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Suppl. Tab. 1. Best BLAST Hit for Each Viral Contig Identified in Leech and Waterhole Samples

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Suppl. Tab. 1. Best BLAST hit for each viral contig identified in leech and waterhole samples. SAMPLE BLAST HIT REF REF. TAXONOMY ID COV E VALUE Contig length (bp) Mapping reads PCR +/- HOST L1 Bat coronavirus EF065516.1 Coronaviridae 72 98 1.00E-42 384 49 x Bos javanicus, Banteng Muntiacus sp., Muntjac Rusa unicolor, Sambar L3 Bat coronavirus EF065516.1 Coronaviridae 72 99 2.00E-26 282 189 x Rusa unicolor, Sambar L4 Lagos bat virus GU170202.1 Rhabdoviridae-Lyssavirus 73 58 3.00E-10 246 27 Rusa unicolor, Sambar L4 Lagos bat virus GU170202.1 Rhabdoviridae-Lyssavirus 72 33 7.00E-09 426 126 L5 Vesicular stomatitis Indiana virus KU296058.1 Rhabdoviridae-Vesiculovirus 69 100 2.00E-70 763 243 x Rusa unicolor, Sambar Sus barbatus, Bearded Pig Tragulus javanicus, Javan Chevrotain L7 Porcine circovirus 2 KF742545.1 Circoviridae 100 100 1.00E-82 175 3 x ✔ Helarctos malayanus, Sun Bear L7 Porcine circovirus 2 MH480645.1 Circoviridae 100 100 2.00E-28 74 3 Rusa unicolor, Sambar L7 Simian foamy virus KP143760.1 Retroviridae 80 96 5.00E-51 251 2 x Sus barbatus, Bearded Pig L7 Giant panda anellovirus MF327544.1 Anelloviridae 82 69 3.00E-49 315 14 x ✔ Tragulus napu, Greater Oriental Chevrotain Trichys fasciculata, Long-tailed Porcupine L8 Torque teno sus virus JF451498.1 Anelloviridae 95 87 9.00E-86 242 3 Mydaus javanensis, Sunda Stink-Badger L8 Porcine parvovirus 3 KP768490.1 Parvoviridae 98 100 2.00E-44 109 7 Rusa unicolor, Sambar Sus barbatus, Bearded Pig L9 Bat coronavirus EF065516.1 Coronaviridae 72 75 2.00E-47 545 14 x Muntiacus atherodes, Bornean Yellow Muntjac Pongo pygmaeus, Bornean Orangutan Rusa unicolor, Sambar L12 Bovine ephemeral fever virus MH756623.1 Rhabdoviridae-Ephemerovirus 67 57 2.00E-17 691 1466 Muntiacus sp., Muntjac L12 Lagos bat virus ABZ81171.1 Rhabdoviridae-Lyssavirus 45 88 2.00E-10 261 3 Pongo pygmaeus, Bornean Orangutan Rusa unicolor, Sambar Sus barbatus, Bearded Pig L14 Porcine parvovirus 4 HM031135.1 Parvoviridae 77 70 5.00E-40 331 9 Aonyx cinereus, Asian Small-clawed otter L14 Porcine parvovirus 4 HM031135.1 Parvoviridae 74 98 1.00E-20 192 85 Arctictis binturong, Binturong L14 Bat coronavirus EF065516.1 Coronaviridae 71 80 7.00E-47 540 136 x Echinosorex gymnura, Moonrat Manis javanica, Sunda Pangolin Rusa unicolor, Sambar Trichys fasciculata, Long-tailed Porcupine L15 Bat coronavirus EF065516.1 Coronaviridae 72 93 2.00E-46 440 561 x Bos javanicus, Banteng Macaca sp., Macaque Muntiacus sp., Muntjac Rusa unicolor, Sambar Sus barbatus, Bearded Pig L17 Bovine ephemeral fever virus MH756623.1 Rhabdoviridae-Ephemerovirus 68 65 2.00E-15 482 224 x Helarctos malayanus, Sun Bear L17 Giant panda anellovirus MF327544.1 Anelloviridae 83 63 4.00E-33 222 12 x ✔ Rusa unicolor, Sambar L18 Bovine ephemeral fever virus MH756623.1 Rhabdoviridae-Ephemerovirus 83 41 4.00E-13 199 3 Helarctos malayanus, Sun Bear Tragulus napu, Greater Oriental Chevrotain L21 Paguma larvata torque teno virus 10-2 LC387545.1 Anelloviridae 91 51 2.00E-21 154 17 x Mydaus javanensis, Sunda Stink-badger L21 Bat coronavirus EF065516.1 Coronaviridae 73 88 5.00E-18 200 12 x Rusa unicolor, Sambar