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  1. Article: Risk Analysis by Age on the Burden of Meningococcal Disease in Spain.

    Rivero-Calle, Irene / Raguindin, Peter Francis / Pardo-Seco, Jacobo / Martinon-Torres, Federico

    Vaccines

    2022  Volume 10, Issue 4

    Abstract: We conducted an age-based risk analysis of meningococcal disease in Spain to provide prospects on a rational vaccine schedule in pediatrics. We used the National Hospital Registry to estimate meningococcal hospitalization rate. Population census for each ...

    Abstract We conducted an age-based risk analysis of meningococcal disease in Spain to provide prospects on a rational vaccine schedule in pediatrics. We used the National Hospital Registry to estimate meningococcal hospitalization rate. Population census for each year was used as the denominator in computing the hospitalization rate. We computed the odds ratio of each age using <1 year old as a reference group. From 1998 to 2017, 13,554 hospitalized cases were diagnosed, with a declining trend across the years. Infants (<1 year, n = 2425) and children (1−14 years, n = 6053) comprised the majority of all hospitalized meningococcal disease in Spain (62.5% or 8474/13,554). The incidence of hospitalization decreased dramatically with age from 56.2/100,000 in <1-year-old children to 1.3/100,000 in >5-year-old children. There was a dramatic decline in risk in 1 year (OR 0.58) to 4 years of age (OR 0.21). The risk continued to decline until 13 years old. Afterward, it had a minimal upward trajectory observed at 14−17 years old (OR 0.08). Infants and adolescents are at continued risk of invasive meningococcal disease in Spain. The highest risk occurs in infants. Surveillance data, together with evidence on long-term immunogenicity and capacity for herd effect, should be considered for a more relevant immunization schedule.
    Language English
    Publishing date 2022-04-12
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2703319-3
    ISSN 2076-393X
    ISSN 2076-393X
    DOI 10.3390/vaccines10040592
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: Superspreading in the emergence of COVID-19 variants.

    Gómez-Carballa, Alberto / Pardo-Seco, Jacobo / Bello, Xabier / Martinón-Torres, Federico / Salas, Antonio

    Trends in genetics : TIG

    2021  Volume 37, Issue 12, Page(s) 1069–1080

    Abstract: Superspreading and variants of concern (VOC) of the human pathogen severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are the main catalyzers of the coronavirus disease 2019 (COVID-19) pandemic. However, measuring their individual impact is ... ...

    Abstract Superspreading and variants of concern (VOC) of the human pathogen severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are the main catalyzers of the coronavirus disease 2019 (COVID-19) pandemic. However, measuring their individual impact is challenging. By examining the largest database of SARS-CoV-2 genomes The Global Initiative on Sharing Avian Influenza Data [GISAID; n >1.2 million high-quality (HQ) sequences], we present evidence suggesting that superspreading has had a key role in the epidemiological predominance of VOC. There are clear signatures in the database compatible with large superspreading events (SSEs) coinciding chronologically with the worst epidemiological scenarios triggered by VOC. The data suggest that, without the randomness effect of the genetic drift facilitated by superspreading, new VOC of SARS-CoV-2 would have had more limited chance of success.
    MeSH term(s) Animals ; COVID-19 ; Humans ; Pandemics ; SARS-CoV-2/classification
    Language English
    Publishing date 2021-09-08
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 619240-3
    ISSN 1362-4555 ; 0168-9525 ; 0168-9479
    ISSN (online) 1362-4555
    ISSN 0168-9525 ; 0168-9479
    DOI 10.1016/j.tig.2021.09.003
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article: Pitfalls of barcodes in the study of worldwide SARS-CoV-2 variation and phylodynamics.

    Pardo-Seco, Jacobo / Gómez-Carballa, Alberto / Bello, Xabier / Martinón-Torres, Federico / Salas, Antonio

    Zoological research

    2021  Volume 42, Issue 1, Page(s) 87–93

    Abstract: Analysis of SARS-CoV-2 genome variation using a minimal number of selected informative sites conforming a genetic barcode presents several drawbacks. We show that purely mathematical procedures for site selection should be supervised by known phylogeny ( ... ...

