Open AccessDOI
Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms.
Francisco Barona-Gómez,Luis Delaye,Erik Díaz-Valenzuela,Fabien Plisson,Arely Cruz-Pérez,Mauricio Díaz-Sánchez,Christian A. García-Sepúlveda,Alejandro Sanchez-Flores,Rafael Pérez-Abreu,Francisco J Valencia-Valdespino,Natali Vega-Magaña,José Francisco Muñoz-Valle,Octavio Patricio García-González,Sofía Bernal-Silva,Andreu Comas-García,Angélica Cibrián-Jaramillo +15 more
- Vol. 7, Iss: 11
TLDR
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.1.28.4) and 20B/P.Abstract:
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.read more
Citations
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Journal ArticleDOI
SARS-CoV-2 Mutations and COVID-19 Clinical Outcome: Mutation Global Frequency Dynamics and Structural Modulation Hold the Key
Ranjeet Maurya,Pallavi Mishra,Aparna Swaminathan,V. Ravi,S. Saifi,Akshay Kanakan,Priyanka Mehta,Priti Devi,Shaista Praveen,Sandeep Budhiraja,Bansidhar Tarai,Shimpa Sharma,Rajesh Khyalappa,Meghnad Joshi,Rajesh Pandey +14 more
TL;DR: A comprehensive analysis of the mutation distribution among the coronavirus disease 2019 (COVID-19) recovered and mortality patients and discovered three mutations within the mortality patients with a high cohort and global distribution, which later became a part of variants of interest (VOIs)/VOCs, suggesting its significant role in enhancing viral characteristics.
Posted ContentDOI
An outbreak of SARS-CoV-2 in big hairy armadillos (Chaetophractus villosus) associated with Gamma variant in Argentina three months after being undetectable in humans
Franco Lucero Arteaga,Mercedes Nabaes Jodar,Mariela Mondino,Ana I. Portu,Mónica Alejandra Boeris,Ana Joly,A. M. Jar,Silvia Leonor Mundo,Eliana F. Castro,Diego Alvarez,Caroline Torres,Mariana Viegas,A. Bratanich +12 more
TL;DR: The detection of SARS-CoV-2 Gamma variant infection in four specimens of Chaetophractus villosus (big hairy armadillo/armadillo peludo) in Argentina raises the question of potential unidentified viral reservoirs.
Journal ArticleDOI
The P323L substitution in the SARS-CoV-2 polymerase (NSP12) confers a selective advantage during infection
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Meynert,Shona C Moore,Mahdad Noursadeghi,Michael Olanipekun,Anthonia Osagie,Massimo Palmarini,Carlo Palmieri,William A. Paxton,Georgios Pollakis,Nicholas C. Price,Andrew Rambaut,David Robertson,Clark D Russell,Vanessa Sancho-Shimizu,Caroline Sands,Janet T Scott,Louise Sigfrid,Tom Solomon,Shiranee Sriskandan,D. Stuart,C. Gail Summers,Olivia Swann,Zoltan Takats,Panteleimon G. Takis,Richard S. Tedder,Aaron Thompson,E. Thomson,Ryan S Thwaites,Lance Turtle,Maria Zambon,Hayley E Hardwick,Chloe Donohue,Fiona Griffiths,Wilna Oosthuyzen,Cara Donegan,Rebecca G Spencer,Lisa Norman,Riinu Pius,Thomas M Drake,Cameron J Fairfield,Stephen R Knight,Kenneth A. 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TL;DR: In this article , through an integrative genomic approach, the authors describe the molecular transition of SARS-CoV-2 by analyzing the viral whole genome sequences from 50 critical COVID-19 patients recruited during the first year of the pandemic in Mexico City.
Journal ArticleDOI
Phylogenetic analysis of SARS-CoV-2 viruses circulating in the South American region: Genetic relations and vaccine strain match
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TL;DR: In order to gain insight into the emergence and evolution of SARS-CoV-2 variants circulating in the South American region, a comprehensive phylogenetic study was performed as discussed by the authors .
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