Understanding the evolution of the SARS-CoV-2 virus in various regions of the world during the Covid-19 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 real-time quantitative PCR screening and phylogenomic reconstructions directed at sequence/structure analysis of the spike glycoprotein revealed 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 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 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. 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.
【저자키워드】 SARS-CoV-2, variants, Mexico, Asymptomatic, nucleocapsid, population genomics, 【초록키워드】 Evolution, vaccination, pandemic, Mutation, adaptive, COVID-19 pandemic, Genome, Genetic, variant, spike glycoprotein, SARS-CoV-2 virus, virus, variants, Spike protein, nucleocapsid protein, Prevalence, Protein, Region, Symptomatic patients, Asymptomatic carriers, Evolution of SARS-CoV-2, understanding, clades, variants of interest, single nucleotide variants, E484K, genomes, Follow-up, receptor-binding motif, disease, quantitative PCR, N-terminal domain, Single nucleotide variant, nucleotide, Frequency, Analysis, complementary, dual, T478K, Clinical data, help, Nucleocapsid proteins, spike and nucleocapsid proteins, phenotypic, carrier, pre-vaccination, Host, Effect, mitigate, highlight, lack, addition, allelic, fixed, baseline, raising, symptomatic and asymptomatic, the SARS-CoV-2 virus, 【제목키워드】 Symptom, variants of interest, Phylogenomics, population genomics, pre-vaccination, reveal,