article · Journal of Medical Virology
The emergence of the SARS-CoV-2 Omicron variant introduced an extensive degree of genetic mutation relative to earlier lineages. Comparative genomic and phylogenetic analysis evaluated whole viral sequences against other known variants to resolve these evolutionary connections. The choice of nucleotide substitution model altered the evolutionary placement: models accounting for transitions and transversions, such as Kimura 80, established that Omicron forms an independent, distant monophyletic clade. In contrast, simpler models positioned Omicron close to the Alpha variant. Across all evaluated genomes, Omicron displayed the highest structural variation, with between 43 and 63 genomic gaps. Based on sequence identity percentages, Alpha is the closest relative, followed by Gamma, Delta, Beta, and Mu. This link suggests that Omicron may have been circulating for longer than previously suspected.
Determining how rapidly mutating viruses evolve is vital for tracking pandemic lineages. By highlighting differences in phylogenetic models and revealing that Omicron may have circulated unrecognised for longer than expected, this work clarifies the genetic divergence of major variants. It underscores the critical requirement for continuous, comprehensive genomic surveillance to detect structural mutations and trace lineage evolution as new strains emerge.
The abstract does not indicate an application pathway, as it reports early-stage fundamental genomic and phylogenetic research. The findings could potentially assist public health bodies and diagnostic test developers in refining genomic surveillance strategies and molecular primers to account for significant sequence gaps, but no specific commercial application or readiness level is described.
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Following the discovery of the SARS-CoV-2 Omicron variant (B.1.1.529), the global COVID-19 outbreak has resurfaced after appearing to be relentlessly spreading over the past 2 years. This new variant showed marked degree of mutation, compared with the previous SARS-CoV-2 variants. This study investigates the evolutionary links between Omicron variant and recently emerged SARS-CoV-2 variants. The entire genome sequences of SARS-CoV-2 variants were obtained, aligned using Clustal Omega, pairwise comparison was computed, differences, identity percent, gaps, and mutations were noted, and the identity matrix was generated. The phylogenetics of Omicron variants were determined using a variety of evolutionary substitution models. The ultrametric and metric clustering methods, such as UPGMA and neighbor-joining (NJ), using nucleotide substitution models that allowed the inclusion of nucleotide transitions and transversions as Kimura 80 models, revealed that the Omicron variant forms a new monophyletic clade that is distant from other SARS-CoV-2 variants. In contrast, the NJ method using a basic nucleotide substitution model such as Jukes-Cantor revealed a close relationship between the Omicron variant and the recently evolved Alpha variant. Based on the percentage of sequence identity, the closest variants were in the following order: Omicron, Alpha, Gamma, Delta, Beta, Mu, and then the SARS-CoV-2 USA isolate. A genome alignment with other variants indicated the greatest number of gaps in the Omicron variant's genome ranging from 43 to 63 gaps. It is possible, given their close relationship to the Alpha variety, that Omicron has been around for much longer than predicted, even though they created a separate monophyletic group. Sequencing initiatives in a systematic and comprehensive manner is highly recommended to study the evolution and mutations of the virus.
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DOI: 10.1002/jmv.27515
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