Computational Exploration of Virus Diversity on Transcriptomic Datasets
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Genome Sequencing by Random Priming Methods for Viral Identification
Genome sequencing by random priming methods for viral identification Rosseel Toon Dissertation submitted in fulfillment of the requirements for the degree of Doctor of Philosophy (PhD) in Veterinary Sciences, Faculty of Veterinary Medicine, Ghent University, 2015 Promotors: Dr. Steven Van Borm Prof. Dr. Hans Nauwynck “The real voyage of discovery consist not in seeking new landscapes, but in having new eyes” Marcel Proust, French writer, 1923 Table of contents Table of contents ....................................................................................................................... 1 List of abbreviations ................................................................................................................. 3 Chapter 1 General introduction ................................................................................................ 5 1. Viral diagnostics and genomics ....................................................................................... 7 2. The DNA sequencing revolution ................................................................................... 12 2.1. Classical Sanger sequencing .................................................................................. 12 2.2. Next-generation sequencing ................................................................................... 16 3. The viral metagenomic workflow ................................................................................. 24 3.1. Sample preparation ............................................................................................... -
Nucleotide Amino Acid Size (Nt) #Orfs Marnavirus Heterosigma Akashiwo Heterosigma Akashiwo RNA Heterosigma Lang Et Al
Supplementary Table 1: Summary of information for all viruses falling within the seven Marnaviridae genera in our analyses. Accession Genome Genus Species Virus name Strain Abbreviation Source Country Reference Nucleotide Amino acid Size (nt) #ORFs Marnavirus Heterosigma akashiwo Heterosigma akashiwo RNA Heterosigma Lang et al. , 2004; HaRNAV AY337486 AAP97137 8587 One Canada RNA virus 1 virus akashiwo Tai et al. , 2003 Marine single- ASG92540 Moniruzzaman et Classification pending Q sR OV 020 KY286100 9290 Two celled USA ASG92541 al ., 2017 eukaryotes Marine single- Moniruzzaman et Classification pending Q sR OV 041 KY286101 ASG92542 9328 One celled USA al ., 2017 eukaryotes APG78557 Classification pending Wenzhou picorna-like virus 13 WZSBei69459 KX884360 9458 One Bivalve China Shi et al ., 2016 APG78557 Classification pending Changjiang picorna-like virus 2 CJLX30436 KX884547 APG79001 7171 One Crayfish China Shi et al ., 2016 Beihai picorna-like virus 57 BHHQ57630 KX883356 APG76773 8518 One Tunicate China Shi et al ., 2016 Classification pending Beihai picorna-like virus 57 BHJP51916 KX883380 APG76812 8518 One Tunicate China Shi et al ., 2016 Marine single- ASG92530 Moniruzzaman et Classification pending N OV 137 KY130494 7746 Two celled USA ASG92531 al ., 2017 eukaryotes Hubei picorna-like virus 7 WHSF7327 KX884284 APG78434 9614 One Pill worm China Shi et al ., 2016 Classification pending Hubei picorna-like virus 7 WHCC111241 KX884268 APG78407 7945 One Insect China Shi et al ., 2016 Sanxia atyid shrimp virus 2 WHCCII13331 KX884278 APG78424 10445 One Insect China Shi et al ., 2016 Classification pending Freshwater atyid Sanxia atyid shrimp virus 2 SXXX37884 KX883708 APG77465 10400 One China Shi et al ., 2016 shrimp Labyrnavirus Aurantiochytrium single Aurantiochytrium single stranded BAE47143 Aurantiochytriu AuRNAV AB193726 9035 Three4 Japan Takao et al. -
The Viruses of Wild Pigeon Droppings
The Viruses of Wild Pigeon Droppings Tung Gia Phan1,2, Nguyen Phung Vo1,3,A´ kos Boros4,Pe´ter Pankovics4,Ga´bor Reuter4, Olive T. W. Li6, Chunling Wang5, Xutao Deng1, Leo L. M. Poon6, Eric Delwart1,2* 1 Blood Systems Research Institute, San Francisco, California, United States of America, 2 Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, United States of America, 3 Pharmacology Department, School of Pharmacy, Ho Chi Minh City University of Medicine and Pharmacy, Ho Chi Minh, Vietnam, 4 Regional Laboratory of Virology, National Reference Laboratory of Gastroenteric Viruses, A´ NTSZ Regional Institute of State Public Health Service, Pe´cs, Hungary, 5 Stanford Genome Technology