Variant analysis of the first Lebanese SARS-CoV-2 isolates

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.

Novel and emerging mutations of SARS-CoV-2: Biomedical implications

“…The results of a study that investigated only eleven full-length genome sequences from Lebanon until Mar 2020, showed that the most prevalent variants were 23403A > G (D614G), clade G, and the second common mutant was 14408C > T, in ORF1ab, resulted in a missense mutation as P4715L, one of the three mutations mostly co-occurred with 23403A > G harboring genome. The pattern of variations in this study was equal to the European countries, at the same time which is rational according to their short distances [92] .…”

SARS-CoV-2 Variants in Lebanon: Evolution and Current Situation

“…The genomes of 11 Lebanese strains were previously analyzed and showed a number of mutations in the ORF of structural and nonstructural proteins [26,27]. A total of 40 single nucleotide variations were detected in the analyzed strains and resulted in amino acid changes, a stop codon, a frameshift, and a deletion.…”

Aptamers for Detection and Diagnostics (ADD): Can mobile systems process optical data from aptamer sensors to identify molecules indicating presence of SARS-CoV-2 virus? Should healthcare explore aptamers as drugs for prevention as well as its use as adjuvants with antibodies and vaccines?

“…With accumulating genome wide errors 495 in coding and non-coding sequences of emerging 496 variants, the impact of errors on SARS-CoV-2 proteins may influence the mortality and morbidity due to SARS-CoV-2 infection. Spike protein RBD is an element in this set and may remain as the prominent antigen of choice for mRNA vaccines, albeit in the short-term.…”