Temporal dynamics of SARS-CoV-2 genome mutations that occurred in vivo on an aircraft.

We analyzed variations in the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome during a flight-related cluster outbreak of coronavirus disease 2019 (COVID-19) in Shenzhen, China, to explore the characteristics of SARS-CoV-2 transmission and intra-host single nucleotide variations (iSNVs) in a confined space. Thirty-three patients with COVID-19 were sampled, and 14 were resampled 3-31 days later. All 47 nasopharyngeal swabs were deep sequenced. iSNVs and similarities in the consensus genome sequence were analyzed. Three SARS-CoV-2 variants of concern, Delta (n=31), Beta (n=1), and C.1.2 (n=1), were detected among the 33 patients. The viral genome sequences from 30 Delta-positive patients had similar SNVs; 14 of these patients provided two successive samples. Overall, the 47 sequenced genomes contained 164 iSNVs. Of the 14 paired (successive) samples, the second samples (T2) contained more iSNVs (median: 3; 95% confidence interval [95%CI]: 2.77-10.22) than did the first samples (T1; median: 2; 95%CI: 1.63-3.74; Wilcoxon test, P=0.021). 38 iSNVs were detected in T1 samples, and only seven were also detectable in T2 samples. Notably, T2 samples from two of the 14 paired samples had additional mutations than the T1 samples. The iSNVs of the SARS-CoV-2 genome exhibited rapid dynamic changes during a flight-related cluster outbreak event. Intra-host diversity increased gradually with time, and new site mutations occurred in vivo without a population transmission bottleneck. Therefore, we could not determine the generational relationship from the mutation site changes alone.

Risk Transmission Mechanism of Domestic Cluster Epidemic Caused by Overseas Imported Cases: Multiple Case Studies Based on Grounded Theory.

The continued severity of the global epidemic situation has led to a rising risk of imported cases in China, and domestic cluster epidemic events caused by imported cases have occurred from time to time, repeatedly causing nation-wide disruption. To deeply explain this phenomenon, this study adopted the grounded theory method, using the 5·21 Guangzhou COVID-19 outbreak and 7·20 Nanjing COVID-19 outbreak as examples to study the risk transmission mechanism of domestic cluster epidemic caused by overseas imported cases. The study found that the risk factors for the phenomenon mainly include the following seven aspects: external protection, operations and supervision, international and domestic environment, contaminated objects, virus characteristics, management efficacy, and individual factors. These risk factors together constitute the "detonator", "risk source", "risk carrier," and "risk amplifier" in the risk transmission process. In addition, this study also found that the transmission mechanism of domestic clusters caused by imported cases is a process of secondary risk amplification. The increase in risk carriers leads to a surge in secondary risks compared with the first, which leads to the outbreak of domestic clusters. Finally, based on the characteristics of the transmission mechanism and risk transmission components, this study provides some suggestions on risk mitigation for public departments to optimize China's epidemic prevention policies.

Reflections on the Cluster Epidemic of COVID-19; Lessons Learned from Wuhan's Experience: A Brief Review.

At present, new coronavirus pneumonia (COVID-19) is circulating worldwide. The pathogen of this coronavirus pneumonia is named SARS-CoV-2. The virus has a long incubation period and is highly contagious. There is currently no specific targeted drug treatment. The focus of anti-epidemic work should be more on prevention and control while cutting off the virus transmission route while treating infected patients, and protecting healthy people. In order to protect the safety and health of the Chinese citizens and to maintain the safety of world public health, the Chinese government and people have made unprecedented efforts to control the epidemic. Many people in the international community have joined in limiting the spread of COVID-19. This article combines the development of COVID-19 epidemic situation in Wuhan, the relevant prevention and control measures of the Wuhan government and local health authorities to share Wuhan's experience on control the cluster epidemic and provide new suggestions and ideas for epidemic prevention and control.

[Investigation on two family clusters of COVID-19 in a county of Baotou city in Inner Mongolia Autonomous Region].

Objective: To investigate the epidemiological characteristics and transmission chain of COVID-19 in two families, and to provide scientific evidence for effective prevention and control measures. Methods: Field epidemiological investigation was conducted for the COVID-19 cases occurred in two families and the close contacts in a county of Baotou city in Inner Mongolia Autonomous Region. Descriptive statistical analysis on epidemiological data was conducted. Results: The infection source of the COVID-19 cases in the two families was a man who had living history in Wuhan. After his return, his parents were infected by him. A few days later, the members of a neighbor family were found to be infected, and relatives of this family were also infected after dining together repeatedly. Finally, ten confirmed cases and three suspected cases of COVID-19 were detected in the two families. Conclusions: Human-to-human transmission of COVID-19 can occur not only in a family but also in neighborhoods. The cases in two families had close relationship, indicating the necessity to strengthen the health education about COVID-19 prevention and control and the management of groups at high risk to reduce the incidence of COVID-19 in families and neighborhoods.

