A COVID-19 case was identified in Beijing on 2020-06-11,ending a run of 55days without local transmissionand starting the second outbreak. Since then, the city has responded quickly and fiercely with a series of control measures, such as large scaleqRT-PCRscreening, locking down affected residential compounds, and closingall schools. With all these efforts,the second outbreak was taken under control within two weeks, and lasted only for 39days (till 2020-07-20) with 368 qRT-PCR positive cases. Mostcases of the outbreak had a history of close contact with Xinfadi (XFD) Wholesale Market. Genetic tracing of SARS-CoV-2 genomesfrom XFD indicated that the outbreak was triggered by imported virus.Specifically it was a memberof the lineage B1.1 (now of the lineage B1.1.29, ) predominately circulatingin Europe rather than in China[4).
Evidences from epidemiological field investigationshowed that a salmon booth (#S14) was the starting point, suggesting that the viruses could have been imported with contaminated frozen food.However, some held a belief thatthe virus wasimported by infected human
Molecular clock-based evolutionaryanalysis of temporally spaced genome data providesa new tool fortiming past events andexploring the mechanism and process of evolution . Generally, the molecular clock positsthat viral genomesaccumulate mutationsat roughly a constantrate, and the process could be affected by certain environmentalfactors. For example, frozen viral isolates do not accumulate genetic mutations while in storage. Thisenvironmental factor, frozen in storage, could help test the contaminated seafoodhypothesis.We therefore performed evolutionary analysis of the SARS-CoV-2 genome data of the isolates collected in the XFD Wholesale Market (denoted as XFD genomes). Weevaluated the amount of genetic changes embedded in these genomesto test whether the contaminated seafood hypothesisworded for the import of virus leading to the second outbreak of COVID-19 in Beijingin 2020.
The evolutionary analysisof SARS-CoV-2 genomes sampled in XFDrevealedthatthe two XFD genomes(IVDC-02-06 and IVDC-01-1)lackedgenetic divergence.If theyfollowedthe previous evolutionary rate, the calculated collection date of these two XFD genomes wereearlier than the record date.This lack of genetic divergence was attributed to frozen storage for the following reasons. First,SARS-CoV-2biologysuggests it be impossible for some virusesstayingin a host or reservoir for several monthswith little or no replication before reactivationand asecond outbreak . Second, it has been reported thatSARS-CoV-2can survive the time and temperatures associated with transportation and storage conditions associated with international food trade. Besides,epidemiological evidence revealed that the outbreak started from a booth of frozen food in the market. Therefore, we hypothesizedthat the contaminated imported food carried the livevirus from the supply chain, survivedinthefrozen storage, and transferredthe virus to the XFD market, thusleadingthe outbreak.
In conclusion, we concludethat the outbreak in XFD market in Beijing was caused by contaminatedfrozen food(or its packaging). Ourfindings, coupled with the reports from China of SARS-CoV-2 being detected on imported frozen food, should alert food safety authorities and the food industry where this virus could pose a non-traditional food safety risk.