0000000001087905
AUTHOR
ÁLvaro Chiner-oms
showing 18 related works from this author
Large genomics datasets shed light on the evolution of the Mycobacterium tuberculosis complex
2019
Review: 5 páginas, 1 figura
Integrative transnational analysis to dissect tuberculosis transmission events along the migratory route from Africa to Europe
2021
páginas, 4 figuras, 3 tablas
Evolutionary Dissection of the Dot/Icm System Based on Comparative Genomics of 58 Legionella Species
2019
14 páginas, 2 figuras, 2 tablas
Detection Of Genomic Variants Of SARS-CoV-2 Circulating In Wastewater By High-Throughput Sequencing
2021
The use of SARS-CoV-2 metagenomics in wastewater can allow the detection of variants circulating at community level. After comparing with clinical databases, we identified three novel variants in the spike gene, and six new variants in the spike detected for the first time in Spain. We finally support the hypothesis that this approach allows the identification of unknown SARS-CoV-2 variants or detected at only low frequencies in clinical genomes.
Evolutionary and phenotypic characterization of spike mutations in a new SARS-CoV-2 Lineage reveals two Variants of Interest
2021
Molecular epidemiology of SARS-CoV-2 aims to monitor the appearance of new variants with the potential to change the virulence or transmissibility of the virus. During the first year of SARS-CoV-2 evolution, numerous variants with possible public health impact have emerged. We have detected two mutations in the Spike protein at amino acid positions 1163 and 1167 that have appeared independently multiple times in different genetic backgrounds, indicating they may increase viral fitness. Interestingly, the majority of these sequences appear in transmission clusters, with the genotype encoding mutations at both positions increasing in frequency more than single-site mutants. This genetic outco…
EvalMSA: A Program to Evaluate Multiple Sequence Alignments and Detect Outliers
2016
8 páginas, 3 figuras, 2 tablas.
Towards next-generation diagnostics for tuberculosis: identification of novel molecular targets by large-scale comparative genomics.
2020
5 páginas, 2 figuras. AVAILABILITY AND IMPLEMENTATION: The database of non-tuberculous mycobacteria assemblies can be accessed at: 10.5281/zenodo.3374377. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online: http://dx.doi.org/10.1093/bioinformatics/btz729
Whole genome sequencing-based analysis of tuberculosis (TB) in migrants: rapid tools for cross-border surveillance and to distinguish between recent …
2019
14 páginas, 7 figuras
Recurrences of multidrug-resistant tuberculosis: Strains involved, within-host diversity, and fine-tuned allocation of reinfections
2020
34 páginas, 13 figuras
Towards next generation diagnostics for tuberculosis: identification of novel molecular targets by large-scale comparative genomics
2019
AbstractTuberculosis remains one of the main causes of death worldwide. The long and cumbersome process of culturingMycobacterium tuberculosiscomplex (MTBC) bacteria has encouraged the development of specific molecular tools for detecting the pathogen. Most of these tools aim to become novel tuberculosis diagnostics, and big efforts and resources are invested in their development, looking for the endorsement of the main public health agencies. Surprisingly, no study had been conducted where the vast amount of genomic data available is used to identify the best MTBC diagnostic markers. In this work, we use large-scale comparative genomics to provide a catalog of 30 characterized loci that ar…
Genomic determinants of speciation and spread of the Mycobacterium tuberculosis complex
2019
14 páginas, 6 figuras
Spatial and temporal distribution of SARS-CoV-2 diversity circulating in wastewater
2022
Wastewater-based epidemiology (WBE) has proven to be an effective tool for epidemiological surveillance of SARS-CoV-2 during the current COVID-19 pandemic. Furthermore, combining WBE together with high-throughput sequencing techniques can be useful for the analysis of SARS-CoV-2 viral diversity present in a given sample. The present study focuses on the genomic analysis of SARS-CoV-2 in 76 sewage samples collected during the three epidemiological waves that occurred in Spain from 14 wastewater treatment plants distributed throughout the country. The results obtained demonstrate that the metagenomic analysis of SARS-CoV-2 in wastewater allows the detection of mutations that define the B.1.1.…
Gene expression models based on a reference laboratory strain are bad predictors of Mycobacterium tuberculosis complex transcriptional diversity
2016
ABSTRACTSpecies of the Mycobacterium tuberculosis complex (MTBC) kill more people every year than any other infectious disease. As a consequence of its global distribution and parallel evolution with the human host the bacteria is not genetically homogeneous. The observed genetic heterogeneity has relevance at different phenotypic levels, from gene expression to epidemiological dynamics. However current systems biology datasets have focused in the laboratory reference strain H37Rv. By using large expression datasets testing the role of almost two hundred transcription factors, we have constructed computational models to grab the expression dynamics of Mycobacterium tuberculosis H37Rv genes.…
GENOMIC EPIDEMIOLOGY OF TUBERCULOSIS: FROM WITHIN HOST EVOLUTION TO GLOBAL MIGRATION PATTERNS
2018
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The first wave of the Spanish COVID-19 epidemic was associated with early introductions and fast spread of a dominating genetic variant
2020
The COVID-19 pandemic has shaken the world since the beginning of 2020. Spain is among the European countries with the highest incidence of the disease during the first pandemic wave. We established a multidisciplinar consortium to monitor and study the evolution of the epidemic, with the aim of contributing to decision making and stopping rapid spreading across the country. We present the results for 2170 sequences from the first wave of the SARS-Cov-2 epidemic in Spain and representing 12% of diagnosed cases until 14th March. This effort allows us to document at least 500 initial introductions, between early February-March from multiple international sources. Importantly, we document the …
Mycobacterium tuberculosis Acquires Limited Genetic Diversity in Prolonged Infections, Reactivations and Transmissions Involving Multiple Hosts
2018
9 páginas, 5 figuras y material suplementario en: https://www.frontiersin.org/articles/10.3389/fmicb.2017.02661/full#supplementary-material
Evolutionary systems biology of the Mycobacterium tuberculosis complex
2019
Tesis doctoral, 214 páginas
Complete analysis of the epidemiological scenario around a SARS-CoV-2 reinfection: previous infection events and subsequent transmission
2021
9 páginas, 3 figuras. The data that support the findings of this study (Fastq files) are publicly available. Fastq files above the GISAID thresholds were deposited at GISAID (hCoV-19/Spain/MD-IBV-99007733/2020, hCoV-19/Spain/MD-IBV-99007151/2020, hCoV-19/Spain/MD-IBV-99007734/2020, and hCoV-19/Spain/MDIBV-99007170/2020). All sequences were also deposited at the ENA (European Nucleotide Archive; https:// www.ebi.ac.uk/ena/browser/home) (ERR5698024, ERR5697187, ERR6459974, ERR5698025, and ERR5697254).