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A total of 14 973 alleles in 29 661 sequenced samples collected between March 2021 and January 2023 by the Mexican Consortium for Genomic Surveillance (CoViGen-Mex) and collaborators were used to construct a thorough map of mutations of the Mexican SARS-CoV-2 genomic landscape containing Intra-Patient Minor Allelic Variants (IPMAVs), which are low-frequency alleles not ordinarily present in a genomic consensus sequence. This additional information proved critical in identifying putative coinfecting variants included alongside the most common variants, B.1.1.222, B.1.1.519, and variants of concern (VOCs) Alpha, Gamma, Delta, and Omicron. A total of 379 coinfection events were recorded in the dataset (a rate of 1.28 %), resulting in the first such catalogue in Mexico. The most common putative coinfections occurred during the spread of Delta or after the introduction of Omicron BA.2 and its descendants. Coinfections occurred constantly during periods of variant turnover when more than one variant shared the same niche and high infection rate was observed, which was dependent on the local variants and time. Coinfections might occur at a higher frequency than customarily reported, but they are often ignored as only the consensus sequence is reported for lineage identification.

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Abdominal obesity is highly prevalent in Mexico and has a poor prognosis in terms of the severity of coronavirus disease (COVID-19) and low levels of antibodies induced by infection and vaccination. We evaluated the humoral immune response induced by COVID-19 and five different vaccination schedules in Mexican individuals with abdominal obesity and the effects of other variables. This prospective longitudinal cohort study included 2084 samples from 389 participants. The levels of anti-S1/S2 and anti-RBD IgG antibodies were measured at various time points after vaccination. A high prevalence of hospitalization and oxygen use was observed in individuals with abdominal obesity (AO) who had COVID-19 before vaccination; however, they also had high levels of anti-S1/S2 and anti-RBD-neutralizing IgG antibodies. The same was true for vaccination-induced antibody levels. However, their longevity was low. Interestingly, we did not observe significant differences in vaccine reactogenicity between abdominally obese and abdominally non-obese groups. Finally, individuals with a higher body mass index, older age, and previous COVID-19 had higher levels of antibodies induced by COVID-19 and vaccination. Therefore, it is important to evaluate other immunological and inflammatory factors to better understand the pathogenesis of COVID-19 in the presence of risk factors and to propose effective vaccination schedules for vulnerable populations.

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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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Obesity is associated with an increased risk of contracting infections. This study aimed to estimate the risk of COVID-19 infection associated with obesity and to assess its role in the specific antibody response against SARS-CoV-2 in 2021. This study included 980 participants from the State of Mexico who participated in a serological survey where they were tested for SARS-CoV-2 IgG anti-S1/S2 and anti-RBD antibodies and asked for height, weight, and previous infection data via a questionnaire. Of the cohort of 980 participants, 451 (46.02%) were seropositive at the time of recruitment (45.2% symptomatic and 54.8% asymptomatic). The risk of SARS-CoV-2 infection with obesity was 2.18 (95% CI: 1.51-3.16), 2.58 (95% CI: 1.63-4.09), and 1.88 (95% CI: 1.18-2.98) for seropositive, asymptomatic, and symptomatic individuals, respectively, compared to those with normal weight. Anti-S1/S2 and anti-RBD IgG antibodies tended to be higher in overweight and obese participants in the seropositive group and stratified by different obesity classes. Additionally, there was a positive correlation between anti-S1/S2 and anti-RBD IgG antibodies and BMI in both men and women in the seropositive group. Obesity is an independent risk factor for SARS-CoV-2 infection when adjusted for confounding variables; however, the relationship between BMI and anti-S1/S2 and anti-RBD IgG antibody levels differed markedly in the presence or absence of symptoms.

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Probiotics play an important role against infectious pathogens, such as Escherichia coli (E. coli), mainly through the production of antimicrobial compounds and their immunomodulatory effect. This protection can be detected both on the live probiotic microorganisms and in their inactive forms (paraprobiotics). Probiotics may affect different cells involved in immunity, such as macrophages. Macrophages are activated through contact with microorganisms or their products (lipopolysaccharides, endotoxins or cell walls). The aim of this work was the evaluation of the effect of two probiotic bacteria (Escherichia coli Nissle 1917 and Bifidobacterium animalis subsp. lactis HN019 on macrophage cell line J774A.1 when challenged with two pathogenic strains of E. coli. Macrophage activation was revealed through the detection of reactive oxygen (ROS) and nitrogen (RNS) species by flow cytometry. The effect varied depending on the kind of probiotic preparation (immunobiotic, paraprobiotic or postbiotic) and on the strain of E. coli (enterohemorrhagic or enteropathogenic). A clear immunomodulatory effect was observed in all cases. A higher production of ROS compared with RNS was also observed.

