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

Hugo G. Castelán-Sánchez; Luis Delaye; Rhys P.D. Inward; Simon Dellicour; Bernardo Gutierrez; Natalia Martinez de la Vina; Celia Boukadida; Oliver G. Pybus; Guillermo de Anda Jáuregui; Plinio Guzmán; Marisol Flores-Garrido; Óscar Fontanelli; Maribel Hernández Rosales; Amilcar Meneses; Gabriela Olmedo-Alvarez; Alfredo Heriberto Herrera-Estrella; Alejandro Sánchez-Flores; José Esteban Muñoz-Medina; Andreu Comas-García; Bruno Gómez-Gil; Selene Zárate; Blanca Taboada; Susana López; Carlos F. Arias; Moritz U.G. Kraemer; Antonio Lazcano; Marina Escalera Zamudio

doi:10.7554/eLife.82069

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

Hugo G. Castelán-Sánchez
, Luis Delaye
, Rhys P.D. Inward
, Simon Dellicour
, Bernardo Gutierrez
, Natalia Martinez de la Vina
, Celia Boukadida
, Oliver G. Pybus
, Guillermo de Anda Jáuregui
, Plinio Guzmán
, Marisol Flores-Garrido
, Óscar Fontanelli
, Maribel Hernández Rosales
, Amilcar Meneses
, Gabriela Olmedo-Alvarez
, Alfredo Heriberto Herrera-Estrella
, Alejandro Sánchez-Flores
, José Esteban Muñoz-Medina
, Andreu Comas-García
, Bruno Gómez-Gil

Selene Zárate, Blanca Taboada, Susana López, Carlos F. Arias, Moritz U.G. Kraemer, Antonio Lazcano, Marina Escalera Zamudio^*

^*Corresponding author for this work

Consorcio Mexicano de Vigilancia Genómica (CoViGen-Mex)
Consejo Nacional de Ciencia y Tecnología
Centro de Investigacion y de Estudios Avanzados del Instituto Politécnico Nacional
University of Oxford
Université Libre de Bruxelles
KU Leuven
Instituto Nacional de Enfermedades Respiratorias
Royal Veterinary College University of London
Instituto Nacional de Medicina Genómica
Astronomer LTD
Universidad Nacional Autónoma de México
Centro de Investigacion y de Estudios Avanzados del IPN
Instituto Mexicano del Seguro Social
Universidad Autónoma de San Luis Potosí, Facultad de Medicina
Unidad Regional Mazatlán en Acuicultura y Manejo Ambiental
Universidad Autonoma de la Ciudad de Mexico
UNAM

Research output: Contribution to journal › Article › peer-review

5 Scopus citations

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.

Original language	English
Article number	e82069
Journal	eLife
Volume	12
DOIs	https://doi.org/10.7554/eLife.82069
State	Published - 27 Jul 2023
Externally published	Yes

Keywords

Humans
Mexico/epidemiology
COVID-19/epidemiology
SARS-CoV-2/genetics
Biological Evolution
Phylogeny

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10.7554/eLife.82069

Cite this

Castelán-Sánchez, H. G., Delaye, L., Inward, R. P. D., Dellicour, S., Gutierrez, B., de la Vina, N. M., Boukadida, C., Pybus, O. G., Jáuregui, G. D. A., Guzmán, P., Flores-Garrido, M., Fontanelli, Ó., Rosales, M. H., Meneses, A., Olmedo-Alvarez, G., Herrera-Estrella, A. H., Sánchez-Flores, A., Muñoz-Medina, J. E., Comas-García, A., ... Zamudio, M. E. (2023). Comparing the evolutionary dynamics of predominant SARS-CoV-2 virus lineages co-circulating in Mexico. eLife, 12, Article e82069. https://doi.org/10.7554/eLife.82069

