Secuenciación del genoma de 9 aislados del virus ectromelia: implicaciones evolutivas y determinantes de virulencia

Tesis doctoral inédita. Universidad Autónoma de Madrid, Facultad de Ciencias, Departamento de Biología Molecular. Fecha de lectura: 12-07-2013La autora de la Tesis Doctoral ha disfrutado de una ayuda Predoctoral de Formarción de Personal Investigador (referencia BES-2008-002202) asociada al proyecto de Investigación SAF2006-0810

Comparative Pathogenesis, Genomics and Phylogeography of Mousepox

Ectromelia virus (ECTV), the causative agent of mousepox, has threatened laboratory mouse colonies worldwide for almost a century. Mousepox has been valuable for the understanding of poxvirus pathogenesis and immune evasion. Here, we have monitored in parallel the pathogenesis of nine ECTVs in BALB/cJ mice and report the full-length genome sequence of eight novel ECTV isolates or strains, including the first ECTV isolated from a field mouse, ECTV-MouKre. This approach allowed us to identify several genes, absent in strains attenuated through serial passages in culture, that may play a role in virulence and a set of putative genes that may be involved in enhancing viral growth in vitro. We identified a putative strong inhibitor of the host inflammatory response in ECTV-MouKre, an isolate that did not cause local foot swelling and developed a moderate virulence. Most of the ECTVs, except ECTV-Hampstead, encode a truncated version of the P4c protein that impairs the recruitment of virions into the A-type inclusion bodies, and our data suggest that P4c may play a role in viral dissemination and transmission. This is the first comprehensive report that sheds light into the phylogenetic and geographic relationship of the worldwide outbreak dynamics for the ECTV species.Peer Reviewe

The genome sequence of the emerging common midwife toad virus identifies an evolutionary intermediate within ranaviruses

Worldwide amphibian population declines have been ascribed to global warming, increasing pollution levels, and other factors directly related to human activities. These factors may additionally be favoring the emergence of novel pathogens. In this report, we have determined the complete genome sequence of the emerging common midwife toad ranavirus (CMTV), which has caused fatal disease in several amphibian species across Europe. Phylogenetic and gene content analyses of the first complete genomic sequence from a ranavirus isolated in Europe show that CMTV is an amphibian-like ranavirus (ALRV). However, the CMTV genome structure is novel and represents an intermediate evolutionary stage between the two previously described ALRV groups. We find that CMTV clusters with several other ranaviruses isolated from different hosts and locations which might also be included in this novel ranavirus group. This work sheds light on the phylogenetic relationships within this complex group of emerging, disease-causing viruses. © 2012, American Society for Microbiology.Peer Reviewe

Complete genome sequence of the European sheatfish virus

Viral diseases are an increasing threat to the thriving aquaculture industry worldwide. An emerging group of fish pathogens is formed by several ranaviruses, which have been isolated at different locations from freshwater and seawater fish species since 1985.We report the complete genome sequence of European sheatfish ranavirus (ESV), the first ranavirus isolated in Europe, which causes high mortality rates in infected sheatfish (Silurus glanis) and in other species. Analysis of the genome sequence shows that ESV belongs to the amphibian- like ranaviruses and is closely related to the epizootic hematopoietic necrosis virus (EHNV), a disease agent geographically confined to the Australian continent and notifiable to the World Organization for Animal HealthThis work was supported by grant AGL 2009-08711 from the Spanish Ministerio de Ciencia e Innovación. Alberto López-Bueno and Carla Mavian are recipients of Ramón y Cajal and Formación de Personal Investigador fellowships, respectively, from the same institutio

The genome sequence of the emerging common midwife toad virus identifies an evolutionary intermediate within ranaviruses

Worldwide amphibian population declines have been ascribed to global warming, increasing pollution levels, and other factors directly related to human activities. These factors may additionally be favoring the emergence of novel pathogens. In this report, we have determined the complete genome sequence of the emerging common midwife toad ranavirus (CMTV), which has caused fatal disease in several amphibian species across Europe. Phylogenetic and gene content analyses of the first complete genomic sequence from a ranavirus isolated in Europe show that CMTV is an amphibian-like ranavirus (ALRV). However, the CMTV genome structure is novel and represents an intermediate evolutionary stage between the two previously described ALRV groups. We find that CMTV clusters with several other ranaviruses isolated from different hosts and locations which might also be included in this novel ranavirus group. This work sheds light on the phylogenetic relationships within this complex group of emerging, disease-causing viruses.This work was supported by grant AGL 2009-08711 from the Spanish Ministerio de Ciencia e Innovación. Alberto López-Bueno and Carla Mavián are recipients of the Ramón y Cajal and Formación del Personal Investigador fellowships, respectively, from the same institutio

