DOCSLIB.ORG

Universidade Federal Do Rio Grande Do Sul Faculdade De Veterinária Programa De Pós-Graduação Em Ciências Veterinárias

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Universidade Federal Do Rio Grande Do Sul Faculdade De Veterinária Programa De Pós-Graduação Em Ciências Veterinárias UNIVERSIDADE FEDERAL DO RIO GRANDE DO SUL FACULDADE DE VETERINÁRIA PROGRAMA DE PÓS-GRADUAÇÃO EM CIÊNCIAS VETERINÁRIAS CARACTERIZAÇÃO DO VIROMA DE SORO DE SUÍNOS, EQUINOS E BOVINOS WILLIAN PINTO PAIM PORTO ALEGRE 2021 UNIVERSIDADE FEDERAL DO RIO GRANDE DO SUL FACULDADE DE VETERINÁRIA PROGRAMA DE PÓS-GRADUAÇÃO EM CIÊNCIAS VETERINÁRIAS CARACTERIZAÇÃO DO VIROMA DE SORO DE SUÍNOS, EQUINOS E BOVINOS Autor: Willian Pinto Paim Tese apresentada como requisito parcial para obtenção do grau de Doutor em Ciências Veterinárias na área de Medicina Veterinária Preventiva e Patologia – Virologia. Orientador: Dr. Cláudio Wageck Canal Coorientador: Dr. Matheus Nunes Weber PORTO ALEGRE 2021 O presente trabalho foi realizado com apoio da Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - Brasil (CAPES) - Código de Financiamento 001. Willian Pinto Paim CARACTERIZAÇÃO DO VIROMA DE SORO DE SUÍNOS, EQUINOS E BOVINOS Aprovada em 09 abril de 2021 APROVADO POR: ________________________________________ Prof. Dr. Cláudio Wageck Canal Orientador e Presidente da Comissão ________________________________________ Prof. Dr. Matheus Nunes Weber Coorientador e Membro da Comissão ________________________________________ Prof. Dra. Franciele Maboni Siqueira Membro da Comissão ________________________________________ Prof. Dr. Franscisco Esmaile Sales de Lima Membro da Comissão ________________________________________ Prof. Dra. Juliana Felipetto Cargnelutti Membro da Comissão DEDICATÓRIA Dedico esta tese aos meus pais, pelo apoio incondicional. AGRADECIMENTOS Agradeço aos meus pais, Tânia e Salatiel, à minha noiva, Camila, e a meus irmãos, Luciana e Marcelo, pelo amor, apoio e suporte para que eu pudesse concretizar este sonho. Em especial aos meus avós, Manoela e Pereci, por todos os conselhos e por tudo que me ensinaram, mesmo tendo nos deixado, serão sempre lembrados. Gostaria também de gradecer a minha segunda família, os Schiavos, pelo apoio que mesmo de longe se fizeram presentes. Aos amigos do laboratório pela assistência e amizade desde o momento em que ingressei no grupo de Virologia da FAVET/UFRGS, até o final do meu doutorado. Agradeço a Mayara Maggioli e Fernando Bauermann por todo o aprendizado proporcionado e por tornar extremamente gratificante o meu período do doutorado sanduíche na Universidade do Estado de Oklahoma nos Estados Unidos. Agradeço ao meu orientador Cláudio Wageck Canal pela oportunidade, confiança e pelos tantos ensinamentos que contribuíram muito para meu crescimento pessoal e profissional. Agradeço ao meu coorientador Matheus Nunes Weber pela amizade, incentivo, paciência, pelos ensinamentos e por toda ajuda até aqui. A todas as pessoas que direta ou indiretamente estiveram envolvidas nessa conquista e por todo o apoio dado. Por fim, agradeço ao Programa de Pós-Graduação em Ciências Veterinárias pela oportunidade de realizar doutorado em um programa de excelência e ao Departamento de Patobiologia Veterinária da Universidade do Estado de Oklahoma pelo auxilio durante o período do doutorado sanduíche. EPÍGRAFE “A ciência se compõe de erros que, por sua vez, são os passos até a verdade”. (Júlio Verne) RESUMO Os suínos, equinos e bovinos possuem uma histórica importância econômica e social. A criação de suínos de exposição para participar em eventos agrícolas é uma atividade relevante na região Centro-Oeste dos Estados Unidos. Os equinos são utilizados para o lazer, esporte, equoterapia e força de tração no trabalho rural. Os bovinos