Variant analysis of SARS-CoV-2 strains with phylogenetic analysis and the Coronavirus Antiviral and Resistance Database

SAYAN M., Arikan A., Isbilen M.

JOURNAL OF COMPARATIVE EFFECTIVENESS RESEARCH, cilt.11, ss.157-167, 2022 (SCI-Expanded) identifier identifier identifier

  • Yayın Türü: Makale / Tam Makale
  • Cilt numarası: 11
  • Basım Tarihi: 2022
  • Doi Numarası: 10.2217/cer-2021-0208
  • Dergi Adı: JOURNAL OF COMPARATIVE EFFECTIVENESS RESEARCH
  • Derginin Tarandığı İndeksler: Science Citation Index Expanded (SCI-EXPANDED), Scopus, EMBASE, MEDLINE
  • Sayfa Sayıları: ss.157-167
  • Anahtar Kelimeler: bioinformatics, COVID-19, next-generation sequencing, phylogenetic analyses, SARS-CoV-2 variants
  • Kocaeli Üniversitesi Adresli: Evet

Özet

Aims: This study determined SARS-CoV-2 variations by phylogenetic and virtual phenotyping analyses. Materials & methods: 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. Results: 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. Conclusion: The Stanford CoV-RDB analysis method appears useful for SARS-CoV-2 lineage surveillance.