    Abstract Analysis of SARS-CoV-2 genome variation using a minimal number of selected informative sites conforming a genetic barcode presents several drawbacks. We show that purely mathematical procedures for site selection should be supervised by known phylogeny (i) to ensure that solid tree branches are represented instead of mutational hotspots with poor phylogeographic proprieties, and (ii) to avoid phylogenetic redundancy. We propose a procedure that prevents information redundancy in site selection by considering the cumulative informativeness of previously selected sites (as a proxy for phylogenetic-based criteria). This procedure demonstrates that, for short barcodes (e.g., 11 sites), there are thousands of informative site combinations that improve previous proposals. We also show that barcodes based on worldwide databases inevitably prioritize variants located at the basal nodes of the phylogeny, such that most representative genomes in these ancestral nodes are no longer in circulation. Consequently, coronavirus phylodynamics cannot be properly captured by universal genomic barcodes because most SARS-CoV-2 variation is generated in geographically restricted areas by the continuous introduction of domestic variants.
    MeSH term(s) Algorithms ; COVID-19/virology ; DNA Barcoding, Taxonomic ; Genetic Variation ; Genome, Viral ; Humans ; Mutation ; Phylogeny ; Phylogeography ; SARS-CoV-2/classification ; SARS-CoV-2/genetics ; SARS-CoV-2/isolation & purification
    Language English
    Publishing date 2021-01-07
    Publishing country China
    Document type Letter
    ISSN 2095-8137
    ISSN 2095-8137
    DOI 10.24272/j.issn.2095-8137.2020.364
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Risk Analysis by Age on the Burden of Meningococcal Disease in Spain

    Irene Rivero-Calle / Peter Francis Raguindin / Jacobo Pardo-Seco / Federico Martinon-Torres

    Vaccines, Vol 10, Iss 592, p

    2022  Volume 592

    Abstract: We conducted an age-based risk analysis of meningococcal disease in Spain to provide prospects on a rational vaccine schedule in pediatrics. We used the National Hospital Registry to estimate meningococcal hospitalization rate. Population census for each ...

    Abstract We conducted an age-based risk analysis of meningococcal disease in Spain to provide prospects on a rational vaccine schedule in pediatrics. We used the National Hospital Registry to estimate meningococcal hospitalization rate. Population census for each year was used as the denominator in computing the hospitalization rate. We computed the odds ratio of each age using <1 year old as a reference group. From 1998 to 2017, 13,554 hospitalized cases were diagnosed, with a declining trend across the years. Infants (<1 year, n = 2425) and children (1–14 years, n = 6053) comprised the majority of all hospitalized meningococcal disease in Spain (62.5% or 8474/13,554). The incidence of hospitalization decreased dramatically with age from 56.2/100,000 in <1-year-old children to 1.3/100,000 in >5-year-old children. There was a dramatic decline in risk in 1 year (OR 0.58) to 4 years of age (OR 0.21). The risk continued to decline until 13 years old. Afterward, it had a minimal upward trajectory observed at 14–17 years old (OR 0.08). Infants and adolescents are at continued risk of invasive meningococcal disease in Spain. The highest risk occurs in infants. Surveillance data, together with evidence on long-term immunogenicity and capacity for herd effect, should be considered for a more relevant immunization schedule.
    Keywords meningococcal vaccines ; meningococcal infections ; invasive diseases ; Neisseria meningitides ; Medicine ; R
    Subject code 610
    Language English
    Publishing date 2022-04-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article ; Online: A Timeframe for SARS-CoV-2 Genomes: A Proof of Concept for Postmortem Interval Estimations.

    Pardo-Seco, Jacobo / Bello, Xabier / Gómez-Carballa, Alberto / Martinón-Torres, Federico / Muñoz-Barús, José Ignacio / Salas, Antonio

    International journal of molecular sciences

    2022  Volume 23, Issue 21

    Abstract: Establishing the timeframe when a particular virus was circulating in a population could be useful in several areas of biomedical research, including microbiology and legal medicine. Using simulations, we demonstrate that the circulation timeframe of an ... ...

    Abstract Establishing the timeframe when a particular virus was circulating in a population could be useful in several areas of biomedical research, including microbiology and legal medicine. Using simulations, we demonstrate that the circulation timeframe of an unknown SARS-CoV-2 genome in a population (hereafter, estimated time of a queried genome [QG];
    MeSH term(s) Humans ; SARS-CoV-2/genetics ; Phylogeny ; COVID-19 ; Genome, Viral ; Mutation
    Language English
    Publishing date 2022-10-25
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2019364-6
    ISSN 1422-0067 ; 1422-0067 ; 1661-6596
    ISSN (online) 1422-0067
    ISSN 1422-0067 ; 1661-6596
    DOI 10.3390/ijms232112899
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Improving Influenza Vaccine Acceptance in Children Leveraging on COVID-19 Vaccination Lessons.

