Analyses of Omicron genomes from India reveal BA.2 as a more transmissible variant

  • Ashwin Atkulwar Department of Zoology, Amolakchand Mahavidyalaya, Godhani Road, Yavatmal-445001, India
  • Aakif Rehman Pace Junior Science College, Dadar, Mumbai, 400028, India
  • Yashal Imaan Mohawk College, 135 Fennell Avenue West Hamilton, L9C OE5, ON Canada
  • Mumtaz Baig Department of Zoology, Laboratory of Molecular and Conservation Genetics, Govt. Vidarbha Institute of Science and Humanities, VMV Road, Amravati 444604, India
Keywords: Omicron, Phylogenomics, SARS-CoV-2, India, Phylodynamics, Reduced Median Network


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.



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How to Cite
Atkulwar, A.; Rehman, A.; Imaan, Y.; Baig, M. Analyses of Omicron Genomes from India Reveal BA.2 As a More Transmissible Variant. European Journal of Biological Research 2023, 13, 10-17.
Research Articles