<?xml version="1.0" encoding="UTF-8"?><xml><records><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Casimiro-Soriguer, Carlos S</style></author><author><style face="normal" font="default" size="100%">Perez-Florido, Javier</style></author><author><style face="normal" font="default" size="100%">Robles, Enrique A</style></author><author><style face="normal" font="default" size="100%">Lara, María</style></author><author><style face="normal" font="default" size="100%">Aguado, Andrea</style></author><author><style face="normal" font="default" size="100%">Rodríguez Iglesias, Manuel A</style></author><author><style face="normal" font="default" size="100%">Lepe, Jose A</style></author><author><style face="normal" font="default" size="100%">García, Federico</style></author><author><style face="normal" font="default" size="100%">Pérez-Alegre, Mónica</style></author><author><style face="normal" font="default" size="100%">Andújar, Eloísa</style></author><author><style face="normal" font="default" size="100%">Jiménez, Victoria E</style></author><author><style face="normal" font="default" size="100%">Camino, Lola P</style></author><author><style face="normal" font="default" size="100%">Loruso, Nicola</style></author><author><style face="normal" font="default" size="100%">Ameyugo, Ulises</style></author><author><style face="normal" font="default" size="100%">Vazquez, Isabel María</style></author><author><style face="normal" font="default" size="100%">Lozano, Carlota M</style></author><author><style face="normal" font="default" size="100%">Chaves, J Alberto</style></author><author><style face="normal" font="default" size="100%">Dopazo, Joaquin</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">The integrated genomic surveillance system of Andalusia (SIEGA) provides a One Health regional resource connected with the clinic.</style></title><secondary-title><style face="normal" font="default" size="100%">Sci Rep</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Sci Rep</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Animals</style></keyword><keyword><style  face="normal" font="default" size="100%">Drug Resistance, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Genome, Bacterial</style></keyword><keyword><style  face="normal" font="default" size="100%">Genomics</style></keyword><keyword><style  face="normal" font="default" size="100%">Humans</style></keyword><keyword><style  face="normal" font="default" size="100%">One Health</style></keyword><keyword><style  face="normal" font="default" size="100%">Virulence Factors</style></keyword><keyword><style  face="normal" font="default" size="100%">Whole Genome Sequencing</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2024</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2024 Aug 19</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">14</style></volume><pages><style face="normal" font="default" size="100%">19200</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;The One Health approach, recognizing the interconnectedness of human, animal, and environmental health, has gained significance amid emerging zoonotic diseases and antibiotic resistance concerns. This paper aims to demonstrate the utility of a collaborative tool, the SIEGA, for monitoring infectious diseases across domains, fostering a comprehensive understanding of disease dynamics and risk factors, highlighting the pivotal role of One Health surveillance systems. Raw whole-genome sequencing is processed through different species-specific open software that additionally reports the presence of genes associated to anti-microbial resistances and virulence. The SIEGA application is a Laboratory Information Management System, that allows customizing reports, detect transmission chains, and promptly alert on alarming genetic similarities. The SIEGA initiative has successfully accumulated a comprehensive collection of more than 1900 bacterial genomes, including Salmonella enterica, Listeria monocytogenes, Campylobacter jejuni, Escherichia coli, Yersinia enterocolitica and Legionella pneumophila, showcasing its potential in monitoring pathogen transmission, resistance patterns, and virulence factors. SIEGA enables customizable reports and prompt detection of transmission chains, highlighting its contribution to enhancing vigilance and response capabilities. Here we show the potential of genomics in One Health surveillance when supported by an appropriate bioinformatic tool. By facilitating precise disease control strategies and antimicrobial resistance management, SIEGA enhances global health security and reduces the burden of infectious diseases. The integration of health data from humans, animals, and the environment, coupled with advanced genomics, underscores the importance of a holistic One Health approach in mitigating health threats.