apresentam um papel essencial na indústria de carne e leite. Além disso, equinos e bovinos são fontes de soro, um produto biológico utilizado na pesquisa e para à fabricação de vacinas. Dessa forma, o conhecimento do status sanitário de suínos, equinos e bovinos é um ponto estratégico para à epidemiologia molecular de agentes virais que causam prejuízos econômicos à saúde animal. O conhecimento limitado da comunidade viral presente no soro desses animais dificulta o esclarecimento das possíveis causas de doenças de etiologia infecciosa. O emprego do sequenciamento de alto desempenho (high-throughput sequencing, HTS) tem permitido a detecção de agentes virais em amostras biológicas de muitas espécies animais. Porém, os soros de suínos de exposição, e lotes de soros equinos e bovinos comerciais de diferentes países ainda carecem de investigação da presença de vírus adventícios através da metagenômica viral. Nesse sentido, o presente estudo visa ampliar o conhecimento sobre a diversidade do viroma do soros desses animais utilizando o HTS. No Capítulo 1, foram analisadas 400 amostras de soros de suínos, divididas em dois pools de 200 amostras cada. Foram obtidas sequências de genomas das famílias Arteriviridae, Circoviridae, Flaviviridae, Herpesviridae, Parvoviridae e Retroviridae. Vinte e três espécies virais foram detectadas, incluindo o primeiro bufavírus suíno nos Estados Unidos. Assim como, o vírus da síndrome respiratória e reprodutiva suína, pestivírus atípico de suíno e circovírus suíno. Além disso, 17 genomas completos foram recuperados e os dois primeiros bocaparvovirus ungulado 3 dos Estados Unidos. No Capítulo 2, foram investigados cinco lotes de soros comerciais de equinos com origem na Nova Zelândia (três lotes), Brasil e dos Estados Unidos (um lote cada). Nestes soros foram detectadas sequências genomicas das famílias Flaviviridae, Herpesviridae e Parvoviridae. Particularmente, hepacivírus e pegivírus equinos foram os mais frequentes. No Capítulo 3, foram sequenciados sete lotes de soros comerciais de bovinos com origem na Nova Zelândia (dois lotes), México (um lote) e dos Estados Unidos (quatro lotes). Os soros de bovinos apresentaram genomas das famílias Adenoviridae, Flaviviridae, Parvoviridae, Picornaviridae, Pneumoviridae, Polyomaviridae, Poxviridae, Reoviridae, Retroviridae e vírus circulares DNA fita simples codificantes de replicase (circular rep-encoding single-stranded, CRESS) (Genomoviridae, Circoviridae e Smacoviridae). Doze genomas completos de parvovírus bovino 2 e 3, bosavírus, hokovírus bovino e poliomavírus bovino 1 foram recuperados. Além disso, foram detectadas sequências relacionadas à crAssphage, um bacteriófago associado a contaminação fecal humana. Portanto, o estudo ilustra os agentes virais presentes nos soros de suínos, equinos e bovinos, buscando contribuir para o conhecimento do viroma presente nos soros desses animias e auxiliar no esclarecimento de possíveis causas de doenças de etiologia infecciosa. Palavras-chave: Sequenciamento de Alto Desempenho , Vírus, Cressdnaviricota, Metagenômica. ABSTRACT Pigs, horses, and cattle have historical economic and social importance. Raising show pigs to participate in agricultural events is a major activity in the Midwest region of the United States. Horses are used for leisure, sport, hippotherapy and traction force in rural work. Cattle play an essential role in the meat and milk industry. In addition, horses and cattle are sources of serum, a biological product used in research and for the manufacture of vaccines. Thus, knowledge of the health status of pigs, horses and cattle is a strategic point for the molecular epidemiology of viral agents that cause economic damage to animal health. The limited knowledge of the viral community present in the serum of