Center, Stanford, California, United States of America, 6 Centre of Influenza Research and School of Public Health, University of Hong Kong, Hong Kong SAR Abstract Birds are frequent sources of emerging human infectious diseases. Viral particles were enriched from the feces of 51 wild urban pigeons (Columba livia) from Hong Kong and Hungary, their nucleic acids randomly amplified and then sequenced. We identified sequences from known and novel species from the viral families Circoviridae, Parvoviridae, Picornaviridae, Reoviridae, Adenovirus, Astroviridae, and Caliciviridae (listed in decreasing number of reads), as well as plant and insect viruses likely originating from consumed food. The near full genome of a new species of a proposed parvovirus genus provisionally called Aviparvovirus contained an unusually long middle ORF showing weak similarity to an ORF of unknown function from a fowl adenovirus. Picornaviruses found in both Asia and Europe that are distantly related to the turkey megrivirus and contained a highly divergent 2A1 region were named mesiviruses. -
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. -
Enteric and Non-Enteric Adenoviruses Associated with Acute Gastroenteritis in Pediatric Patients in Thailand, 2011 to 2017
RESEARCH ARTICLE Enteric and non-enteric adenoviruses associated with acute gastroenteritis in pediatric patients in Thailand, 2011 to 2017 1,2 1,2 3,4 1,2 Kattareeya Kumthip , Pattara Khamrin , Hiroshi Ushijima , Niwat ManeekarnID * 1 Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand, 2 Center of Excellence in Emerging and Re-emerging Diarrheal Viruses, Chiang Mai University, Chiang Mai, Thailand, 3 Department of Developmental Medical Sciences, School of International Health, Graduate School of a1111111111 Medicine, The University of Tokyo, Tokyo, Japan, 4 Division of Microbiology, Department of Pathology and a1111111111 Microbiology, Nihon University School of Medicine, Tokyo, Japan a1111111111 * [email protected] a1111111111 a1111111111 Abstract Human adenovirus (HAdV) is known to be a common cause of diarrhea in children world- OPEN ACCESS wide. Infection with adenovirus is responsible for 2±10% of diarrheic cases. To increase a Citation: Kumthip K, Khamrin P, Ushijima H, better understanding of the prevalence and epidemiology of HAdV infection, a large scale Maneekarn N (2019) Enteric and non-enteric and long-term study was needed. We implemented a multi-year molecular detection and adenoviruses associated with acute gastroenteritis characterization study of HAdV in association with acute gastroenteritis in Chiang Mai, Thai- in pediatric patients in Thailand, 2011 to 2017. PLoS ONE 14(8): e0220263. https://doi.org/ land from 2011 to 2017. Out of 2,312 patients, HAdV was detected in 165 cases (7.2%). The 10.1371/journal.pone.0220263 positive rate for HAdV infection was highest in children of 1 and 2 years of age compared to Editor: Wenyu Lin, Harvard Medical School, other age groups. -
Quito's Virome: Metagenomic Analysis of Viral Diversity in Urban Streams of Ecuador's Capital City
Science of the Total Environment 645 (2018) 1334–1343 Contents lists available at ScienceDirect Science of the Total Environment journal homepage: www.elsevier.com/locate/scitotenv Quito's virome: Metagenomic analysis of viral diversity in urban streams of Ecuador's capital city Laura Guerrero-Latorre a,⁎, Brigette Romero a, Edison Bonifaz a, Natalia Timoneda b, Marta Rusiñol b, Rosina Girones b, Blanca Rios-Touma c a Grupo de investigación Biodiversidad, Medio Ambiente y Salud (BIOMAS), Facultad de Ingenierías y Ciencias Aplicadas (FICA), Ingeniería en Biotecnología, Universidad de las Américas, Quito, Ecuador b Laboratory of Virus Contaminants of Water and Food, Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Catalonia, Spain c Grupo de investigación Biodiversidad, Medio Ambiente y Salud (BIOMAS), Facultad de Ingenierías y Ciencias Aplicadas (FICA), Ingeniería Ambiental, Universidad de las Américas, Quito, Ecuador HIGHLIGHTS GRAPHICAL ABSTRACT • First viral metagomic study of highly impacted surface waters in Latin America • The study describes human viral patho- gens present in urban rivers of Quito. • Several viral families detected contain- ing emergent species firstly reported in Ecuador. article info abstract Article history: In Quito, the microbiological contamination of surface water represents a public health problem, mainly due to Received 25 May 2018 the lack of sewage treatment from urban wastewater. Contaminated water contributes to the transmission of Received in revised form 16 July 2018 many enteric pathogens through direct consumption, agricultural and recreational use. Among the different Accepted 16 July 2018 pathogens present in urban discharges, viruses play an important role on disease, being causes of gastroenteritis, Available online 23 July 2018 hepatitis, meningitis, respiratory infections, among others. -
