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

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.

Two-year follow-up of the COVID-19 pandemic in Mexico.

Background: After the initial outbreak in China (December 2019), the World Health Organization declared COVID-19 a pandemic on March 11th, 2020. This paper aims to describe the first 2 years of the pandemic in Mexico. Design and methods: This is a population-based longitudinal study. We analyzed data from the national COVID-19 registry to describe the evolution of the pandemic in terms of the number of confirmed cases, hospitalizations, deaths and reported symptoms in relation to health policies and circulating variants. We also carried out logistic regression to investigate the major risk factors for disease severity. Results: From March 2020 to March 2022, the coronavirus disease 2019 (COVID-19) pandemic in Mexico underwent four epidemic waves. Out of 5,702,143 confirmed cases, 680,063 were hospitalized (11.9%), and 324,436 (5.7%) died. Even if there was no difference in susceptibility by gender, males had a higher risk of death (CFP: 7.3 vs. 4.2%) and hospital admission risk (HP: 14.4 vs. 9.5%). Severity increased with age. With respect to younger ages (0-17 years), the 60+ years or older group reached adjusted odds ratios of 9.63 in the case of admission and 53.05 (95% CI: 27.94-118.62) in the case of death. The presence of any comorbidity more than doubled the odds ratio, with hypertension-diabetes as the riskiest combination. While the wave peaks increased over time, the odds ratios for developing severe disease (waves 2, 3, and 4 to wave 1) decreased to 0.15 (95% CI: 0.12-0.18) in the fourth wave. Conclusion: The health policy promoted by the Mexican government decreased hospitalizations and deaths, particularly among older adults with the highest risk of admission and death. Comorbidities augment the risk of developing severe illness, which is shown to rise by double in the Mexican population, particularly for those reported with hypertension-diabetes. Factors such as the decrease in the severity of the SARS-CoV2 variants, changes in symptomatology, and advances in the management of patients, vaccination, and treatments influenced the decrease in mortality and hospitalizations.

Omicron-BA.1 Dispersion Rates in Mexico Varied According to the Regional Epidemic Patterns and the Diversity of Local Delta Subvariants.

PURPOSE: The Omicron subvariant BA.1 of SARS-CoV-2 was first detected in November 2021 and quickly spread worldwide, displacing the Delta variant. In this work, a characterization of the spread of this variant in Mexico is presented. METHODS: The time to fixation of BA.1, the diversity of Delta sublineages, the population density, and the level of virus circulation during the inter-wave interval were determined to analyze differences in BA.1 spread. RESULTS: BA.1 began spreading during the first week of December 2021 and became dominant in the next three weeks, causing the fourth COVID-19 epidemiological surge in Mexico. Unlike previous variants, BA.1 did not exhibit a geographically distinct circulation pattern. However, a regional difference in the speed of the replacement of the Delta variant was observed. CONCLUSIONS: Viral diversity and the relative abundance of the virus in a particular area around the time of the introduction of a new lineage seem to have influenced the spread dynamics, in addition to population density. Nonetheless, if there is a significant difference in the fitness of the variants, or if the time allowed for the competition is sufficiently long, it seems the fitter virus will eventually become dominant, as observed in the eventual dominance of the BA.1.x variant in Mexico.

The Alpha Variant (B.1.1.7) of SARS-CoV-2 Failed to Become Dominant in Mexico.

