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Computational Exploration of Virus Diversity on Transcriptomic Datasets

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Computational Exploration of Virus Diversity on Transcriptomic Datasets Digitaler Anhang der Dissertation zur Erlangung des Doktorgrades (Dr. rer. nat.) der Mathematisch-Naturwissenschaftlichen Fakultät der Rheinischen Friedrich-Wilhelms-Universität Bonn vorgelegt von Simon Käfer aus Andernach Bonn 2019 Table of Contents 1 Table of Contents 1 Preliminary Work - Phylogenetic Tree Reconstruction 3 1.1 Non-segmented RNA Viruses ........................... 3 1.2 Segmented RNA Viruses ............................. 4 1.3 Flavivirus-like Superfamily ............................ 5 1.4 Picornavirus-like Viruses ............................. 6 1.5 Togavirus-like Superfamily ............................ 7 1.6 Nidovirales-like Viruses .............................. 8 2 TRAVIS - True Positive Details 9 2.1 INSnfrTABRAAPEI-14 .............................. 9 2.2 INSnfrTADRAAPEI-16 .............................. 10 2.3 INSnfrTAIRAAPEI-21 ............................... 11 2.4 INSnfrTAORAAPEI-35 .............................. 13 2.5 INSnfrTATRAAPEI-43 .............................. 14 2.6 INSnfrTBERAAPEI-19 .............................. 15 2.7 INSytvTABRAAPEI-11 .............................. 16 2.8 INSytvTALRAAPEI-35 .............................. 17 2.9 INSytvTBORAAPEI-47 .............................. 18 2.10 INSswpTBBRAAPEI-21 .............................. 19 2.11 INSeqtTAHRAAPEI-88 .............................. 20 2.12 INShkeTCLRAAPEI-44 .............................. 22 2.13 INSeqtTBNRAAPEI-11 .............................. 23 2.14 INSeqtTCJRAAPEI-20 .............................. 24 2.15 INSeqtTCZRAAPEI-47 .............................. 25 2.16 INSeqtTDXRAAPEI-19 .............................. 27 2.17 INSlupTBDRAAPEI-17 .............................. 28 2.18 INSlupTBKRAAPEI-31 .............................. 29 2.19 INSlupTBMRAAPEI-34 .............................. 30 2.20 INSlupTBURAAPEI-45 .............................. 31 2.21 INSlupTAFRAAPEI-44 .............................. 32 2.22 INSntgTABRAAPEI-216 ............................. 33 2.23 INSlupTASRAAPEI-89 .............................. 34 2.24 INSqiqTBFRAAPEI-61 .............................. 36 2.25 INSqiqTBLRAAPEI-83 .............................. 37 2.26 INSqiqTBNRABPEI-90 .............................. 38 2.27 INSqiqTCTRAAPEI-75 .............................. 40 2 Table of Contents 2.28 INSlupTATRAAPEI-90 .............................. 41 2.29 INSqiqTCXRAAPEI-90 .............................. 42 2.30 INSqiqTDLRAAPEI-72 .............................. 43 2.31 INSobdTDTRAAPEI-18 .............................. 44 2.32 INSobdTDYRAAPEI-30 .............................. 45 2.33 INSerlTCGRAAPEI-32 .............................. 47 2.34 INSkzdTABRAAPEI-136 ............................. 48 2.35 INSkzdTACRAAPEI-171 ............................. 49 2.36 INSofmTBLRAAPEI-71 .............................. 50 2.37 INSofmTCYRAAPEI-79 .............................. 51 2.38 INSqiqTDDRABPEI-136 ............................. 52 2.39 INSfkjTBIRAAPEI-202 .............................. 53 2.40 INSerlTAKRAAPEI-83 .............................. 54 2.41 INSfkjTBMRAAPEI-206 ............................. 