these animals makes it difficult to clarify the possible causes of diseases of infectious etiology. The use of high-throughput sequencing (HTS) has allowed the detection of viral agents in biological samples of many animal species. However, the sera from show pigs, and batches of commercial equine and bovine sera from different countries still need to be investigated for the presence of adventitious viruses through viral metagenomics. In this sense, the present study aims to expand the knowledge about the diversity of the sera virome of these animals using the HTS. In Chapter 1, 400 swine serum samples were analyzed, divided into two pools of 200 samples each. Genome sequences were obtained from the Arteriviridae, Circoviridae, Flaviviridae, Herpesviridae, Parvoviridae and Retroviridae families. Twenty-three viral species were detected, including the first porcine bufavirus in the United States. As well as the porcine reproductive and respiratory syndrome virus, porcine atypical pestivirus and porcine circovirus. In addition, 17 complete genomes were retrieved and the first two ungulate bocaparvovirus 3 from the United States. In Chapter 2, five batches of commercial equine sera originating in New Zealand (three batches), Brazil and the United States (one batch each) were investigated. In these sera, genomic sequences of the Flaviviridae, Herpesviridae and Parvoviridae families were detected. In particular, equine hepacivirus and pegivirus were the most frequent. In Chapter 3, seven batches of commercial bovine sera from New Zealand (two batches), Mexico (one batch) and the United States (four batches) were sequenced. Bovine sera showed genomes of the Adenoviridae, Flaviviridae, Parvoviridae, Picornaviridae, Pneumoviridae, Polyomaviridae, Poxviridae, Reoviridae, Retroviridae and circular Rep-encoding single-stranded (CRESS) DNA virus (Genomoviridae, Circoviridae e Smacoviridae). Twelve complete genomes of bovine parvovirus 2 and 3, bosavirus, bovine hokovirus and bovine polyomavirus 1 were recovered. Furthermore, sequences related to crAssphage, a bacteriophage associated with human fecal contamination, were detected. Therefore, the study illustrates the viral agents present in the pigs, horses, and cattle sera, seeking to contribute to the knowledge of
Load more

Recommended publications
  • Madarak Polyomavírusainak És CRESS DNS Vírusainak Összehasonlító Genomvizsgálata
    Állatorvostudományi Egyetem Aujeszky Aladár Elméleti Állatorvostudományok Doktori Program Madarak polyomavírusainak és CRESS DNS vírusainak összehasonlító genomvizsgálata PhD értekezés Szabóné Kaszab Eszter 2021 Témavezető és témabizottsági tagok: ………………………………… dr. Fehér Enikő Állatorvostudományi Kutatóintézet Új kórokozók témacsoport témavezető Készült 8 példányban. Ez a …… sz. példány ………………………………….. Szabóné Kaszab Eszter 2 Tartalomjegyzék 1. Rövidítések jegyzéke ............................................................................................... 5 2. Összefoglalás .......................................................................................................... 7 3. Summary ................................................................................................................. 8 4. Bevezetés ................................................................................................................ 9 5. Irodalmi áttekintés...................................................................................................10 5.1. A Circoviridae család jellemzése ...................................................................10 5.1.1. A Circovirus nemzetség ........................................................................12 5.1.2. A Cyclovirus nemzetség ........................................................................18 5.2. A CRESS DNS vírusok jellemzése ................................................................19 5.3. A polyomavírusok jellemzése ........................................................................22