During the coronavirus disease 2019 (COVID-19) pandemic, the emergence and rapid increase of the B.1.1.7 (Alpha) lineage of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), first identified in the United Kingdom in September 2020, was well documented in different areas of the world and became a global public health concern because of its increased transmissibility. The B.1.1.7 lineage was first detected in Mexico during December 2020, showing a slow progressive increase in its circulation frequency, which reached its maximum in May 2021 but never became predominant. In this work, we analyzed the patterns of diversity and distribution of this lineage in Mexico using phylogenetic and haplotype network analyses. Despite the reported increase in transmissibility of the B.1.1.7 lineage, in most Mexican states, it did not displace cocirculating lineages, such as B.1.1.519, which dominated the country from February to May 2021. Our results show that the states with the highest prevalence of B.1.1.7 were those at the Mexico-U.S. border. An apparent pattern of dispersion of this lineage from the northern states of Mexico toward the center or the southeast was observed in the largest transmission chains, indicating possible independent introduction events from the United States. However, other entry points cannot be excluded, as shown by multiple introduction events. Local transmission led to a few successful haplotypes with a localized distribution and specific mutations indicating sustained community transmission. IMPORTANCE The emergence and rapid increase of the B.1.1.7 (Alpha) lineage of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) throughout the world were due to its increased transmissibility. However, it did not displace cocirculating lineages in most of Mexico, particularly B.1.1.519, which dominated the country from February to May 2021. In this work, we analyzed the distribution of B.1.1.7 in Mexico using phylogenetic and haplotype network analyses. Our results show that the states with the highest prevalence of B.1.1.7 (around 30%) were those at the Mexico-U.S. border, which also exhibited the highest lineage diversity, indicating possible introduction events from the United States. Also, several haplotypes were identified with a localized distribution and specific mutations, indicating that sustained community transmission occurred in the country.

Metagenomic analysis reveals differences in the co-occurrence and abundance of viral species in SARS-CoV-2 patients with different severity of disease.

BACKGROUND: SARS-CoV-2 infections have a wide spectrum of clinical manifestations whose causes are not completely understood. Some human conditions predispose to severe outcome, like old age or the presence of comorbidities, but many other facets, including coinfections with other viruses, remain poorly characterized. METHODS: In this study, the eukaryotic fraction of the respiratory virome of 120 COVID-19 patients was characterized through whole metagenomic sequencing. RESULTS: Genetic material from respiratory viruses was detected in 25% of all samples, whereas human viruses other than SARS-CoV-2 were found in 80% of them. Samples from hospitalized and deceased patients presented a higher prevalence of different viruses when compared to ambulatory individuals. Small circular DNA viruses from the Anneloviridae (Torque teno midi virus 8, TTV-like mini virus 19 and 26) and Cycloviridae families (Human associated cyclovirus 10), Human betaherpesvirus 6, were found to be significantly more abundant in samples from deceased and hospitalized patients compared to samples from ambulatory individuals. Similarly, Rotavirus A, Measles morbillivirus and Alphapapilomavirus 10 were significantly more prevalent in deceased patients compared to hospitalized and ambulatory individuals. CONCLUSIONS: Results show the suitability of using metagenomics to characterize a broader peripheric virological landscape of the eukaryotic virome in SARS-CoV-2 infected patients with distinct disease outcomes. Identified prevalent viruses in hospitalized and deceased patients may prove important for the targeted exploration of coinfections that may impact prognosis.

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

The COVID-19 disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus started its deadly journey into a global pandemic in Wuhan, China, in December 2019, where it was first isolated. Subsequently, multiple variants of the virus have been identified worldwide. In this review, we discuss the overall landscape of the pandemic in Mexico, including its most prevalent variants, their surveillance at a genomic level, and how they impacted the epidemiology of the disease. We also evaluate the heterologous vaccination in Mexico and how it may have influenced group immunity and helped mitigate the pandemic. Finally, we present an integrated view that could help us to understand the pandemic and serve as an example of the situation in Latin America.

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

In this study, we analyzed the sequences of SARS-CoV-2 isolates of the Delta variant in Mexico, which has completely replaced other previously circulating variants in the country due to its transmission advantage. Among all the Delta sublineages that were detected, 81.5 % were classified as AY.20, AY.26, and AY.100. According to publicly available data, these only reached a world prevalence of less than 1%, suggesting a possible Mexican origin. The signature mutations of these sublineages are described herein, and phylogenetic analyses and haplotype networks are 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 main 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 variant associated with the third wave of the COVID-19 pandemic in Mexico and highlights the importance of SARS-CoV-2 genomic surveillance for the timely identification of emerging variants that may impact public health.