55 2.42 INSofmTCERAAPEI-22 .............................. 57 2.43 INSofmTCFRAAPEI-26 .............................. 58 2.44 INSinlTAARABPEI-43 ............................... 59 2.45 INSinlTAPRAAPEI-33 ............................... 60 2.46 INSinlTAWRAAPEI-44 .............................. 61 2.47 RINSinlTCARAAPEI-55 .............................. 62 2.48 RINSinlTCNRAAPEI-33 .............................. 63 2.49 RINSymlTABRAAPEI-202 ............................ 64 2.50 RINSwvkTAURAAPEI-56 ............................. 65 2.51 ANIsrmTAAWRAAPEI-225 ............................ 66 2.52 WHANIsrmTMAFRAAPEI-14 .......................... 67 2.53 WHANIsrmTMCHRAAPEI-56 .......................... 68 2.54 INSeqtTBBRAAPEI-75 .............................. 69 2.55 INSobdTDIRAAPEI-84 .............................. 71 1. PRELIMINARY WORK - PHYLOGENETIC TREE RECONSTRUCTION 3 1 Preliminary Work - Phylogenetic Tree Reconstruction 1.1 Non-segmented RNA Viruses non-segmented RNA virus (-) 0.3 II 1KV_mono_000165 III KM817639-Shuangao_Insect_Virus... 1KV_mono_000207 1KV_mono_000169 1KV_mono_000166 1KV_mono_000067 1KV_mono_000135 1KV_mono_000172 1KV_mono_000223 1KV_mono_000138 1KV_mono_000020 1KV_mono_000109 KM817645-Wuhan_Ant_Virus_1KV_mono_000061 1KV_mono_000111 1KV_mono_000195 NC_025382-Spodoptera_frugiperd... NC_025253-Farmington_virus_(st... 1KV_mono_000179 1KV_mono_000117 KM817652-Wuhan_Insect_virus_6_... KM817649-Wuhan_House_Fly_Virus... 1KV_mono_000035 1KV_mono_000011 NC_007642-Lettuce_necrotic_yel... 1KV_mono_000123 KM817659-Wuhan_Mosquito_Virus_... KM817636-Shayang_Fly_Virus_3_(... 1KV_mono_000148 KM817650-Wuhan_Insect_virus_4_... KM817642-Tacheng_Tick_Virus_7_... NC_016136-Potato_yellow_dwarf_... KM817637-Shuangao_Bedbug_Virus... KM817647-Wuhan_Fly_Virus_3_(st... HM849039-Soybean_cyst_nematode... KM817651-Wuhan_Insect_virus_5_... 1KV_mono_000023 1KV_mono_000098 Rhabdoviridae 1KV_mono_000114 1KV_mono_000204 1KV_mono_000171 NC_002251-Northern_cereal_mosa... KM817634-Sanxia_Water_Strider_... 1KV_mono_000016 1KV_mono_000084 1KV_mono_000118 1KV_mono_000013 1KV_mono_000191 1KV_mono_000054 KM817631-Jingshan_Fly_Virus_2_... 1KV_mono_000027 KF823814-Fox_fecal_rhabdovirus... 1KV_mono_000150 1KV_mono_000039 1KV_mono_000201 NC_025401-Sunguru_virus_(strip... KM817638-Shuangao_Fly_Virus_2_... NC_025405-Niakha_virus_(stripp... 1KV_mono_000062 1KV_mono_000115 1KV_mono_000232 NC_025399-Oak-Vale_virus_ 1KV_mono_000102 1KV_mono_000040 1KV_mono_000063 1KV_mono_000139 NC_018629-Ikoma_lyssavirus_(st... 1KV_mono_000147 Anphevirus 1KV_mono_000002 IV 1KV_mono_000188 KM817643-Taishun_Tick_Virus_(s... 1KV_mono_000053 1KV_mono_000024 NC_001542-Rabies_virus_(stripp... 1KV_mono_000124 KM817661-Xincheng_Mosquito_Vir... NC_025393-Arboretum_virus 1KV_mono_000051 1KV_mono_000094 Lyssavirus 1KV_mono_000192 1KV_mono_000203 1KV_mono_000096 KM205018-Bahia_Grande_virus_(s... NC_025340-Long_Island_tick_rha... 1KV_mono_000177 1KV_mono_000164 NC_025359-Moussa_virus_(stripp... 1KV_mono_000043 NC_025354-Curionopolis_virus 1KV_mono_000031 1KV_mono_000092 1KV_mono_000095 1KV_mono_000030 KF360973-North_Creek_virus_(st... 1KV_mono_000082 1KV_mono_000091 NC_025384-Culex_tritaeniorhync... 