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Review Articles

Viral metagenomics as an emerging and powerful tool in veterinary medicine

Pages 107-114 | Received 06 Jun 2011, Accepted 29 Jun 2011, Published online: 02 Aug 2011

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Harindranath Cholleti, Mikael Berg, Juliette Hayer & Anne-Lie Blomström. (2018) Vector-borne viruses and their detection by viral metagenomics. Infection Ecology & Epidemiology 8:1.
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Shu-xuan Deng, Ming-sheng Cai, Wei Cui, Jin-lu Huang & Mei-li Li. (2014) Evaluation of the immune response in Shitou geese (Anser anser domesticus) following immunization with GPV-VP1 DNA-based and live attenuated vaccines. Veterinary Quarterly 34:4, pages 180-184.
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Vivien G Dugan, Kazima Saira & Elodie Ghedin. (2012) Large-Scale Sequencing and the Natural History of Model Human RNA Viruses. Future Virology 7:6, pages 563-573.
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Gabriela B. Caldas-Garcia, Vinícius Castro Santos, Paula Luize Camargos Fonseca, João Paulo Pereira de Almeida, Marco Antônio Costa & Eric Roberto Guimarães Rocha Aguiar. (2023) The Viromes of Six Ecosystem Service Provider Parasitoid Wasps. Viruses 15:12, pages 2448.
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Claudio L. Afonso & Anna M. Afonso. (2023) Next-Generation Sequencing for the Detection of Microbial Agents in Avian Clinical Samples. Veterinary Sciences 10:12, pages 690.
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Dávid Smoľak, Slavomíra Šalamúnová, Anna Jacková, Mária Haršányová, Jaroslav Budiš, Tomáš Szemes & Štefan Vilček. (2022) Analysis of RNA virome in rectal swabs of healthy and diarrheic pigs of different age. Comparative Immunology, Microbiology and Infectious Diseases 90-91, pages 101892.
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Alba Folgueiras-González, Robin van den Braak, Martin Deijs, Wikke Kuller, Steven Sietsma, Valentijn Thuring, Lia van der Hoek & Ad de Groof. (2021) Dynamics of the Enteric Virome in a Swine Herd Affected by Non-PCV2/PRRSV Postweaning Wasting Syndrome. Viruses 13:12, pages 2538.
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Viviane Saporiti, Giovanni Franzo, Marina Sibila & Joaquim Segalés. (2021) Porcine circovirus 3 (PCV‐3) as a causal agent of disease in swine and a proposal of PCV‐3 associated disease case definition. Transboundary and Emerging Diseases 68:6, pages 2936-2948.
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Seung-Ho Lee, Kijin Kim, Jongwoo Kim, Jin Sun No, Kyungmin Park, Shailesh Budhathoki, Seung Ho Lee, Jingyeong Lee, Seung Hye Cho, Seungchan Cho, Geum-Young Lee, Jusun Hwang, Heung-Chul Kim, Terry A. Klein, Chang-Sub Uhm, Won-Keun Kim & Jin-Won Song. (2021) Discovery and Genetic Characterization of Novel Paramyxoviruses Related to the Genus Henipavirus in Crocidura Species in the Republic of Korea. Viruses 13:10, pages 2020.
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Seung-Ho Lee, Jin Sun No, Kijin Kim, Shailesh Budhathoki, Kyungmin Park, Geum-Young Lee, Seungchan Cho, Bong-Hyun Kim, Seunghee Cho, Jongwoo Kim, Jingyeong Lee, Seung Hye Cho, Heung-Chul Kim, Terry A. Klein, Chang-Sub Uhm, Won-Keun Kim & Jin-Won Song. (2021) Novel Paju Apodemus paramyxovirus 1 and 2, harbored by Apodemus agrarius in the Republic of Korea. Virology 562, pages 40-49.
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Tarka Raj Bhatta, Anthony Chamings & Soren Alexandersen. (2021) Exploring the Cause of Diarrhoea and Poor Growth in 8–11-Week-Old Pigs from an Australian Pig Herd Using Metagenomic Sequencing. Viruses 13:8, pages 1608.
