Comparing the evolutionary dynamics of predominant SARS-CoV-2 virus lineages co-circulating in Mexico

Castelán-Sánchez, HG; Delaye, L; Inward, RPD; Dellicour, S; Gutierrez, B; de la Vina, NM; Boukadida, C; Pybus, OG; Jáuregui, GD; Guzmán, P; Flores-Garrido, M; Fontanelli, O; Rosales, MH; Meneses, A; Olmedo-Alvarez, G; Herrera-Estrella, AH; Sánchez-Flores, A; Muñoz-Medina, JE; Comas-García, A; Gómez-Gil, B; Zárate, S; Taboada, B; López, S; Arias, CF; Kraemer, MU; Lazcano, A; Zamudio, ME

doi:10.7554/eLife.82069

Comparing the evolutionary dynamics of predominant SARS-CoV-2 virus lineages co-circulating in Mexico

Castelán-Sánchez, HG; Delaye, L; Inward, RPD; Dellicour, S; Gutierrez, B; de la Vina, NM; Boukadida, C; Pybus, OG; Jáuregui, GD; Guzmán, P; Flores-Garrido, M; Fontanelli, O; Rosales, MH; Meneses, A; Olmedo-Alvarez, G; Herrera-Estrella, AH; Sánchez-Flores, A; Muñoz-Medina, JE; Comas-García, A; Gómez-Gil, B; Zárate, S; Taboada, B; López, S; Arias, CF; Kraemer, MU; Lazcano, A; Zamudio, ME

Authors

HG Castelán-Sánchez

L Delaye

RPD Inward

S Dellicour

B Gutierrez

NM de la Vina

C Boukadida

OG Pybus

GD Jáuregui

P Guzmán

M Flores-Garrido

O Fontanelli

MH Rosales

A Meneses

G Olmedo-Alvarez

AH Herrera-Estrella

A Sánchez-Flores

JE Muñoz-Medina

A Comas-García

B Gómez-Gil

S Zárate

B Taboada

S López

CF Arias

MU Kraemer

A Lazcano

ME Zamudio

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.

Citation

Castelán-Sánchez, H., Delaye, L., Inward, R., Dellicour, S., Gutierrez, B., de la Vina, N., …Zamudio, M. (2023). Comparing the evolutionary dynamics of predominant SARS-CoV-2 virus lineages co-circulating in Mexico. eLife, 12, https://doi.org/10.7554/eLife.82069

Journal Article Type	Article
Acceptance Date	Jul 23, 2023
Online Publication Date	Aug 16, 2023
Publication Date	2023
Deposit Date	Jul 12, 2024
Publicly Available Date	Jul 12, 2024
Print ISSN	2050-084X
Publisher	eLife Sciences Publications
Peer Reviewed	Peer Reviewed
Volume	12
DOI	https://doi.org/10.7554/eLife.82069
Keywords	genomic epidemiology; phylodynamics; SARS-CoV-2; COVID-19; Latin America; Viruses; EMERGENCE; B.1.1.7