Analyses of Omicron genomes from India reveal BA.2 as a more transmissible variant
In the current study, the phylodynamics and phylogenomics of Omicron variants are being examined to provide insight into their evolution. We analyzed 564 genomes deposited to the GISAID database from various states of India. A Pangolin COVID-19 Lineage Assigner tool was used to assign lineages to all retrieved genomes. Maximum likelihood (MLE) tree construction and Reduced Median Joining (RM) network were performed. For phylodynamic analysis, the basic reproduction number (R0) was estimated. A Maximum likelihood tree (MLE) confirms the separation of genomes into two distinct clades, BA. 1. and BA. 2. A very high reproduction number (R0) of 2.445 was estimated for the lineage BA.2. Telangana has the highest R0 value in the country, indicating a high prevalence of the BA.2 lineage. The construction of the Reduced Median (RM) network reveals an evolution of some autochthonous haplogroups and haplotypes, which further supports the rapid evolution of Omicron as opposed to its previous variants. Phylogenomic analyses using maximum likelihood (ML) and RM also reveal the likelihood of the emergence of sub-sublineages and novel haplogroups respectively. Due to the recombinant nature and high transmissibility of the Omicron virus, we suggest continuous and more widespread genome sequencing in all states of India to track the evolution of SARS-CoV-2.
2. World Health Organization Classification of Omicron (B.1.1.529): SARS-CoV-2 Variant of Concern; https://www.who.int/news-room/statements/26-11-2021-classification-of-omicron-(b.1.1.529)-sars-cov-2-variant-of-concern; 2021.
3. Spreeuwenberg P, Kroneman M, Paget J. Reassessing the Global Mortality Burden of the 1918 Influenza Pandemic. Am J Epidemiol. 2018; 187(12): 2561-2567.
4. Biondi-Zoccai G, Landoni G, Carnevale R, Cavarretta E, Sciarretta S, Frati G. SARS-CoV-2 and COVID-19: facing the pandemic together as citizens and cardiovascular practitioners. Minerva Cardioangiol. 2020; 68(2): 61-64.
5. Woo P C, Huang Y, Lau S K, Yuen KY. Corona virus genomics and bioinformatics analysis. Viruses. 2010; 2(8): 1804-1820.
6. Zhang YZ, Holmes EC. A genomic perspective on the origin and emergence of SARS-CoV-2. Cell. 2020; 181(2): 223-227.
7. Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2010; 4: 772-780.
8. Rozas J, Ferrer-Mata A, Sánchez-DelBarrio C, Guirao-Rico S, Librado P, Ramos-Onsins SE, et al. DnaSP 6: DNA sequence polymorphism analysis of large datasets. Mol Biol Evol. 2017; 34: 3299-3302.
9. Toole AO, Scher E, Underwood A, Jackson B, Hill V, McCrone JT, et al. BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis. PLoS Comput Biol. 2019; 15(4): e1006650.
10. Bouckaert R, Vaughan TG, Barido-Sottani J, Duchêne S, Fourment M, Gavryushkina A, et al. BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis. PLoS Comput Biol. 2019; 15(4): e1006650.
11. Rambaut A, Drummond AJ, Xie D, Baele G, Suchard MA. Posterior summarisation in Bayesian phylogenetics using Tracer 1.7. Syst Biol. 2018: syy032.
12. Bandelt HJ, Forster P, Roehl A. Median-joining networks for inferring intraspecific phylogenies. Mol Biol Evol. 1999; 16: 37-48.
13. Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O. New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0. Syst Biol. 2010; 59(3): 307-321.
14. Lyngse FP, Kirkeby CT, Denwood M, Christiansen LE, Molbak K, Moller CH, et al. Transmission of SARS-CoV-2 Omicron VOC subvariants BA.1 and BA.2: Evidence from Danish Households. medRxiv. 2022: 2022.01.28.22270044.
15. Liu IS, Guo Y, Guo Y, Liu L, Chan JF, Huang Y, et al. Antibody evasion properties of SARS-CoV-2 Omicron sublineages. Nature. 2022; 604(7906): 553-556.
16. Loconsole D, Bisceglia L, Centrone F, Sallustio A, Accogli M, Dalfino L, et al. Autochthonous Outbreak of SARS-CoV-2 Omicron Variant in Booster-Vaccinated (3 Doses) Healthcare Workers in Southern Italy: Just the Tip of the Iceberg? Vaccines. 2022; 10(2): 283.
17. Kumar S, Thambiraja TS, Karuppanan K, Subramaniam G. Omicron and Delta variant of SARS-CoV-2: A comparative computational study of spike protein. J Med Virol. 2022; 94(4): 1641-1649.
18. Yamasoba D, Kimura I, Nasser H, Morioka Y, Nao N, Ito J, et al. Genotype to Phenotype Japan (G2P-Japan) Consortium, Sawa H, Saito A, Irie T, Tanaka S, Matsuno K, Fukuhara T, Ikeda T, Sato K. Virological characteristics of the SARS-CoV-2 Omicron BA.2 spike. Cell. 2022; 185(12): 2103-2115.e19.
19. Syed AM, Ciling A, Taha TY, Chen IP, Khalid MM, Sreekumar B, et al. Omicron mutations enhance infectivity and reduce antibody neutralization of SARS-CoV-2 virus-like particles. Proc Natl Acad Sci USA. 2022; 119(31): e2200592119.
20. Yu J, Collier AY, Rowe M, Mardas F, Ventura JD, Wan H, et al. Neutralization of the SARS-CoV-2 Omicron BA.1 and BA.2 Variants. N Engl J Med. 2022; 386(16): 1579-1580.
21. Makarenkov V, Mazoure B, Rabusseau G, Legendre P. Horizontal gene transfer and recombination analysis of SARS-CoV-2 genes helps discover its close relatives and shed light on its origin. BMC Ecol Evol. 2021; 21(1): 5.
22. Frantz Laurent AF, Bradley DG, Larson G, Orlando L. Animal domestication in the era of ancient genomics. Nat Rev Genet. 2020; 21(8): 449-460.
23. Zerjal T, Xue Y, Bertorelle G, Wells RS, Bao W, Zhu S, et al. The genetic legacy of the Mongols. Am J Hum Genet. 2003; 72(3): 717-721.
24. Forster P, Forster L, Renfrew C, Forster M. Phylogenetic network analysis of SARS-CoV-2 genomes. Proc Natl Acad Sci. USA. 2020; 117: 9241-9243.
25. Farah S, Atkulwar A, Praharaj M R, Khan R, Gandham R, Baig M. Phylogenomics and phylodynamics of SARS-CoV-2 genomes retrieved from India. Future Virol. 2020; 15: 747-753.
This work is licensed under a Creative Commons Attribution 4.0 International License.