    [Show full text]
  • Multiple Origins of Prokaryotic and Eukaryotic Single-Stranded DNA Viruses from Bacterial and Archaeal Plasmids
    ARTICLE https://doi.org/10.1038/s41467-019-11433-0 OPEN Multiple origins of prokaryotic and eukaryotic single-stranded DNA viruses from bacterial and archaeal plasmids Darius Kazlauskas 1, Arvind Varsani 2,3, Eugene V. Koonin 4 & Mart Krupovic 5 Single-stranded (ss) DNA viruses are a major component of the earth virome. In particular, the circular, Rep-encoding ssDNA (CRESS-DNA) viruses show high diversity and abundance 1234567890():,; in various habitats. By combining sequence similarity network and phylogenetic analyses of the replication proteins (Rep) belonging to the HUH endonuclease superfamily, we show that the replication machinery of the CRESS-DNA viruses evolved, on three independent occa- sions, from the Reps of bacterial rolling circle-replicating plasmids. The CRESS-DNA viruses emerged via recombination between such plasmids and cDNA copies of capsid genes of eukaryotic positive-sense RNA viruses. Similarly, the rep genes of prokaryotic DNA viruses appear to have evolved from HUH endonuclease genes of various bacterial and archaeal plasmids. Our findings also suggest that eukaryotic polyomaviruses and papillomaviruses with dsDNA genomes have evolved via parvoviruses from CRESS-DNA viruses. Collectively, our results shed light on the complex evolutionary history of a major class of viruses revealing its polyphyletic origins. 1 Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio av. 7, Vilnius 10257, Lithuania. 2 The Biodesign Center for Fundamental and Applied Microbiomics, School of Life Sciences, Center for Evolution and Medicine, Arizona State University, Tempe, AZ 85287, USA. 3 Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Rondebosch, 7700 Cape Town, South Africa.
    [Show full text]
  • Small Circular DNA Viruses: the Muddy Viral “Playground” of Recombinant, Reassortant, and Highly Diverse Viruses
    Small Circular DNA Viruses: The muddy viral “playground” of recombinant, reassortant, and highly diverse viruses @Varsani_lab Arizona State University, USA University of Canterbury, New Zealand University of Cape Town, South Africa Arvind Varsani Nucleotide substitutions Recombination Reassortment Viral evolution Viral Nucleotide substitutions Recombination Reassortment Viral evolution Viral Nucleotide substitutions Recombination Reassortment Viral evolution Viral I II III IV V dsDNA ssDNA VI VII dsRNA ssRNA(+) ssRNA(-) ssRNA(RT) dsDNA(RT) viruses Archaea Bacteria Diatoms Fungi Invertebrates Plants Vertebrates Unknown Anelloviridae – circular (~2.1 - 3.8kb) Bacillidnaviridae - circular (~4.5 - 6kb) Circoviridae – circular (~1.6 - 2.3kb) Geminiviridae – circular (~2.7kb; monopartite, bipartite, associated with α/β satellites) Genomovirdae – circular (1.8 -2.3 kb) ssDNA Inoviridae – circular (~5.8 - 8.7kb) Microviridae – circular (~4.5 - 6kb) Nanoviridae – circular (~1.2kb; multicomponent viruses; associated with satellites) Parvoviridae – linear (~3.7 - 6kb) Pleolipoviridae* – circular ssDNA; circular dsDNA or liner dsDNA (7-16kb) Smacoviridae* - circular (2.3 - 2.9kb) ssDNA viruses Chimerism in Rep Geminiviruses MSV: ~2 x 10-4 subs/site/year SSRV: ~3 x 10-4 subs/site/year EACMV: ~1 x 10-3 subs/site/year TYLCV: ~3 x 10-4 subs/site/year Nanoviruses FBNYV: ~1 x 10-3 subs/site/year BBTV: ~3 x 10-4 subs/site/year Circoviruses BFDV: ~2 x 10-3 subs/site/year PCV-2: ~1 x 10-3 subs/site/year Parvoviruses CPV: ~2 x 10-4 - 8 x 10-5 subs/site/year
    [Show full text]
