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Article ; Online: Is SARS-CoV-2 an oncogenic virus?

Gómez-Carballa, Alberto / Martinón-Torres, Federico / Salas, Antonio

2022 Volume 85, Issue 5, Page(s) 573–607

MeSH term(s)	COVID-19 ; Humans ; Oncogenic Viruses ; RNA, Viral ; SARS-CoV-2
Chemical Substances	RNA, Viral
Language	English
Publishing date	2022-08-09
Publishing country	England
Document type	Letter ; Research Support, Non-U.S. Gov't ; Comment
ZDB-ID	424417-5
ISSN	1532-2742 ; 0163-4453
ISSN (online)	1532-2742
ISSN	0163-4453
DOI	10.1016/j.jinf.2022.08.005
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Zs.A 1501: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (1.OG) ab Jg. 2022: Lesesaal (EG)
Zs.MG 48: Show issues

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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
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Zs.A 2272: Show issues

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Article ; Online: CD14 and Related Genes in Respiratory Morbidity After Respiratory Syncytial Virus Infection.

Gómez-Carballa, Alberto / Pischedda, Sara / Rivero-Calle, Irene / Montoto-Louzao, Julian / Martinón-Torres, Federico / Salas, Antonio

The Journal of infectious diseases

2022 Volume 226, Issue 7, Page(s) 1295–1297

MeSH term(s)	Humans ; Morbidity ; Palivizumab ; Respiratory Syncytial Virus Infections/epidemiology ; Respiratory Syncytial Virus Infections/genetics ; Respiratory Syncytial Virus, Human/genetics
Chemical Substances	Palivizumab (DQ448MW7KS)
Language	English
Publishing date	2022-06-17
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Comment
ZDB-ID	3019-3
ISSN	1537-6613 ; 0022-1899
ISSN (online)	1537-6613
ISSN	0022-1899
DOI	10.1093/infdis/jiac248
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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
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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
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Article ; Online: Extraordinary claims require extraordinary evidence in asserted mtDNA biparental inheritance.

Salas, Antonio / Schönherr, Sebastian / Bandelt, Hans-Jürgen / Gómez-Carballa, Alberto / Weissensteiner, Hansi

Forensic science international. Genetics

2020 Volume 47, Page(s) 102274

Abstract: A breakthrough article published in PNAS by Luo et al. challenges a central dogma in biology which states that the mitochondrial DNA (mtDNA) in humans is inherited exclusively from the mother. We re-analyzed original FASTQ files and results reported by ... ...

Abstract	A breakthrough article published in PNAS by Luo et al. challenges a central dogma in biology which states that the mitochondrial DNA (mtDNA) in humans is inherited exclusively from the mother. We re-analyzed original FASTQ files and results reported by Luo et al. to investigate methodological issues (e.g. nuclear mitochondrial DNA or NUMTs, DNA rearrangements) that could lead to biological misinterpretations. A comprehensive analysis of their data reveals several methodological and analytical issues that must be carefully addressed before challenging the current paradigm. We first show that the probability of the findings described by the authors is extremely small (most likely below 10
MeSH term(s)	Cell Nucleus ; DNA, Mitochondrial ; Haplotypes ; Humans ; Mitochondria/genetics
Chemical Substances	DNA, Mitochondrial
Language	English
Publishing date	2020-03-12
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Comment
ZDB-ID	2493339-9
ISSN	1878-0326 ; 1872-4973
ISSN (online)	1878-0326
ISSN	1872-4973
DOI	10.1016/j.fsigen.2020.102274
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Zs.A 6764: Show issues

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Article: Sensogenomics of music and Alzheimer's disease: An interdisciplinary view from neuroscience, transcriptomics, and epigenomics.

Navarro, Laura / Gómez-Carballa, Alberto / Pischedda, Sara / Montoto-Louzao, Julián / Viz-Lasheras, Sandra / Camino-Mera, Alba / Hinault, Thomas / Martinón-Torres, Federico / Salas, Antonio

Frontiers in aging neuroscience

2023 Volume 15, Page(s) 1063536

Abstract: Introduction: The relationship between music and Alzheimer's disease (AD) has been approached by different disciplines, but most of our outstanding comes from neuroscience.: Methods: First, we systematically reviewed the state-of-the-art of ... ...

