis of 772 complete severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes from early in the Boston-area epidemic revealed numerous introductions of the virus, a small number of which led to most cases. The data revealed two superspreading events. One, in a skilled nursing facility, led to rapid transmission and significant mortality in this vulnerable population but little broader spread, whereas other introductions into the facility had little effect. The second, at an international business conference, produced sustained community transmission and was exported, resulting in extensive regional, national, and international spread. The two events also differed substantially in the genetic variation they generated, suggesting varying transmission dynamics in superspreading events. Our results show how genomic epidemiology can help to understand the link between individual clusters and wider community spread.

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Datasets Mentioned

BETA
GISAID

Software Mentioned

ggtree
Augur pipeline
BEAST1
Kraken2
augur
R package adegenet
R
ggplot2
tidyverse
viral

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