  • Description of a Novel Species of Torque Teno Sus Virus (Ttsuv) and First Insights on Immunization Against Ttsuvs in Naturally Infected Pigs
    Description of a novel species of Torque teno sus virus (TTSuV) and first insights on immunization against TTSuVs in naturally infected pigs Memòria presentada per l’ Alexandra Jiménez Melsió per optar al grau de Doctora en el programa de Bioquímica, Biologia Molecular i Biomedicina del Departament de Bioquímica i Biologia Molecular de la Universitat Autònoma de Barcelona Dra. Tuija Kekarainen Dr. Joaquim Segalés i Coma Dra. Anna Bassols Teixidó Directora Director Tutora Alexandra Jiménez Melsió Doctoranda Bellaterra, setembre 2015 La Dra. Tuija Kekarainen, investigadora del Centre de Recerca en Sanitat Animal (CReSA), i el Dr. Joaquim Segalés i Coma, professor titular del Departament de Sanitat i d’Anatomia Animals de la Facultat de Veterinària de la Universitat Autònoma de Barcelona (UAB) i investigador adscrit al CReSA, com a co-directors, i la Dra. Anna Bassols Teixidó, professora titular del Departament de Bioquímica i Biologia Molecular de la UAB, com a tutora acadèmica, Certifiquen: Que la memòria de tesi doctoral titulada: “Description of a novel species of Torque teno sus virus (TTSuV) and first insights on immunization against TTSuVs in naturally infected pigs “ presentada per l’Alexandra Jiménez Melsió s’ha realitzat sota la seva direcció en el CReSA i n’autoritzen la seva presentació per tal de ser avaluada per la comissió corresponent per l’obtenció del grau de Doctora del programa de Bioquímica, Biologia Molecular i Biomedicina del Departament de Bioquímica i Biologia Molecular de la Universitat Autònoma de Barcelona. I per tal que consti, als efectes oportuns, signem el present certificat a Bellaterra, a 28 de setembre del 2015.
    [Show full text]
  • New Viral Facets in Oral Diseases: the EBV Paradox
    International Journal of Molecular Sciences Review New Viral Facets in Oral Diseases: The EBV Paradox Lilit Tonoyan 1,*, Séverine Vincent-Bugnas 1,2 , Charles-Vivien Olivieri 1 and Alain Doglio 1,3,* 1 Faculté de Chirurgie Dentaire, Université Côte d’Azur, EA 7354 MICORALIS (Microbiologie Orale, Immunothérapie et Santé), 06357 Nice, France; [email protected] (S.V.-B.); [email protected] (C.-V.O.) 2 Pôle Odontologie, Centre Hospitalier Universitaire de Nice, 06001 Nice, France 3 Unité de Thérapie Cellulaire et Génique, Centre Hospitalier Universitaire de Nice, 06103 Nice, France * Correspondence: [email protected] (L.T.); [email protected] (A.D.) Received: 3 October 2019; Accepted: 20 November 2019; Published: 22 November 2019 Abstract: The oral cavity contributes to overall health, psychosocial well-being and quality of human life. Oral inflammatory diseases represent a major global health problem with significant social and economic impact. The development of effective therapies, therefore, requires deeper insights into the etiopathogenesis of oral diseases. Epstein–Barr virus (EBV) infection results in a life-long persistence of the virus in the host and has been associated with numerous oral inflammatory diseases including oral lichen planus (OLP), periodontal disease and Sjogren’s syndrome (SS). There is considerable evidence that the EBV infection is a strong risk factor for the development and progression of these conditions, but is EBV a true pathogen? This long-standing EBV paradox yet needs to be solved. This review discusses novel viral aspects of the etiopathogenesis of non-tumorigenic diseases in the oral cavity, in particular, the contribution of EBV in OLP, periodontitis and SS, the tropism of EBV infection, the major players involved in the etiopathogenic mechanisms and emerging contribution of EBV-pathogenic bacteria bidirectional interaction.