[Contagiousness and secondary attack rate of 2019 novel coronavirus based on cluster epidemics of COVID-19 in Guangzhou].

Objective: To analyze the contagiousness and secondary attack rate of 2019 novel coronavirus in cluster epidemics in Guangzhou and provide evidence for the prevention and control of COVID-19. Methods: All the individuals identified to be infected with 2019-nCoV in Guangzhou, including confirmed cases and asymptomatic cases, were included and classified as imported cases and local cases. The first case of each cluster epidemic was defined as index case, and the number of subsequent infections was calculated to evaluate the contagiousness and secondary attack rate of 2019 novel coronavirus in the shortest incubation period of 1-3 days. Results: As of 18 February, 2020, a total of 349 cases of 2019-nCoV infection, including 339 confirmed cases (97.13%) and 10 asymptomatic cases (2.87%) were reported in Guangzhou. There were 68 clusters involving 217 2019-nCoV infection cases (210 confirmed cases and 7 asymptomatic cases). The median number of subsequent infections caused by an index case in a cluster epidemic was 3, among which 2 were confirmed cases and 1 was asymptomatic cases, respectively. The average number of contagiousness was 2.18 in shorted incubation period of 1-3 days (The average number of infected cases were 2.18 cases by the index case in a cluster epidemic), the average infection number in family members was 1.86, and the infection ratio of family member transmission was 85.32% (1.86/2.18). The secondary attack rate in close contacts with shortest incubation period of 1-3 days was 17.12%-18.99%, the secondary attack rate in family members was 46.11%-49.56%. Conclusions: The cluster epidemic of COVID-19 in Guangzhou mainly occurred in families, the contagiousness was high. It is necessary to strengthen the prevention and control to reduce the community transmission of COVID-19.

[Investigation on a cluster epidemic of COVID-19 in a supermarket in Liaocheng, Shandong province].

Objective: To explore clustered epidemic of COVID-19 in Liaocheng city and analyze infection status and chain of transmission of the cases. Methods: A joint investigation team of emergency response for COVID-19 epidemic by CDC professional workers of Liaocheng city and district at two levels on January 30, 2020. According to a indicator case from ZH supermarkets, close contacts and related subjects were tracked and screened on February 1, including ZH supermarket employees, family members having contact history with related cases during January 13-26, supermarket clients during January 16-30 and family members of related cases. an epidemiological investigation was carried on and their swab of nose/throat were collected and were sent to Liaocheng CDC laboratory, real-time fluorescence quantitative RT-PCR was used to detect nucleic acids of SARS-CoV-2. Results: a total of 8 437 people were screened during January 30 to February 9, 2020 (120 employees of supermarket, 93 family members, and 8224 clients of supermarket). The epidemic was caused by ZH cases and brought clustered cases in four families. A total 25 cases of SARS-CoV-2 infection, the total infection rate of subjects was 0.30% (25/8 437) with 22 confirmed cases (0.26%, 22/8 437) and 3 asymptomatic patients (0.04%, 3/8 437), asymptomatic patients accounted for 12.00% (3/25) of all infection cases. The infection rates of supermarket employees, family members of confirmed cases and supermarket clients were 9.17% (11/120), 12.90% (12/93) and 0.02% (2/8 224). Conclusions: This was a cluster epidemic caused by one imported case of COVID-19 in a supermarket of Liaocheng city. Prevention and control of cluster epidemic should be focused on chain of community transmission and family cluster cases. It must also be an attention for transmission risk of asymptomatic patients.

[Epidemiological investigation on a cluster epidemic of COVID-19 in a collective workplace in Tianjin].

Objective: To investigate and analysis the epidemiological characteristics of a cluster epidemic of COIVD-19 in a collective workplace in Tianjin, evduate the prevention and control measures based on limited evidence and experience in early period of COVID-19 epidemic. Methods: Descriptive research method was used to describe the distribution and other epidemiological characteristics of the cluster cases of COVID-19. Results: Since the onset of the first index case on January 15, ten confirmed COVID-19 cases had occurred in the workplace, and the epidemic had spread from the workplace to 4 families, infecting 7 family members. The median age of 17 cases was 55 (19-79) years. All the 10 employee cases were males, and in the family cases, 3 were males and 4 were females. Of the employee cases, 8 worked in CW workshop and 2 worked in administrative office building. The median exposure-onset interval of all the cases was 4 days, and the median exposure-onset interval was 4.5 days in the employee cases and 4 days in the family cases. The median onset-medical care seeking interval was 4 days in the non-isolated cases, 2.5 days in the cases with home isolation after onset, and 0.5 day in the cases with home isolation before onset. Conclusions: The clustering of COVID-19 cases was observed in this workplace in Tianjin, which affected 4 families. In the early stage of the epidemic, accurate and rapid blocking and control measures can completely prevent the large-scale spread of COVID-19.