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">1</style></issue></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Casimiro-Soriguer, Carlos S</style></author><author><style face="normal" font="default" size="100%">Perez-Florido, Javier</style></author><author><style face="normal" font="default" size="100%">Lara, María</style></author><author><style face="normal" font="default" size="100%">Camacho-Martinez, Pedro</style></author><author><style face="normal" font="default" size="100%">Merino-Diaz, Laura</style></author><author><style face="normal" font="default" size="100%">Pupo-Ledo, Inmaculada</style></author><author><style face="normal" font="default" size="100%">de Salazar, Adolfo</style></author><author><style face="normal" font="default" size="100%">Fuentes, Ana</style></author><author><style face="normal" font="default" size="100%">Viñuela, Laura</style></author><author><style face="normal" font="default" size="100%">Chueca, Natalia</style></author><author><style face="normal" font="default" size="100%">Martinez-Martinez, Luis</style></author><author><style face="normal" font="default" size="100%">Lorusso, Nicola</style></author><author><style face="normal" font="default" size="100%">Lepe, Jose A</style></author><author><style face="normal" font="default" size="100%">Dopazo, Joaquin</style></author><author><style face="normal" font="default" size="100%">García, Federico</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Molecular and phylogenetic characterization of the monkeypox outbreak in the South of Spain.</style></title><secondary-title><style face="normal" font="default" size="100%">Health Sci Rep</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Health Sci Rep</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2024</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2024 Mar</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">7</style></volume><pages><style face="normal" font="default" size="100%">e1965</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;&lt;b&gt;BACKGROUND AND AIM: &lt;/b&gt;Until the May 2022 Monkeypox (MPXV) outbreak, which spread rapidly to many non-endemic countries, the virus was considered a viral zoonosis limited to some African countries. The Andalusian circuit of genomic surveillance was rapidly applied to characterize the MPXV outbreak in the South of Spain.&lt;/p&gt;&lt;p&gt;&lt;b&gt;METHODS: &lt;/b&gt;Whole genome sequencing was used to obtain the genomic profiles of samples collected across the south of Spain, representative of all the provinces of Andalusia. Phylogenetic analysis was used to study the relationship of the isolates and the available sequences of the 2022 outbreak.&lt;/p&gt;&lt;p&gt;&lt;b&gt;RESULTS: &lt;/b&gt;Whole genome sequencing of a total of 160 MPXV viruses from the different provinces that reported cases were obtained. Interestingly, we report the sequences of MPXV viruses obtained from two patients who died. While one of the isolates bore no noteworthy mutations that explain a potential heightened virulence, in another patient the second consecutive genome sequence, performed after the administration of tecovirimat, uncovered a mutation within the A0A7H0DN30 gene, known to be a prime target for tecovirimat in its Vaccinia counterpart. In general, a low number of mutations were observed in the sequences reported, which were very similar to the reference of the 2022 outbreak (OX044336), as expected from a DNA virus. The samples likely correspond to several introductions of the circulating MPXV viruses from the last outbreak. The virus sequenced from one of the two patients that died presented a mutation in a gene that bears potential connections to drug resistance. This mutation was absent in the initial sequencing before treatment.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">3</style></issue></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Perez-Florido, Javier</style></author><author><style face="normal" font="default" size="100%">Casimiro-Soriguer, Carlos S</style></author><author><style face="normal" font="default" size="100%">Ortuno, Francisco</style></author><author><style face="normal" font="default" size="100%">Fernandez-Rueda, Jose L</style></author><author><style face="normal" font="default" size="100%">Aguado, Andrea</style></author><author><style face="normal" font="default" size="100%">Lara, María</style></author><author><style face="normal" font="default" size="100%">Riazzo, Cristina</style></author><author><style face="normal" font="default" size="100%">Rodriguez-Iglesias, Manuel A</style></author><author><style face="normal" font="default" size="100%">Camacho-Martinez, Pedro</style></author><author><style face="normal" font="default" size="100%">Merino-Diaz, Laura</style></author><author><style face="normal" font="default" size="100%">Pupo-Ledo, Inmaculada</style></author><author><style face="normal" font="default" size="100%">de Salazar, Adolfo</style></author><author><style face="normal" font="default" size="100%">Viñuela, Laura</style></author><author><style face="normal" font="default" size="100%">Fuentes, Ana</style></author><author><style face="normal" font="default" size="100%">Chueca, Natalia</style></author><author><style face="normal" font="default" size="100%">García, Federico</style></author><author><style face="normal" font="default" size="100%">Dopazo, Joaquin</style></author><author><style face="normal" font="default" size="100%">Lepe, Jose A</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Detection of High Level of Co-Infection and the Emergence of Novel SARS CoV-2 Delta-Omicron and Omicron-Omicron Recombinants in the Epidemiological Surveillance of Andalusia.