Re-emergence of COVID-19 in Beijing was triggered by frozen virus: evidence from molecular clock

The COVID-19 outbreak in Xinfadi (XFD) Wholesale market in Beijing, China in June, 2020 caused 368 reported cases within 39 days. Genetic evidences indicated that imported SARS-CoV-2 (belong to the lineage B1.1.29) initiated this outbreak. However, the transmission route of the virus is still unknown. We obtained from public database three SARS-CoV-2 genomes isolated in XFD (XFD genomes) and adopted the leaf-dating method to calculate their expected collection dates using temporal calibrating information from other 241 genomes collected in mainland of China. All three XFD genomes were calculated to have earlier collection dates than the recorded (Bayes factor >1), and hence exhibited a lack of genetic divergence. We additionally combined the XFD genomes with other 225 genomes subsampled from those of the lineage B1.1.29, among which five sequences were also included for control analysis. Two of three XFD genomes were calculated to have earlier collection dates than the recorded (Bayes factor >1), while no control genomes provided such evidence. According to present understanding of SARS-CoV-2, a lack of genetic divergence is most likely due to being frozen. Considering the fact that the XFD outbreak started from a booth of frozen food, we judged that the XFD outbreak was caused by contaminated frozen food. Our results provided molecular evidence for the source of COVID-19 outbreak in Beijing XFD, which highlights new targets for SARS-CoV-2 surveillance for the public health.