Explanipedia

K-FluDB: A Novel K-Mer Based Database for Enhanced Genomic Surveillance of Influenza A Viruses Open

Alejandro Uscanga Junco, Lorena Díaz‐González, Blanca Taboada · 2025

Motivation Influenza A viruses frequently cause seasonal outbreaks and pandemics due to their genetic diversity and reassortment potential. Existing genomic surveillance tools face challenges with redundant databases, delaying subtype iden…

Circulation of RSV Subtypes A and B Among Mexican Children During the 2021–2022 and 2022–2023 Seasons Open

Selene Zárate, Blanca Taboada, Karina Torres-Rivera, Patricia Bautista‐Carbajal, Miguel Leonardo García-León , et al. · 2025

Respiratory syncytial virus (RSV) remains a leading cause of pneumonia in young children in Mexico and worldwide. To investigate RSV dynamics in Mexico, we conducted a multicenter study from August 2021 to July 2023 in six hospitals across…

VirDetect-AI: a residual and convolutional neural network–based metagenomic tool for eukaryotic viral protein identification Open

Alvan O. Zárate, Lorena Díaz‐González, Blanca Taboada · 2024

This study addresses the challenging task of identifying viruses within metagenomic data, which encompasses a broad array of biological samples, including animal reservoirs, environmental sources, and the human body. Traditional methods fo…

Exploration of low-frequency allelic variants of SARS-CoV-2 genomes reveals coinfections in Mexico occurred during periods of VOCs turnover Open

Rodrigo García-López, Blanca Taboada, Selene Zárate, José Esteban Muñoz‐Medina, Ángel Gustavo Salas-Lais , et al. · 2024

Graphical abstract Coinfections occurring within a single sample can be detected by exploring all mutations in a genomic set as these have full profiles commonly observed in lower prevalence.

SARS-CoV-2 Omicron variants BA.4 and BA.5 dominated the fifth COVID-19 epidemiological wave in Mexico Open

Blanca Taboada, Selene Zárate, Rodrigo García-López, José Esteban Muñoz‐Medina, Bruno Gómez‐Gil , et al. · 2023

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 a…

Longitudinal anti-SARS-CoV-2 antibody immune response in acute and convalescent patients Open

Horacio Pérez-Juárez, Angélica Serrano-Vázquez, Héctor Godínez–Álvarez, Enrique González, Liliana Rojas-Velázquez , et al. · 2023

Despite global efforts to assess the early response and persistence of SARS-CoV-2 antibodies in patients infected with or recovered from COVID-19, our understanding of the factors affecting its dynamics remains limited. This work aimed to …

Comparing the evolutionary dynamics of predominant SARS-CoV-2 virus lineages co-circulating in Mexico Open

Hugo G. Castelán‐Sánchez, Luis Delaye, Rhys Inward, Simon Dellicour, Bernardo Gutiérrez , et al. · 2023

Over 200 different SARS-CoV-2 lineages have been observed in Mexico by November 2021. To investigate lineage replacement dynamics, we applied a phylodynamic approach and explored the evolutionary trajectories of five dominant lineages that…

SARS-CoV-2 Omicron variants BA.4 and BA.5 dominated the fifth COVID-19 epidemiological wave in Mexico Open

Blanca Taboada, Selene Zárate, Rodrigo García-López, José Esteban Muñoz‐Medina, Bruno Gómez‐Gil , et al. · 2023

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 a…

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

Rodrigo García-López, Xaira Rivera-Gutiérrez, Mauricio Rosales-Rivera, Selene Zárate, José Esteban Muñoz‐Medina , et al. · 2023

Author response: Comparing the evolutionary dynamics of predominant SARS-CoV-2 virus lineages co-circulating in Mexico Open

Hugo G. Castelán‐Sánchez, Luis Delaye, Rhys Inward, Simon Dellicour, Bernardo Gutiérrez , et al. · 2023

Full text Figures and data Side by side Abstract Editor's evaluation Introduction Results Discussion Methods Appendix 1 Data availability References Decision letter Author response Article and author information Metrics Abstract Over 200 d…