</style></title><secondary-title><style face="normal" font="default" size="100%">Int J Mol Sci</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Int J Mol Sci</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2023</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2023 Jan 26</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">24</style></volume><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Recombination is an evolutionary strategy to quickly acquire new viral properties inherited from the parental lineages. The systematic survey of the SARS-CoV-2 genome sequences of the Andalusian genomic surveillance strategy has allowed the detection of an unexpectedly high number of co-infections, which constitute the ideal scenario for the emergence of new recombinants. Whole genome sequence of SARS-CoV-2 has been carried out as part of the genomic surveillance programme. Sample sources included the main hospitals in the Andalusia region. In addition to the increase of co-infections and known recombinants, three novel SARS-CoV-2 delta-omicron and omicron-omicron recombinant variants with two break points have been detected. Our observations document an epidemiological scenario in which co-infection and recombination are detected more frequently. Finally, we describe a family case in which co-infection is followed by the detection of a recombinant made from the two co-infecting variants. This increased number of recombinants raises the risk of emergence of recombinant variants with increased transmissibility and pathogenicity.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">3</style></issue></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Loucera, Carlos</style></author><author><style face="normal" font="default" size="100%">Perez-Florido, Javier</style></author><author><style face="normal" font="default" size="100%">Casimiro-Soriguer, Carlos S</style></author><author><style face="normal" font="default" size="100%">Ortuno, Francisco M</style></author><author><style face="normal" font="default" size="100%">Carmona, Rosario</style></author><author><style face="normal" font="default" size="100%">Bostelmann, Gerrit</style></author><author><style face="normal" font="default" size="100%">Martínez-González, L Javier</style></author><author><style face="normal" font="default" size="100%">Muñoyerro-Muñiz, Dolores</style></author><author><style face="normal" font="default" size="100%">Villegas, Román</style></author><author><style face="normal" font="default" size="100%">Rodríguez-Baño, Jesús</style></author><author><style face="normal" font="default" size="100%">Romero-Gómez, Manuel</style></author><author><style face="normal" font="default" size="100%">Lorusso, Nicola</style></author><author><style face="normal" font="default" size="100%">Garcia-León, Javier</style></author><author><style face="normal" font="default" size="100%">Navarro-Marí, Jose M</style></author><author><style face="normal" font="default" size="100%">Camacho-Martinez, Pedro</style></author><author><style face="normal" font="default" size="100%">Merino-Diaz, Laura</style></author><author><style face="normal" font="default" size="100%">Salazar, Adolfo de</style></author><author><style face="normal" font="default" size="100%">Viñuela, Laura</style></author><author><style face="normal" font="default" size="100%">Lepe, Jose A</style></author><author><style face="normal" font="default" size="100%">García, Federico</style></author><author><style face="normal" font="default" size="100%">Dopazo, Joaquin</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Assessing the Impact of SARS-CoV-2 Lineages and Mutations on Patient Survival.</style></title><secondary-title><style face="normal" font="default" size="100%">Viruses</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Viruses</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">COVID-19</style></keyword><keyword><style  face="normal" font="default" size="100%">Genome, Viral</style></keyword><keyword><style  face="normal" font="default" size="100%">Humans</style></keyword><keyword><style  face="normal" font="default" size="100%">mutation</style></keyword><keyword><style  face="normal" font="default" size="100%">Pandemics</style></keyword><keyword><style  face="normal" font="default" size="100%">Phylogeny</style></keyword><keyword><style  face="normal" font="default" size="100%">SARS-CoV-2</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2022</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2022 Aug 27</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">14</style></volume><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;&lt;b&gt;OBJECTIVES: &lt;/b&gt;More than two years into the COVID-19 pandemic, SARS-CoV-2 still remains a global public health problem. Successive waves of infection have produced new SARS-CoV-2 variants with new mutations for which the impact on COVID-19 severity and patient survival is uncertain.