As of July 2022, the SARS-CoV-2 Omicron BA.5 variant has become an epidemic in Japan. The recently emerged Omicron BA.2.75 has further concerned the world. Studies have developed a mathematical model to predict and compare the infectivities of different SARS-CoV-2 variants such as Wuhan, Alpha, Beta, Gamma, Delta, and Omicron BA.1 and BA.2 variants.
In the present study, researchers predicted the comparative risk of infection by recently emerging variants such as the SARS-CoV-2 Omicron BA.2.75 variant compared to that against preexisting variants.
The team assessed the evolutionary distance of viral spike (S) genes between the Wuhan variant and Omicron BA.4, BA.5, or BA.2.75. The S gene sequences were collected by searching the EpiCoV database of the Global Initiative on Sharing All Influenza Data (GISAID) for the one having a complete S gene sequence. The docking affinity associated with the receptor-binding domain (RBD) of each S protein of these variants with angiotensin-converting enzyme-2 (ACE-2) was assessed via cluster analysis and docking simulation.
The amino acid sequences related to the S proteins were collected from the CoVariants website that classified the variants as per Nextstrain clades, wherein the Omicron BA.4 variant was classified as 22A, Omicron BA.5 as 22B, and Omicron BA.2.75 as 22D. Since BA.4 and BA.5 had similar S proteins, the S gene and amino acid sequences were grouped together for the study.
The study results showed that the SARS-CoV-2 variants that had a longer evolutionary distance from the SARS-CoV-2 Wuhan variant were more likely to lead to an epidemic. The Omicron BA.2.75 variant was found to have the highest docking affinity of the viral S protein with the ACE2 protein. Compared to the Omicron BA.2 variant, while BA.4 and BA.5 had longer S gene evolutionary distances, the docking affinity observed was lower.
Furthermore, compared to BA.2, BA.2.75 displayed longer evolutionary distances along with higher docking affinity. This indicated that BA.2.75 has a higher ability to enter host cells, while the currently available SARS-CoV-2 vaccines are less effective against this variant.
The study findings showed that the infectivity of the SARS-CoV-2 Omicron BA.2.75 variant was significantly high due to the long S gene evolutionary distance and the docking simulation for the viral S protein with ACE2. The researchers believe that Omicron BA.2.75 poses a higher risk of causing a global health crisis.
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