L22 Bat coronavirus EF065516.1 Coronaviridae 72 92 1.00E-42 402 126 x Rusa unicolor, Sambar L22 Bovine ephemeral fever virus MH756623.1 Rhabdoviridae-Ephemerovirus 67 60 3.00E-16 643 1128 x L23 Bat coronavirus EF065516.1 Coronaviridae 73 69 2.00E-18 255 7 x Hemigalus derbyanus, Banded Civet L23 Bovine ephemeral fever virus MH756623.1 Rhabdoviridae-Ephemerovirus 84 32 5.00E-14 254 5 Rusa unicolor, Sambar L23 Vesicular stomatitis Indiana virus KU296058.1 Rhabdoviridae-Vesiculovirus 77 95 2.00E-22 167 2 x L25 Bat coronavirus EF065516.1 Coronaviridae 71 94 3.00E-38 414 106 x Viverra tangalunga, Malay Civet L25 Paguma larvata torque teno virus 10-2 LC387545.1 Anelloviridae 91 30 4.00E-21 265 11 x ✔ L26 Lagos bat virus GU170202.1 Rhabdoviridae-Lyssavirus 73 40 4.00E-10 351 22 Viverra tangalunga, Malay Civet L27 Bovine ephemeral fever virus MH756623.1 Rhabdoviridae-Ephemerovirus 84 20 8.00E-14 394 24 Rusa unicolor, Sambar L28 Bovine ephemeral fever virus MH756623.1 Rhabdoviridae-Ephemerovirus 84 25 6.00E-14 320 28 Rusa unicolor, Sambar L30 Bat coronavirus EF065516.1 Coronaviridae 72 95 7.00E-24 240 43 x Bos javanicus, Banteng Felis Catus, Domestic Cat Hemigalus derbyanus, Banded Civet Hystrix brachyura, Malayan Porcupine Muntiacus sp., Muntjac Rusa unicolor, Sambar LEECHES L34 Bovine ephemeral fever virus MH756623.1 Rhabdoviridae-Ephemerovirus 84 24 6.00E-14 330 17 Bos javanicus, Banteng Macaca nemestrina, Southern Pig-tailed Macaque Muntiacus sp., Muntjac Rusa unicolor, Sambar Sus barbatus, Bearded Pig L36 Giant panda anellovirus MF327544.1 Anelloviridae 92 79 8.00E-24 106 9 x Helarctos malayanus, Sun Bear Viverra tangalunga, Malay Civet L37 Torque teno sus virus JX444426.1 Anelloviridae 96 71 3.00E-22 100 2 x ✔ Helarctos malayanus, Sun Bear L37 Bat coronavirus EF065516.1 Coronaviridae 72 97 2.00E-46 423 232 x Rusa unicolor, Sambar L37 Bovine ephemeral fever virus MH756623.1 Rhabdoviridae-Ephemerovirus 68 45 9.00E-16 692 348 x Sus barbatus, Bearded Pig Tragulus napu, Greater Oriental Chevrotain L38 Bat coronavirus EF065516.1 Coronaviridae 70 81 8.00E-48 609 398 x Munticaus atherodes, Bornean Yellow Muntjac L38 Vesicular stomatitis Indiana virus KU296058.1 Rhabdoviridae-Vesiculovirus 72 76 1.00E-58 626 58 x Rusa uncolor, Sambar Tragulus sp., Chevrotain Trichys fasciculata, Long-tailed Porcupine L39 Paguma larvata torque teno virus 5-1 LC387539.1 Anelloviridae 92 82 4.00E-35 285 20 x Helarctos malayanus, Sun Bear L39 Paguma larvata torque teno virus 5-2 LC387540.1 Anelloviridae 83 58 3.00E-43 305 15 x Rusa unicolor, Sambar L39 Paguma larvata torque teno virus 1-2 LC387537.1 Anelloviridae 87 68 1.00E-39 211 15 x L39 Paguma larvata torque teno virus 5-2 LC387540.1 Anelloviridae 86 69 4.00E-42 386 18 x L39 Paguma larvata torque teno virus 5-2 LC387540.1 Anelloviridae 85 75 4.00E-41 304 22 x L39 Paguma larvata torque teno virus 5-2 LC387540.1 Anelloviridae 86 59 6.00E-42 481 36 x L39 Giant panda anellovirus MF327546.1 Anelloviridae 81 75 9.00E-42 247 4 x L40 Bat coronavirus EF065516.1 Coronaviridae 72 97 3.00E-29 292 79 x Echinosorex gymnura, Moonrat L40 Bovine ephemeral fever virus MH756623.1 Rhabdoviridae-Ephemerovirus 84 16 1.00E-13 507 139 x Tragulus napu, Greater Oriental Chevrotain L44 Vesicular stomatitis Indiana virus KU296058.1 Rhabdoviridae-Vesiculovirus 