&lt;/p&gt;&lt;p&gt;&lt;b&gt;METHODS: &lt;/b&gt;A total of 764 SARS-CoV-2 genomes, sequenced from COVID-19 patients, hospitalized from 19th February 2020 to 30 April 2021, along with their clinical data, were used for survival analysis.&lt;/p&gt;&lt;p&gt;&lt;b&gt;RESULTS: &lt;/b&gt;A significant association of B.1.1.7, the alpha lineage, with patient mortality (log hazard ratio (LHR) = 0.51, C.I. = [0.14,0.88]) was found upon adjustment by all the covariates known to affect COVID-19 prognosis. Moreover, survival analysis of mutations in the SARS-CoV-2 genome revealed 27 of them were significantly associated with higher mortality of patients. Most of these mutations were located in the genes coding for the S, ORF8, and N proteins.&lt;/p&gt;&lt;p&gt;&lt;b&gt;CONCLUSIONS: &lt;/b&gt;This study illustrates how a combination of genomic and clinical data can provide solid evidence for the impact of viral lineage on patient survival.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">9</style></issue></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Ortuno, Francisco M</style></author><author><style face="normal" font="default" size="100%">Loucera, Carlos</style></author><author><style face="normal" font="default" size="100%">Casimiro-Soriguer, Carlos S</style></author><author><style face="normal" font="default" size="100%">Lepe, Jose A</style></author><author><style face="normal" font="default" size="100%">Camacho Martinez, Pedro</style></author><author><style face="normal" font="default" size="100%">Merino Diaz, Laura</style></author><author><style face="normal" font="default" size="100%">de Salazar, Adolfo</style></author><author><style face="normal" font="default" size="100%">Chueca, Natalia</style></author><author><style face="normal" font="default" size="100%">García, Federico</style></author><author><style face="normal" font="default" size="100%">Perez-Florido, Javier</style></author><author><style face="normal" font="default" size="100%">Dopazo, Joaquin</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Highly accurate whole-genome imputation of SARS-CoV-2 from partial or low-quality sequences.</style></title><secondary-title><style face="normal" font="default" size="100%">Gigascience</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Gigascience</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Genome, Viral</style></keyword><keyword><style  face="normal" font="default" size="100%">Phylogeny</style></keyword><keyword><style  face="normal" font="default" size="100%">SARS-CoV-2</style></keyword><keyword><style  face="normal" font="default" size="100%">Whole Genome Sequencing</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2021</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2021 12 02</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">10</style></volume><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;&lt;b&gt;BACKGROUND: &lt;/b&gt;The current SARS-CoV-2 pandemic has emphasized the utility of viral whole-genome sequencing in the surveillance and control of the pathogen. An unprecedented ongoing global initiative is producing hundreds of thousands of sequences worldwide. However, the complex circumstances in which viruses are sequenced, along with the demand of urgent results, causes a high rate of incomplete and, therefore, useless sequences. Viral sequences evolve in the context of a complex phylogeny and different positions along the genome are in linkage disequilibrium. Therefore, an imputation method would be able to predict missing positions from the available sequencing data.&lt;/p&gt;&lt;p&gt;&lt;b&gt;RESULTS: &lt;/b&gt;We have developed the impuSARS application, which takes advantage of the enormous number of SARS-CoV-2 genomes available, using a reference panel containing 239,301 sequences, to produce missing data imputation in viral genomes. ImpuSARS was tested in a wide range of conditions (continuous fragments, amplicons or sparse individual positions missing), showing great fidelity when reconstructing the original sequences, recovering the lineage with a 100% precision for almost all the lineages, even in very poorly covered genomes (&lt;20%).&lt;/p&gt;&lt;p&gt;&lt;b&gt;CONCLUSIONS: &lt;/b&gt;Imputation can improve the pace of SARS-CoV-2 sequencing production by recovering many incomplete or low-quality sequences that would be otherwise discarded. ImpuSARS can be incorporated in any primary data processing pipeline for SARS-CoV-2 whole-genome sequencing.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">12</style></issue><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/34865008?dopt=Abstract</style></custom1></record></records></xml>