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SARS-CoV-2 is the causal agent of COVID-19; the first report of SARS-CoV-2 infection was in December 2019 in Wuhan, China. This virus has since caused the largest pandemic in history, and the number of deaths and infections has been significant. Nevertheless, the development of vaccines has helped to reduce both deaths and infections. Comorbidities such as diabetes, hypertension, heart and lung diseases, and obesity have been identified as additional risk factors for infection and the progression of COVID-19. Additionally, latent toxoplasmosis has been reported to be a risk factor for acquiring COVID-19 in some studies, but other studies have suggested a negative association between these two infections. Furthermore, in patients after vaccination or with COVID-19 and coinfection, an increase in the lethality and mortality of toxoplasmosis has been observed. Therefore, the objective of the current study is to determine the association of toxoplasmosis with COVID-19 in patients diagnosed with COVID-19. Serum samples from 384 patients previously diagnosed with COVID-19 using IgG antibodies against the S1/S2 antigens of SARS-CoV-2 were collected. Subsequently, anti-Toxoplasma IgG and IgM antibodies were analyzed with ELISA. Statistical analysis was performed using SPSS Version 20.0 frequencies, percentages, 2 × 2 tables, and the Pearson correlation coefficient. IgG and IgM anti-Toxoplasma antibodies were positive in 105/384 (27.34%) and (26/191) 13.6% of patients, respectively. The positivity for both infections was higher in patients aged >40 years old. Subjects who were overweight or obese were mainly positive for both IgG antibodies against S1/S2 SARS-CoV-2 and Toxoplasma antibodies. In conclusion, the coinfection rate was 21.7%. The prevalence of S1/S2 SARS-CoV-2 was 308/384 (80.2%), and the percentage of Toxoplasma antibodies was 27.34%.

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Latin America is one of the regions in which the COVID-19 pandemic has a stronger impact, with more than 72 million reported infections and 1.6 million deaths until June 2022. Since this region is ecologically diverse and is affected by enormous social inequalities, efforts to identify genomic patterns of the circulating SARS-CoV-2 genotypes are necessary for the suitable management of the pandemic. To contribute to the genomic surveillance of the SARS-CoV-2 in Latin America, we extended the number of SARS-CoV-2 genomes available from the region by sequencing and analyzing the viral genome from COVID-19 patients from seven countries (Argentina, Brazil, Costa Rica, Colombia, Mexico, Bolivia, and Peru). Subsequently, we analyzed the genomes circulating mainly during 2021 including records from GISAID database from Latin America. A total of 1,534 genome sequences were generated from seven countries, demonstrating the laboratory and bioinformatics capabilities for genomic surveillance of pathogens that have been developed locally. For Latin America, patterns regarding several variants associated with multiple re-introductions, a relatively low percentage of sequenced samples, as well as an increment in the mutation frequency since the beginning of the pandemic, are in line with worldwide data. Besides, some variants of concern (VOC) and variants of interest (VOI) such as Gamma, Mu and Lambda, and at least 83 other lineages have predominated locally with a country-specific enrichments. This work has contributed to the understanding of the dynamics of the pandemic in Latin America as part of the local and international efforts to achieve timely genomic surveillance of SARS-CoV-2.

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The WHO has approved the use of several vaccines during the COVID-19 pandemic; experience over the last 2 years has indicated that dose demand can only be covered using more than one design. Therefore, having scientific evidence of the performance of the different vaccines applied in a country is highly relevant. In Mexico, 5 vaccines against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) were used, allowing a cohort study to analyze the generation of anti-S1/S2 IgG antibodies and anti-RBD antibodies with neutralizing activity at 0, 21, 90, and 180 days after vaccination. Five groups of participants were formed on the basis of the type of vaccine received and were divided on the basis of whether they previously had or did not have COVID-19. After completing the vaccination schedule, the seroprevalence was 95.5, 97.5, 81.0, 95.2, and 90.0% (BNT162b2, AZD1222, Convidecia, Sputnik V, and CoronaVac, respectively). Among the participants without COVID-19 prior to vaccination, the largest amount of antibodies in the 90-day period was observed in the BNT162b2 group, and the amount of antibodies in the Sputnik V group decreased the least over time. Even though the percentages of seroconversion obtained in this study were lower than those currently reported in other parts of the world, the tested vaccines are able, in most cases, to induce a good production of IgG antibodies anti-S1/S2 and neutralizing capacity. The fact that there are people who have not produced antibodies during the study leaves open some questions that must be investigated to avoid the appearance of serious cases of COVID-19. IMPORTANCE Since the start of the vaccination programs against COVID-19 in 2020, it was evident that due to global shortages, the demand for the dose required in Mexico could only be covered by acquiring different vaccines. Therefore, determining the effectiveness of these and the longevity of acquired immunity is extremely important in a scenario where SARS-CoV-2 circulation becomes endemic and booster doses are required periodically. Our data reveal significant differences both in the generation of antibodies as well as in their longevity for the vaccines applied in the country but suggest that, in general, the Mexican population can reach a high capacity to neutralize the virus, therefore, regarding less the variant for which they were designed.

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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.

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OBJECTIVE: In this study, we investigated the impact of the SARS-CoV-2 vaccination on seroprevalence in a cohort of healthcare workers (HCW) at an ophthalmic medical center. METHODS: IgG antibodies against the N, S1, and S2 antigens of SARS-CoV-2 as well as their serum neutralizing activity were determined. RESULTS: In the present study, we observed that 98.4% of HCW were seropositive for S1/S2 proteins of SARS-CoV-2 due to the national vaccination program. Interestingly, 78.4% of the participants had anti-N protein antibodies, suggesting previous COVID-19 infection. We also evaluated the neutralizing antibodies and found that the mean value was high (90.7%). CONCLUSION: These results indicate that our HCWs cohort presented a robust hybrid humoral response owing to the massive national vaccination program and natural infections.

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