72 90 7.00E-60 535 28 x Rusa unicolor, Sambar L44 Bat coronavirus EF065516.1 Coronaviridae 72 98 1.00E-41 381 28 x Tragulus napu, Greater Oriental Chevrotain L46 Feline foamy virus AB052798.1 Retroviridae 79 93 4.00E-32 185 48 x Rusa unicolor, Sambar Tragulus napu, Greater Oriental Chevrotain L49 Berrimah virus HM461974.1 Rhabdoviridae-Ephemerovirus 82 34 2.00E-11 227 5 Muntiacus atherodes, Bornean Yellow Muntjac L51 Lagos bat virus GU170202.1 Rhabdoviridae-Lyssavirus 73 50 6.00E-10 516 185 x Muntiacus atherodes, Bornean Yellow Muntjac Rusa unicolor, Sambar L54 Bovine ephemeral fever virus MH756623.1 Rhabdoviridae-Ephemerovirus 84 23 7.00E-14 351 336 Rusa unicolor, Sambar Sus barbatus, Bearded Pig L55 Lagos bat virus GU170202.1 Rhabdoviridae-Lyssavirus 66 54 7.00E-19 909 866 x ✔ Rusa unicolor, Sambar L56 Berrimah virus HM461974.1 Rhabdoviridae-Ephemerovirus 82 11 8.00E-11 710 379 Rusa unicolor, Sambar Sus barbatus, Bearded Pig L57 Bovine ephemeral fever virus MH756623.1 Rhabdoviridae-Ephemerovirus 67 47 1.00E-14 660 391 x Rusa unicolor, Sambar L58 Berrimah virus HM461974.1 Rhabdoviridae-Ephemerovirus 82 26 3.00E-11 300 20 Rusa unicolor, Sambar L58 Lagos bat virus GU170202.1 Rhabdoviridae-Lyssavirus 65 61 2.00E-25 1038 3055 x ✔ L59 Porcine circovirus 2 MH480645.1 Circoviridae 100 100 6.00E-59 131 3 x ✔ Macaca nemestrina, Southern Pig-tailed macaque Rusa unicolor, Sambar L60 Bat coronavirus EF065516.1 Coronaviridae 71 85 1.00E-30 383 96 x Bos javanicus, Banteng Muntiacus sp., Muntjac Rusa unicolor, Sambar L62 Lagos bat virus GU170202.1 Rhabdoviridae-Lyssavirus 73 66 8.00E-10 210 50 Pongo pygmaeus, Bornean Orangutan Tragulus javanicus, Javan Chevrotain Trichys fasciculata, Long-tailed Porcupine L64 Lagos bat virus JX901139.1 Rhabdoviridae-Lyssavirus 72 26 2E-11 622 19 Tragulus napu, Greater Oriental Chevrotain L64 Feline foamy virus AB052798.1 Retroviridae 80 94 2.00E-44 228 5 x L64 Simian foamy virus KP143760.1 Retroviridae 82 100 6.00E-20 113 1 L68 Bat coronavirus EF065516.1 Coronaviridae 70 94 1.00E-50 538 742 x Bos javanicus, Banteng L68 Vesicular stomatitis Indiana virus KU296058.1 Rhabdoviridae-Vesiculovirus 72 89 2.00E-60 552 124 x Rusa unicolor, Sambar L68 Bovine ephemeral fever virus MH756623.1 Rhabdoviridae-Ephemerovirus 68 65 6.00E-16 484 124 x Sus barbatus, Bearded Pig Tragulus napu, Greater Oriental Chevrotain WM3 Equid herpesvirus 1 MF975656.1 Herpesviridae 100 75 1.00E-89 251 42 x ✔ WM3 Equid alphaherpesvirus 3 YP_009054948 Herpesviridae 100 71 1.00E-40 306 16 WM20 Equid herpesvirus 1 MF975656.1 Herpesviridae 100 100 0.00E+00 394 4 x ✔ SM20 Equine adenovirus 2 YP_009162356 Adenoviridae 100 95 2.00E-32 170 6 ST38 Equus caballus papillomavirus 1 NP_620510 Papillomaviridae 63 61 1.00E-21 385 4 ✔ WATER SM3 enJSRV-13 endogenous virus Jaagsiekte sheep EF680296 Retroviridae 100 76 7E-61 176 4 x SM3 enJSRV-5 endogenous virus Jaagsiekte sheep EF680305.1 Retroviridae 100 73 4E-57 171 2 SM3 Enzootic nasal tumour virus of goats strain Shaanxi4 KU980912.1 Retroviridae 100 100 1E-62 140 2 SM3 Enzootic nasal tumour virus of goats isolate CQ1 MK164400 Retroviridae 100 98 5E-82 176 3 PCR if a PCR was tried on this sample to confirm the viral hit +/- if the PCR gave positive amplifiCation or not HOST leech host assigment code (code correspondence on the right).
