Comparing the evolutionary dynamics of predominant SARS-CoV-2 virus lineages co-circulating in Mexico
- Consejo Nacional de Ciencia y Tecnología, Mexico
- CINVESTAV-Unidad Irapuato, Mexico
- University of Oxford, United Kingdom
- KU Leuven, Belgium
- Instituto Nacional de Enfermedades Respiratorias, Mexico
- Instituto Nacional de Medicina Genómica, Mexico
- Astronomer LTD, Mexico
- Universidad Nacional Autónoma de México, Mexico
- CINVESTAV-IPN, Mexico
- Instituto Mexicano del Seguro Social, Mexico
- Universidad Autónoma de San Luis Potosí, Mexico
- Unidad Regional Mazatlán en Acuicultura y Manejo Ambiental, Mexico
- Universidad Autónoma de la Ciudad de México, Mexico
- Universidad Nacional Autónoma de Méxic, Mexico
Abstract
Over 200 different SARS-CoV-2 lineages have been observed in Mexico by November 2021. To investigate lineage replacement dynamics, we applied a phylodynamic approach and explored the evolutionary trajectories of five dominant lineages that circulated during the first year of local transmission. For most lineages, peaks in sampling frequencies coincided with different epidemiological waves of infection in Mexico. Lineages B.1.1.222 and B.1.1.519 exhibited similar dynamics, constituting clades that likely originated in Mexico and persisted for >12 months. Lineages B.1.1.7, P.1 and B.1.617.2 also displayed similar dynamics, characterized by multiple introduction events leading to a few successful extended local transmission chains that persisted for several months. For the largest B.1.617.2 clades, we further explored viral lineage movements across Mexico. Many clades were located within the south region of the country, suggesting that this area played a key role in the spread of SARS-CoV-2 in Mexico.
Data availability
Virus genome IDs and GISAID accession numbers for the sequences used in each dataset are provided in the Supplementary file 1 file. All genomic and epidemiological data supporting the findings of this study is publicly available from GISAID/GenBank, from the Ministry Of Health Mexico102, and/or from the 'Our World in Data' coronavirus pandemic web portal 29. For the GISAID data used, the corresponding acknowledgement table is available on the 'GISAID Data Acknowledgement Locator' under the EPI_SET_20220405qd and EPI_SET_20220215at keys 49. Our bioinformatic pipeline implementing a migration data and phylogenetically-informed sequence subsampling approach is publicly available at https://github.com/rhysinward/Mexico_subsampling.
Article and author information
Author details
José Esteban Muñoz-Medina
Marina Escalera Zamudio
Funding
FNRS (F.4515.22)
- Simon Dellicour
UNAM (DGAPA-PAPIIT (IN214421)
- Antonio Lazcano
UNAM (DGAPA-PAPIME (PE204921))
- Antonio Lazcano
Research Foundation Flanders (G098321N)
- Simon Dellicour
European Horizon 2020 project MOOD (874850)
- Simon Dellicour
Leverhulme Trust (ECF-2019-542)
- Marina Escalera Zamudio
European Horizon 2020 project MOOD (874850)
- Oliver Pybus
European Horizon 2020 project MOOD (874850)
- Moritz U G Kraemer
CONACyT Vigilancia Genómica del Virus SARS-CoV-2 en México-2022"" (PP-F003)
- Carlos F Arias
Ministry of Education, Science, Technology and Innovation of Mexico City (057)
- Carlos F Arias
AHF Global Public Health Institute at the University of Miami (Genomic surveillance for SARS-CoV-2 variants in Mexico"")
- Carlos F Arias
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Copyright
© 2023, Castelán-Sánchez et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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Comparing the evolutionary dynamics of predominant SARS-CoV-2 virus lineages co-circulating in Mexico
eLife 12:e82069.
https://doi.org/10.7554/eLife.82069
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