ArticleMicrobial genomics2021
Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms.
Article in Microbial genomics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
19 citing papers in PubMed, 23 citations in OpenAlex.
- Genomic surveillance and phylo-evolutionary analysis of SARS-CoV-2 variants in Osun state, Nigeria during the second wave of COVID-19 pandemic.BMC medical genomics · 2025Article
- SARS-CoV-2 Variants: Genetic Insights, Epidemiological Tracking, and Implications for Vaccine Strategies.International journal of molecular sciences · 2025Review
- An Outbreak of SARS-CoV-2 in Captive Armadillos Associated with Gamma Variant in Argentina.EcoHealth · 2024Article
- Review
- SARS-CoV-2 population dynamics in immunocompetent individuals in a closed transmission chain shows genomic diversity over the course of infection.Genome medicine · 2024Article
- The TRAF3-DYRK1A-RAD54L2 complex maintains ACE2 expression to promote SARS-CoV-2 infection.Journal of virology · 2024Article
- Sequence signatures within the genome of SARS-CoV-2 can be used to predict host source.Microbiology spectrum · 2024Article
- Nsp3-N interactions are critical for SARS-CoV-2 fitness and virulence.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- The P323L substitution in the SARS-CoV-2 polymerase (NSP12) confers a selective advantage during infection.Genome biology · 2023Article
- CurSa: scripts to curate metadata and sample genomes from GISAID for analysis and display in nextstrain and microreact.Biology methods & protocols · 2023Article
- Prevalence of symptoms, comorbidities, and reinfections in individuals infected with Wild-Type SARS-CoV-2, Delta, or Omicron variants: a comparative study in western Mexico.Frontiers in public health · 2023Article
- Molecular transition of SARS-CoV-2 from critical patients during the first year of the COVID-19 pandemic in Mexico City.Frontiers in cellular and infection microbiology · 2023Article
- Phylogenetic analysis of SARS-CoV-2 viruses circulating in the South American region: Genetic relations and vaccine strain match.Virus research · 2022Article
- Molecular epidemiology and genetic characterization of SARS-CoV-2 in Kuwait: A descriptive study.Frontiers in microbiology · 2022Article
- Two Years of Evolutionary Dynamics of SARS-CoV-2 in Mexico, With Emphasis on the Variants of Concern.Frontiers in microbiology · 2022Article
- SARS-CoV-2 Mutations and COVID-19 Clinical Outcome: Mutation Global Frequency Dynamics and Structural Modulation Hold the Key.Frontiers in cellular and infection microbiology · 2022Article
- Insights on the SARS-CoV-2 genome variability: the lesson learned in Brazil and its impacts on the future of pandemics.Microbial genomics · 2021Article
- SARS-CoV-2 new variants: Characteristic features and impact on the efficacy of different vaccines.Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie · 2021Review
- Effectiveness of BNT162b2 COVID-19 Vaccine in Preventing Severe Symptomatic Infection among Healthcare Workers.Medicina (Kaunas, Lithuania) · 2021Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
16 authors at 5 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Understanding the evolution of the SARS-CoV-2 virus in various regions of the world during the Covid-19 pandemic is essential to help mitigate the effects of this devastating disease. We describe the phylogenomic and population genetic patterns of the virus in Mexico during the pre-vaccination stage, including asymptomatic carriers. A real-time quantitative PCR screening and phylogenomic reconstructions directed at sequence/structure analysis of the spike glycoprotein revealed mutation of concern E484K in genomes from central Mexico, in addition to the nationwide prevalence of the imported variant 20C/S:452R (B.1.427/9). Overall, the detected variants in Mexico show spike protein mutations in the N-terminal domain (i.e. R190M), in the receptor-binding motif (i.e. T478K, E484K), within the S1-S2 subdomains (i.e. P681R/H, T732A), and at the basis of the protein, V1176F, raising concerns about the lack of phenotypic and clinical data available for the variants of interest we postulate: 20B/478K.V1 (B.1.1.222 or B.1.1.519) and 20B/P.4 (B.1.1.28.4). Moreover, the population patterns of single nucleotide variants from symptomatic and asymptomatic carriers obtained with a self-sampling scheme confirmed the presence of several fixed variants, and differences in allelic frequencies among localities. We identified the mutation N:S194L of the nucleocapsid protein associated with symptomatic patients. Phylogenetically, this mutation is frequent in Mexican sub-clades. Our results highlight the dual and complementary role of spike and nucleocapsid proteins in adaptive evolution of SARS-CoV-2 to their hosts and provide a baseline for specific follow-up of mutations of concern during the vaccination stage.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.