    Ares-Gomez, Sonia / Mallah, Narmeen / Pardo-Seco, Jacobo / Nartallo-Penas, Victoria / Mirás-Carballal, Susana / Rodriguez-Tenreiro-Sánchez, Carmen / Rivero-Calle, Irene / Piñeiro-Sotelo, Marta / Durán-Parrondo, Carmen / Martinón-Torres, Federico

    Archivos de bronconeumologia

    2023  Volume 59, Issue 8, Page(s) 531–533

    MeSH term(s) Humans ; Child ; Influenza Vaccines ; COVID-19 Vaccines ; COVID-19/prevention & control ; Vaccination ; Influenza, Human/epidemiology ; Influenza, Human/prevention & control
    Chemical Substances Influenza Vaccines ; COVID-19 Vaccines
    Language Spanish
    Publishing date 2023-03-21
    Publishing country Spain
    Document type Case Reports
    ZDB-ID 733126-5
    ISSN 1579-2129 ; 0300-2896
    ISSN (online) 1579-2129
    ISSN 0300-2896
    DOI 10.1016/j.arbres.2023.03.011
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Mapping genome variation of SARS-CoV-2 worldwide highlights the impact of COVID-19 super-spreaders.

    Gómez-Carballa, Alberto / Bello, Xabier / Pardo-Seco, Jacobo / Martinón-Torres, Federico / Salas, Antonio

    Genome research

    2020  Volume 30, Issue 10, Page(s) 1434–1448

    Abstract: The human pathogen severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the major pandemic of the twenty-first century. We analyzed more than 4700 SARS-CoV-2 genomes and associated metadata retrieved from public repositories. ... ...

    Abstract The human pathogen severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the major pandemic of the twenty-first century. We analyzed more than 4700 SARS-CoV-2 genomes and associated metadata retrieved from public repositories. SARS-CoV-2 sequences have a high sequence identity (>99.9%), which drops to >96% when compared to bat coronavirus genome. We built a mutation-annotated reference SARS-CoV-2 phylogeny with two main macro-haplogroups, A and B, both of Asian origin, and more than 160 sub-branches representing virus strains of variable geographical origins worldwide, revealing a rather uniform mutation occurrence along branches that could have implications for diagnostics and the design of future vaccines. Identification of the root of SARS-CoV-2 genomes is not without problems, owing to conflicting interpretations derived from either using the bat coronavirus genomes as an outgroup or relying on the sampling chronology of the SARS-CoV-2 genomes and TMRCA estimates; however, the overall scenario favors haplogroup A as the ancestral node. Phylogenetic analysis indicates a TMRCA for SARS-CoV-2 genomes dating to November 12, 2019, thus matching epidemiological records. Sub-haplogroup A2 most likely originated in Europe from an Asian ancestor and gave rise to subclade A2a, which represents the major non-Asian outbreak, especially in Africa and Europe. Multiple founder effect episodes, most likely associated with super-spreader hosts, might explain COVID-19 pandemic to a large extent.
    MeSH term(s) Animals ; Asia/epidemiology ; Base Sequence/genetics ; Betacoronavirus/genetics ; COVID-19 ; Chiroptera/virology ; Chromosome Mapping ; Coronavirus Infections/epidemiology ; Europe/epidemiology ; Evolution, Molecular ; Genetic Variation/genetics ; Genome, Viral/genetics ; Humans ; Pandemics ; Phylogeny ; Phylogeography ; Pneumonia, Viral/epidemiology ; SARS-CoV-2 ; Sequence Homology, Nucleic Acid
    Keywords covid19
    Language English
    Publishing date 2020-09-02
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1284872-4
    ISSN 1549-5469 ; 1088-9051 ; 1054-9803
    ISSN (online) 1549-5469
    ISSN 1088-9051 ; 1054-9803
    DOI 10.1101/gr.266221.120
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Pitfalls of barcodes in the study of worldwide SARS-CoV-2 variation and phylodynamics

    Jacobo Pardo-Seco / Alberto Gómez-Carballa / Xabier Bello / Federico Martinón-Torres / Antonio Salas

    Zoological Research, Vol 42, Iss 1, Pp 87-

    2021  Volume 93

    Abstract: Analysis of SARS-CoV-2 genome variation using a minimal number of selected informative sites conforming a genetic barcode presents several drawbacks. We show that purely mathematical procedures for site selection should be supervised by known phylogeny ( ... ...

