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Genetic diversity of SARS-CoV-2 Omicron variants’ spike gene in Vietnam

Quan Ke Thai, Phuoc Huynh, Yen Le Thi, Huyen Nguyen Thi Thuong

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Int. J. Biosci.21(3), 166-176, September 2022

DOI: http://dx.doi.org/10.12692/ijb/21.3.166-176


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The recently emerging Omicron is of prime concern because this variant has been the cause of current large outbreaks. Omicron becomes more dangerous when numerous content mutations in the Spike (S) gene lead to more than 30 substitutions of amino acids in spike protein. Omicron variant had been identified as Variants Of Concern (VOC) when it had transmission rate overtake previous VOCs. In this report, we focus on analyzing the genetic diversity of the S gene of Omicron variants in Vietnam. Our results indicate the high level of haplotype diversity when confirmed 362 haplotypes and the haplotype diversity index at 0.9160 ± 0.0037. The analysis of nucleotide diversity display nucleotide diversity at 0.0053 ± 0.0026 and recorded 318 polymorphic sites with the average number of mutations of 40 ± 9. Almost missense mutations appeared in the RBD region, and deletion and insertion occurred in the NTD region. Besides, we note conserved mutation in the S gene of Omicron in Vietnam, namely C21618T G21987A T22200G G22578A C22674T T22679C C22686T A22688G G22775A A22786C G22813T T22882G G22992A C22995A A23013C A23040G A23055G A23063T T23075C A23403G C23525T T23599G C23604A C23854A G23948T A24424T T24469A, and C25000T. Furthermore, the genetic networks of the S gene provided more correlation between infection and mutation in this gene. Ultimately, we propose the close relation between BA.2 and BA.4, BA.5 through the network, in which necessary focus T22917G (L452R), T23018G (F486V), and other novel mutations will appear in the S gene. The network provided the whole picture of Omicron variants in Vietnam, supporting the tracing of the source of a new outbreak in the future.


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Genetic diversity of SARS-CoV-2 Omicron variants’ spike gene in Vietnam

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