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title = "Comparing the evolutionary dynamics of predominant SARS-CoV-2 virus lineages co-circulating in 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.",

keywords = "Humans, Mexico/epidemiology, COVID-19/epidemiology, SARS-CoV-2/genetics, Biological Evolution, Phylogeny",

author = "Castel{\'a}n-S{\'a}nchez, \{Hugo G.\} and Luis Delaye and Inward, \{Rhys P.D.\} and Simon Dellicour and Bernardo Gutierrez and \{de la Vina\}, \{Natalia Martinez\} and Celia Boukadida and Pybus, \{Oliver G.\} and J{\'a}uregui, \{Guillermo de Anda\} and Plinio Guzm{\'a}n and Marisol Flores-Garrido and {\'O}scar Fontanelli and Rosales, \{Maribel Hern{\'a}ndez\} and Amilcar Meneses and Gabriela Olmedo-Alvarez and Herrera-Estrella, \{Alfredo Heriberto\} and Alejandro S{\'a}nchez-Flores and Mu{\~n}oz-Medina, \{Jos{\'e} Esteban\} and Andreu Comas-Garc{\'i}a and Bruno G{\'o}mez-Gil and Selene Z{\'a}rate and Blanca Taboada and Susana L{\'o}pez and Arias, \{Carlos F.\} and Kraemer, \{Moritz U.G.\} and Antonio Lazcano and Zamudio, \{Marina Escalera\}",

note = "{\textcopyright} 2023, Castel{\'a}n-S{\'a}nchez, Delaye, Inward et al.",

year = "2023",

month = jul,

day = "27",

doi = "10.7554/eLife.82069",

language = "Ingl{\'e}s",

volume = "12",

journal = "eLife",

issn = "2050-084X",

publisher = "eLife Sciences Publications Ltd",

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Castelán-Sánchez, HG, Delaye, L, Inward, RPD, Dellicour, S, Gutierrez, B, de la Vina, NM, Boukadida, C, Pybus, OG, Jáuregui, GDA, Guzmán, P, Flores-Garrido, M, Fontanelli, Ó, 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, MUG, Lazcano, A & Zamudio, ME 2023, 'Comparing the evolutionary dynamics of predominant SARS-CoV-2 virus lineages co-circulating in Mexico', eLife, vol. 12, e82069. https://doi.org/10.7554/eLife.82069

TY - JOUR

T1 - Comparing the evolutionary dynamics of predominant SARS-CoV-2 virus lineages co-circulating in Mexico

AU - Castelán-Sánchez, Hugo G.

AU - Delaye, Luis

AU - Inward, Rhys P.D.

AU - Dellicour, Simon

AU - Gutierrez, Bernardo

AU - de la Vina, Natalia Martinez

AU - Boukadida, Celia

AU - Pybus, Oliver G.

AU - Jáuregui, Guillermo de Anda

AU - Guzmán, Plinio

AU - Flores-Garrido, Marisol

AU - Fontanelli, Óscar

AU - Rosales, Maribel Hernández

AU - Meneses, Amilcar

AU - Olmedo-Alvarez, Gabriela

AU - Herrera-Estrella, Alfredo Heriberto

AU - Sánchez-Flores, Alejandro

AU - Muñoz-Medina, José Esteban

AU - Comas-García, Andreu

AU - Gómez-Gil, Bruno

AU - Zárate, Selene

AU - Taboada, Blanca

AU - López, Susana

AU - Arias, Carlos F.

AU - Kraemer, Moritz U.G.

AU - Lazcano, Antonio

AU - Zamudio, Marina Escalera

PY - 2023/7/27

Y1 - 2023/7/27

N2 - 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.

AB - 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.

KW - Humans

KW - Mexico/epidemiology

KW - COVID-19/epidemiology

KW - SARS-CoV-2/genetics

KW - Biological Evolution

KW - Phylogeny

UR - https://www.scopus.com/pages/publications/85175631039

U2 - 10.7554/eLife.82069

DO - 10.7554/eLife.82069

M3 - Artículo

C2 - 37498057

AN - SCOPUS:85175631039

SN - 2050-084X

VL - 12

JO - eLife

JF - eLife

M1 - e82069

ER -

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

Abstract

Keywords

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