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Alexandra Corduneanu, Andrei Daniel Mihalca, Attila D. Sándor, Sándor Hornok, Maja Malmberg, Natalia Pin Viso & Erik Bongcam-Rudloff. (2021) The heart microbiome of insectivorous bats from Central and South Eastern Europe. Comparative Immunology, Microbiology and Infectious Diseases 75, pages 101605.
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Donath DamianReuben MaghembeModester DamasJonas Johansson WensmanMikael Berg. (2020) Application of Viral Metagenomics for Study of Emerging and Reemerging Tick-Borne Viruses. Vector-Borne and Zoonotic Diseases 20:8, pages 557-565.
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Pooja Arya & Ravindra. 2020. Recent Advancements in Microbial Diversity. Recent Advancements in Microbial Diversity 537 559 .
Eszter Kaszab, Andor Doszpoly, Gianvito Lanave, Atul Verma, Krisztián Bányai, Yashpal Singh Malik & Szilvia Marton. 2020. Genomics and Biotechnological Advances in Veterinary, Poultry, and Fisheries. Genomics and Biotechnological Advances in Veterinary, Poultry, and Fisheries 29 73 .
Tarka Raj Bhatta, Anthony Chamings, Jessy Vibin & Soren Alexandersen. (2019) Detection and characterisation of canine astrovirus, canine parvovirus and canine papillomavirus in puppies using next generation sequencing. Scientific Reports 9:1.
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Cecilia Osunmakinde, Ramganesh Selvarajan, Timothy Sibanda, Bhekie Mamba & Titus Msagati. (2018) Overview of Trends in the Application of Metagenomic Techniques in the Analysis of Human Enteric Viral Diversity in Africa’s Environmental Regimes. Viruses 10:8, pages 429.
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Anne-Lie Blomström, Xingyu Ye, Caroline Fossum, Per Wallgren & Mikael Berg. (2018) Characterisation of the Virome of Tonsils from Conventional Pigs and from Specific Pathogen-Free Pigs. Viruses 10:7, pages 382.
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Laura Inés Cuervo-Soto, Silvio Alejandro López-Pazos & Ramón Alberto Batista-García. 2018. Farm Animals Diseases, Recent Omic Trends and New Strategies of Treatment. Farm Animals Diseases, Recent Omic Trends and New Strategies of Treatment.
Anbu K. Karuppannan, Alessandra Marnie M. G. de Castro & Tanja Opriessnig. 2018. Advanced Techniques in Diagnostic Microbiology. Advanced Techniques in Diagnostic Microbiology 317 344 .
Sonia Monteil-Bouchard, Sarah Temmam & Christelle Desnues. 2018. The Human Virome. The Human Virome 25 36 .
Mette Myrmel, Veslemøy Oma, Mamata Khatri, Hanne H. Hansen, Maria Stokstad, Mikael Berg & Anne-Lie Blomström. (2017) Single primer isothermal amplification (SPIA) combined with next generation sequencing provides complete bovine coronavirus genome coverage and higher sequence depth compared to sequence-independent single primer amplification (SISPA). PLOS ONE 12:11, pages e0187780.
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Paloma S. Moreno, Josef Wagner, Caroline S. Mansfield, Matthew Stevens, James R. Gilkerson & Carl D. Kirkwood. (2017) Characterisation of the canine faecal virome in healthy dogs and dogs with acute diarrhoea using shotgun metagenomics. PLOS ONE 12:6, pages e0178433.
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Todd P. Knutson, Binu T. Velayudhan & Douglas G. Marthaler. (2017) A porcine enterovirus G associated with enteric disease contains a novel papain-like cysteine protease. Journal of General Virology 98:6, pages 1305-1310.
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Elizabeth Fahsbender, Jennifer M. Burns, Stacy Kim, Simona Kraberger, Greg Frankfurter, Alice A. Eilers, Michelle R. Shero, Roxanne Beltran, Amy Kirkham, Robert McCorkell, Rachel K. Berngartt, Maketalena F. Male, Grant Ballard, David G. Ainley, Mya Breitbart & Arvind Varsani. (2017) Diverse and highly recombinant anelloviruses associated with Weddell seals in Antarctica. Virus Evolution 3:1.