    [Show full text]
  • Metatranscriptomics to Characterize Respiratory Virome, Microbiome, and Host Response Directly from Clinical Samples
    Metatranscriptomics to characterize respiratory virome, microbiome, and host response directly from clinical samples Seesandra Rajagopala ( [email protected] ) Vanderbilt University Medical Center Nicole Bakhoum Vanderbilt University Medical Center Suman Pakala Vanderbilt University Medical Center Meghan Shilts Vanderbilt University Medical Center Christian Rosas-Salazar Vanderbilt University Medical Center Annie Mai Vanderbilt University Medical Center Helen Boone Vanderbilt University Medical Center Rendie McHenry Vanderbilt University Medical Center Shibu Yooseph University of Central Florida https://orcid.org/0000-0001-5581-5002 Natasha Halasa Vanderbilt University Medical Center Suman Das Vanderbilt University Medical Center https://orcid.org/0000-0003-2496-9724 Article Keywords: Metatranscriptomics, Virome, Microbiome, Next-Generation Sequencing (NGS), RNA-Seq, Acute Respiratory Infection (ARI), Respiratory Syncytial Virus (RSV), Coronavirus (CoV) Posted Date: October 15th, 2020 DOI: https://doi.org/10.21203/rs.3.rs-77157/v1 Page 1/31 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Page 2/31 Abstract We developed a metatranscriptomics method that can simultaneously capture the respiratory virome, microbiome, and host response directly from low-biomass clinical samples. Using nasal swab samples, we have demonstrated that this method captures the comprehensive RNA virome with sucient sequencing depth required to assemble complete genomes. We nd a surprisingly high-frequency of Respiratory Syncytial Virus (RSV) and Coronavirus (CoV) in healthy children, and a high frequency of RSV-A and RSV-B co-infections in children with symptomatic RSV. In addition, we have characterized commensal and pathogenic bacteria, and fungi at the species-level. Functional analysis of bacterial transcripts revealed H.
    [Show full text]
  • Viral Diversity in Tree Species
    Universidade de Brasília Instituto de Ciências Biológicas Departamento de Fitopatologia Programa de Pós-Graduação em Biologia Microbiana Doctoral Thesis Viral diversity in tree species FLÁVIA MILENE BARROS NERY Brasília - DF, 2020 FLÁVIA MILENE BARROS NERY Viral diversity in tree species Thesis presented to the University of Brasília as a partial requirement for obtaining the title of Doctor in Microbiology by the Post - Graduate Program in Microbiology. Advisor Dra. Rita de Cássia Pereira Carvalho Co-advisor Dr. Fernando Lucas Melo BRASÍLIA, DF - BRAZIL FICHA CATALOGRÁFICA NERY, F.M.B Viral diversity in tree species Flávia Milene Barros Nery Brasília, 2025 Pages number: 126 Doctoral Thesis - Programa de Pós-Graduação em Biologia Microbiana, Universidade de Brasília, DF. I - Virus, tree species, metagenomics, High-throughput sequencing II - Universidade de Brasília, PPBM/ IB III - Viral diversity in tree species A minha mãe Ruth Ao meu noivo Neil Dedico Agradecimentos A Deus, gratidão por tudo e por ter me dado uma família e amigos que me amam e me apoiam em todas as minhas escolhas. Minha mãe Ruth e meu noivo Neil por todo o apoio e cuidado durante os momentos mais difíceis que enfrentei durante minha jornada. Aos meus irmãos André, Diego e meu sobrinho Bruno Kawai, gratidão. Aos meus amigos de longa data Rafaelle, Evanessa, Chênia, Tati, Leo, Suzi, Camilets, Ricardito, Jorgito e Diego, saudade da nossa amizade e dos bons tempos. Amo vocês com todo o meu coração! Minha orientadora e grande amiga Profa Rita de Cássia Pereira Carvalho, a quem escolhi e fui escolhida para amar e fazer parte da família.
