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

Castelán-Sánchez, Hugo G; Delaye, Luis; Inward, Rhys; Dellicour, Simon; Gutierrez, Bernardo; Viña, Natalia Martínez de la; Boukadida, Célia; Pybus, Oliver G.; Anda-Jáuregui, Guillermo de; Guzmán, Plinio; Flores-Garrido, Marisol; Fontanelli, Oscar; Hernández-Rosales, Maribel; Viveros, Amilcar Meneses; Olmedo-Álvarez, Gabriela; Herrera‐Estrella, Alfredo; Sánchez-Flores, Alejandro; Comas‐García, Andreu; Gómez‐Gil, Bruno; Zárate, Selene; Taboada, Blanca; López, Susana; Arias, Carlos F.; Kraemer, Moritz U. G.; Lazcano, Antonio; Escalera-Zamudio, Marina

doi:10.7554/elife.82069

Cited by 6 publications

(3 citation statements)

References 73 publications

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“…This contrasts with a scenario of worldwide mobility restrictions with fewer successful introductions, resulting in viruses spreading mostly through continuous chains of transmission within Mexico as well as locally acquired mutations that cause geographical clustering. For instance, it has been reported that seven introductions resulted in transmission chains for the Alpha variant, whereas Gamma and Delta had two and six, respectively [ 42 ]. Although the methodology employed in the present study differs and is focused on each subvariant’s early introduction events, this work identified 10 to 17 Mexican clades in these early trees.…”

Section: Discussionmentioning

confidence: 99%

SARS-CoV-2 Omicron variants BA.4 and BA.5 dominated the fifth COVID-19 epidemiological wave in Mexico

Taboada,

Zárate,

García-López

et al. 2023

Microbial Genomics

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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' abundance, 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 the most abundant, BA.2.9, BA.2.12.1, BA.5.1, BA.5.2, BA.5.2.1 and BA.4.1, circulated 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 significant entry point and contributed to introducing and evolving novel variants in Mexico. Furthermore, a differential distribution was observed for certain subvariants among specific States through time, which may have contributed to the overall increased diversity observed during this wave compared to the previous ones. This study highlights the importance of sustaining genomic surveillance to identify novel variants that may impact public health.

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Section: Discussionmentioning

confidence: 99%

SARS-CoV-2 Omicron variants BA.4 and BA.5 dominated the fifth COVID-19 epidemiological wave in Mexico

Taboada,

Zárate,

García-López

et al. 2023

Microbial Genomics

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“…This may be because MPXV experienced a stochastic evolutionary event, that led to further diversification of MPXV and contributed to its spread different geographic locations and its possible adaptation to new hosts within these regions 27 Our results reveled that the ancestors of the branches containing Mexican isolates could be traced to the United Kingdom, Portugal, and Canada. This suggests that the sequenced MPXV genomes in Mexico originated from these countries, possibly through travel-associated transmission, as has been observed for other viruses such as SARS-CoV-2, where multiple introductions occur, and only a few viruses manage to establish local transmission chains throughout the country 28,29 .…”

Section: Discussionmentioning

confidence: 76%

Genetic Insights into the Microevolutionary Dynamics and Early Introductions of Human Monkeypox Virus in Mexico

Gómez-Sánchez,

Castelán-Sánchez,

Martínez-Castilla

et al. 2023

Preprint

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The recent global outbreak of Monkeypox, caused by the Monkeypox virus (MPVX) emerged in Europe in 2022 and rapidly spread to over 40 countries. The Americas are currently facing the highest impact, reporting over 50,000 cases by early 2023. Here, we analyze 880 MPXV isolates worldwide to gain insights into the evolutionary patterns and initial introduction events of the virus in Mexico. We found that MPXV entered Mexico on multiple occasions, from the United Kingdom, Portugal, and Canada, and subsequently spread locally in different regions of Mexico. Additionally, we show that MPXV has an open pangenome, highlighting the role of gene turnover in shaping its genomic diversity, rather than SNPs variations, which do not contribute significantly to genome diversity. Although the genome presents multiple SNP sites in coding regions, these remain under purifying selection, suggesting their evolutionary conservation. One notable exception is the amino acid site 63 of the protein encoded by the Cop-A4L gene, intricately related to viral maturity, for which we picked up a strong signal of positive selection. Ancestral state reconstruction deduced that the ancestral state at site 63 corresponds to the amino acid valine, present only in isolates of clade I. However, the isolates of the current outbreak evolved for threonine at site 63. Finally, our findings contribute to the knowledge of the evolutionary processes of the Monkeypox virus.

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“…Secondly, although we have focused on the VOC/VOI that emerged in the LAC, the exclusion of countries from North America and Europe might preclude the identification of transition events between such countries and the LAC. For example, USA and Mexico were shown to have a related Gamma epidemic, with genomes clustering together, especially for the P.1.17 Gamma sublineage 46 . However, the exclusion of countries from Europe and North America probably did not have a great impact on the inferred spread patterns of Lambda and Mu due to the very low prevalence of those variants outside South America.…”

Section: Discussionmentioning

confidence: 99%

Dispersion patterns of SARS-CoV-2 variants Gamma, Lambda and Mu in Latin America and the Caribbean

Gräf,

Martinez,

Bello

et al. 2024

Nat Commun

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Latin America and Caribbean (LAC) regions were an important epicenter of the COVID-19 pandemic and SARS-CoV-2 evolution. Through the COVID-19 Genomic Surveillance Regional Network (COVIGEN), LAC countries produced an important number of genomic sequencing data that made possible an enhanced SARS-CoV-2 genomic surveillance capacity in the Americas, paving the way for characterization of emerging variants and helping to guide the public health response. In this study we analyzed approximately 300,000 SARS-CoV-2 sequences generated between February 2020 and March 2022 by multiple genomic surveillance efforts in LAC and reconstructed the diffusion patterns of the main variants of concern (VOCs) and of interest (VOIs) possibly originated in the Region. Our phylogenetic analysis revealed that the spread of variants Gamma, Lambda and Mu reflects human mobility patterns due to variations of international air passenger transportation and gradual lifting of social distance measures previously implemented in countries. Our results highlight the potential of genetic data to reconstruct viral spread and unveil preferential routes of viral migrations that are shaped by human mobility patterns.

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

Cited by 6 publications

References 73 publications

SARS-CoV-2 Omicron variants BA.4 and BA.5 dominated the fifth COVID-19 epidemiological wave in Mexico

SARS-CoV-2 Omicron variants BA.4 and BA.5 dominated the fifth COVID-19 epidemiological wave in Mexico

Genetic Insights into the Microevolutionary Dynamics and Early Introductions of Human Monkeypox Virus in Mexico

Dispersion patterns of SARS-CoV-2 variants Gamma, Lambda and Mu in Latin America and the Caribbean

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