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    Evidence to support safe return to clinical practice by oral health professionals in Canada during the COVID-19 pandemic: A report prepared for the Office of the Chief Dental Officer of Canada. November 2020 update This evidence synthesis was prepared for the Office of the Chief Dental Officer, based on a comprehensive review under contract by the following: Paul Allison, Faculty of Dentistry, McGill University Raphael Freitas de Souza, Faculty of Dentistry, McGill University Lilian Aboud, Faculty of Dentistry, McGill University Martin Morris, Library, McGill University November 30th, 2020 1 Contents Page Introduction 3 Project goal and specific objectives 3 Methods used to identify and include relevant literature 4 Report structure 5 Summary of update report 5 Report results a) Which patients are at greater risk of the consequences of COVID-19 and so 7 consideration should be given to delaying elective in-person oral health care? b) What are the signs and symptoms of COVID-19 that oral health professionals 9 should screen for prior to providing in-person health care? c) What evidence exists to support patient scheduling, waiting and other non- treatment management measures for in-person oral health care? 10 d) What evidence exists to support the use of various forms of personal protective equipment (PPE) while providing in-person oral health care? 13 e) What evidence exists to support the decontamination and re-use of PPE? 15 f) What evidence exists concerning the provision of aerosol-generating 16 procedures (AGP) as part of in-person
  • Virus Pathogen Resource (Vipr) New Features in Vipr

    Virus Pathogen Resource (Vipr) New Features in Vipr

    November 2012 Virus Pathogen Resource (ViPR) New Features in ViPR genome sequences with incomplete CDS. tool to allow primer design for a group of target News and Events Currently, the annotation pipeline has been sequences in the future . implemented to predict mature viral proteins for In response to user feedback, we have also added Join the ViPR User Advisory many taxa in the Arenaviridae , Bunyaviridae , end-of-line position numbers in the primer design Group to help us better serve Caliciviridae , Coronaviridae , Flaviviridae , and sequence input sequence box. This feature will the scientific community Togaviridae families in ViPR . help ensure accurate selection of the desired ViPR is a bioinformatics resources built for the target region within the displayed sequence. virology research community. We are calling for users to join the ViPR User Advisory Group to provide feedback and advise on ViPR Rock your development. Click here for details . protein structure IRD/ViPR hands-on workshops ViPR provides a ViPR will be providing a hands-on workshop customized at Mount Sinai School of Medicine, New interactive York, NY, December 5 . Please contact Ryan protein Camping ( [email protected] ) for structure workshop registration. viewer for virus-related protein structures obtained from the Protein Data Bank . In addition to PCR primer design tool enhanced choosing from a variety of structure display Sequence Conservation/ ViPR has recently implemented a PCR primer options , including ball & stick, line, space, primary Variation Analysis tutorial design tool , which uses the Primer3 algorithm to The Analyze Sequence Variation (SNP) tool in structure, secondary structure, etc., you can now predict the optimal set(s) of PCR primers for a ViPR provides the ability to quickly quantify rock a structure back and forth to get a better 3D particular sequence .
  • The Jungle Times

    The Jungle Times

    The Jungle Times Independent newsletter of: Est. 2008 Issue: 113 Inside this issue: Page 7: 10 years of DGFC Page 2: Arrivals Page 3: Visitors Page 5: Departures Page 6: Aberystwyth Field Course Page 7: 10 years of DGFC Page 8: State Action Plans Page 8: State Action Plans Page 9: Science Corner Page 10: Conservation Corner Page 11: Game September 2018 Page 2 Arrivals Jessica Shuttleworth Our final PTY of the year joins us from Oxfordshire. Jess studies Biological Sciences at Cardiff University and is particularly interested in Ecology and Conservation. She has always loved animals since growing up on a pig farm and her love of the outdoors was solidified when trekking through Norway for 3 weeks. She is looking forward to seeing all of Borneo’s amazing wildlife before carrying out her own project here at DG. September 2018 Page 3 Visitors Sabrina Herold Sabrina came from Switzerland to visit for 10 days to experience life at DGFC. She took part in many activities including night walks, primate boats, bird boats and tracking our collared tarsiers. Sabrina also helped to create a welcome pack for future PTYs and volunteers at DG to help future students get more of an idea of the centre before they arrive. Thank you Sabrina! September 2018 Page 4 Visitors – Cardiff University Professor Andrew Weightman, Dr Alison Weightman, Sarah Evans and Professor Susan Baker This month the centre had some visitors from Cardiff University! Professor Andy Weightman from Cardiff School of Biosciences, Sarah Evans, Manager of Cardiff Sustainable Places Research Institute, Professor Susan Baker from Cardiff School of Social Sciences and Dr Alison Weightman visited Borneo this month to attend the ten year anniversary celebration of DGFC.