In this study, we performed a comprehensive epidemiological and genomic analysis of SARS-CoV-2 genomes from ten patients in Shaoxing, a mid-sized city outside of the epicenter Hubei province, China, during the early stage of the outbreak (late January to early February, 2020).
More...In this study, we performed a comprehensive epidemiological and genomic analysis of SARS-CoV-2 genomes from ten patients in Shaoxing, a mid-sized city outside of the epicenter Hubei province, China, during the early stage of the outbreak (late January to early February, 2020). We obtained viral genomes with > 99% coverage and a mean depth of 296X demonstrating that viral genomic analysis is feasible via metagenomics sequencing directly on nasopharyngeal samples with SARS-CoV-2 Real-time PCR C t values less than 28. We found that a cluster of 4 patients with travel history to Hubei shared the exact same virus with patients from Wuhan, Taiwan, Belgium and Australia,
highlighting how quickly this virus spread to the globe. The virus from another cluster of
husband and wife without travel history but with a sick contact of a confirmed case from
another city outside of Hubei accumulated significantly more mutations (9 SNPs vs
average 4 SNPs), suggesting a complex and dynamic nature of this outbreak. We also
found 70% patients in this study had the S genotype, consistent with an early study
showing a higher prevalence of S genotype out of Hubei than that inside Hubei. We
calculated an average mutation rate of 1.37x10 -3 nucleotide substitution per site per
year, which is similar to that of other coronaviruses. Our findings add to the growing
knowledge of the epidemiological and genomic characteristics of SARS-CoV-2 that are
important for guiding outbreak containment and vaccine development. The moderate
mutation rate of this virus also lends hope that development of an effective, long-lasting
vaccine may be possible. Less...