Genomic Characterization of SARS-CoV-2 Isolated from Patients with Distinct Disease Outcomes in Mexico
Por:
Boukadida, Celia, Taboada, Blanca, Escalera-Zamudio, Marina, Isa, Pavel, Ramírez-González J.E., Vazquez-Perez J.A., Muñoz-Medina J.E., Grajales-Muniz, Concepcion, Gonzalez-Torres, Carolina, Gaytán-Cervantes F.J., Rincon-Rubio, Alma, Matias-Florentino, Margarita, Paz-Juárez H.E., Sanchez-Flores, Alejandro, Mendieta-Condado, Edgar, Barrera-Badillo, Gisela, Hernandez-Rivas, Lucia, Lopez, Susana, Lopez-Martinez, Irma, Avila-Rios, Santiago, Arias, Carlos F.
Publicada:
1 feb 2022
Resumen:
The coronavirus disease 2019 (COVID-19), caused by the severe acute
respiratory syndrome coronavirus-2 (SARS-CoV-2), has shown a wide
spectrum of clinical manifestations ranging from asymptomatic infections
to severe disease and death. Pre-existing medical conditions and age
have been mainly linked to the development of severe disease; however,
the potential association of viral genetic characteristics with
different clinical conditions remains unclear. SARS-CoV-2 variants with
increased transmissibility were detected early in the pandemics, and
several variants with potential relevance for public health are
currently circulating around the world. In this study, we characterized
57 complete SARS-CoV-2 genomes during the exponential growth phase of
the early epidemiological curve in Mexico, in April 2020. Patients were
categorized under distinct disease severity outcomes: mild disease or
ambulatory care, severe disease or hospitalized, and deceased. To reduce
bias related to risk factors, the patients were less than 60 years old
and with no diagnosed comorbidities A trait-association phylogenomic
approach was used to explore genotype-phenotype associations,
represented by the co-occurrence of mutations, disease severity outcome
categories, and clusters of Mexican sequences. Phylogenetic results
revealed a higher genomic diversity compared to the initial viruses
detected during the early stage of the local epidemic. We identified a
total of 90 single nucleotide variants compared to the Wuhan-Hu-1
genome, including 54 nonsynonymous mutations. We did not find evidence
for the co-occurrence of mutations associated with specific disease
outcomes. Therefore, in the group of patients studied, disease severity
was likely mainly driven by the host genetic background and other
demographic factors.
IMPORTANCE The genetic association of severe acute respiratory syndrome
coronavirus-2 (SARS-CoV-2) with different clinical conditions remains
unclear and needs further investigation. In this study, we characterized
57 complete SARS-CoV-2 genomes from patients in Mexico with distinct
disease severity outcomes: mild disease or ambulatory care, severe
disease or hospitalized, and deceased. To reduce bias related to risk
factors the patients were less than 60 years old and with no diagnosed
comorbidities. We did not find evidence for the co-occurrence of
mutations associated with specific disease outcomes. Therefore, in the
group of patients studied, disease severity was likely mainly driven by
the host genetic background and other demographic factors.
Filiaciones:
Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, Mexico
Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, Mexico
Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Morelos, Cuernavaca, Mexico
Department of Zoology, Oxford University, Oxford, United Kingdom
Instituto de Diagnóstico y Referencia Epidemiológicos, Dirección General de Epidemiología, Mexico City, Mexico
División de Laboratorios de Vigilancia e Investigación Epidemiológica, Instituto Mexicano del Seguro Social, Mexico City, Mexico
Coordinación de Control Técnico de Insumos, Instituto Mexicano del Seguro Social, Mexico City, Mexico
División de Desarrollo de la Investigación, Instituto Mexicano del Seguro Social, Mexico City, Mexico
Unidad Universitaria de Secuenciación Masiva y Bioinformática, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Morelos, Cuernavaca, Mexico
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