Exploration of low-frequency allelic variants of SARS-CoV-2 genomes reveals coinfections in Mexico occurred during periods of VOCs turnover
Artículo
Te invitamos a leer el artículo "Exploration of low-frequency allelic variants of SARS-CoV-2 genomes reveals coinfections in Mexico occurred during periods of VOCs turnover" publicado en Microbial Genomics, a cargo del profesor investigador Dr. Alfredo Heriberto Herrera Estrella y su equipo de trabajo de la UGA-Langebio.
Autores: Rodrigo García-López / Blanca Taboada, Selene Zárate / José Esteban Muñoz-Medina / Angel Gustavo Salas-Lais / Alfredo Herrera-Estrella / Celia Boukadida / Joel Armando Vazquez-Perez / Bruno Gómez-Gil / Alejandro Sanchez-Flores / Carlos F. Arias.
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, Mexico City, Mexico
- Coordinación de Calidad de Insumos y Laboratorios Especializados, Instituto Mexicano del Seguro Social, Mexico City, Mexico
- Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, Guanajuato, Mexico
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, Mexico
- Laboratorio de Biología Molecular de Enfermedades Emergentes y EPOC, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, Mexico
- Centro de Investigación en Alimentación y Desarrollo AC, Unidad Mazatlán, Mazatlán, Sinaloa, Mexico
- Unidad Universitaria de Secuenciación Masiva y Bioinformática, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico.
Felicitamos al estudiantado y profesorado que contribuyeron en esta investigación por su arduo trabajo.
Summary:
Coinfections occurring within a single sample can be detected by exploring all mutations in a genomic set as these have full profiles commonly observed in lower prevalence.
A total of 14 973 alleles in 29 661 sequenced samples collected between March 2021 and January 2023 by the Mexican Consortium for Genomic Surveillance (CoViGen-Mex) and collaborators were used to construct a thorough map of mutations of the Mexican SARS-CoV-2 genomic landscape containing Intra-Patient Minor Allelic Variants (IPMAVs), which are low-frequency alleles not ordinarily present in a genomic consensus sequence. This additional information proved critical in identifying putative coinfecting variants included alongside the most common variants, B.1.1.222, B.1.1.519, and variants of concern (VOCs) Alpha, Gamma, Delta, and Omicron. A total of 379 coinfection events were recorded in the dataset (a rate of 1.28 %), resulting in the first such catalogue in Mexico. The most common putative coinfections occurred during the spread of Delta or after the introduction of Omicron BA.2 and its descendants. Coinfections occurred constantly during periods of variant turnover when more than one variant shared the same niche and high infection rate was observed, which was dependent on the local variants and time. Coinfections might occur at a higher frequency than customarily reported, but they are often ignored as only the consensus sequence is reported for lineage identification.