Genomic Sequencing and Phylogenomics of Cowpox Virus

Cowpox virus (CPXV; genus Orthopoxvirus; family Poxviridae) is the causative agent of cowpox, a self-limiting zoonotic infection. CPXV is endemic in Eurasia, and human CPXV infections are associated with exposure to infected animals. In the Fennoscandian region, five CPXVs isolated from cats and humans were collected and used in this study. We report the complete sequence of their genomes, which ranged in size from 220–222 kbp, containing between 215 and 219 open reading frames. The phylogenetic analysis of 87 orthopoxvirus strains, including the Fennoscandian CPXV isolates, confirmed the division of CPXV strains into at least five distinct major clusters (CPXV-like 1, CPXV-like 2, VACV-like, VARV-like and ECTV-Abatino-like) and can be further divided into eighteen sub-species based on the genetic and patristic distances. Bayesian time-scaled evolutionary history of CPXV was reconstructed employing concatenated 62 non-recombinant conserved genes of 55 CPXV. The CPXV evolution rate was calculated to be 1.65 × 10−5 substitution/site/year. Our findings confirmed that CPXV is not a single species but a polyphyletic assemblage of several species and thus, a reclassification is warranted

Sampling bias and incorrect rooting make phylogenetic network tracing of SARS-COV-2 infections unreliable.

There is obvious interest in gaining insights into the epidemiology and evolution of the virus that has recently emerged in humans as the cause of the coronavirus disease 2019 (COVID-19) pandemic. The recent paper by Forster et al. (1), analyzed 160 SARS-CoV-2 full genomes available (https://www.gisaid.org/) in early March 2020. The central claim is the identification of three main SARS-CoV-2 types, named A, B, and C, circulating in different proportions among Europeans and Americans (types A and C) and East Asian (type B). According to a median-joining network analysis, variant A is proposed to be the ancestral type because it links to the sequence of a coronavirus from bats, used as an outgroup to trace the ancestral origin of the human strains. The authors further suggest that the “ancestral Wuhan B-type virus is immunologically or environmentally adapted to a large section of the East Asian population, and may need to mutate to overcome resistance outside East Asia”. There are several serious flaws with their findings and interpretation. First, and most obviously, the sequence identity between SARS-CoV-2 and the bat virus is only 96.2%, implying that these viral genomes (which are nearly 30,000 nucleotides long) differ by more than 1,000 mutations. Such a distant outgroup is unlikely to provide a reliable root for the network. Yet, strangely, the branch to the bat virus, in Figure 1 of the paper, is only 16 or 17 mutations in length. Indeed, the network seems to be mis-rooted because (see Supplementary Figure 4) a virus from Wuhan from week 0 (24th December 2019) is portrayed as a descendant of a clade of viruses collected in weeks 1-9 (presumably from many places outside China), which makes no evolutionary (2), nor epidemiological sense (3).N

Comparative Pathogenesis, Genomics and Phylogeography of Mousepox

Ectromelia virus (ECTV), the causative agent of mousepox, has threatened laboratory mouse colonies worldwide for almost a century. Mousepox has been valuable for the understanding of poxvirus pathogenesis and immune evasion. Here, we have monitored in parallel the pathogenesis of nine ECTVs in BALB/cJ mice and report the full-length genome sequence of eight novel ECTV isolates or strains, including the first ECTV isolated from a field mouse, ECTV-MouKre. This approach allowed us to identify several genes, absent in strains attenuated through serial passages in culture, that may play a role in virulence and a set of putative genes that may be involved in enhancing viral growth in vitro. We identified a putative strong inhibitor of the host inflammatory response in ECTV-MouKre, an isolate that did not cause local foot swelling and developed a moderate virulence. Most of the ECTVs, except ECTV-Hampstead, encode a truncated version of the P4c protein that impairs the recruitment of virions into the A-type inclusion bodies, and our data suggest that P4c may play a role in viral dissemination and transmission. This is the first comprehensive report that sheds light into the phylogenetic and geographic relationship of the worldwide outbreak dynamics for the ECTV species

Complete genome sequence of the European sheatfish virus

Viral diseases are an increasing threat to the thriving aquaculture industry worldwide. An emerging group of fish pathogens is formed by several ranaviruses, which have been isolated at different locations from freshwater and seawater fish species since 1985.Wereport the complete genome sequence of European sheatfish ranavirus (ESV), the first ranavirus isolated in Europe, which causes high mortality rates in infected sheatfish (Silurus glanis) and in other species. Analysis of the genome sequence shows that ESV belongs to the amphibian-like ranaviruses and is closely related to the epizootic hematopoietic necrosis virus (EHNV), a disease agent geographically confined to the Australian continent and notifiable to the World Organization for Animal Health. © 2012, American Society for Microbiology.Spanish Ministerio de Ciencia e InnovaciónPeer Reviewe

ARCA: the interactive database for arbovirus reported cases in the Americas

Abstract Background Accurate case report data are essential to understand arbovirus dynamics, including spread and evolution of arboviruses such as Zika, dengue and chikungunya viruses. Giving the multi-country nature of arbovirus epidemics in the Americas, these data are not often accessible or are reported at different time scales (weekly, monthly) from different sources. Results We developed a publicly available and user-friendly database for arboviral case data in the Americas: ARCA. ARCA is a relational database that is hosted on the ARCA website. Users can interact with the database through the website by submitting queries through the website, which generates displays results and allows users to download these results in different, convenient file formats. Users can choose to view arboviral case data through a table which containscontaining the number of cases for a particular week, a plot, or through a map. Conclusion Our ARCA database is a useful tool for arboviral epidemiology research allowing for complex queries, data visualization, integration, and formatting