Célia Boukadida
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View article: Alterations of the gut microbiome in HIV infection highlight human anelloviruses as potential predictors of immune recovery
Alterations of the gut microbiome in HIV infection highlight human anelloviruses as potential predictors of immune recovery Open
View article: Exploration of low-frequency allelic variants of SARS-CoV-2 genomes reveals coinfections in Mexico occurred during periods of VOCs turnover
Exploration of low-frequency allelic variants of SARS-CoV-2 genomes reveals coinfections in Mexico occurred during periods of VOCs turnover Open
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.
View article: Comparing the evolutionary dynamics of predominant SARS-CoV-2 virus lineages co-circulating in Mexico
Comparing the evolutionary dynamics of predominant SARS-CoV-2 virus lineages co-circulating in Mexico Open
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…
View article: Author response: Comparing the evolutionary dynamics of predominant SARS-CoV-2 virus lineages co-circulating in Mexico
Author response: Comparing the evolutionary dynamics of predominant SARS-CoV-2 virus lineages co-circulating in Mexico Open
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…
View article: Two-year follow-up of the COVID-19 pandemic in Mexico
Two-year follow-up of the COVID-19 pandemic in Mexico Open
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…
View article: Evaluation of tools for taxonomic classification of viruses
Evaluation of tools for taxonomic classification of viruses Open
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…
View article: Metagenomic analysis reveals differences in the co-occurrence and abundance of viral species in SARS-CoV-2 patients with different severity of disease
Metagenomic analysis reveals differences in the co-occurrence and abundance of viral species in SARS-CoV-2 patients with different severity of disease Open
View article: 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 Open
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…
View article: Evaluation of tools for the taxonomical classification of viruses
Evaluation of tools for the taxonomical classification of viruses Open
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…
View article: Evaluation of tools for the taxonomical classification of viruses
Evaluation of tools for the taxonomical classification of viruses Open
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…
View article: Comparing the evolutionary dynamics of predominant SARS-CoV-2 virus lineages co-circulating in Mexico
Comparing the evolutionary dynamics of predominant SARS-CoV-2 virus lineages co-circulating in Mexico Open
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…
View article: Comparative Dynamics of Delta and Omicron SARS-CoV-2 Variants across and between California and Mexico
Comparative Dynamics of Delta and Omicron SARS-CoV-2 Variants across and between California and Mexico Open
Evolutionary analysis using viral sequence data can elucidate the epidemiology of transmission. Using publicly available SARS-CoV-2 sequence and epidemiological data, we developed discrete phylogeographic models to interrogate the emergenc…
View article: Comparing the evolutionary dynamics of predominant SARS-CoV-2 virus lineages co-circulating in Mexico
Comparing the evolutionary dynamics of predominant SARS-CoV-2 virus lineages co-circulating in Mexico Open
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…
View article: Antibody and Memory B-Cell Immunity in a Heterogeneously SARS-CoV-2-Infected and -Vaccinated Population
Antibody and Memory B-Cell Immunity in a Heterogeneously SARS-CoV-2-Infected and -Vaccinated Population Open
The majority of studies on SARS-CoV-2 vaccine-elicited immunity and immune evasion have focused on single vaccines corresponding to those distributed in high-income countries. However, in low- and middle-income countries, vaccine deploymen…
View article: Dominance of Three Sublineages of the SARS-CoV-2 Delta Variant in Mexico
Dominance of Three Sublineages of the SARS-CoV-2 Delta Variant in Mexico Open
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…
View article: Dominance of Three Sublineages of the SARS-CoV-2 Delta Variant in Mexico
Dominance of Three Sublineages of the SARS-CoV-2 Delta Variant in Mexico Open
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,…
View article: 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 Open
