In a recent study published in bioRxiv* Prepress server, researchers implemented a file in silico An analysis to estimate the relative risks of recently emerged coronavirus-2 (SARS-CoV-2) variants of severe acute respiratory syndrome.
The coronavirus pandemic 2019 (COVID-19) has caused unprecedented illness and death around the world. The continued emergence of new variants of SARS-CoV-2, with greater infectivity, virulence, transmissibility, and immuno-evasiveness, is challenging effectiveness COVID-19 vaccines and other therapeutic agents such as monoclonal antibodies.
During the early days of 2023, the BQ.1 variant, the XBB.1 variant, and the XBB.1.5 variant of Omicron were identified and estimated to enhance the risk of epidemics in the coming times. Continuous SARS-CoV-2 surveillance efforts and genomic research are essential to improve understanding of the viral characteristics of novel SARS-CoV-2 variants and guide the development of updated, broader, and more effective anti-SARS-CoV-2 therapies.
The authors of this study previously investigated the degree of infectivity for SARS-CoV-2 variants, Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), Delta (B.1.617.2), Omicron (B.1.1.529) Sub-variants, BA.1, Omicron BA.2 sub-variant and Omicron BA.2.75 in terms of ratio for each Wuhan strain is 1 SARS-CoV-2 and evolutionary distances variant genes (S) from Wuhan-Hu ancestors -1S
In this study, the authors extend their previous analysis by estimating the epidemiological risk of the recently emerged BQ.1 variant, the XBB.1 variant, and the XBB.1.5 variant of Omicron.
Molecular docking simulations of the S protein receptor-binding domain (RBD) of the interactions of BQ.1, XBB.1 and XBB.1.5 with the ACE2 (angiotensin-converting enzyme 2) receptor of the host were performed to evaluate the binding affinities of SARS-CoV-2. COV-2 variants and sub-variants, with ACE2.
Elevated gene sequences for the variants were retrieved from the NCBI database, and information about mutations of the S variant protein was obtained from https://covariants.org website.
In addition, the evolutionary distances of the spike genes of the SARS-CoV-2 Alpha variant, Beta variant, Gamma variant, Delta variant, Omicron BA.1 variant, Omicron BA.2 variant, Omicron BA.4/5 variant, and Omicron BA variant. 2.75 variant, Omicron BQ.1 variant, Omicron XBB.1 variant and Omicron XBB.1.5 variant) of the S genes of the Wuhan-Hu-1 strain, Omicron BA.1 and Omicron BA.4/5 variants, in absolute terms, to assess the evolutionary changes of SARS-CoV-2.
The Omicron XBB.1.5 sub-variant showed the greatest affinity for ACE2 binding, indicating the greatest infectivity, impaired effects of COVID-19 vaccines, and the greatest propensity to cause a future pandemic. The evolutionary distances of Omicron BQ.1 subvariant, Omicron XBB.1 subvariant, and Omicron XBB.1.5 subvariant showed that the BQ.1 variant had a short phylogenetic distance from Omicron BA.4/5, indicating that Omicron BA. 4/5 vaccines based on the sub-variant would be equivalently effective against the BQ.1 sub-variant.
Moreover, the long hauls of the XBB.1 variant and the XBB.1.5 sub-variant of the Wuhan-Hu-1 S gene indicated that current COVID-19 vaccines would be less effective against the sub-variants, underlining the need for updated vaccines.
ACE2-binding affinities for Spike Proteins (in terms of lineage per SARS-CoV-2 Wuhan-Hu-1 strain) of Wuhan-Hu-1 strain Alpha variant, Beta variant, Gamma variant, Delta variant, Omicron’s BA.1 subvariant, Omicron’s BA.2 subvariant, Omicron’s variant BA.4/5, Omicron BA.2.75 variant sub, Omicron BQ.1 variant, Omicron BQ.1 variant, Omicron XBB.1 variant, and XBB.1.5 variant were 1.0, 1.2, 1.2, 1.3, 2.1, 1.6, and 2.5 2.2, 2.9, 3.1, 1.9 and 3.0, respectively.
Evolutionary distances of spike genes (from the Wuhan-Hu-1 strain gene) × 10-3 for Alpha, Beta, Gamma, Delta, BA.1, Omicron BA.2, Omicron BA.4/5, Omicron BA.2.75, Omicron BQ.1, Omicron BQ.1, Omicron XBB.1 and XBB.1.5, in The absolute values were 2.1, 2.1, 3.5, 3.2, 11.5, 8.3, 9.2, 10.9, 10.0, 12.4 and 13.1, respectively.
Evolutionary distances of spike genes from BA.1 × 10-3 For the Omicron BA.2 variant, BA.4/5 variant, BA.2.75 variant, BQ.1 variant, XBB.1 variant and XBB.1.5 variant, in absolute terms, 5.6, 6.5, 8.3, 7.4, 9.8, and 10.4 were respectively respectively. Evolutionary distances of spike genes BQ.1 variant, XBB.1 variant and XBB.1.5 variant of Omicron from Omicron BA.4/5 subvariant x 10-3in absolute terms, were 2.9, 0.9, 4.4, and 5.1, respectively.
Overall, the results of the study showed that the XBB.1.5 variant of Omicron had the greatest association with human ACE2 and the greatest evolutionary distance than the height genes of Wuhan-Hu-1, Omicron BA.1 and Omicron BA.4/5. The results indicated that XBB.1.5 may be more infective than previously circulating variants, underlining the need for the greatest caution for XBB.1.5 infection.
bioRxiv publishes preliminary scientific reports that are not peer-reviewed and therefore should not be considered conclusive, directing clinical practice/health-related behaviour, or treated as hard information.