Dominance of Three Sublineages of the SARS-CoV-2 Delta Variant in Mexico

Blanca Taboada; Selene Zárate; José Esteban Muñoz-Medina; Alejandro Sanchez-Flores; Rodrigo García-López; Alfredo Herrera-Estrella; Celia Boukadida; Bruno Gómez-Gil; Nelly Selem Mojica; Mauricio Rosales-Rivera; Angel Gustavo Salas-Lais; Rosa María Gutiérrez-Ríos; Antonio Loza; Xaira Rivera-Gutierrez; Joel Armando Vazquez-Perez; Margarita Matías-Florentino; Marissa Pérez-García; Santiago Ávila-Ríos; Juan Manuel Hurtado; Carla Herrera-Nájera; José Núñez-Contreras; Brenda Sarquiz-Martínez; Víctor García-Arias; María Santiago-Mauricio; Bernardo Martínez-Miguel; Julissa Enciso-Ibarra; Cristóbal Cháidez-Quiróz; Pavel Isa; Rosa María Wong-Chew; María-Eugenia Jiménez-Corona; Susana López; Carlos F. Arias

doi:10.20944/preprints202205.0131.v1

A peer-reviewed article of this Preprint also exists.

Taboada, B.; Zárate, S.; García-López, R.; Muñoz-Medina, J.E.; Sanchez-Flores, A.; Herrera-Estrella, A.; Boukadida, C.; Gómez-Gil, B.; Mojica, N.S.; Rosales-Rivera, M.; Salas-Lais, A.G.; Gutiérrez-Ríos, R.M.; Loza, A.; Rivera-Gutierrez, X.; Vazquez-Perez, J.A.; Matías-Florentino, M.; Pérez-García, M.; Ávila-Ríos, S.; Hurtado, J.M.; Herrera-Nájera, C.I.; Núñez-Contreras, J.J.; Sarquiz-Martínez, B.; García-Arias, V.E.; Santiago-Mauricio, M.G.; Martínez-Miguel, B.; Enciso-Ibarra, J.; Cháidez-Quiróz, C.; Iša, P.; Wong-Chew, R.M.; Jiménez-Corona, M.-E.; López, S.; Arias, C.F. Dominance of Three Sublineages of the SARS-CoV-2 Delta Variant in Mexico. Viruses 2022, 14, 1165. Taboada, B.; Zárate, S.; García-López, R.; Muñoz-Medina, J.E.; Sanchez-Flores, A.; Herrera-Estrella, A.; Boukadida, C.; Gómez-Gil, B.; Mojica, N.S.; Rosales-Rivera, M.; Salas-Lais, A.G.; Gutiérrez-Ríos, R.M.; Loza, A.; Rivera-Gutierrez, X.; Vazquez-Perez, J.A.; Matías-Florentino, M.; Pérez-García, M.; Ávila-Ríos, S.; Hurtado, J.M.; Herrera-Nájera, C.I.; Núñez-Contreras, J.J.; Sarquiz-Martínez, B.; García-Arias, V.E.; Santiago-Mauricio, M.G.; Martínez-Miguel, B.; Enciso-Ibarra, J.; Cháidez-Quiróz, C.; Iša, P.; Wong-Chew, R.M.; Jiménez-Corona, M.-E.; López, S.; Arias, C.F. Dominance of Three Sublineages of the SARS-CoV-2 Delta Variant in Mexico. Viruses 2022, 14, 1165.

Abstract

In this study, we analyzed sequences of SARS-CoV-2 isolates of the Delta variant in Mexico, which completely replaced other previously circulating variants in the country due to its transmission advantage. Among Delta sublineages detected, 81.5 % were classified as AY.20, AY.26, and AY.100. According to publicly available data, these sublineages only reached a world prevalence of less than 1%, suggesting a possible Mexican origin. The signature mutations of these sublineages are described, and phylogenetic analyses and haplotype networks were used to track their spread across the country. Other frequently detected sublineages include AY.3, AY.62, AY.103, and AY.113. Over time, the principal sublineages showed different geographical distributions, with AY.20 predominant in Central Mexico, AY.26 in the North, and AY.100 in the Northwest and South/Southeast. This work describes the circulation, from May to November 2021, of the primary sublineages of the Delta variants associated to the third wave of the COVID-19 pandemic in Mexico and reinforces the importance of SARS-CoV-2 genomic surveillance for timely identification of emerging variants that may impact public health.

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Copyright: This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Dominance of Three Sublineages of the SARS-CoV-2 Delta Variant in Mexico

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