Abstract
The spread of SARS-CoV-2 in Beijing before May, 2020 resulted from transmission following both domestic and global importation of cases. Here we present genomic surveillance data on 102 imported cases, which account for 17.2% of the total cases in Beijing. Our data suggest that all of the cases in Beijing can be broadly classified into one of three groups: Wuhan exposure, local transmission and overseas imports. We classify all sequenced genomes into seven clusters based on representative high-frequency single nucleotide polymorphisms (SNPs). Genomic comparisons reveal higher genomic diversity in the imported group compared to both the Wuhan exposure and local transmission groups, indicating continuous genomic evolution during global transmission. The imported group show region-specific SNPs, while the intra-host single nucleotide variations present as random features, and show no significant differences among groups. Epidemiological data suggest that detection of cases at immigration with mandatory quarantine may be an effective way to prevent recurring outbreaks triggered by imported cases. Notably, we also identify a set of novel indels. Our data imply that SARS-CoV-2 genomes may have high mutational tolerance.
Highlights
The spread of SARS-CoV-2 in Beijing before May, 2020 resulted from transmission following both domestic and global importation of cases
The coronavirus disease 2019 (COVID-19) is an emerging disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)
None of the family members had been to Wuhan, but one of them could be linked to another patient with Wuhan exposure
Summary
The spread of SARS-CoV-2 in Beijing before May, 2020 resulted from transmission following both domestic and global importation of cases. Our data suggest that all of the cases in Beijing can be broadly classified into one of three groups: Wuhan exposure, local transmission and overseas imports. Upon implementation of a series of interventions, including routine screening and quarantine of travelers, self-isolation and detection, contact restrictions, and social distancing measures, the number of new infections in China has decreased, and the disease has been well controlled[8–10]. As Europe and the United States became the epicenters of disease outbreak, China started to experience case importations from abroad. We perform deep SARS-CoV-2 genome sequencing followed by bioinformatic analysis on the clinical samples we collected during the abovementioned two periods in Beijing. We summarize the characteristics of the viral genome sequences, including several notable changes in the viral genomic features during these periods
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