Genome-wide characteristics and evolutionary analysis of Omicron variant BN.1 in Lincang City, Yunnan Province (2022)
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目的 了解2022年云南省临沧市8例SARS-CoV-2感染者的病毒全基因组测序结果及进化情况。 方法 2022年10月30日至11月4日采集临沧市8例SARS-CoV-2感染者的鼻咽拭子样本进行MiniSeq illumina二代测序获得病毒的全基因组序列。应用在线分析平台判断病毒的类型，利用分子进化遗传分析软件鉴别基因的变异位点，与参考基因组进行比对，构建生物进化树。 结果 8份样本ORF1ab基因的Ct值为19.16~23.64，N基因为16.71~24.08。全基因组序列显示，基因测序准确度Q30为90.1%（>80%），簇密度为256 K/mm2。与武汉参考株（GenBank登录号：MN908947.3）序列比较，共检测出1份95处核苷酸突变位点，6份94处核苷酸突变位点，1份93处核苷酸突变位点。病毒分型结果显示，所有样本均属于奥密克戎变异株BN.1进化分支。进化分析结果显示，8份样本差异数小于3，属于同一条传播链。 结论 此次疫情病例为同一传染源，首例病例发病前有边境地区（缅甸）活动史，再结合云南省发生BN.1变异株疫情的地区均处于与缅甸交接处和基因测序结果等情况，综合分析本次疫情为境外（缅甸）输入新的病毒感染的可能性较大。 Objective To investigate the whole genome sequencing and evolutionary status of SARS-CoV-2 in 8 COVID-19 cases in Lincang City, Yunnan Province in 2022. Methods Nasal and throat swab samples were collected from 8 patients with COVID-19 in Lincang City, Yunnan Province from October 30 to November 4, 2022 for MiniSeq Illumina second-generation sequencing to obtain the complete viral genome sequence. The types of viruses were determined by online analysis platform. The gene mutation sites were identified using molecular evolutionary genetics analysis software, and a reference genome was compared to build a biological evolutionary tree. Results In 8 samples, the Ct values of the ORF1ab gene were ranged from 19.16 to 23.64, and those of N gene were ranged from 16.71 to 24.08. The whole genome sequence showed that the accuracy of the gene sequencing Q30 was 90.1% (>80%), and the cluster density was 256 K/mm2. Compared with the sequence of the Wuhan reference strain (GenBank registration number: MN908947.3), 1 sample had 95 nucleotide mutation sites, 6 samples had 94 nucleotide mutation sites, and 1 sample had 93 nucleotide mutation sites. The virus typing results indicated that it belonged to the Omicron variant BN.1 evolutionary branch. Evolutionary analysis showed that the differences among 8 samples were less than 3, indicating that they belonged to the same transmission chain. Conclusions The epidemic in Lincang City is from the same source of infection. The first case had a history of activity in border areas (Myanmar) before the onset. Combined with the occurrence of the variant BN.1 branch epidemic in Yunnan Province where locates at the border with Myanmar, and the gene sequencing results, it is highly probable that this epidemic is caused by a new virus imported from abroad (Myanmar).
Objective To investigate the whole genome sequencing and evolutionary status of SARS-CoV-2 in 8 COVID-19 cases in Lincang City, Yunnan Province in 2022. Methods Nasal and throat swab samples were collected from 8 patients with COVID-19 in Lincang City, Yunnan Province from October 30 to November 4, 2022 for MiniSeq Illumina second-generation sequencing to obtain the complete viral genome sequence. The types of viruses were determined by online analysis platform. The gene mutation sites were identified using molecular evolutionary genetics analysis software, and a reference genome was compared to build a biological evolutionary tree. Results In 8 samples, the Ct values of the ORF1ab gene were ranged from 19.16 to 23.64, and those of N gene were ranged from 16.71 to 24.08. The whole genome sequence showed that the accuracy of the gene sequencing Q30 was 90.1% (>80%), and the cluster density was 256 K/mm2. Compared with the sequence of the Wuhan reference strain (GenBank registration number: MN908947.3), 1 sample had 95 nucleotide mutation sites, 6 samples had 94 nucleotide mutation sites, and 1 sample had 93 nucleotide mutation sites. The virus typing results indicated that it belonged to the Omicron variant BN.1 evolutionary branch. Evolutionary analysis showed that the differences among 8 samples were less than 3, indicating that they belonged to the same transmission chain. Conclusions The epidemic in Lincang City is from the same source of infection. The first case had a history of activity in border areas (Myanmar) before the onset. Combined with the occurrence of the variant BN.1 branch epidemic in Yunnan Province where locates at the border with Myanmar, and the gene sequencing results, it is highly probable that this epidemic is caused by a new virus imported from abroad (Myanmar).
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