    [Show full text]
  • Unravelling the Evolutionary Relationships of Hepaciviruses Within and Across Rodent Hosts
    bioRxiv preprint doi: https://doi.org/10.1101/2020.10.09.332932; this version posted October 9, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Unravelling the evolutionary relationships of hepaciviruses within and across rodent hosts Magda Bletsa1, Bram Vrancken1, Sophie Gryseels1;2, Ine Boonen1, Antonios Fikatas1, Yiqiao Li1, Anne Laudisoit3, Sebastian Lequime1, Josef Bryja4, Rhodes Makundi5, Yonas Meheretu6, Benjamin Dudu Akaibe7, Sylvestre Gambalemoke Mbalitini7, Frederik Van de Perre8, Natalie Van Houtte8, Jana Teˇsˇ´ıkova´ 4;9, Elke Wollants1, Marc Van Ranst1, Jan Felix Drexler10;11, Erik Verheyen8;12, Herwig Leirs8, Joelle Gouy de Bellocq4 and Philippe Lemey1∗ 1Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven – University of Leuven, Leuven, Belgium 2Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, USA 3EcoHealth Alliance, New York, USA 4Institute of Vertebrate Biology of the Czech Academy of Sciences, Brno, Czech Republic 5Pest Management Center – Sokoine University of Agriculture, Morogoro, Tanzania 6Department of Biology and Institute of Mountain Research & Development, Mekelle University, Mekelle, Ethiopia 7Department of Ecology and Animal Resource Management, Faculty of Science, Biodiversity Monitoring Center, University of Kisangani, Kisangani, Democratic Republic
    [Show full text]
  • Diversity and Evolution of Novel Invertebrate DNA Viruses Revealed by Meta-Transcriptomics
    viruses Article Diversity and Evolution of Novel Invertebrate DNA Viruses Revealed by Meta-Transcriptomics Ashleigh F. Porter 1, Mang Shi 1, John-Sebastian Eden 1,2 , Yong-Zhen Zhang 3,4 and Edward C. Holmes 1,3,* 1 Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life & Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia; [email protected] (A.F.P.); [email protected] (M.S.); [email protected] (J.-S.E.) 2 Centre for Virus Research, Westmead Institute for Medical Research, Westmead, NSW 2145, Australia 3 Shanghai Public Health Clinical Center and School of Public Health, Fudan University, Shanghai 201500, China; [email protected] 4 Department of Zoonosis, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, China * Correspondence: [email protected]; Tel.: +61-2-9351-5591 Received: 17 October 2019; Accepted: 23 November 2019; Published: 25 November 2019 Abstract: DNA viruses comprise a wide array of genome structures and infect diverse host species. To date, most studies of DNA viruses have focused on those with the strongest disease associations. Accordingly, there has been a marked lack of sampling of DNA viruses from invertebrates. Bulk RNA sequencing has resulted in the discovery of a myriad of novel RNA viruses, and herein we used this methodology to identify actively transcribing DNA viruses in meta-transcriptomic libraries of diverse invertebrate species. Our analysis revealed high levels of phylogenetic diversity in DNA viruses, including 13 species from the Parvoviridae, Circoviridae, and Genomoviridae families of single-stranded DNA virus families, and six double-stranded DNA virus species from the Nudiviridae, Polyomaviridae, and Herpesviridae, for which few invertebrate viruses have been identified to date.
    [Show full text]
  • The Intestinal Virome of Malabsorption Syndrome-Affected and Unaffected
    Virus Research 261 (2019) 9–20 Contents lists available at ScienceDirect Virus Research journal homepage: www.elsevier.com/locate/virusres The intestinal virome of malabsorption syndrome-affected and unaffected broilers through shotgun metagenomics T ⁎ Diane A. Limaa, , Samuel P. Cibulskib, Caroline Tochettoa, Ana Paula M. Varelaa, Fabrine Finklera, Thais F. Teixeiraa, Márcia R. Loikoa, Cristine Cervac, Dennis M. Junqueirad, Fabiana Q. Mayerc, Paulo M. Roehea a Laboratório de Virologia, Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básicas da Saúde (ICBS), Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil b Laboratório de Virologia, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil c Laboratório de Biologia Molecular, Instituto de Pesquisas Veterinárias Desidério Finamor (IPVDF), Eldorado do Sul, RS, Brazil d Centro Universitário Ritter dos Reis - UniRitter, Health Science Department, Porto Alegre, RS, Brazil ARTICLE INFO ABSTRACT Keywords: Malabsorption syndrome (MAS) is an economically important disease of young, commercially reared broilers, Enteric disorders characterized by growth retardation, defective feather development and diarrheic faeces. Several viruses have Virome been tentatively associated to such syndrome. Here, in order to examine potential associations between enteric Broiler chickens viruses and MAS, the faecal viromes of 70 stool samples collected from diseased (n = 35) and healthy (n = 35) High-throughput sequencing chickens from seven flocks were characterized and compared. Following high-throughput sequencing, a total of 8,347,319 paired end reads, with an average of 231 nt, were generated. Through analysis of de novo assembled contigs, 144 contigs > 1000 nt were identified with hits to eukaryotic viral sequences, as determined by GenBank database.