    Abstract Analysis of SARS-CoV-2 genome variation using a minimal number of selected informative sites conforming a genetic barcode presents several drawbacks. We show that purely mathematical procedures for site selection should be supervised by known phylogeny (i) to ensure that solid tree branches are represented instead of mutational hotspots with poor phylogeographic proprieties, and (ii) to avoid phylogenetic redundancy. We propose a procedure that prevents information redundancy in site selection by considering the cumulative informativeness of previously selected sites (as a proxy for phylogenetic-based criteria). This procedure demonstrates that, for short barcodes (e.g., 11 sites), there are thousands of informative site combinations that improve previous proposals. We also show that barcodes based on worldwide databases inevitably prioritize variants located at the basal nodes of the phylogeny, such that most representative genomes in these ancestral nodes are no longer in circulation. Consequently, coronavirus phylodynamics cannot be properly captured by universal genomic barcodes because most SARS-CoV-2 variation is generated in geographically restricted areas by the continuous introduction of domestic variants.
    Keywords sars-cov-2 ; covid-19 ; phylogeny ; phylodynamics ; barcode ; informative subtype markers ; Zoology ; QL1-991
    Subject code 572
    Language English
    Publishing date 2021-01-01T00:00:00Z
    Publisher Science Press, PR China
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  9. Article ; Online: Biogeographical informativeness of Y-STR haplotypes.

    Pardo-Seco, Jacobo / Gómez-Carballa, Alberto / Bello, Xabier / Martinón-Torres, Federico / Salas, Antonio

    Science bulletin

    2019  Volume 64, Issue 19, Page(s) 1381–1384

    Language English
    Publishing date 2019-07-26
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 2816140-3
    ISSN 2095-9281 ; 2095-9273
    ISSN (online) 2095-9281
    ISSN 2095-9273
    DOI 10.1016/j.scib.2019.07.025
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Identification of a Minimal 3-Transcript Signature to Differentiate Viral from Bacterial Infection from Best Genome-Wide Host RNA Biomarkers: A Multi-Cohort Analysis.

    Gómez-Carballa, Alberto / Barral-Arca, Ruth / Cebey-López, Miriam / Bello, Xabier / Pardo-Seco, Jacobo / Martinón-Torres, Federico / Salas, Antonio

    International journal of molecular sciences

    2021  Volume 22, Issue 6

    Abstract: The fight against the spread of antibiotic resistance is one of the most important challenges facing health systems worldwide. Given the limitations of current diagnostic methods, the development of fast and accurate tests for the diagnosis of viral and ... ...

    Abstract The fight against the spread of antibiotic resistance is one of the most important challenges facing health systems worldwide. Given the limitations of current diagnostic methods, the development of fast and accurate tests for the diagnosis of viral and bacterial infections would improve patient management and treatment, as well as contribute to reducing antibiotic misuse in clinical settings. In this scenario, analysis of host transcriptomics constitutes a promising target to develop new diagnostic tests based on the host-specific response to infections. We carried out a multi-cohort meta-analysis of blood transcriptomic data available in public databases, including 11 different studies and 1209 samples from virus- (
    MeSH term(s) Area Under Curve ; Bacterial Infections/genetics ; Bacterial Infections/microbiology ; Biomarkers ; Cohort Studies ; Computational Biology/methods ; Gene Expression Profiling ; Host-Pathogen Interactions/genetics ; Humans ; Meta-Analysis as Topic ; ROC Curve ; Transcriptome ; Virus Diseases/genetics ; Virus Diseases/virology
    Chemical Substances Biomarkers
    Language English
    Publishing date 2021-03-19
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2019364-6
    ISSN 1422-0067 ; 1422-0067 ; 1661-6596
    ISSN (online) 1422-0067
    ISSN 1422-0067 ; 1661-6596
    DOI 10.3390/ijms22063148
    Database MEDical Literature Analysis and Retrieval System OnLINE

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