Early Genomic, Epidemiological, and Clinical Description of the SARS-CoV-2 Omicron Variant in Mexico City

Cedro‐Tanda, Alberto; Gómez-Romero, Laura; Anda-Jáuregui, Guillermo de; Garnica-López, Dora; Alfaro-Mora, Yair; Sanchez-Xochipa, Sonia; García-García, Eulices F.; Mendoza-Vargas, Alfredo; Frías-Jiménez, Emmanuel; Moreno, Bernardo; Campos‐Romero, Abraham; Moreno-Camacho, José L; Alcántar‐Fernández, Jonathan; Ortiz-Ramirez, Jesus; Benitez-González, Mariana; Trejo-González, Roxana; Aguirre-Chavarría, Daniel; Núñez-Martínez, Marcela Elizabeth; Uribe-Figueroa, Laura; Angulo, Ofelia; Ruiz, Rosaura; Hidalgo-Miranda, Alfredo; Herrera, Luis A.

doi:10.3390/v14030545

Cited by 29 publications

(22 citation statements)

References 32 publications

(41 reference statements)

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“…As in other countries, in Mexico, several variants classified as VOC, VOI, and VUM have been detected, particularly Delta, Alpha, Gamma, Mu [7], and more recently Omicron [8].…”

Section: Introductionsupporting

confidence: 54%

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Clinical and Virological Features of patients hospitalized with different types of COVID-19 vaccination in Mexico City

Hernández‐Terán

GarciaDiego

Villanueva-Reza

et al. 2022

Preprint

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Coronavirus disease 2019 (COVID-19) vaccines are very effective at protecting against severe disease and death. However, the impact of the vaccine used, viral variants, and host factors on disease severity remain poorly understood. Here we compared COVID-19 clinical presentations and outcomes in vaccinated and unvaccinated patients in Mexico City. From March to September 2021, clinical and demographic characteristics were obtained from 1,014 individuals with a documented SARS-CoV-2 infection, and viral variants were identified in a subset of 386 patients. We compared unvaccinated, partially vaccinated, and fully vaccinated patients, stratifying by age groups. We fitted multivariate statistical models to evaluate the impact of vaccination status, SARS-CoV-2 lineages, vaccine types, and clinical parameters. Most hospitalized patients were unvaccinated. In patients over 61 years old, mortality was significantly higher in unvaccinated compared to fully vaccinated individuals. In patients aged 31 to 60 years, vaccinated patients were more likely to be outpatients (46%) than unvaccinated individuals (6.1%). We found immune disease and age above 61 years old as risk factors. While fully vaccination was found as the most protective factor against in-hospital death. This study suggests that vaccination is essential to reduce mortality in a comorbid population such as that of Mexico.

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“…As in other countries, in Mexico, several variants classified as VOC, VOI, and VUM have been detected, particularly Delta, Alpha, Gamma, Mu [7], and more recently Omicron [8].…”

Section: Introductionsupporting

confidence: 54%

“…As in other countries, in Mexico, several variants classified as VOC, VOI, and VUM have been detected, particularly Delta, Alpha, Gamma, Mu [7], and more recently Omicron [8]. Moreover, B.1.1.519 was detected as the predominant lineage in Mexico during late 2020 and the first months of 2021 [9].…”

Section: Introductionmentioning

confidence: 99%

Clinical and Virological Features of patients hospitalized with different types of COVID-19 vaccination in Mexico City

Hernández‐Terán

GarciaDiego

Villanueva-Reza

et al. 2022

Preprint

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“…For example, the R346K amino acid change, previously detected in lineage Mu (B.1.621) (Laiton-Donato et al 2021, 2) is associated with increased resistance to convalescent plasma therapy, and less neutralization of antibodies (Liu et al 2022). The substitution R346K was previously reported in genomes from Mexico City with a prevalence of 40% in the capital and according to phylogenetic analyses, the sequences from Mexico City form a monophyletic clade (Cedro-Tanda et al 2022). Genomes with the R346K mutation now designated as BA.1.1 sub-lineage (Mohandas et al 2022) which predominated in Mexico and spread throughout the country.…”

