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Variations in spike gene of SARS-CoV-2 isolated in Vietnam

Quan Ke Thai, Phuoc Huynh, Duc Minh Le

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Int. J. Biosci.21(5), 83-92, November 2022

DOI: http://dx.doi.org/10.12692/ijb/21.5.83-92

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Abstract

The S gene encodes the spike protein, which plays an important role in the life cycle of SARS-CoV-2. Many mutations in the S gene demonstrate the increase in the transmission rate, helping viral can escape the immune system and monoclonal antibodies. This study aims to track the genetic diversity of the S gene of SARS-CoV-2 isolated in Vietnam during the four waves of the pandemic. A total of 5478 S gene sequences were extracted and classified into 1093 haplotypes, giving the mean number of pairwise differences at 27.491490 ± 12.039763 and the haplotype diversity index at 0.9089 ± 0.0031. In addition, we recorded the nucleotide diversity index at 0.007176 ± 0.003475 with 802 polymorphic sites. We found that indel mutations appear mainly in the NTD coding region, and amino acid substitutions appear most in the RBD coding region. In the RBD region, we also recorded mutations that increase the transmission rate for SARS-CoV-2 with a large proportion in Vietnam: G22578A (G339D), C22686T (S375F), G22813T (K417N), T22917G (L452R), C22995A (T478K) and A23063T (N501Y). In addition, the furin cleavage site also recorded three important mutations in enhancing transmissibility namely A23403G (D614G) and C23604A/G (P681H/R). The mean nucleotide difference between haplotypes in the cluster of Delta variants was 1.989772 ± 1.123948 nucleotides. The Omicron cluster has a tremendous nucleotide difference of 17.951297 ± 7.970441 nucleotides. The analysis results showed the whole picture of variations in the spike gene of SARS-CoV-2 in Vietnam, supporting the management of new variants imported into Vietnam.

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Variations in spike gene of SARS-CoV-2 isolated in Vietnam

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