对 SARS-CoV-2 株的变异分析与系统发生分析以及冠状病毒抗病毒和耐药性数据库。
Variant analysis of SARS-CoV-2 strains with phylogenetic analysis and the Coronavirus Antiviral and Resistance Database.
机构信息
Kocaeli University, Research & Education Hospital, PCR Unit, 41380, Kocaeli, Turkey.
Near East University, DESAM Research Institute, 99138, Nicosia, Northern Cyprus.
出版信息
J Comp Eff Res. 2022 Feb;11(3):157-167. doi: 10.2217/cer-2021-0208. Epub 2022 Jan 11.
This study determined SARS-CoV-2 variations by phylogenetic and virtual phenotyping analyses. Strains isolated from 143 COVID-19 cases in Turkey in April 2021 were assessed. Illumina NexteraXT library preparation kits were processed for next-generation ]sequencing. Phylogenetic (neighbor-joining method) and virtual phenotyping analyses (Coronavirus Antiviral and Resistance Database [CoV-RDB] by Stanford University) were used for variant analysis. B.1.1.7-1/2 (n = 103, 72%), B.1.351 (n = 5, 3%) and B.1.525 (n = 1, 1%) were identified among 109 SARS-CoV-2 variations by phylogenetic analysis and B.1.1.7 (n = 95, 66%), B.1.351 (n = 5, 4%), B.1.617 (n = 4, 3%), B.1.525 (n = 2, 1.4%), B.1.526-1 (n = 1, 0.6%) and missense mutations (n = 15, 10%) were reported by CoV-RDB. The two methods were 85% compatible and B.1.1.7 (alpha) was the most frequent SARS-CoV-2 variation in Turkey in April 2021. The Stanford CoV-RDB analysis method appears useful for SARS-CoV-2 lineage surveillance.
本研究通过系统进化和虚拟表型分析来确定 SARS-CoV-2 的变异情况。评估了 2021 年 4 月在土耳其的 143 例 COVID-19 病例中分离出的菌株。使用 Illumina NexteraXT 文库制备试剂盒进行下一代测序。通过系统进化（邻接法）和虚拟表型分析（斯坦福大学的冠状病毒抗病毒和耐药数据库[CoV-RDB]）进行变异分析。通过系统进化分析，在 109 种 SARS-CoV-2 变异中鉴定出 B.1.1.7-1/2（n=103，72%）、B.1.351（n=5，3%）和 B.1.525（n=1，1%），而 CoV-RDB 报告了 B.1.1.7（n=95，66%）、B.1.351（n=5，4%）、B.1.617（n=4，3%）、B.1.525（n=2，1.4%）、B.1.526-1（n=1，0.6%）和错义突变（n=15，10%）。两种方法的兼容性为 85%，B.1.1.7（alpha）是 2021 年 4 月土耳其最常见的 SARS-CoV-2 变异株。斯坦福 CoV-RDB 分析方法似乎可用于 SARS-CoV-2 谱系监测。
Zotero 插件