Viruses in Transplantation - Not Always Enemies
Viruses in transplantation - not always enemies Virome and transplantation ECCMID 2018 - Madrid Prof. Laurent Kaiser Head Division of Infectious Diseases Laboratory of Virology Geneva Center for Emerging Viral Diseases University Hospital of Geneva ESCMID eLibrary © by author Conflict of interest None ESCMID eLibrary © by author The human virome: definition? Repertoire of viruses found on the surface of/inside any body fluid/tissue • Eukaryotic DNA and RNA viruses • Prokaryotic DNA and RNA viruses (phages) 25 • The “main” viral community (up to 10 bacteriophages in humans) Haynes M. 2011, Metagenomic of the human body • Endogenous viral elements integrated into host chromosomes (8% of the human genome) • NGS is shaping the definition Rascovan N et al. Annu Rev Microbiol 2016;70:125-41 Popgeorgiev N et al. Intervirology 2013;56:395-412 Norman JM et al. Cell 2015;160:447-60 ESCMID eLibraryFoxman EF et al. Nat Rev Microbiol 2011;9:254-64 © by author Viruses routinely known to cause diseases (non exhaustive) Upper resp./oropharyngeal HSV 1 Influenza CNS Mumps virus Rhinovirus JC virus RSV Eye Herpes viruses Parainfluenza HSV Measles Coronavirus Adenovirus LCM virus Cytomegalovirus Flaviviruses Rabies HHV6 Poliovirus Heart Lower respiratory HTLV-1 Coxsackie B virus Rhinoviruses Parainfluenza virus HIV Coronaviruses Respiratory syncytial virus Parainfluenza virus Adenovirus Respiratory syncytial virus Coronaviruses Gastro-intestinal Influenza virus type A and B Human Bocavirus 1 Adenovirus Hepatitis virus type A, B, C, D, E Those that cause -
Elucidating Viral Communities During a Phytoplankton Bloom on the West Antarctic Peninsula
fmicb-10-01014 May 10, 2019 Time: 14:46 # 1 ORIGINAL RESEARCH published: 14 May 2019 doi: 10.3389/fmicb.2019.01014 Elucidating Viral Communities During a Phytoplankton Bloom on the West Antarctic Peninsula Tomás Alarcón-Schumacher1,2†, Sergio Guajardo-Leiva1†, Josefa Antón3 and Beatriz Díez1,4* 1 Department of Molecular Genetics and Microbiology, Pontificia Universidad Católica de Chile, Santiago, Chile, 2 Max Planck Institute for Marine Microbiology, Bremen, Germany, 3 Department of Physiology, Genetics, and Microbiology, University of Alicante, Alicante, Spain, 4 Center for Climate and Resilience Research (CR2), University of Chile, Santiago, Chile In Antarctic coastal waters where nutrient limitations are low, viruses are expected to play a major role in the regulation of bloom events. Despite this, research in viral identification and dynamics is scarce, with limited information available for the Southern Ocean (SO). This study presents an integrative-omics approach, comparing variation in the viral and microbial active communities on two contrasting sample conditions from Edited by: a diatom-dominated phytoplankton bloom occurring in Chile Bay in the West Antarctic David Velazquez, Autonomous University of Madrid, Peninsula (WAP) in the summer of 2014. The known viral community, initially dominated Spain by Myoviridae family (∼82% of the total assigned reads), changed to become dominated Reviewed by: by Phycodnaviridae (∼90%), while viral activity was predominantly driven by dsDNA Carole Anne Llewellyn, ∼ ∼ Swansea University, United Kingdom members of the Phycodnaviridae ( 50%) and diatom infecting ssRNA viruses ( 38%), Márcio Silva de Souza, becoming more significant as chlorophyll a increased. A genomic and phylogenetic Fundação Universidade Federal do characterization allowed the identification of a new viral lineage within the Myoviridae Rio Grande, Brazil family. -
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. -
Comparative Viral Metagenomics from Chicken Feces and Farm Dust in the Netherlands