Abstract	Introduction: The relationship between music and Alzheimer's disease (AD) has been approached by different disciplines, but most of our outstanding comes from neuroscience. Methods: First, we systematically reviewed the state-of-the-art of neuroscience and cognitive sciences research on music and AD (>100 studies), and the progress made on the therapeutic impact of music stimuli in memory. Next, we meta-analyzed transcriptomic and epigenomic data of AD patients to search for commonalities with genes and pathways previously connected to music in genome association, epigenetic, and gene expression studies. Results: Our findings indicate that >93% of the neuroscience/ cognitive sciences studies indicate at least one beneficial effect of music on patients with neurodegenerative diseases, being improvements on memory and cognition the most frequent outcomes; other common benefits were on social behavior, mood and emotion, anxiety and agitation, quality of life, and depression. Out of the 334 music-related genes, 127 (38%) were found to be linked to epigenome/transcriptome analysis in AD (vs. healthy controls); some of them ( Discussion: The present study indicate that the vast majority of neuroscientific studies unambiguously show that music has a beneficial effect on health, being the most common benefits relevant to Alzheimer's disease. These findings illuminate a new roadmap for genetic research in neurosciences, and musical interventions in AD and other neurodegenerative conditions.
Language	English
Publishing date	2023-02-03
Publishing country	Switzerland
Document type	Systematic Review
ZDB-ID	2558898-9
ISSN	1663-4365
ISSN	1663-4365
DOI	10.3389/fnagi.2023.1063536
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Article ; Online: Lung transcriptomics of K18-hACE2 mice highlights mechanisms and genes involved in the MVA-S vaccine-mediated immune response and protection against SARS-CoV-2 infection.

Gómez-Carballa, Alberto / Albericio, Guillermo / Montoto-Louzao, Julián / Pérez, Patricia / Astorgano, David / Rivero-Calle, Irene / Martinón-Torres, Federico / Esteban, Mariano / Salas, Antonio / García-Arriaza, Juan

Antiviral research

2023 Volume 220, Page(s) 105760

Abstract: Unravelling the molecular mechanism of COVID-19 vaccines through transcriptomic pathways involved in the host response to SARS-CoV-2 infection is key to understand how vaccines work, and for the development of optimized COVID-19 vaccines that can prevent ...

Abstract	Unravelling the molecular mechanism of COVID-19 vaccines through transcriptomic pathways involved in the host response to SARS-CoV-2 infection is key to understand how vaccines work, and for the development of optimized COVID-19 vaccines that can prevent the emergence of SARS-CoV-2 variants of concern (VoCs) and future outbreaks. In this study, we investigated the effects of vaccination with a modified vaccinia virus Ankara (MVA)-based vector expressing the full-length SARS-CoV-2 spike protein (MVA-S) on the lung transcriptome from susceptible K18-hACE2 mice after SARS-CoV-2 infection. One dose of MVA-S regulated genes related to viral infection control, inflammation processes, T-cell response, cytokine production and IFN-γ signalling. Down-regulation of Rhcg and Tnfsf18 genes post-vaccination with one and two doses of MVA-S may represent a mechanism for controlling infection immunity and vaccine-induced protection. One dose of MVA-S provided partial protection with a distinct lung transcriptomic profile to healthy animals, while two doses of MVA-S fully protected against infection with a transcriptomic profile comparable to that of non-vaccinated healthy animals. This suggests that the MVA-S booster generates a robust and rapid antigen-specific immune response preventing virus infection. Notably, down-regulation of Atf3 and Zbtb16 genes in mice vaccinated with two doses of MVA-S may contribute to vaccine control of innate immune system and inflammation processes in the lungs during SARS-CoV-2 infection. This study shows host transcriptomic mechanisms likely involved in the MVA-S vaccine-mediated immune response against SARS-CoV-2 infection, which could help in improving vaccine dose assessment and developing novel, well-optimized SARS-CoV-2 vaccine candidates against prevalent or emerging VoCs.
MeSH term(s)	Humans ; Animals ; Mice ; Vaccinia virus/genetics ; COVID-19 Vaccines/genetics ; Antibodies, Viral ; COVID-19/prevention & control ; SARS-CoV-2/genetics ; Vaccines ; Gene Expression Profiling ; Immunity ; Lung ; Inflammation
Chemical Substances	spike protein, SARS-CoV-2 ; COVID-19 Vaccines ; K-18 conjugate ; Antibodies, Viral ; Vaccines
Language	English
Publishing date	2023-11-21
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	306628-9
ISSN	1872-9096 ; 0166-3542
ISSN (online)	1872-9096
ISSN	0166-3542
DOI	10.1016/j.antiviral.2023.105760
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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
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Zs.A 3729: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (2.OG) ab Jg. 2022: Lesesaal (EG)
Zs.MG 8: Show issues

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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
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