The genomic signature deciphered during the ongoing pandemic period is valuable to understand the virus evolutionary patterns and spread across the globe. In the current study, the scientists studied 5,000 suspected COVID-19 cases to investigate the virus introduction events and its spread in central India with data collected from 10 different districts. To identify confirmed COVID-19 cases, they performed a reverse transcriptase quantitative polymerase chain reaction, which led to identifying 136 SARS-CoV-2 positive cases.
Of 136 cases, 26 were selected for the whole genome sequencing analysis based on the patient’s travel history, age, and contact history. By comparing the whole genome sequences of experimental SARS-CoV-2 strains with the globally circulating ones, the scientists identified 38 amino acid substitution mutations compared to the Wuhan strain. Of these variations, the majority (n=24) were observed in ORF1 ab protein, followed by spike protein (n=5), nucleocapsid (n=4), ORF 3a (n=2), and envelope protein, membrane protein, and ORF 7a (n=1 for each protein).
Through thorough analysis, the amino acid substitution was observed in the spike protein. They identified that 17 viral strains from 4 districts had D614G mutation, making the virus more infectious and rapidly expanding the COVID-19 pandemic. Notably, the scientists identified nonsynonymous substitutions in experimental viral strains. These substitution mutations were A97V in RNA-dependent RNA polymerase, P13L in nucleocapsid protein, and T2016K in non-structural protein 3.
The current study reveals that the exponential rise of SARS-CoV-2 positive cases in central India is associated with multiple viral introduction events with diverse geographical linkage, as well as viral expansion within the regions. The phylogenetic data reveal links of viral introduction from Italy, the UK, France, and Southeast and Central Asia. The evolution of the virus in the studied regions is evidenced by the cluster-wise segregation of SARS-CoV-2.
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