Dataset Information

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

ABSTRACT: 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.

SUBMITTER: Taboada B

PROVIDER: S-EPMC9229647 | biostudies-literature | 2022 May

REPOSITORIES: biostudies-literature

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

Taboada Blanca B Zárate Selene S García-López Rodrigo R Muñoz-Medina José Esteban JE Sanchez-Flores Alejandro A Herrera-Estrella Alfredo A Boukadida Celia C Gómez-Gil Bruno B Selem Mojica Nelly N Rosales-Rivera Mauricio M Salas-Lais Angel Gustavo AG Gutiérrez-Ríos Rosa María RM Loza Antonio A Rivera-Gutierrez Xaira X Vazquez-Perez Joel Armando JA Matías-Florentino Margarita M Pérez-García Marissa M Ávila-Ríos Santiago S Hurtado Juan Manuel JM Herrera-Nájera Carla Ivón CI Núñez-Contreras José de Jesús JJ Sarquiz-Martínez Brenda B García-Arias Víctor Eduardo VE Santiago-Mauricio María Guadalupe MG Martínez-Miguel Bernardo B Enciso-Ibarra Julissa J Cháidez-Quiróz Cristóbal C Iša Pavel P Wong-Chew Rosa María RM Jiménez-Corona María-Eugenia ME López Susana S Arias Carlos F CF

Viruses 20220527 6

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 de ...[more]

PMID: 35746637

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Project description:BackgroundSeveral vaccines with demonstrated efficacy for coronavirus disease 2019 (Covid-19) are available. The purpose of this study was to evaluate the COVID mRNA based and adenovector based vaccines' differential effectiveness during the time of circulation of the Delta variant and determine what impact this would have on population health and cost effectiveness.MethodsWe used de-identified claims in a research database that included vaccination status and Covid-positivity status. Individuals ≥18 years, fully vaccinated with Ad26.COV2·S/J&J/Janssen, mRNA-1273/Moderna, or BNT162b2/Pfizer-BioNTech by September 30, 2021, were included. Outcomes were SARS-CoV-2-infection, emergency department visits, outpatient visits, inpatient hospitalizations, intensive care unit (ICU) transfers, death, and hospice transfers through September 30, 2021.ResultsAmong ∼6.5 million fully vaccinated individuals in the UHC Medicare Advantage and our commercially insured research database, mRNA-1273 performed better than BNT162b2 for infection, composite-hospitalization (hospitalization/ICU transfer/hospice transfer/death), and composite-ICU transfer (ICU transfer/hospice transfer/death) caused by B.1.612.7 (delta) variant infection. 26 CE.COV2.S performed worse than BNT162b2 for infection, composite-hospitalization, and composite-ICU transfers. The number needed to vaccinate (NNV) with mRNA1273 to prevent one hospitalization at 90 days was 3130 compared to 26 CE.COV2·S and 15,472 compared to BNT162b2. The NNV with mRNA1273 to prevent one ICU transfer at 90 days was 6358 compared to 26 CE.COV2·S and 34,279 compared to BNT162b2. For every one million individuals vaccinated with BNT162b compared to mRNA-1273, the approximate incremental inpatient cost would be $405,000 and the approximate incremental ICU cost would be $662,000.ConclusionsThe two-dose mRNA vaccines' effectiveness significantly exceeded the single-dose Ad26.COV2·S vaccine's effectiveness from population health and cost-effectiveness perspectives. The mRNA1273 vaccine showed slightly more effectiveness than the BNT162b vaccine.

Project description:BackgroundThe SARS-CoV-2 Delta variant was first identified in the U.S. in March 2021 and has rapidly become the predominant lineage across the U.S. due to increased transmissibility, immune evasion and vaccine breakthrough. The aim of this study was to better understand the genetic diversity and the potential impact of mutations observed in SARS-CoV-2 viruses circulating in the U.S. in vaccinated individuals.ResultsWhole genome sequencing was performed on thirty-four SARS-CoV-2 positive samples using the Oxford Nanopore MinION. Evolutionary genomic analysis revealed two novel mutations, ORF1b:V2354F and a premature stop codon, ORF7a:Q94*, identified in a cluster of SARS-CoV-2 Delta isolates collected from vaccinated individuals in Colorado. The ORF1b:V2354F mutation, corresponding to NSP15:V303F, may induce a conformational change and result in a disruption to a flanking beta-sheet structure. The premature stop codon, ORF7a:Q94*, truncates the transmembrane protein and cytosolic tail used to mediate protein transport. This may affect protein localization to the ER-Golgi. In addition to these novel mutations, the cluster of vaccinated isolates contain an additional mutation in the spike protein, at position 112, compared to the Delta variant defining mutations. This mutation, S112L, exists in isolates previously obtained in the U.S. The S112L mutation substitutes a bulky hydrophobic side chain for a polar side chain, which results in a non-conservative substitution within the protein that may affect antibody-binding affinity. Additionally, the vaccinated cluster of isolates contains non-synonymous mutations within ORF8 and NSPs which further distinguish this cluster from the respective ancestral Delta variant.ConclusionsThese results show there is an emerging sub-lineage of the ancestral Delta variant circulating in the U.S. As mutations emerge in constellations, those with a potentially beneficial advantage to the virus may continue to circulate while others will cease.

Dataset Information

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

Publications

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

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