ABSTRACT
Objective: To understand the genomic characteristics of SARS-CoV-2 from 40 imported cases with confirmed COVID-19 in Sichuan during January and March 2022. Methods: Total viral RNA was extracted from respiratory samples of 182 confirmed COVID-19 cases who entered China through Chendu International Airport from January to March 2022. Mutation nucleic acid detection kit was used to identify the mutant strains and Illumina sequencing platform was applied for whole genome sequence(WGS) of virus. SARS-CoV-2 reference sequences were downloaded from NCBI database for genetic evolution and antigen variation analysis. The Nextclade and Pangolin online virus analysis platform were used to determine the virus family and type, and to analyze the mutation loci of the virus. The phylogenetic tree was constructed, along with the epidemiological data of cases to analyze the source and correlation of viruses. Results: Among 182 imported COVID-19 cases,B.1.617.2 mutations were identified in 3 cases and B.1.1.529 mutations were detected in 57 cases.A total of 40 SARS-CoV-2 whole genome sequences with coverage>95% were obtained in this study. Nextclade typing analysis showed that 3 sequences belonged to 21J(Delta),5 sequences belonged to 21K(Omicron)and the remaining 32 sequences belonged to 21L(Omicron). Pangolin typing analysis showed that the 3 sequences of 21J(Delta)belonged to AY.4,AY.109and B.1.617.2, the 5sequences of 21K(Omicron)all belonged to BA.1.1, and the remaining 32 sequences of 21L(Omicron)belonged to BA.2. Our sequence results were99.7% consistency with the Omicron variants sequences in current GISAID database. Compared with the reference sequence strain Wuhan-Hu-1(NC_045512.2),45,47and 42nucleotide variation sites and 36,25 and 36amino acid variation sites were found in the 3 sequences of 21J(Delta). There were average 59(26-64)nucleotide mutation sites and 48(10-53)amino acid mutation sites in the 5sequences of 21K(Omicron). The median number of nucleotide mutation sites of 71(66-76)and amino acid mutation sites of 53(40-56)were identified in the 32sequences of 21L(Omicron). Phylogenetic tree analysis showed that 40SARS-CoV-2WGSs were all related to the current variants of concern(VOC). Conclusions Continuous: sequencing of SARS-CoV-2whole genome from imported cases with confirmed COVID-19is of great significance for the prevention and control of the outbreak and prevalence of local epidemic caused by imported viruses in Sichuan.
ABSTRACT
Objective To understand the genomic characteristics of SARS-CoV-2 from 40 imported cases with confirmed COVID-19 in Sichuan during January and March 2022. Methods Total viral RNA was extracted from respiratory samples of 182 confirmed COVID-19 cases who entered China through Chendu International Airport from January to March 2022.Mutation nucleic acid detection kit was used to identify the mutant strains and Illumina sequencing platform was applied for whole genome sequence（WGS） of virus.SARS-CoV-2 reference sequences were downloaded from NCBI database for genetic evolution and antigen variation analysis.The Nextclade and Pangolin online virus analysis platform were used to determine the virus family and type,and to analyze the mutation loci of the virus.The phylogenetic tree was constructed,along with the epidemiological data of cases to analyze the source and correlation of viruses. Results Among 182 imported COVID-19 cases,B.1.617.2 mutations were identified in 3 cases and B.1.1.529 mutations were detected in 57 cases.A total of 40 SARS-CoV-2 whole genome sequences with coverage>95% were obtained in this study.Nextclade typing analysis showed that 3 sequences belonged to 21J（Delta）,5 sequences belonged to 21K（Omicron）and the remaining 32 sequences belonged to 21L（Omicron）.Pangolin typing analysis showed that the 3 sequences of 21J（Delta）belonged to AY.4,AY.109and B.1.617.2,the 5sequences of 21K（Omicron）all belonged to BA.1.1,and the remaining 32 sequences of 21L（Omicron）belonged to BA.2.Our sequence results were99.7% consistency with the Omicron variants sequences in current GISAID database.Compared with the reference sequence strain Wuhan-Hu-1（NC＿045512.2）,45,47and 42nucleotide variation sites and 36,25 and 36amino acid variation sites were found in the 3 sequences of 21J（Delta）.There were average 59（26-64）nucleotide mutation sites and 48（10-53）amino acid mutation sites in the 5sequences of 21K（Omicron）.The median number of nucleotide mutation sites of 71（66-76）and amino acid mutation sites of 53（40-56）were identified in the 32sequences of 21L（Omicron）.Phylogenetic tree analysis showed that 40SARS-CoV-2WGSs were all related to the current variants of concern（VOC）. Conclusions Continuous sequencing of SARS-CoV-2whole genome from imported cases with confirmed COVID-19is of great significance for the prevention and control of the outbreak and prevalence of local epidemic caused by imported viruses in Sichuan.
ABSTRACT
Objectives: To explore and understand the SARS-CoV-2 seroprevalence of convalescents, the association between antibody levels and demographic factors, and the seroepidemiology of convalescents of COVID-19 till March 2021. Methods: We recruited 517 voluntary COVID-19 convalescents in Sichuan Province and collected 1,707 serum samples till March 2021. Then we reported the seroprevalence and analyzed the associated factors. Results: Recent travel history was associated with IgM levels. Convalescents who had recent travel history were less likely to be IgM antibody negative [OR = 0.232, 95% CI: (0.128, 0.420)]. Asymptomatic cases had, approximately, twice the odds of being IgM antibody negative compared with symptomatic cases [OR = 2.583, 95% CI: (1.554, 4.293)]. Participants without symptoms were less likely to be IgG seronegative than those with symptoms [OR = 0.511, 95% CI: (0.293, 0.891)]. Convalescents aged 40-59 were less likely to be IgG seronegative than those aged below 20 [OR = 0.364, 95% CI: (0.138, 0.959)]. The duration of positive IgM antibodies persisted 365 days while the IgG persisted more than 399 days. Conclusions: Our findings suggested that recent travel history might be associated with the antibody levels of IgM, while age could be associated with the antibody levels of IgG. Infection type could be associated with both antibody levels of IgM and IgG that declined quicker in asymptomatic cases.
Subject(s)
COVID-19 , SARS-CoV-2 , Antibodies, Viral , China/epidemiology , Humans , Immunoglobulin G , Seroepidemiologic StudiesABSTRACT
The SARS-CoV-2 virus, the causative agent of COVID-19, is undergoing constant mutation. Here, we utilized an integrative approach combining epidemiology, virus genome sequencing, clinical phenotyping, and experimental validation to locate mutations of clinical importance. We identified 35 recurrent variants, some of which are associated with clinical phenotypes related to severity. One variant, containing a deletion in the Nsp1-coding region (Δ500-532), was found in more than 20% of our sequenced samples and associates with higher RT-PCR cycle thresholds and lower serum IFN-ß levels of infected patients. Deletion variants in this locus were found in 37 countries worldwide, and viruses isolated from clinical samples or engineered by reverse genetics with related deletions in Nsp1 also induce lower IFN-ß responses in infected Calu-3 cells. Taken together, our virologic surveillance characterizes recurrent genetic diversity and identified mutations in Nsp1 of biological and clinical importance, which collectively may aid molecular diagnostics and drug design.