The New SARS-CoV-2 Variants and Their Epidemiological Impact in Mexico

García-López, Rodrigo; Laresgoiti-Servitje, Estibalitz; Lemus-Martin, Roselyn; Sánchez-Flores, Alejandro; Sanders‐Velez, Carlos

doi:10.1128/mbio.01060-21

Cited by 9 publications

(14 citation statements)

References 57 publications

(60 reference statements)

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“…This has been in part thanks to an unprecedented collaborative sequencing effort carried out by the government (INMEGEN, InDRE) and multiple academic institutions (CoViGen-Mex). The resulting sequences have enabled the study of the variant turnover in the country throughout the three years of the pandemic [ 6 , 7 ]. As pointed out in previous studies [ 8 , 9 ], the Yucatan Peninsula (States of Campeche, Quintana Roo, and Yucatan) is one of the primary entry points for SARS-CoV-2 variants in Mexico due to its large influx of tourists and commercial activities in the areas surrounding Merida and Cancun.…”

Section: Introductionmentioning

confidence: 99%

SARS-CoV-2 BW lineage, a fast-growing Omicron variant from southeast Mexico bearing relevant escape mutations

et al. 2023

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Purpose The swift expansion of the BW.1 SARS-CoV-2 variant coincided with a rapid increase of COVID-19 cases occurring in Southeast Mexico in October, 2022, which marked the start of Mexico’s sixth epidemiological wave. In Yucatan, up to 92% (58 of 73) of weekly sequenced genomes between epidemiological week 42 and 47 were identified as either BW.1 or its descendant, BW.1.1 in the region, during the last trimester of 2022. In the current study, a comprehensive genomic comparison was carried out to characterize the evolutionary history of the BW lineage, identifying its origins and its most important mutations. Methods An alignment of all the genomes of the BW lineage and its parental BA.5.6.2 variant was carried out to identify their mutations. A phylogenetic and ancestral sequence reconstruction analysis with geographical inference, as well as a longitudinal analysis of point mutations, were performed to trace back their origin and contrast them with key RBD mutations in variant BQ.1, one of the fastest-growing lineages to date. Results Our ancestral reconstruction analysis portrayed Mexico as the most probable origin of the BW.1 and BW.1.1 variants. Two synonymous substitutions, T7666C and C14599T, support their Mexican origin, whereas other two mutations are specific to BW.1: S:N460K and ORF1a:V627I. Two additional substitutions and a deletion are found in its descending subvariant, BW.1.1. Mutations found in the receptor binding domain, S:K444T, S:L452R, S:N460K, and S:F486V in BW.1 have been reported to be relevant for immune escape and are also key mutations in the BQ.1 lineage. Conclusions BW.1 appears to have arisen in the Yucatan Peninsula in Southeast Mexico sometime around July 2022 during the fifth COVID-19 wave. Its rapid growth may be in part explained by the relevant escape mutations also found in BQ.1.

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Section: Introductionmentioning

confidence: 99%

SARS-CoV-2 BW lineage, a fast-growing Omicron variant from southeast Mexico bearing relevant escape mutations

et al. 2023

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“…In Mexico, from 2020 to March 2022, 10% of COVID-19 patients required hospitalization, and the lethality rate was less than 1% [García-López et al 2022]. Hospitalized patients had a higher lethality rate of around 40%.…”

Section: Discussionmentioning

confidence: 99%

“…Patients under the age of 65 who require hospitalization have a mortality rate of less than 50%, which increases significantly with advancing age. Patients aged 85 years or older have the highest mortality rate, reaching up to 60% [García-López et al, 2022]. Connecting specific virus mutations to particular cases is challenging due to their rarity.…”

Section: Discussionmentioning

confidence: 99%

“…Finally, the Omicron variant and its respective lineages entered in December 2021, initiating the fourth wave becoming the variant with the highest daily case count. This variant and the recombinant XBB sublineage have spread even among vaccinated populations [García-López et al, 2022]. It is unclear whether the reported regional mutations are related to the alarming case-fatality rates in Mexico.…”

Section: Introductionmentioning

confidence: 99%

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Mortality-Associated Sars-Cov-2 Genomic Variants From Patients Hospitalized for Severe Pneumonia in Aguascalientes, Mexico From 2020 to 2023

Gomez,

Gamboa,

Ceapa

et al. 2024

Preprint

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The SARS-CoV-2 virus has caused a global health crisis, resulting in a significant loss of human lives. It is essential to report disease and mutation associations to provide ideas for public health interventions and preventive measures. In this study, to determine the association between genomic variants and the severity of pneumonia caused by SARS-CoV-2, a sequencing analysis of 150 patient samples with confirmed COVID-19 was conducted. These samples were collected between 2021 and 2023 and isolated in Aguascalientes, Mexico. The patient cohort had males and females ranging from 0 to 91 years old. Males accounted for 66% of the population analyzed. The Delta variant was the most prevalent lineage associated with deaths in 2021-2022, while the B.1.1.529 lineages emerged in mid-2022. Currently, the XBB lineage is the most commonly identified in Mexico. New mutations L95M and L46M in ORF 8 and ORF 9 were discovered in 30% and 20% of the sequences and are uniquely present in the studied population. These mutations are positively associated with patient death. This study provides valuable data to aid in understanding the evolution of SARS-CoV-2 in specific populations and explores the severity of the disease and mutation correlations.

