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

Research Paper | September 12, 2022

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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

Abbas Q, Kusakin A. 2022. Follow-up investigation and detailed mutational characterization of the SARS-CoV-2 Omicron variant lineages (BA.1, BA.2, BA.3 and BA.1.1). bioRxiv: 2022.2002.2025.481941. http://dx.doi.org/10.1101/2022.02.25.481941.

Alouane T, Laamarti M. 2020. Genomic Diversity and Hotspot Mutations in 30,983 SARS-CoV-2 Genomes: Moving Toward a Universal Vaccine for the “Confined Virus”? Pathogens 9(10). http://dx.doi.org/10.3390/pathogens9100829.

Berrio A, Gartner V. 2020. Positive selection within the genomes of SARS-CoV-2 and other Coronaviruses independent of impact on protein function. Peer J 8, e10234. http://dx.doi.org/10.7717/peerj.10234.

Callaway E, Ledford H. 2021. How bad is Omicron? What scientists know so far. Nature 600(7888), 197-199. http://dx.doi.org/10.1038/d41586-021-03614-z.

Campbell F, Archer B. 2021. Increased transmissibility and global spread of SARS-CoV-2 variants of concern as at June 2021. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 26(24), 2100509. http://dx.doi.org/10.2807/15607917.ES.2021.26.24.2100509.

Candido KL, Eich CR. 2022. Spike protein of SARS-CoV-2 variants: a brief review and practical implications. Braz J Microbiol. http://dx.doi.org/10.1007/s42770-022-00743-z.

Chaguza C, Coppi A. 2022. Rapid emergence of SARS-CoV-2 Omicron variant is associated with an infection advantage over Delta in vaccinated persons. Med (New York, N.Y.): http://dx.doi.org/10.1016/j.medj.2022.1003.1010.

Chau NVV, Hong NTT. 2021. Rapid whole-genome sequencing to inform COVID-19 outbreak response in Vietnam. The Journal of infection 82(6), 276-316. http://dx.doi.org/10.1016/j.jinf.2021.03.017.

Chaw SM, Tai JH. 2020. The origin and underlying driving forces of the SARS-CoV-2 outbreak. J Biomed Sci 27(1), 73. http://dx.doi.org/10.1186/s12929-020-00665-8.

Colson P, Delerce J. 2022. First cases of infection with the 21L/BA.2 Omicron variant in Marseille, France. J Med Virol 94(7), 3421-3430. http://dx.doi.org/10.1002/jmv.27695.

Di Giacomo S, Mercatelli D. 2021. Preliminary report on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike mutation T478K. J Med Virol 93(9), 5638-5643. http://dx.doi.org/10.1002/jmv.27062.

Durmaz B, Abdulmajed O. 2020. Mutations Observed in the SARS-CoV-2 Spike Glycoprotein and Their Effects in the Interaction of Virus with ACE-2 Receptor. Medeniyet Medical Journal 35(3), 253-260. http://dx.doi.org/10.5222/MMJ.2020.98048.

Excoffier L, Lischer HE.  2010. Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Mol Ecol Resour 10(3), 564-567. http://dx.doi.org/10.1111/j.1755-0998.2010.02847.x.

Fall A, Eldesouki RE. 2022. A Quick Displacement of the SARS-CoV-2 variant Delta with Omicron: Unprecedented Spike in COVID-19 Cases Associated with Fewer Admissions and Comparable Upper Respiratory Viral Loads. medRxiv : the preprint server for health sciences: 2022.2001.2026.22269927. http://dx.doi.org/10.1101/2022.01.26.22269927.

Fan LQ, Hu XY. 2021. Biological Significance of the Genomic Variation and Structural Dynamics of SARS-CoV-2 B.1.617. Frontiers in microbiology 12, 750725-750725. http://dx.doi.org/10.3389/fmicb.2021.750725.

Goher SS, Ali F. 2021. The Delta Variant Mutations in the Receptor Binding Domain of SARS-CoV-2 Show Enhanced Electrostatic Interactions with the ACE2. Med Drug Discov: 100114. http://dx.doi.org/10.1016/j.medidd.2021.100114.

He X, Hong W. 2021. SARS-CoV-2 Omicron variant: Characteristics and prevention. MedComm 2(4), 838-845. http://dx.doi.org/10.1002/mco2.110.

Hoang VT, Pham TD. 2022. Seroprevalence of SARS-CoV-2 among high-density communities and hyper-endemicity of COVID-19 in Vietnam. Trop Med Int Health. http://dx.doi.org/10.1111/tmi.13744.

Kim Y, Gaudreault NN. 2022. Effects of Spike Mutations in SARS-CoV-2 Variants of Concern on Human or Animal ACE2-Mediated Virus Entry and Neutralization 10(3), e0178921. http://dx.doi.org/10.1128/spectrum.01789-21.

