tetano
Editor, Senior Moderator
Genomics
. 2020 Oct 19;S0888-7543(20)31980-7.
doi: 10.1016/j.ygeno.2020.10.021. Online ahead of print.
Variant analysis of the first Lebanese SARS-CoV-2 isolates
Mhamad Abou-Hamdan[SUP] 1 [/SUP], Kassem Hamze[SUP] 1 [/SUP], Ali Abdel Sater[SUP] 2 [/SUP], Haidar Akl[SUP] 1 [/SUP], Nabil El-Zein[SUP] 1 [/SUP], Israa Dandache[SUP] 1 [/SUP], Fadi Abdel-Sater[SUP] 3 [/SUP]
Affiliations
Abstract
Recently the first genome sequences for 11 SARS-CoV-2 isolates from Lebanon became available. Here, we report the detection of variants within the genome of these strains. Pairwise alignment analysis using blastx was performed between these sequences and the UniProtKB data for the SARS-CoV-2 coronavirus to identify amino acid variations. Variants analysis was performed using multiple Bioinformatics tools. We noticed for the first time 18 mutations that have never been reported before. Among those, a frame shift (8651A>) in NSP4, a stop codon 6887A > T in NSP3 and two missense mutations in spike S2 were found. In addition, we found 28 variants in ORF1ab alone. A previously reported variant, 23403A > G, in the spike protein S2 was mostly seen. Two other known mutations 25563G > T in ORF3a and 14408C > T in ORF1ab were detected respectively in 6 and 8 out of the 11 isolates. Our results may help to prognose forthcoming infections in this region.
Keywords: Lebanese isolates; Missense; Novel mutations; Severe acute respiratory syndrome coronavirus 2.
. 2020 Oct 19;S0888-7543(20)31980-7.
doi: 10.1016/j.ygeno.2020.10.021. Online ahead of print.
Variant analysis of the first Lebanese SARS-CoV-2 isolates
Mhamad Abou-Hamdan[SUP] 1 [/SUP], Kassem Hamze[SUP] 1 [/SUP], Ali Abdel Sater[SUP] 2 [/SUP], Haidar Akl[SUP] 1 [/SUP], Nabil El-Zein[SUP] 1 [/SUP], Israa Dandache[SUP] 1 [/SUP], Fadi Abdel-Sater[SUP] 3 [/SUP]
Affiliations
- PMID: 33091548
- PMCID: PMC7572353
- DOI: 10.1016/j.ygeno.2020.10.021
Abstract
Recently the first genome sequences for 11 SARS-CoV-2 isolates from Lebanon became available. Here, we report the detection of variants within the genome of these strains. Pairwise alignment analysis using blastx was performed between these sequences and the UniProtKB data for the SARS-CoV-2 coronavirus to identify amino acid variations. Variants analysis was performed using multiple Bioinformatics tools. We noticed for the first time 18 mutations that have never been reported before. Among those, a frame shift (8651A>) in NSP4, a stop codon 6887A > T in NSP3 and two missense mutations in spike S2 were found. In addition, we found 28 variants in ORF1ab alone. A previously reported variant, 23403A > G, in the spike protein S2 was mostly seen. Two other known mutations 25563G > T in ORF3a and 14408C > T in ORF1ab were detected respectively in 6 and 8 out of the 11 isolates. Our results may help to prognose forthcoming infections in this region.
Keywords: Lebanese isolates; Missense; Novel mutations; Severe acute respiratory syndrome coronavirus 2.