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…
View article: The Alpha Variant (B.1.1.7) of SARS-CoV-2 Failed to Become Dominant in Mexico
The Alpha Variant (B.1.1.7) of SARS-CoV-2 Failed to Become Dominant in Mexico Open
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…
View article: Antibody and memory B-cell immunity in a heterogeneously SARS-CoV-2 infected and vaccinated population
Antibody and memory B-cell immunity in a heterogeneously SARS-CoV-2 infected and vaccinated population Open
Global population immunity to SARS-CoV-2 is accumulating through heterogenous combinations of infection and vaccination. Vaccine distribution in low- and middle-income countries has been variable and reliant on diverse vaccine platforms. W…
View article: Genomic Characterization of SARS-CoV-2 Isolated from Patients with Distinct Disease Outcomes in Mexico
Genomic Characterization of SARS-CoV-2 Isolated from Patients with Distinct Disease Outcomes in Mexico Open
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…
View article: 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
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
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…
View article: Dysbiosis and structural disruption of the respiratory microbiota in COVID-19 patients with severe and fatal outcomes
Dysbiosis and structural disruption of the respiratory microbiota in COVID-19 patients with severe and fatal outcomes Open
The COVID-19 outbreak has caused over three million deaths worldwide. Understanding the pathology of the disease and the factors that drive severe and fatal clinical outcomes is of special relevance. Studying the role of the respiratory mi…
View article: Genetic Analysis of SARS-CoV-2 Variants in Mexico during the First Year of the COVID-19 Pandemic
Genetic Analysis of SARS-CoV-2 Variants in Mexico during the First Year of the COVID-19 Pandemic Open
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…
View article: Emergence and spread of the potential variant of interest (VOI) B.1.1.519 of SARS-CoV-2 predominantly present in Mexico
Emergence and spread of the potential variant of interest (VOI) B.1.1.519 of SARS-CoV-2 predominantly present in Mexico Open
SARS-CoV-2 variants emerged in late 2020, and at least three variants of concern (B.1.1.7, B.1.351, and P1) have been reported by WHO. These variants have several substitutions in the spike protein that affect receptor binding; they exhibi…
View article: Dysbiosis and structural disruption of the respiratory microbiota in COVID-19 patients with severe and fatal outcomes
Dysbiosis and structural disruption of the respiratory microbiota in COVID-19 patients with severe and fatal outcomes Open
COVID-19 outbreak has caused over 3 million deaths worldwide. Understanding disease pathology and the factors that drive severe and fatal clinical outcomes is of special relevance. Studying the role of the respiratory microbiota in COVID-1…
View article: Emergence and spread of the potential variant of interest (VOI) B.1.1.519 predominantly present in Mexico
Emergence and spread of the potential variant of interest (VOI) B.1.1.519 predominantly present in Mexico Open
SARS-CoV-2 variants have emerged in late 2020 and there are at least three variants of concern (B.1.1.7, B.1.351, P1) reported by WHO. These variants have several substitutions in the Spike protein that affect receptor binding; they presen…
View article: Genomic Analysis of Early SARS-CoV-2 Variants Introduced in Mexico
Genomic Analysis of Early SARS-CoV-2 Variants Introduced in Mexico Open
Understanding the introduction, spread, and establishment of SARS-CoV-2 within distinct human populations as well as the evolution of the pandemics is crucial to implement effective control strategies. In this work, we report that the init…
View article: Congenital Zika Syndrome and Extra-Central Nervous System Detection of Zika Virus in a Pre-term Newborn in Mexico
Congenital Zika Syndrome and Extra-Central Nervous System Detection of Zika Virus in a Pre-term Newborn in Mexico Open
Our findings demonstrate the ability of congenitally-acquired ZIKV to produce disseminated infections and the viral tropism towards epithelial cells.
View article: Expansion of the enteric virome in untreated HIV infection
Expansion of the enteric virome in untreated HIV infection Open
View article: Impact of HIV-associated immunodeficiency on the enteric bacterial microbiome
Impact of HIV-associated immunodeficiency on the enteric bacterial microbiome Open