1KV_mono_000007 1KV_mono_000209 1KV_mono_000228 JX297815-Bas-Congo_virus_ 1KV_mono_000036 KM817629-Bole_Tick_Virus_2_(st... 1KV_mono_000081 1KV_mono_000107 KM817640-Tacheng_Tick_Virus_3_... I 1KV_mono_000021 1KV_mono_000065 KM817660-Wuhan_Tick_Virus_1_(s... 1KV_mono_000048 1KV_mono_000100 NC_013135-Drosophila_melanogas... V KM817657-Wuhan_Louse_Fly_Virus... 1KV_mono_000042 KM817655-Wuhan_Louse_Fly_Virus... 1KV_mono_000060 KM817656-Wuhan_Louse_Fly_Virus...NC_007020-Tupaia_virus_(stripp... 1KV_mono_000106 1KV_mono_000200 1KV_mono_000058 1KV_mono_000224 NC_002526-Bovine_ephemeral_fev... KM817630-Huangpi_Tick_Virus_3_... KM817658-Wuhan_Louse_Fly_Virus... NC_020804-Tibrogargan_virus_(s... 1KV_mono_000012 NC_011639-Wongabel_virus_ 1KV_mono_000212 NC_025387-Scopthalmus_maximus_... NC_001560-Vesicular_stomatitis... 1KV_mono_000078 1KV_mono_000131 VI NC_002803-Spring_viraemia_of_c... KM817653-Wuhan_Insect_virus_7_... NC_020803-Perch_rhabdovirus NC_024702-Soybean_cyst_nematode... KM817654-Wuhan_Louse_Fly_Virus... KM350503-Santa_barbara_virus NC_012703-Nyamini_virusNC_024376-Sierra_Nevada_virus_... 1KV_mono_000167 1KV_mono_000077 KM817648-Wuhan_House_Fly_Virus... NC_025341-Fikirini_bat_rhabdov... NC_025362-Xiburema_virus KM817646-Wuhan_Fly_Virus_2 KM817646-Wuhan_Fly_Virus_2 KM817662-Yongjia_Tick_Virus 1KV_mono_000181 KM817635-Shayang_Fly_Virus_2 1KV_mono_000028 1KV_mono_000071 1KV_mono_000001 1KV_mono_000206 Nyamiviridae 1KV_mono_000068 1KV_mono_000052 NC_024296-Avian_Bornavirus. Vesiculovirus 1KV_mono_000009 1KV_mono_000015 1KV_mono_000004 1KV_mono_000198 1KV_mono_000199 NC_001607-Borna_disease_virus_... 1KV_mono_000180 1KV_mono_000162 1KV_mono_000044 1KV_mono_000006 NC_024778-Reptile_Bornavirus 1KV_mono_000059 1KV_mono_000152 1KV_mono_000116 1KV_mono_000174 1KV_mono_000149 KM817644-Wenzhou_Crab_Virus_1_... 1KV_mono_000156 Bornaviridae 1KV_mono_000194 1KV_mono_000141 VII 1KV_mono_000099 1KV_mono_000110 KM817598-Shayang_Fly_Virus_1_(... 1KV_mono_000022 Crustavirus 1KV_mono_000087 KM817613-Shuangao_Lacewing_Vir... KM817632-Lishi_Spider_Virus_2_... KM817614-Shuangao_Insect_Virus... 1KV_mono_000033 1KV_mono_000029 1KV_mono_000041 KM817641-Tacheng_Tick_Virus_6_... 1KV_mono_000101 1KV_mono_000154 KM817603-Wenzhou_Crab_Virus_3_... KM817633-Sanxia_Water_Strider_... VIII KM817599-Tacheng_Tick_Virus_4_... 1KV_mono_000113 Chengtivirus 1KV_mono_000057 1KV_mono_000047 1KV_mono_000190 Arlivirus KC601997-Sclerotinia_sclerotio... 1KV_mono_000046 1KV_mono_000049 Wastrivirus 1KV_mono_000055 1KV_mono_000225 1KV_mono_000142 Mymonaviridae KM817595-Changping_Tick_Virus_... KM817600-Tacheng_Tick_Virus_5_... 1KV_mono_000155 NC_001652-Infectious_hematopoi... 1KV_mono_000034 XIII 1KV_mono_000104 KJ746903-Deer_tick_mononegavir... KM817611-Wuhan_Tick_Virus_2_(s... KM817594-Changping_Tick_Virus_... 1KV_mono_000170 Novirhabdovirus KM817609-Wuhan_Louse_Fly_Virus... 1KV_mono_000090 1KV_mono_000076 1KV_mono_000050 1KV_mono_000132 KM817606-Wuhan_Louse_Fly_Virus... IX 1KV_mono_000227 KM817612-Shuangao_Fly_Virus_1_... 1KV_mono_000134 KM817597-Lishi_Spider_Virus_1_... NC_025403-Achimota_virus_1_(st... NC_025403-Achimota_virus_1_(st... 1KV_mono_000105 KM817601-Wenzhou_Crab_Virus_2_...KM817610-Wuhan_Mosquito_Virus_..
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    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

    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

    (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

    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.