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-GilSelene Zárate, Blanca Taboada, Susana López, Carlos F. Arias, Moritz U.G. Kraemer, Antonio Lazcano, Marina Escalera Zamudio

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Resumen

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.

Idioma original	Inglés
Número de artículo	e82069
Publicación	eLife
Volumen	12
DOI	https://doi.org/10.7554/eLife.82069
Estado	Publicada - 27 jul. 2023
Publicado de forma externa	Sí

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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, Artículo 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",

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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 - http://www.scopus.com/inward/record.url?scp=85175631039&partnerID=8YFLogxK

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

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