Kumar S, Thambiraja TS. 2022. Omicron and Delta variant of SARS-CoV-2: A comparative computational study of spike protein. Journal of Medical Virology 94(4), 1641-1649. http://dx.doi.org/10.1002/jmv.27526.

Kumar V, Singh J. 2021. Possible Link between Higher Transmissibility of Alpha, Kappa and Delta Variants of SARS-CoV-2 and Increased Structural Stability of Its Spike Protein and hACE2 Affinity. International journal of molecular sciences 22(17), 9131. http://dx.doi.org/10.3390/ijms22179131.

Kupferschmidt K, Vogel G. 2021. How bad is Omicron? Some clues are emerging. Science 374(6573), 1304-1305. http://dx.doi.org/10.1126/science.acx9782.

Lan J, Ge J. 2020. Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor. Nature 581(7807), 215-220. http://dx.doi.org/10.1038/s41586-020-2180-5.

Leigh JW, Bryant D. 2015. popart: full-feature software for haplotype network construction. Methods in Ecology and Evolution 6(9), 1110-1116. https://doi.org/10.1111/2041-210X.12410.

Lubinski B, Frazier LE. 2021. Spike protein cleavage-activation mediated by the SARS-CoV-2 P681R mutation: a case-study from its first appearance in variant of interest (VOI) A.23.1 identified in Uganda. bioRxiv : the preprint server for biology: 2021.2006.2030.450632. http://dx.doi.org/10.1101/2021.06.30.450632.

Mohapatra RK, Kandi V. 2022. The recently emerged BA.4 and BA.5 lineages of Omicron and their global health concerns amid the ongoing wave of COVID-19 pandemic – Correspondence. Int J Surg 103, 106698. http://dx.doi.org/10.1016/j.ijsu.2022.106698.

Motozono C, Toyoda M. 2021. SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. Cell Host Microbe 29(7), 1124-1136 e1111. http://dx.doi.org/10.1016/j.chom.2021.06.006.

Nguyen TP, Wong ZS. 2021. Rapid impact assessments of COVID-19 control measures against the Delta variant and short-term projections of new confirmed cases in Vietnam. J Glob Health 11, 03118. http://dx.doi.org/10.7189/jogh.11.03118.

Ni D, Lau K.  2021. Structural analysis of the Spike of the Omicron SARS-COV-2 variant by cryo-EM and implications for immune evasion. bioRxiv: 2021.2012.2027.474250. http://dx.doi.org/10.1101/2021.12.27.474250.

O’Toole A,. Pybus OG. 2022. Pango lineage designation and assignment using SARS-CoV-2 spike gene nucleotide sequences. BMC Genomics 23(1), 121. http://dx.doi.org/10.1186/s12864-022-08358-2.

Ou J, Lan W. 2022. Tracking SARS-CoV-2 Omicron diverse spike gene mutations identifies multiple inter-variant recombination events. Signal Transduct Target Ther 7(1), 138. http://dx.doi.org/10.1038/s41392-022-00992-2.

Ovsyannikova IG, Haralambieva IH. 2020. The role of host genetics in the immune response to SARS-CoV-2 and COVID-19 susceptibility and severity. Immunol Rev 296(1), 205-219. http://dx.doi.org/10.1111/imr.12897.

Papanikolaou V, Chrysovergis A. 2022. From delta to Omicron: S1-RBD/S2 mutation/deletion equilibrium in SARS-CoV-2 defined variants. Gene 814, 146134-146134. http://dx.doi.org/10.1016/j.gene.2021.146134.

Phuong HVM, Tung TS. 2021. Novel Mutation of SARS-CoV-2, Vietnam, July 2020. Emerging infectious diseases 27(5), 1519-1521. http://dx.doi.org/10.3201/eid2705.210013.

Ren SY, Wang WB. 2022. Omicron variant (B.1.1.529) of SARS-CoV-2: Mutation, infectivity, transmission, and vaccine resistance. World journal of clinical cases 10(1), 1-11. http://dx.doi.org/10.12998/wjcc.v10.i1.1.

Singh D, Yi SV. 2021. On the origin and evolution of SARS-CoV-2. Exp Mol Med 53(4), 537-547. http://dx.doi.org/10.1038/s12276-021-00604-z.

Tegally H, Moir M. 2022. Continued Emergence and Evolution of Omicron in South Africa: New BA.4 and BA.5 lineages. medRxiv: 2022.2005.2001.22274406. http://dx.doi.org/10.1101/2022.05.01.22274406.

Thai PQ, Rabaa MA. 2021. The First 100 Days of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Control in Vietnam. Clin Infect Dis 72(9), e334-e342. http://dx.doi.org/10.1093/cid/ciaa1130.

Wei C, Shan KJ. 2021. Evidence for a mouse origin of the SARS-CoV-2 Omicron variant. J Genet Genomics 48(12), 1111-1121. http://dx.doi.org/10.1016/j.jgg.2021.12.003