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“…Conducted on both local and global scales, these studies have facilitated the tracking of SARS-CoV-2 transmission, the identification of viral mutations, and the spatiotemporal mapping of the virus’s progression. The insights gained have been instrumental in informing public health responses to the pandemic [ 18 , 19 , 20 , 21 , 22 , 23 ]. In Cyprus, the impact of SARS-CoV-2 has been diligently studied since the early stages of the COVID-19 pandemic from April 2020 to October 2021 [ 24 , 25 ].…”

Section: Introductionmentioning

confidence: 99%

Unraveling the Dynamics of Omicron (BA.1, BA.2, and BA.5) Waves and Emergence of the Deltacron Variant: Genomic Epidemiology of the SARS-CoV-2 Epidemic in Cyprus (Oct 2021–Oct 2022)

Chrysostomou,

Vrancken,

Haralambous

et al. 2023

Viruses

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Commencing in December 2019 with the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), three years of the coronavirus disease 2019 (COVID-19) pandemic have transpired. The virus has consistently demonstrated a tendency for evolutionary adaptation, resulting in mutations that impact both immune evasion and transmissibility. This ongoing process has led to successive waves of infections. This study offers a comprehensive assessment spanning genetic, phylogenetic, phylodynamic, and phylogeographic dimensions, focused on the trajectory of the SARS-CoV-2 epidemic in Cyprus. Based on a dataset comprising 4700 viral genomic sequences obtained from affected individuals between October 2021 and October 2022, our analysis is presented. Over this timeframe, a total of 167 distinct lineages and sublineages emerged, including variants such as Delta and Omicron (1, 2, and 5). Notably, during the fifth wave of infections, Omicron subvariants 1 and 2 gained prominence, followed by the ascendancy of Omicron 5 in the subsequent sixth wave. Additionally, during the fifth wave (December 2021–January 2022), a unique set of Delta sequences with genetic mutations associated with Omicron variant 1, dubbed “Deltacron”, was identified. The emergence of this phenomenon initially evoked skepticism, characterized by concerns primarily centered around contamination or coinfection as plausible etiological contributors. These hypotheses were predominantly disseminated through unsubstantiated assertions within the realms of social and mass media, lacking concurrent scientific evidence to validate their claims. Nevertheless, the exhaustive molecular analyses presented in this study have demonstrated that such occurrences would likely lead to a frameshift mutation—a genetic aberration conspicuously absent in our provided sequences. This substantiates the accuracy of our initial assertion while refuting contamination or coinfection as potential etiologies. Comparable observations on a global scale dispelled doubt, eventually leading to the recognition of Delta-Omicron variants by the scientific community and their subsequent monitoring by the World Health Organization (WHO). As our investigation delved deeper into the intricate dynamics of the SARS-CoV-2 epidemic in Cyprus, a discernible pattern emerged, highlighting the major role of international connections in shaping the virus’s local trajectory. Notably, the United States and the United Kingdom were the central conduits governing the entry and exit of the virus to and from Cyprus. Moreover, notable migratory routes included nations such as Greece, South Korea, France, Germany, Brazil, Spain, Australia, Denmark, Sweden, and Italy. These empirical findings underscore that the spread of SARS-CoV-2 within Cyprus was markedly influenced by the influx of new, highly transmissible variants, triggering successive waves of infection. This investigation elucidates the emergence of new waves of infection subsequent to the advent of highly contagious and transmissible viral variants, notably characterized by an abundance of mutations localized within the spike protein. Notably, this discovery decisively contradicts the hitherto hypothesis of seasonal fluctuations in the virus’s epidemiological dynamics. This study emphasizes the importance of meticulously examining molecular genetics alongside virus migration patterns within a specific region. Past experiences also emphasize the substantial evolutionary potential of viruses such as SARS-CoV-2, underscoring the need for sustained vigilance. However, as the pandemic’s dynamics continue to evolve, a balanced approach between caution and resilience becomes paramount. This ethos encourages an approach founded on informed prudence and self-preservation, guided by public health authorities, rather than enduring apprehension. Such an approach empowers societies to adapt and progress, fostering a poised confidence rooted in well-founded adaptation.

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The New SARS-CoV-2 Variants and Their Epidemiological Impact in Mexico

Cited by 9 publications

References 57 publications

SARS-CoV-2 BW lineage, a fast-growing Omicron variant from southeast Mexico bearing relevant escape mutations

SARS-CoV-2 BW lineage, a fast-growing Omicron variant from southeast Mexico bearing relevant escape mutations

Mortality-Associated Sars-Cov-2 Genomic Variants From Patients Hospitalized for Severe Pneumonia in Aguascalientes, Mexico From 2020 to 2023

Unraveling the Dynamics of Omicron (BA.1, BA.2, and BA.5) Waves and Emergence of the Deltacron Variant: Genomic Epidemiology of the SARS-CoV-2 Epidemic in Cyprus (Oct 2021–Oct 2022)

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