Comparative analysis of SARS-CoV-2 variants with two high-throughput sequencing platforms

Whole-genome sequencing of upper respiratory tract specimens from patients with confirmed COVID-19 in Henan Province was performed to compare the performance of the Illumina and Oxford Nanopore sequencing platforms, thus providing a reference for whole-genome monitoring of the novel coronavirus (SARS-CoV-2). Ten samples from COVID-19 cases in Henan Province from June 2021 to January 2022 were collected and sequenced with Illumina and Nanopore high-through-put sequencing technology to obtain full genome sequences of the novel coronavirus, which were compared with the Wuhan reference sequence (Wuhan-Hu-1). Bioinformatics software (CLC) was used for sequence alignment analysis. Three of the ten samples were Omicron (BA.1) variants with 55,61 nucleotide variation sites. One sample was an Alpha (B.1.1.7) variant with 41 nucleotide variation sites. Six samples were Delta (8.1.617.2) variants with 35,42,47 nucleotide variation sites. The sequence identity of mutation sites in six samples was 100%, and the mutation sites in the S genome segment of seven samples were consistent. For samples with a Ct value < 33, both next-generation and third-generation sequencing achieved high genome coverage and sequencing depth. A significant difference in coverage was observed between second-generation sequencing and third-generation sequencing (t=-2.037, P < 0.06). However, the coverage at different time points of the third-generation sequencing did not significantly differ (F=2.498, P > 0.05). The needs for SARS-CoV-2 mutant detection could be met through use of either high-throughput sequencing platform. The identification of mutations in the novel coronavirus through Illumina high-throughput sequencing was more accurate, whereas Nanopore high-throughput sequencing technology could be used for rapid detection and typing of different novel coronaviruses.

Research on transmission pattern of SARS-CoV-2

Objective: Taking the three outbreaks caused by Delta variant (B.1.617.2) in Guangzhou, Guangdong Province, Nanjing, Jiangsu Province and Zhengzhou, Henan Province as examples, to explore different transmission pattern of SARS-CoV-2 epidemic and to provide basis for scientific prevention and control.

Analyses of the nucleic acids of SARS-CoV-2 from pharyngeal swabs and fecal specimens in COVID-19 patients and asymptomatic SARS-CoV-2 infected persons at different exposure times

The coronavirus disease 2019 (COVID-19) pandemic has become a public-health crisis worldwide. Accurate identification of the virus that causes COVID-19, SARS-CoV-2, carriers of SARS-CoV-2, and infected people is crucial for the prevention and control of this pandemic. Detection of the nucleic acids (NAs) of SARS-CoV-2 is one of the main criteria for COVID-19 diagnosis. Pharyngeal swabs (PSs) and fecal specimens (FSs) tend to be positive for SARS-CoV-2. However, there have been no reports of differences in the detection results of SARS-CoV-2 NAs in PSs and FSs of COVID-19 patients and asymptomatic SARS-CoV-2 infected persons at different exposure times. Forty-six patients diagnosed with COVID 19 in Nanyang City, China, from 2 February to 17 February 2020 and 27 asymptomatic SARS-CoV-2 infected persons screened through epidemiologic history and PSs and FSs at different exposure times were evaluated through detection of SARS-CoV-2 NAs. COVID-19 patients and asymptomatic SARS-CoV-2 infected persons had the highest positive rate of NAs in PSs at week 2 and the highest positive rate for NAs in FSs at week 3. The positive rate of NAs in PSs was significantly higher than that of FSs (P < 0.05). The difference in the positive rate of NAs in PSs between the two groups at 1, 3, and 4 weeks was significant (P < 0.05). The difference in the positive rate of NM in FSs between the two groups at 1-4 weeks was not significant (P > 0.05). The time for SARS-CoV-2 NAs to test positive in FSs lagged behind that for SARS-CoV-2 NAs to test positive in PSs (P > 0.05). The time for SARS-CoV-2 NAs to test positive in the PSs and FSs of asymptomatic SARS-CoV-2 infected persons lagged behind that for COVID-19 patients (P > 0.05). There was no significant difference in the average cycle threshold (Ct) value of the ORFlab gene and N gene of PSs and FSs between COVID-19 patients and asymptomatic SARS-Cov-2 infected persons at each exposure time tested (P > 0.05). The more severe the COVID-19, the higher was the positive rate of SARS-CoV-2 NAs in PSs and FSs, and the shorter was the time taken for SARS-CoV-2 NAs to test positive (P < 0.05). The re-positive rate of asymptomatic SARS-CoV-2 infected persons was 14.81% (4/27), higher than that of COVID-19 patients (6.52%;3/46), and the difference was significant (X2=8.193, P=0.016). Our study suggests that SARS-CoV-2 has a fecal mouth transmission route. The time taken for SARS-CoV-2 NM from FSs to turn positive lags behind that for SARS-CoV-2 NAs in PSs to turn positive, and the positive rate is lower. Test specimens should be selected according to different exposure times. Attention should he paid to younger asymptomatic SARS-CoV-2 infected persons.

Recommendations for emergency management of rural major infectious diseases in non-epicenter areas: taking village B during COVID-19 as an example

This paper analyzed the key issues and challenges confronted in the governance of Village B in the non-epicenter area in rural areas of China during the COVID-19 pandemic. It clarified the weak points in the prevention and control of infectious diseases in Village B. A triple emergency management mechanism of "people-materials-environment" in rural areas should be established. It came up with constructive recommendations for scientifically and effectively responding to public health emergencies in rural non-epicenter areas, which is helpful to improve the rationality, legality and scientific effectiveness of the construction of emergency response mechanisms in rural areas.

Epidemic dynamics of COVID-19 in Xinyang City, Henan Province. (Special Issue: Spatio-temporal dynamics analysis, risk assessment and emergency management for COVID-19 epidemic.) [Chinese]

Objective: To explore epidemic dynamics of coronavirus disease 2019 (COVID-19) in Xinyang City so as to provide scientific basis for optimizing the prevention and control strategies and evaluating the effects of intervention.

The strategies of "early detection, early report, early assessment, and early control" in vector prevention and control

Since the outbreak of coronavirus disease 2019 (COVID-19), the social prevention and control measures of "early detection, early report, early isolation, and early treatment" have been widely used in the public health field and are widely accepted by the general public. In the practice of integrated vector management, Henan province gives full play to the advantages of mobilization and coordination of the Patriotic Health Campaign, establishes a work path of "early detection, early report, early assessment, and early control", the strategies of "four early". It defines the responsibilities of government, departments, territories, and individuals, and clarifies the working concepts of integrated vector management, which helps to form societal forces and promote the development of vector control in Henan province. This article analyzes the strategies of "four early" in integrated vector management in Henan province, in order to provide a reference for vector management strategies in China.