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Anne-Lie Blomström, Caroline Fossum, Per Wallgren & Mikael Berg. (2016) Viral Metagenomic Analysis Displays the Co-Infection Situation in Healthy and PMWS Affected Pigs. PLOS ONE 11:12, pages e0166863.
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Branko Rihtman, Sean Meaden, Martha R.J. Clokie, Britt Koskella & Andrew D. Millard. (2016) Assessing Illumina technology for the high-throughput sequencing of bacteriophage genomes. PeerJ 4, pages e2055.
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Stephanie M. Rosales & Rebecca Vega Thurber. (2015) Brain Meta-Transcriptomics from Harbor Seals to Infer the Role of the Microbiome and Virome in a Stranding Event. PLOS ONE 10:12, pages e0143944.
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Dana M. Lindemann, James W. Carpenter, Jerome C. Nietfeld, Estehela Gonzalez, Mackenzie Hallman & Ben M. Hause. (2015) MULTICENTRIC T-CELL LYMPHOMA AND CUTANEOUS HEMANGIOSARCOMA IN A CAPTIVE CHEETAH ( ACINONYX JUBATUS ) . Journal of Zoo and Wildlife Medicine 46:4, pages 961-966.
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Toon Rosseel, Orkun Ozhelvaci, Graham Freimanis & Steven Van Borm. (2015) Evaluation of convenient pretreatment protocols for RNA virus metagenomics in serum and tissue samples. Journal of Virological Methods 222, pages 72-80.
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Wray W. Grimaldi, Phil J. Seddon, Phil O’B. Lyver, Shinichi Nakagawa & Daniel M. Tompkins. (2014) Infectious diseases of Antarctic penguins: current status and future threats. Polar Biology 38:5, pages 591-606.
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Richard J. Hall, Jenny L. Draper, Fiona G. G. Nielsen & Bas E. Dutilh. (2015) Beyond research: a primer for considerations on using viral metagenomics in the field and clinic. Frontiers in Microbiology 6.
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Steven Van Borm, Sándor Belák, Graham Freimanis, Alice Fusaro, Fredrik Granberg, Dirk Höper, Donald P. King, Isabella Monne, Richard Orton & Toon Rosseel. 2015. Veterinary Infection Biology: Molecular Diagnostics and High-Throughput Strategies. Veterinary Infection Biology: Molecular Diagnostics and High-Throughput Strategies 415 436 .
T. Rosseel, B. Pardon, K. De Clercq, O. Ozhelvaci & S. Van Borm. (2014) False-Positive Results in Metagenomic Virus Discovery: A Strong Case for Follow-Up Diagnosis. Transboundary and Emerging Diseases 61:4, pages 293-299.
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Sarah Temmam, Bernard Davoust, Jean-Michel Berenger, Didier Raoult & Christelle Desnues. (2014) Viral Metagenomics on Animals as a Tool for the Detection of Zoonoses Prior to Human Infection?. International Journal of Molecular Sciences 15:6, pages 10377-10397.
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GuangCheng Xie, JieMei Yu & ZhaoJun Duan. (2013) New strategy for virus discovery: viruses identified in human feces in the last decade. Science China Life Sciences 56:8, pages 688-696.
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Anne-Lie Blomström, Karl Ståhl, Charles Masembe, Edward Okoth, Ademun Rose Okurut, Patrick Atmnedi, Stephen Kemp, Richard Bishop, Sándor Belák & Mikael Berg. (2012) Viral metagenomic analysis of bushpigs (Potamochoerus larvatus) in Uganda identifies novel variants of Porcine parvovirus 4 and Torque teno sus virus 1 and 2. Virology Journal 9:1.
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Tae Woong Whon, Min-Soo Kim, Seong Woon Roh, Na-Ri Shin, Hae-Won Lee & Jin-Woo Bae. (2012) Metagenomic Characterization of Airborne Viral DNA Diversity in the Near-Surface Atmosphere. Journal of Virology 86:15, pages 8221-8231.
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Eric Delwart. (2012) Animal virus discovery: improving animal health, understanding zoonoses, and opportunities for vaccine development. Current Opinion in Virology 2:3, pages 344-352.
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