    [Show full text]
  • Unfolded Protein Response in Hepatitis C Virus Infection
    REVIEW ARTICLE published: 20 May 2014 doi: 10.3389/fmicb.2014.00233 Unfolded protein response in hepatitis C virus infection Shiu-Wan Chan* Faculty of Life Sciences, The University of Manchester, Manchester, UK Edited by: Hepatitis C virus (HCV) is a single-stranded, positive-sense RNA virus of clinical Hirofumi Akari, Kyoto University, importance. The virus establishes a chronic infection and can progress from chronic Japan hepatitis, steatosis to fibrosis, cirrhosis, and hepatocellular carcinoma (HCC). The Reviewed by: mechanisms of viral persistence and pathogenesis are poorly understood. Recently Ikuo Shoji, Kobe University Graduate School of Medicine, Japan the unfolded protein response (UPR), a cellular homeostatic response to endoplasmic Kohji Moriishi, University of reticulum (ER) stress, has emerged to be a major contributing factor in many human Yamanashi, Japan diseases. It is also evident that viruses interact with the host UPR in many different ways *Correspondence: and the outcome could be pro-viral, anti-viral or pathogenic, depending on the particular Shiu-Wan Chan, Faculty of Life type of infection. Here we present evidence for the elicitation of chronic ER stress in Sciences, The University of Manchester, Michael Smith HCV infection. We analyze the UPR signaling pathways involved in HCV infection, the Building, Oxford Road, various levels of UPR regulation by different viral proteins and finally, we propose several Manchester M13 9PT, UK mechanisms by which the virus provokes the UPR. e-mail: shiu-wan.chan@ manchester.ac.uk Keywords: hepatitis C virus, unfolded protein response, endoplasmic reticulum stress, hepacivirus, virus-host interaction INTRODUCTION (LDLs) and very low-density lipoproteins (VLDLs) to form the Hepatitis C virus (HCV) infection produces a clinically important lipoviroparticles (Andre et al., 2002).
    [Show full text]
  • Single Stranded DNA Viruses Associated with Capybara Faeces Sampled in Brazil
    viruses Article Single Stranded DNA Viruses Associated with Capybara Faeces Sampled in Brazil Rafaela S. Fontenele 1,2, Cristiano Lacorte 2, Natalia S. Lamas 2, Kara Schmidlin 1, Arvind Varsani 1,3,* and Simone G. Ribeiro 2,* 1 The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA 2 Embrapa Recursos Genéticos e Biotecnologia, Brasília, DF 70770-017, Brazil 3 Structural Biology Research Unit, Department of Clinical Laboratory Sciences, University of Cape Town, Observatory, Cape Town 7925, South Africa * Correspondence: [email protected] (A.V.); [email protected] (S.G.R.); Tel.: +1-480-727-2093 (A.V.); +55-61-3448-4666/3448-4703 (S.G.R.) Received: 14 June 2019; Accepted: 31 July 2019; Published: 2 August 2019 Abstract: Capybaras (Hydrochoerus hydrochaeris), the world’s largest rodents, are distributed throughout South America. These wild herbivores are commonly found near water bodies and are well adapted to rural and urban areas. There is limited information on the viruses circulating through capybaras. This study aimed to expand the knowledge on the viral diversity associated with capybaras by sampling their faeces. Using a viral metagenomics approach, we identified diverse single-stranded DNA viruses in the capybara faeces sampled in the Distrito Federal, Brazil. A total of 148 complete genomes of viruses in the Microviridae family were identified. In addition, 14 genomoviruses (family Genomoviridae), a novel cyclovirus (family Circoviridae), and a smacovirus (family Smacoviridae) were identified. Also, 37 diverse viruses that cannot be assigned to known families and more broadly referred to as unclassified circular replication associated protein encoding single-stranded (CRESS) DNA viruses were identified.
    [Show full text]