Where does the virus of the clustering epidemic in the Beijing Xinfadi market come from? Here comes the latest conclusion!
On October 23, Tsinghua University, Beijing Center for Disease Control and Prevention, Institute of pathogenic biology, Chinese Academy of Medical Sciences, Peking University, and Beijing Institute of Genomics, Chinese Academy of Sciences, jointly published a paper in the National Science Review on October 23. Through the analysis of nucleic acid sequencing and virus genome sequence of relevant cases, environment, and food samples, combined with comprehensive epidemiological survey and big data analysis Analysis, the researchers revealed that the source of the virus in the epidemic is very likely to be the cold chain imported food in the high incidence area of the overseas epidemic, and put forward that cold chain transportation may be a new way for the transmission of the novel coronavirus.
On June 11, 2020, a patient with a novel coronavirus infection suddenly appeared, breaking the calm of Beijing without new cases for 56 consecutive days. The patient was treated immediately and his condition was quickly controlled, but where he was infected with the virus has become a mystery.
Combined with the epidemiological investigation and big data analysis of the indicator cases, through the investigation of the areas and contacts, the city further found that two environmental samples from the Beijing Xinfadi market were positive for NCV nucleic acid. Subsequently, 538 employees of the Xinfadi market received viral nucleic acid screening, and 45 were positive. The Xinfadi market has become the focus of attention. The relevant departments of Beijing Municipality resolutely took measures to close the market in order to effectively curb the spread of the epidemic.
In mid-June, Beijing further promoted nucleic acid screening, and a total of 368 people were found to be nucleic acid positive for novel coronavirus. These infected persons were directly or indirectly related to Xinfadi Market: 169 of them were staff of the Xinfadi market, 103 of them had been to the Xinfadi market from May 30 to June 12, and the remaining 96 were contacts of the above-mentioned personnel. No early transmission chain or independent transmission chain independent of the market was found, suggesting that the new source market was the single source of the outbreak.
Distribution of infected workers on the first floor of the Xinfadi comprehensive trading hall (beef and mutton Hall).
Combined with the epidemiological survey of the Xinfa market, the researchers preliminarily determined that the source of infection was probably the No. S14 stalls in the aquatic area on the first floor of the comprehensive trading hall (beef and mutton Hall). All the 7 staff members of the stall were confirmed cases of Xinguan, and the symptoms appeared relatively early. According to the epidemic model, 5 customers were positive for the detection of novel coronavirus antibodies, and all of them visited booth S14. These five customers and their close contacts have not visited the medium and high-risk areas or contacted the personnel from the medium and high-risk areas in the past 14 days, which further indicates that the epidemic situation is transmitted from the new market.
The analysis of viral genome sequence from the cases and environmental samples of the new outbreak market showed that the virus sequence had obvious mutation characteristics, which was different from the domestic and imported cases previously found in China, indicating that the epidemic situation should be a single overseas import.
The research team further used the self-developed low viral load sample processing method to conduct high-throughput nucleic acid sequencing on 110 cases and environmental samples and obtained 72 high-quality genome sequences of the novel coronavirus. It was found that there were 8 characteristic mutation sites in these sequences, which had never been found in Chinese indigenous and imported cases. Compared with the NCV gene sequence database, it was found that the viruses with seven other mutation sites except c6026t were mainly found in Europe. These results further suggest that the virus of this epidemic should be imported from abroad.
The analysis of the virus genome sequence from the cases and environmental samples in the new outbreak area showed that the virus sequence had obvious mutation characteristics, which was different from the domestic and imported cases previously found in China, indicating that the epidemic situation should be a single overseas import.
Based on the above results, it was confirmed that the staff of stall No. S14 had no contact with suspected or confirmed novel coronavirus infection, and no new infection cases were reported in Beijing from May to early June, suggesting that the virus is likely to be imported from abroad. Further investigation showed that among the items sold at stall No. S14, chilled salmon was the only one from abroad, and the stall owner had purchased salmon from a supplier with complete packaging imported from countries with the Covid-19 epidemic situation on May 30 and then cut and retail them in the market. For this reason, the researchers sampled and tested the cold storage of all salmon suppliers in the Xinfadi market, and found that five fish swab samples of a certain supplier were positive for NCV nucleic acid, and the viral genome sequence obtained from sequencing of one unopened fish swab sample was highly homologous with the virus in human and environmental samples in this epidemic situation.
The virus activity in fish can not be proved because the virus can not be isolated from fish. However, the combination of high-quality virus genome sequence analysis and epidemiological investigation indicates that cold chain imported food from high-risk areas of the overseas epidemic is very likely to be the source of the concentrated epidemic virus in the new market. In the process of publication, China CDC reported that novel coronavirus was isolated from cold chain food obtained in Qingdao, which further suggested that cold chain food may be an important way of novel coronavirus transmission. The study provides important evidence for revealing the virus source of the clustering epidemic in the Beijing Xinfa market and provides an important basis for optimizing the control strategy of epidemic normalization.
In the study, many institutions carried out sincere cooperation. Among them, the novel coronavirus pneumonia prevention and control group of Beijing Center for Disease Control and prevention participated in the field investigation, sample collection, and nucleic acid screening. The research team of Wang Jianwei and Ren Lili from the Institute of pathogenic biology, the Chinese Academy of Medical Sciences completed the sample pre-processing process in the P3 laboratory. The rapid genome sequencing sample processing method developed by Wang Jianbin of Tsinghua University and Huang Yanyi of Peking University provides the technical basis and experimental support for accurate and rapid virus sequencing of key samples of this epidemic. Li Mingkun of Beijing Institute of Genomics, Chinese Academy of Sciences, has completed the analysis of key sample sequences.
Pang Xinghuo, chief physician of Beijing Center for Disease Control and prevention, Wu Shuangsheng, chief physician, Ren Lili, researcher of Institute of pathogenic biology, Chinese Academy of Medical Sciences, and Ma Wentai, a graduate student of Beijing Institute of Genomics, Chinese Academy of Sciences, were co-authors of the paper. (reporter Ren Min)
The official account of the advanced biology and innovation center of structural biology, Tsinghua University.