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. 2020 Sep 3:11:573430.
doi: 10.3389/fmicb.2020.573430. eCollection 2020.

Comprehensive Genome Analysis of 6,000 USA SARS-CoV-2 Isolates Reveals Haplotype Signatures and Localized Transmission Patterns by State and by Country

Lishuang Shen  1 , Jennifer Dien Bard  1   2 , Jaclyn A Biegel  1   2 , Alexander R Judkins  1   2 , Xiaowu Gai  1   2
Affiliations

Comprehensive Genome Analysis of 6,000 USA SARS-CoV-2 Isolates Reveals Haplotype Signatures and Localized Transmission Patterns by State and by Country

Lishuang Shen et al. Front Microbiol. .

Abstract

Genomic analysis of SARS-CoV-2 sequences is crucial in determining the effectiveness of prudent safer at home measures in the United States (US). By haplotype analysis of 6,356 US isolates, we identified a pattern of strongly localized outbreaks at the city-, state-, and country-levels, and temporal transmissions. This points to the effectiveness of existing travel restriction policies and public health measures in reducing the transmission of SARS-CoV-2.

Keywords: COVID-19; SARS-CoV-2; haplotype; localized outbreak; temporal transmission; variant.

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Figures

FIGURE 1
FIGURE 1
Maximum likelihood phylogenetic tree of isolates carrying US-specific haplotypes and 2,000 randomly selected non-US isolates. Blue, isolates with Washington-specific haplotypes; Pink, Children’s Hospital Los Angeles (CHLA) and other California isolates; Green, New York-specific, Red, other states’ isolates with USA-specific haplotypes; Light blue, UK and Australia isolates; Black, Other non-US isolates. Blue labels, the clade names. A total of 1107 isolates from US-specific haplotypes were included in the phylogenetic analysis. Non-US isolates belonging to any haplotypes were randomly sampled at about 10% to reach 2000 isolates. Each branch in the phylogenetic tree may represent a group of isolates. The tree is rooted at the outgroup MN996532 (EPI_ISL_402131, bat/Yunnan/RaTG13/2013).
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