key: cord-0897747-6ys3uogb authors: Banerjee, Arinjay; Mossman, Karen; Grandvaux, Nathalie title: Molecular determinants of SARS-CoV-2 variants date: 2021-07-27 journal: Trends Microbiol DOI: 10.1016/j.tim.2021.07.002 sha: ee7d8241ec69d8a1c426f48ab0b3fd0077fe087b doc_id: 897747 cord_uid: 6ys3uogb SARS-CoV-2 evolution is expected given the nature of virus replication. Selection and establishment of variants in the human population depend on viral fitness, and molecular and immunological selection pressures. Here we discuss how mechanisms of replication and recombination may contribute to the emergence of current and future variants of SARS-CoV-2. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in December 2019 to cause a worldwide pandemic. Rapid sharing of information by researchers enabled the development of vaccines in record time. However, as SARS-CoV-2 continues to spread, it is evolving. This evolution should come as no surprise, since RNA viruses are known to mutate, given their error-prone replication process. As SARS-CoV-2 circulates, mounting selection pressures, such as natural infection-and vaccine-mediated immunity will influence the selection of viral variants. In this forum article, we discuss how two processesreplication and recombination -contribute to the generation of current and future SARS-CoV-2 variants. Coronaviruses (CoV) such as SARS-CoV-2 are RNA viruses that use an RNA-dependent RNA polymerase (RdRp) to generate genomic copies. The RdRp is intrinsically error-prone, thus promoting virus evolution through replication-associated changes ( Figure 1 ). The mutation rate is kept low by the proofreading activity of a virus-encoded 3' exonuclease, such as nsp14 for SARS-CoV-2. Despite proofreading activity, SARS-CoV-2 accumulates genetic changes over time as evidenced by emerging variants. Understanding the molecular factors that lead to the generation of SARS-CoV-2 variants, along with extrinsic factors that lead to the selection and establishment of these variants is critical to control the ongoing pandemic. The COVID-19 pandemic has also reignited interest in studying wildlife reservoirs. Selection analyses suggest viruses in wildlife reservoirs. It remains unknown if infected bats produce a more diverse quasivariant population of sarbecoviruses compared to other permissive mammalian species. The biochemical make-up of different cell types from different hosts may impact CoV replication and rate of error. For example, the catalytic reaction of viral polymerases requires certain substrates, the quality and quantity of which may differ between cell types or cells from alternate hosts [2] . Host factors, including enzymes, can also impact the evolution of viral variants. Inherent differences in the coding sequence of host enzymes, such as TMPRSS2, become more prominent between distantly related mammalian species. When a zoonotic virus such as SARS-CoV-2 spills over to a new mammalian species, the virus interacts with a different ortholog of TMPRSS2. Although the spike protein may be sufficiently cleaved in this new host to facilitate cellular entry, over time the virus population is likely to evolve and select for variants with higher cleavage efficiency with the TMPRSS2 ortholog in the new animal species [3] . Indeed, furin cleavage sites in SARS-CoV-2-related CoVs (SARS2r-CoVs) discovered in bats differ in their sequence from human isolates of SARS-CoV-2 [4] , suggesting possible species-specific adaptation in host protease utilization by the virus. differences since they can only be captured by ultra-high-resolution single virion protein sequencing, the technology for which is in its infancy. The SARS-CoV-2 genomic mutation rate in humans is estimated at 0.8 -2.38 x 10 -3 nucleotide substitution per site per year largely based on analysis of sequencing data archived in public repositories [5] . Emerging studies are attempting to confirm this mutation rate using experimental investigations [6] . In comparison, mutations rates for influenza A virus and Middle have an average mutation rate of 3-6 x 10 -4 nucleotide substitutions per site per year [8] . Emerging experimental data suggest that SARS-CoV-2 is capable of mutating and accumulating changes when facing a new cell type, albeit in the absence of immune surveillance in a single cell-type infection model [6] . A clinical study also reported the rapid evolution of SARS-CoV-2 variants in the presence of antibodies from convalescent plasma therapy [11] . While random errors during replication may induce genetic mutations in SARS-CoV-2, multiple extrinsic factors such as individual and population-level immunity play a vital role in the selection of these variants. More research is warranted to fully understand the cellular and molecular drivers of genomic mutation and selection in SARS-CoV-2. As SARS-CoV-2 accumulates new genetic changes, we shall need to reassess the mutation rate to better understand the contribution of replication-associated random mutations and its impact on SARS-CoV-2 transmission and emergence of new variants. Recently, eight potential recombination events among SARS-CoV-2 genomes have been identified. Four of eight were noted within structural genes, while two of eight were noted within the spike gene. It is important to note that these recombination events were not found across all subsampled datasets [15] , and the frequency of SARS-CoV-2 recombination and factors that influence the rate of recombination still remain elusive. It is vital to monitor SARS-CoV-2 recombination as part of ongoing surveillance and diagnostic efforts, especially among circulating variants and also with other beta-CoVs. These studies will be crucial to assess the evolutionary trajectory of SARS-CoV-2 within the ongoing pandemic, along with predicting the long-term efficacy of vaccine-and natural infection-mediated immunity. Tissue and cell tropism, and receptor distribution are important determinants of co-infection by two closely related CoVs, and hence, the probability of recombination. However, little is known about other viral and host factors that are required to permit or facilitate CoV recombination. Much work remains to be done to fully characterize the replication machinery of SARS-CoV-2 and the fidelity of its RdRp in different species. Understanding the replication process will be critical to determine if SARS-CoV-2 is more prone to replication-induced errors and/or recombination, relative to other high pathogenic CoVs, such as SARS-CoV and MERS-CoV. Natural selection in the evolution of SARS-CoV-2 in bats created a generalist virus and highly capable human pathogen Viral polymerases 2020) SARS Coronavirus Redux Evidence for SARS-CoV-2 related coronaviruses circulating in bats and pangolins in Southeast Asia Mutation Rates and Selection on Synonymous Mutations in SARS-CoV-2 Mutation rate of SARS-CoV-2 and emergence of mutators during experimental evolution Moderate mutation rate in the SARS coronavirus genome and its implications Current understanding of middle east respiratory syndrome coronavirus infection in human and animal models Analysis of the evolution and variation of the human influenza A virus nucleoprotein gene from 1933 to 1990 Research on SARS-CoV-2 in NG's lab is supported by funds from Fonds de Recherche du This work was also supported by CIHR COVID-19 priority funding awarded to principal investigator KM and co-investigator AB. VIDO receives operational funding for its CL3 facility (InterVac) from the Canada Foundation for Innovation through the Major Science Initiatives.