Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4, B.1.1.222 or B.1.1.519 and B.1.243 with mutations in the Spike protein and the Nucleocapsid.

Understanding the evolution of SARS-CoV-2 virus in various regions of the world during the Covid19 pandemic is essential to help mitigate the effects of this devastating disease. We describe the phylogenomic and population genetic patterns of the virus in Mexico during the pre-vaccination stage, including asymptomatic carriers. A RT-qPCR screening and phylogenomics reconstructions directed a sequence/structure analysis of the Spike glycoprotein, revealing mutation of concern E484K in genomes from central Mexico, in addition to the nationwide prevalence of the imported variant 20C/S:452R (B.1.427/9). Overall, the detected variants in Mexico show Spike protein mutations in the N-terminal domain (i.e., R190M), in the receptor-binding motif (i.e., T478K, E484K), within the S1-S2 subdomains (i.e., P681R/H, T732A), and at the basis of the protein, V1176F, raising concerns about the lack of phenotypic and clinical data available for the variants of interest (VOI) we postulate: 20B/478K.V1 (B.1.1.222 or B.1.1.519) and 20B/P.4 (B.1.1.28.4). Moreover, the population patterns of Single Nucleotide Variants (SNVs) from symptomatic and asymptomatic carriers obtained with a self-sampling scheme confirmed the presence of several fixed variants, and differences in allelic frequencies among localities. We identified the mutation N:S194L of the Nucleocapsid protein associated with symptomatic patients. Phylogenetically, this mutation is frequent in Mexican sub-clades, so we propose an additional VOI, 20A/N:194L.V2 (B.1.243). Our results highlight the dual and complementary role of Spike and Nucleocapsid proteins in adaptive evolution of SARS-CoV-2 to their hosts and provide a baseline for specific follow-up of mutations of concern during the vaccination stage. the population-level SNVs ‘allelic imbalance’, of the allele, polymorphic biallelic site. statistical of the allelic imbalance within hosts to the expression of Wilcoxon test collapsing all polymorphic sites within groups. one-way ANOVA to test the individual effects of allelic imbalance at each polymorphic site to the of visualization and statistical analysis Positions of mutations of concern in the Spike protein of SARS-CoV-2. We extracted the Electron Microscopy structure (7A94, Benton et al. 2020) of the trimeric Spike (S) glycoprotein of SARS-CoV-2 bound to one Angiotensin-Converting Enzyme-2 (ACE2). We depicted different domains and subdomains of S in various colors and textures (cartoon, surfaces) using MacPyMOL v.1. 7 (Schrodinger LLC, https://pymol.org/). We rendered 3D representations with ray before proceeding to screen captures. We marked the important mutations S477N, T478K, E484K, D614G, P681H/R and T732A. scenario (ii), which has been implicated in regional outbreaks in India et al. 2021), the proposed new Mexican lineage of scenario (i) includes the two San Luis Potosi E484K-containing variants identified after RT-qPCR screening (lineages B.1 and B.1.319), and the Oaxaca E484Q variant appearing early on during the pandemia, which corresponds to lineage B.1. 243. The potential for evolving the dangerous E484K/Q mutation within this Mexican lineage is supported by the recent detection of the sub-lineage B.1. 243.1 in Arizona, USA, which includes mutation E484K (Skidmore et al. 2021). All together, these observations have led us to propose the lineage B.1. 243 in Mexico as a VOI, which we believe warrants further investigation and direct surveillance as it accumulates dangerous Nucleocapsid and Spike protein mutations during the vaccination stage.