The nuts and bolts of recombination in the generation of SARS-CoV-2 variants; from XA to XBB

Abstract

Abstract Since the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), new variants with enhanced transmissibility and pathogenicity have surfaced. The World Health Organization has designated five such variants—Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), Delta (B.1.617.2), and Omicron (B.1.1.529)—as variants of concern. Each variant exhibits distinct characteristics, with many displaying a combination of point mutations and insertions/deletions (indels). These genetic alterations, including mutations, recombinations, and rearrangements, contribute to the emergence of new strains that may exhibit modified phenotypes. However, identifying recombinant forms can be challenging due to their resemblance to other lineages. It is critical to monitor the evolution of new recombinant variants, particularly in light of the potential for vaccine-resistant strains and their accelerated propagation. Recombination has played a pivotal role in the development of certain SARS-CoV-2 variants, such as XA, XD, XF, XE, and XBB, among others. This report delves into the significance of recombination in the evolution of SARS-CoV-2 variants, especially Omicron sublineages, underscoring the necessity for continuous surveillance of the SARS-CoV-2 genome to identify newly emerged recombinant variants.