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SARS-CoV-2 Omicron variants BA.4 and BA.5 dominated the fifth COVID-19 epidemiological wave in Mexico
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  • Blanca Taboada,
  • Selene Zarate ,
  • Rodrigo García-López,
  • José Muñoz-Medina,
  • Bruno Gómez-Gil,
  • Alfredo Herrera-Estrella,
  • Alejandro Sanchez-Flores,
  • Angel Gustavo Salas Lais,
  • Benjamin Roche,
  • Gabriela Martínez-Morales,
  • Hermilo Domínguez Zárate,
  • Célida Duque Molina,
  • Ricardo Avilés Hernández,
  • Susana López,
  • Carlos F. Arias
Blanca Taboada
Universidad Nacional Autonoma de Mexico Instituto de Biotecnologia

Corresponding Author:blanca.taboada@ibt.unam.mx

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Selene Zarate
Universidad Autonoma de la Ciudad de Mexico - Plantel Del Valle
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Rodrigo García-López
Universidad Nacional Autonoma de Mexico Instituto de Biotecnologia
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José Muñoz-Medina
Instituto Mexicano del Seguro Social
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Bruno Gómez-Gil
Centro de Investigacion en Alimentacion y Desarrollo AC
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Alfredo Herrera-Estrella
Laboratorio Nacional de Genomica para la Biodiversidad
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Alejandro Sanchez-Flores
Universidad Nacional Autonoma de Mexico Instituto de Biotecnologia
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Angel Gustavo Salas Lais
Instituto Mexicano del Seguro Social
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Benjamin Roche
MiVEGEC
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Gabriela Martínez-Morales
Instituto Mexicano del Seguro Social
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Hermilo Domínguez Zárate
Instituto Mexicano del Seguro Social
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Célida Duque Molina
Instituto Mexicano del Seguro Social
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Ricardo Avilés Hernández
Instituto Mexicano del Seguro Social
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Susana López
Universidad Nacional Autonoma de Mexico Instituto de Biotecnologia
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Carlos F. Arias
Universidad Nacional Autonoma de Mexico Instituto de Biotecnologia
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Abstract

In Mexico, the BA.4 and BA.5 Omicron variants dominated the fifth epidemic wave (summer 2022), superseding BA.2, which had circulated during the inter-wave period. The present study uses genome sequencing and statistical and phylogenetic analyses to examine these variants’ prevalence, distribution, and genetic diversity in Mexico from April to August 2022. Over 35% of the sequenced genomes in this period corresponded to the BA.2 variant, 8% to the BA.4, and 56% to the BA.5 variant. Multiple subvariants were identified, but only BA.2.9, BA.2.12.1, BA.5.1, BA.5.2, BA.5.2.1, and BA.4.1 circulated throughout the fifth wave across the entire country, not forming geographical clusters. Contrastingly, other subvariants exhibited a geographically restricted distribution, most notably in the Southeast region, which showed a distinct subvariant dynamic. This study supports previous results showing that this region may be a major entry point and may have contributed to the introduction and evolution of novel variants in Mexico. Furthermore, a differential distribution was observed for certain subvariants among specific States throughout time, which may have contributed to the overall increased diversity observed during this wave compared to the previous one. This study highlights the importance of sustaining genomic surveillance to identify novel variants that may impact public health.