塞内加尔城市环境中 SARS-CoV-2 的基因组流行病学研究。
Genomic Epidemiology of SARS-CoV-2 in Urban Settings in Senegal.
机构信息
Institut de Recherche en Santé, de Surveillance Epidémiologique et de Formation, Dakar 7325, Senegal.
IHU-Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005 Marseille, France.
出版信息
Viruses. 2023 May 24;15(6):1233. doi: 10.3390/v15061233.
We used whole genome sequencing to identify and analyze mutations in SARS-CoV-2 in urban settings during the deadliest wave of the COVID-19 epidemic-from March to April 2021-in Senegal. Nasopharyngeal samples testing positive for SARS-CoV-2 were sequenced on the Illumina NovaSeq 6000 sequencing system using the COVIDSeq protocol. A total of 291 genotypable consensus genome sequences were obtained. Phylogenetic analyses grouped the genomes into 16 distinct PANGOLIN lineages. The major lineage was B.1.1.420, despite circulation of the Alpha variant of concern (VOC). A total of 1125 different SNPs, identified relative to the Wuhan reference genome, were detected. These included 13 SNPs in non-coding regions. An average density of 37.2 SNPs per 1000 nucleotides was found, with the highest density occurring in ORF10. This analysis allowed, for the first time, the detection of a Senegalese SARS-CoV-2 strain belonging to the P.1.14 (GR/20J, Gamma V3) sublineage of the Brazilian P.1 lineage (or Gamma VOC). Overall, our results highlight substantial SARS-CoV-2 diversification in Senegal during the study period.
我们使用全基因组测序来鉴定和分析 2021 年 3 月至 4 月塞内加尔 COVID-19 大流行期间城市环境中 SARS-CoV-2 的突变。使用 COVIDSeq 方案，在 Illumina NovaSeq 6000 测序系统上对鼻咽拭子样本进行测序，这些样本检测出 SARS-CoV-2 呈阳性。共获得 291 个可分型的共识基因组序列。系统发育分析将基因组分为 16 个不同的 PANGOLIN 谱系。主要谱系是 B.1.1.420，尽管有令人担忧的 Alpha 变体（VOC）的传播。相对于武汉参考基因组，共检测到 1125 个不同的 SNP。这些 SNP 包括非编码区的 13 个。平均每 1000 个核苷酸有 37.2 个 SNP，最高密度出现在 ORF10 中。该分析首次检测到属于巴西 P.1 谱系的 P.1.14（GR/20J，Gamma V3）次谱系的塞内加尔 SARS-CoV-2 株（或 Gamma VOC）。总的来说，我们的研究结果强调了研究期间塞内加尔 SARS-CoV-2 的大量多样化。
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