bioRxiv preprint doi: https://doi.org/10.1101/2021.03.09.434704; this version posted March 10, 2021. 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 4.0 International license. Comparative viral metagenomics from chicken feces and farm dust in the Netherlands Kirsty T. T. Kwoka#, Myrna M. T. de Rooijb, Aniek B. Messinkb, Inge M. Woutersb, Lidwien A. M. Smitb, Dick J.J. Heederikb, Marion P. G. Koopmansa, My V. T. Phana a Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands b Institute for Risk Assessment Sciences (IRAS), Utrecht University, Utrecht, The Netherlands Running Head: Virome of Dutch farmed chicken feces and farm dust # Address correspondence to Kirsty T. T. Kwok, [email protected]. Keywords: fecal virome; virome; dust; airborne farm dust; viral metagenomics; picornavirus; astrovirus; calicivirus; poultry Word counts for main text: 4019 words (max = 5000 words) 1 bioRxiv preprint doi: https://doi.org/10.1101/2021.03.09.434704; this version posted March 10, 2021. 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 4.0 International license. 1 ABSTRACT (250 words, word limit = 250 words) 2 Livestock animals housed in close proximity to humans can act as sources or intermediate hosts 3 facilitating animal-to-human transmission of zoonotic diseases. -
(Iowa State University College of Veterinary Medicine) and ("4/29/2019"[Date
PubMed (iowa state university college of veterinary medicine) AND ("4/29/2019"[Date Format: Summary Sort by: Most Recent Per page: 200 Search results Items: 1 to 200 of 2111 The Rho-independent transcription terminator for the porA gene enhances expression of the major outer membrane 1. protein and Campylobacter jejuni virulence in abortion induction. Dai L, Wu Z, Xu C, Sahin O, Yaeger M, Plummer PJ, Zhang Q. Infect Immun. 2019 Sep 30. pii: IAI.00687-19. doi: 10.1128/IAI.00687-19. [Epub ahead of print] PMID: 31570559 Administration of a Synbiotic Containing Enterococcus faecium Does Not Significantly Alter Fecal Microbiota Richness 2. or Diversity in Dogs With and Without Food-Responsive Chronic Enteropathy. Pilla R, Guard BC, Steiner JM, Gaschen FP, Olson E, Werling D, Allenspach K, Salavati Schmitz S, Suchodolski JS. Front Vet Sci. 2019 Aug 30;6:277. doi: 10.3389/fvets.2019.00277. eCollection 2019. PMID: 31552278 Free PMC Article Genetic Parameter Estimation and Genomic Prediction of Duroc Boars' Sperm Morphology Abnormalities. 3. Zhao Y, Gao N, Cheng J, El-Ashram S, Zhu L, Zhang C, Li Z. Animals (Basel). 2019 Sep 23;9(10). pii: E710. doi: 10.3390/ani9100710. PMID: 31547493 Free Article Immune thrombocytopenia (ITP): Pathophysiology update and diagnostic dilemmas. 4. LeVine DN, Brooks MB. Vet Clin Pathol. 2019 Sep 19. doi: 10.1111/vcp.12774. [Epub ahead of print] Review. PMID: 31538353 A Porcine circovirus type 2b (PCV2b)-based experimental vaccine is effective in the PCV2b-Mycoplasma 5. hyopneumoniae coinfection pig model. Opriessnig T, Castro AMMG, Karuppanan AK, Gauger PC, Halbur PG, Matzinger SR, Meng XJ. -
Mini Review Picobirnavirus: a Putative Emerging Threat to Humans And
Advances in Animal and Veterinary Sciences Mini Review Picobirnavirus: A Putative Emerging Threat to Humans and Animals JOBIN JOSE KATTOOR, SHUBHANKAR SIRCAR, SHARAD SAURAB, SHANMUGANATHAN SUBRAMANIYAN, KULDEEP DHAMA, YASHPAL SINGH MALIK* ICAR-Indian Veterinary Research Institute, Izatnagar 243122, Bareilly, Uttar Pradesh, India. Abstract | Diarrheal diseases remain fatal threat to human and animal population with the emergence of new types of pathogens. Among them, viral gastroenteritis plays a lion share with a number ranging over 100 different types including emerging and re-emerging types of viruses. Recent viral metagenomics studies confirm the co-existence of viruses in gastrointestinal tract of several different host species. A Picobirnavirus, consisting of 2 segments, has recently attained attention due to its wide host range and genetic variability. Until 2011, these small viruses were not consid- ered as a separate virus family, when a new family (Picobirnaviridae) was approved by the International Committee on Taxonomy of Viruses (ICTV). Currently two distinct genogroups (GG-I and GG-II) and one predicted genogroup (GG-III) are included in the Picobirnaviridae family. Recently, picobirnavirus infections have been reported from al- most all species including wild animals where persistent infection of the virus is also reported. Picobirnaviruses (PBVs) are also reported as opportunistic pathogens in immuno compromised hosts including HIV infected patients. Presence of atypical picobirnaviruses with shorter genomic segments along with genetic closeness of animal and human PBVs and its ability to infect immuno-compromised hosts pose a heavy threat for all human and animal. Currently RNA dependent RNA polymerase based RT-PCR detection is considered as a rapid and sensitive method for detection of PBV.