The fecal and oropharyngeal eukaryotic viromes of healthy infants during the first year of life are personal Open

Xaira Rivera-Gutiérrez, Patricia Morán, Blanca Taboada, Angélica Serrano-Vázquez, Pavel Iša , et al. · 2023

Using a metagenomic sequencing approach, we described and compared the diversity and dynamics of the oropharyngeal and fecal eukaryotic virome of nine asymptomatic children in a semi-rural community setting located in the State of Morelos,…

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

Selene Zárate, Blanca Taboada, Mauricio Rosales-Rivera, Rodrigo García-López, José Esteban Muñoz‐Medina , et al. · 2023

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. Metho…

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

Antonio Loza, Rosa María Wong‐Chew, María Eugenia Jiménez-Corona, Selene Zárate, Susana López , et al. · 2023

Background After the initial outbreak in China (December 2019), the World Health Organization declared COVID-19 a pandemic on March 11 th , 2020. This paper aims to describe the first 2 years of the pandemic in Mexico. Design and methods T…

SARS-CoV-2 BW.1, a fast-growing Omicron variant from southeast Mexico bearing relevant escape mutations Open

Rodrigo García-López, Xaira Rivera-Gutiérrez, Mauricio Rosales-Rivera, Blanca Taboada, Selene Zárate , et al. · 2022

Purpose The swift growth of the BW.1 SARS-CoV-2 variant coincides with a new rapid increase of COVID-19 cases occurring in Southeast Mexico in October, 2022, putting an end to a period of low transmission after Mexico’s fifth epidemiologic…

Evaluation of tools for taxonomic classification of viruses Open

Elizabeth Cadenas-Castrejón, Jérôme Verleyen, Célia Boukadida, Lorena Díaz‐González, Blanca Taboada · 2022

Viruses are the most abundant infectious agents on earth, and they infect living organisms such as bacteria, plants and animals, among others. They play an important role in the balance of different ecosystems by modulating microbial popul…

Regional epidemic dynamics and Delta variant diversity resulted in varying rates of spread of Omicron-BA.1 in Mexico Open

Selene Zárate, Blanca Taboada, Mauricio Rosales-Rivera, Rodrigo García-López, José Esteban Muñoz‐Medina , et al. · 2022

The Omicron subvariant BA.1 of SARS-CoV-2 was first detected in November 2021 and quickly spread worldwide, displacing the Delta variant. In Mexico, this subvariant began spreading during the first week of December 2021 and became dominant…

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

Pavel Iša, Blanca Taboada, Rodrigo García-López, Célia Boukadida, José Ernesto Ramírez–González , et al. · 2022

Clinical and Virological Features of Patients Hospitalized with Different Types of COVID-19 Vaccination in Mexico City Open

Alejandra Hernández‐Terán, Pamela Garcíadiego-Fossas, Marco Villanueva-Reza, Célia Boukadida, Blanca Taboada , et al. · 2022

Coronavirus disease 2019 (COVID-19) vaccines effectively protect against severe disease and death. However, the impact of the vaccine used, viral variants, and host factors on disease severity remain poorly understood. This work aimed to c…

Evaluation of tools for the taxonomical classification of viruses Open

Elizabeth Cadenas-Castrejón, Jérôme Verleyen, Célia Boukadida, Lorena Díaz‐González, Blanca Taboada · 2022

50G (1942_50GL), 500G (1943_500GL) and 1000G (1752_1000GL) sets are simulated reads previously reported Tangherlini et al. [1], and represent large reads like contigs. FISH-I (FISH_1_Q_sS_dup_HNoM_RbNoM), PB3(PB3_Q_sS_dup_HNoM_RbNoM), I5-8…

Evaluation of tools for the taxonomical classification of viruses Open

Elizabeth Cadenas-Castrejón, Jérôme Verleyen, Célia Boukadida, Lorena Díaz‐González, Blanca Taboada · 2022

