Vaccines, Vol. 11, Pages 45: Immunological Studies to Understand Hybrid/Recombinant Variants of SARS-CoV-2

Hybrid variants are a growing cause of concern in the current scenario because they have the potential to again increase positive cases globally by gaining enhanced virulence and transmission rates on recombination between two variants of distinct lineages [14].The variants of SAR-CoV-2 are usually generated by point mutation; however, the hybrid variants are generated by recombination between the genetic content of two different variants or lineages. The cause of mutations is attributed to the erroneous proofreading activity of RNA polymerase. Studies prove that the mechanism to produce novel variants of SARS-CoV-2 by point mutation is of lower efficiency when compared with recombination. Nonetheless, the initial high prevalence of SARS-CoV-2 and COVID-19 cases globally aided the virus in producing successful variants through point mutations. Furthermore, the occurrence of several peaks of COVID-19 incidences indicates the characteristics of the virus-like high transmission rates and retention of survival benefits facilitated by the accumulation of missense mutations. The recombination is the advantageous mechanism for SARS-CoV-2 as it happens between two different lineages with enhanced features, such as higher virulence and transmission rates, leading to continuous circulation and evolution of the virus [24]. The recombinations are classified based on the site of the crossover. In the case of homologous recombination, the crossover happens at the same location in both parental strands whereas, in non-homologous recombination, the crossover takes place at different locations giving rise to anomalous structures. Recombination in RNA viruses is regarded as a result of the selection of genomic traits for the regulation of gene expression, as well as the natural selection of certain genotypes produced by this approach [25].Studies reveal that during the present pandemic situation, there are numerous variants of SARS-CoV-2 that are co-existing in the environment. In cases where two variants co-infect a host, they undergo recombination of the genetic material in the host cell, generating a novel hybrid subvariant, such as Deltacron (XD and XF) and XE. The Deltacron subvariants, as the name suggests, originate from Delta and Omicron lineages [21]. It was first reported in France [26]. The hybrid subvariants, Deltacron and XE, had rapidly transmitted to all six continents. The nomenclature of hybrid variants contains “X” to signify the recombination between two different lineages of the virus [21]. The XD, XE, and XF are the hybrid subvariants generated from the Omicron variant by recombination. XD and XF are hybrids created from lineages of Delta and Omicron strains. According to the formal nomenclature, Deltacron is denoted as BA.1xAY.4. Due to its high potential for future outbreaks, Deltacron is categorized in the list of Variants being Monitored (VBMs) [21]. XD was created by recombination between the Delta and BA.1 variant of Omicron, whereas recombination of BA.1 and UK Delta variants created the XF variant [14,24]. On the other hand, the XE subvariant was created by recombination between BA.1 and BA.2 variants of Omicron [27]. The unique mutation found in the XD hybrid is at the site NSP2 E172D. Studies report that the XD subvariants infect all age groups and genders. The spike proteins, as well as the structural proteins of XE, are obtained from the BA.2 variant of Omicron where the 5′ region of the genome is from BA.1. Several studies have reported that the hybrids with either the spike or structural protein from a single parental lineage exhibit similarity to its corresponding parent. Mutations at the site NSP3 C3241T, V1069I, and NSP12 C14599T are the three important characteristic mutations identified in XE but absent in BA.1 and BA.2 [26]. The subvariant XE contains the mutations corresponding to BA.1 for the non-structural protein (NSP) region 1–6, whereas the remaining regions of the genome contain the mutations corresponding to BA.2. Furthermore, there are also three exclusive mutations (C3241T at the NSP3 region, C14599T at the NSP12 region, and V1069I at the NSP3 region) in XE that is absent in the BA.1 and BA.2 genome. The mutation at V1069I leads to the cleavage of viral proteins [28]. It possesses 10-fold greater transmission rates than the parent Omicron variant [27]. The XE subvariant gained high global prevalence, especially in the UK, Japan, China, and Canada. Consequently, this subvariant is being tracked and monitored by the WHO and included in the list of VOCs [21,27]. Studies have also reported the BNT162b2 vaccines are ineffective in eliciting an immune response in patients infected by XE subvariant [21]. Further, the WHO emphasized the systematic tracking of XE predicting its high transmissibility compared to any other strain or variant of SARS-CoV-2 [26]. There are several other variants, such as XQ, XG, XJ, and XK discovered in European countries, including the UK, Denmark, Finland, and Belgium, respectively [21]. A recent study has reported that the Omicron variant has also emerged due to recombination between the parent strain of SARS-CoV-2 with the B.35 lineage [26].Recombination is typically used to create hybrid variants; however, certain genome alterations have also been discovered to be associated with improved traits of the variant, including resistance to therapy, evasion of immunity provided by infection or vaccination, increased pathogenicity, etc. [9]. The emergence of novel hybrids is attributed to the overall low vaccination rate globally. This allows the virus to survive and circulate in individuals that belong to unvaccinated children and adult populations, immunosuppressed patients, or adult populations over 75 years of age. The easing of COVID-19 countermeasures and curbs also provides an environment to circulate and develop recombinants with other co-existing variants [27]. Recombination can generate highly virulent variants that result in enhanced fitness of the variant for survival in the environment. A significant raise in vaccination, especially for the susceptible population, is essentially required to combat the infections by the hybrid variants [21]. When compared with the other variants of SARS-CoV-2, the hybrid variants of the virus exhibit high transmission rates and global circulation, as is evident from their prevalence on the five continents of the world [24].

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