Section: Discussionmentioning

confidence: 85%

Genome evolution and early introductions of the SARS-CoV-2 Omicron Variant in Mexico

Castelán-Sánchez

Martinez-Castilla

Martinez

et al. 2022

Preprint

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A new variant of SARS-CoV-2 Omicron (Pango lineage designation B.1.1.529), was first reported to the World Health Organization (WHO) by South African health authorities on November 24, 2021. The Omicron variant possesses numerous mutations associated with increased transmissibility and immune escape properties. In November 2021, Mexican authorities reported Omicron's presence in the country. In this study, we infer the first introductory events of Omicron and the impact that human mobility can have on the spread of the virus. We also evaluated the adaptive evolutionary processes in Mexican SARS-CoV-2 genomes during the first month of circulation of Omicron. We infer 173 introduction events of Omicron in Mexico in the first two months of detection; subsequently, of the introductions, there was an increase in the prevalence for January. This higher prevalence of the novel variant results in a peak of cases reported, on average, six weeks after a higher mobility trend was reported. The peak of cases reported is due to the BA.1.1 Omicron sub-lineage dominated, followed by BA.1 and BA.15 sub-lineages in the country from January to February 2022. Additionally, we identified the presence of diversifying natural selection in the genomes of Omicron and found mainly five non-synonymous mutations in the RDB domain of the Spike protein, all of them related to evasion of the immune response. In contrast, the other proteins in the genome are highly conserved however, there are homoplasies mutations in non-structural proteins, indicating a parallel evolution.

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“…However, it is necessary to consider that outbreaks of different SARS-CoV-2 variants could promote specific symptoms 36 , 37 ; then, continuous surveillance would help to improve our knowledge about natural immunity responses against the virus for a comprehensive understanding of the clinical manifestations of COVID-19.…”

Section: Discussionmentioning

confidence: 99%

Seroconversion dynamic and SARS-CoV-2 seropositivity in unvaccinated population during the first and second outbreaks in Mexico

Fernández-Rojas¹,

Esparza²,

Campos‐Romero³

et al. 2022

Sci Rep

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Serosurveillance helps establish reopening guidelines and determine the immunity levels in different populations to reach herd immunity. Then, there is an urgent need to estimate seroprevalence population wide. In Mexico, information about COVID-19 cases and related deaths is scarce. Also, there is no official serosurveillance, limiting our knowledge of the impact of the SARS-CoV-2 pandemic. Here, we report the prevalence of anti-SARS-CoV-2 antibodies in 522,690 unvaccinated people from July 5th to December 31st, 2020. The overall seroprevalence was 32.8% and highest in adults aged 30–39 years (38.5%) than people under 20 years (33.0%) or older (28.9%). Moreover, in a cohort of 1655 individuals confirmed COVID-19 by PCR, we found that symptomatic people (HR = 2.56) increased seroconversion than presymptomatic. Also, we identified that the most discriminative symptoms for COVID-19 that could predict seroconversion were anosmia and ageusia (HR = 1.70), fever, myalgia/arthralgia, and cough (HR = 1.75). Finally, we found that obese people had lower seroconversion (HR = 0.53) than healthy people, but the opposite happens in diabetic people (HR = 1.39). These findings reveal that around one-third of Mexican outpatients had anti-SARS-CoV-2 antibodies before vaccination. Also, some symptoms improve empirically COVID-19 diagnosis and seroconversion. This information could help fine-tune vaccination schemes and the reopening and back-to-work algorithms.

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Early Genomic, Epidemiological, and Clinical Description of the SARS-CoV-2 Omicron Variant in Mexico City

Cited by 29 publications

References 32 publications

Clinical and Virological Features of patients hospitalized with different types of COVID-19 vaccination in Mexico City

Clinical and Virological Features of patients hospitalized with different types of COVID-19 vaccination in Mexico City

Genome evolution and early introductions of the SARS-CoV-2 Omicron Variant in Mexico

Seroconversion dynamic and SARS-CoV-2 seropositivity in unvaccinated population during the first and second outbreaks in Mexico

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