50G (1942_50GL), 500G (1943_500GL) and 1000G (1752_1000GL) sets are simulated reads previously reported Tangherlini et al. [1], and represent large reads like contigs. FISH-I (FISH_1_Q_sS_dup_HNoM_RbNoM), PB3(PB3_Q_sS_dup_HNoM_RbNoM), I5-8…

Comparing the evolutionary dynamics of predominant SARS-CoV-2 virus lineages co-circulating in Mexico Open

Hugo G. Castelán‐Sánchez, Luis Delaye, Rhys Inward, Simon Dellicour, Bernardo Gutiérrez , et al. · 2022

Up to November 2021, over 200 different SARS-CoV-2 lineages circulated in Mexico. To investigate lineage replacement dynamics, we applied a phylodynamic approach to explore the evolutionary trajectories of five dominant lineages that circu…

Comparing the evolutionary dynamics of predominant SARS-CoV-2 virus lineages co-circulating in Mexico Open

Hugo G. Castelán‐Sánchez, Luis Delaye, Rhys Inward, Simon Dellicour, Bernardo Gutiérrez , et al. · 2022

Over 200 different SARS-CoV-2 lineages have been observed in Mexico by November 2021. To investigate lineage replacement dynamics, we applied a phylodynamic approach and explored the evolutionary trajectories of five dominant lineages that…

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

Blanca Taboada, Selene Zárate, Rodrigo García-López, José Esteban Muñoz‐Medina, Alejandro Sánchez‐Flores , et al. · 2022

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 subli…

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

Blanca Taboada, Selene Zárate, José Esteban Muñoz‐Medina, Alejandro Sánchez‐Flores, Rodrigo García-López , et al. · 2022

In this study, we analyzed sequences of SARS-CoV-2 isolates of the Delta variant in Mexico, which completely replaced other previously circulating variants in the country due to its transmission advantage. Among Delta sublineages detected,…

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

Alejandra Hernández‐Terán, Pamela GarciaDiego, Marco Villanueva-Reza, Célia Boukadida, Blanca Taboada , et al. · 2022

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…

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

Selene Zárate, Blanca Taboada, José Esteban Muñoz‐Medina, Pavel Iša, Alejandro Sánchez‐Flores , et al. · 2022

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 lin…

High Prevalence and Diversity of Caliciviruses in a Community Setting Determined by a Metagenomic Approach Open

Xaira Rivera-Gutiérrez, Patricia Morán, Blanca Taboada, Angélica Serrano-Vázquez, Pavel Iša , et al. · 2022

Human caliciviruses are important etiological agents of acute gastroenteritis in children under 5 years of age. Several studies have characterized their association with childhood diarrhea and their presence in nondiarrheal stool samples.

Genomic Characterization of SARS-CoV-2 Isolated from Patients with Distinct Disease Outcomes in Mexico Open

Célia Boukadida, Blanca Taboada, Marina Escalera‐Zamudio, Pavel Iša, José Ernesto Ramírez–González , et al. · 2022

The genetic association of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) with different clinical conditions remains unclear and needs further investigation. In this study, we characterized 57 complete SARS-CoV-2 genomes from…

Additional file 1 of Metagenomic analysis reveals differences in the co-occurrence and abundance of viral species in SARS-CoV-2 patients with different severity of disease Open

Pavel Iša, Blanca Taboada, Rodrigo García-López, Célia Boukadida, José Ernesto Ramírez–González , et al. · 2022

Additional file 1: Table S1. Patients included in the study. Information of samples included in study, sample ID, age, and sex of patients, place of collection, date of sample and start of the symptoms, clinical status, comorbidities, samp…

Genetic Analysis of SARS-CoV-2 Variants in Mexico during the First Year of the COVID-19 Pandemic Open

Blanca Taboada, Selene Zárate, Pavel Iša, Célia Boukadida, Joel Armando Vázquez-Pérez , et al. · 2021

During the first year of the SARS-CoV-2 pandemic in Mexico, more than two million people were infected. In this study, we analyzed full genome sequences from 27 February 2020 to 28 February 2021 to characterize the geographical and tempora…

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