{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,19]],"date-time":"2026-03-19T22:32:42Z","timestamp":1773959562768,"version":"3.50.1"},"reference-count":53,"publisher":"MDPI AG","issue":"8","license":[{"start":{"date-parts":[[2021,8,14]],"date-time":"2021-08-14T00:00:00Z","timestamp":1628899200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>Six foals with interstitial pneumonia of undetermined etiology from Southern California were analyzed by viral metagenomics. Spleen, lung, and colon content samples obtained during necropsy from each animal were pooled, and nucleic acids from virus-like particles enriched for deep sequencing. The recently described equine copiparvovirus named eqcopivirus, as well as three previously uncharacterized viruses, were identified. The complete ORFs genomes of two closely related protoparvoviruses, and of a bocaparvovirus, plus the partial genome of a picornavirus were assembled. The parvoviruses were classified as members of new ungulate protoparvovirus and bocaparvovirus species in the Parvoviridae family. The picornavirus was classified as a new species in the Salivirus genus of the Picornaviridae family. Spleen, lung, and colon content samples from each foal were then tested for these viral genomes by nested PCR and RT-PCR. When present, parvoviruses were detected in both feces and spleen. The picornavirus, protoparvovirus, and eqcopivirus genomes were detected in the lungs of one animal each. Three foals were co-infected with the picornavirus and either a protoparvovirus, bocaparvovirus, or eqcopivirus. Two other foals were infected with a protoparvovirus only. No viral infection was detected in one animal. The complete ORFs of the first equine protoparvoviruses and bocaparvovirus, the partial ORF of the third equine picornavirus, and their detection in tissues of foals with interstitial pneumonia are described here. Testing the involvement of these viruses in fatal interstitial pneumonia or other equine diseases will require larger epidemiological and\/or inoculation studies.<\/jats:p>","DOI":"10.3390\/v13081612","type":"journal-article","created":{"date-parts":[[2021,8,15]],"date-time":"2021-08-15T22:51:27Z","timestamp":1629067887000},"page":"1612","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":11,"title":["New Parvoviruses and Picornavirus in Tissues and Feces of Foals with Interstitial Pneumonia"],"prefix":"10.3390","volume":"13","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-7903-6986","authenticated-orcid":false,"given":"Eda","family":"Altan","sequence":"first","affiliation":[{"name":"Vitalant Research Institute, San Francisco, CA 94118, USA"},{"name":"Department of Laboratory Medicine, University of California at San Francisco, San Francisco, CA 94118, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6027-7958","authenticated-orcid":false,"given":"Alvin","family":"Hui","sequence":"additional","affiliation":[{"name":"Vitalant Research Institute, San Francisco, CA 94118, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0643-4809","authenticated-orcid":false,"given":"Yanpeng","family":"Li","sequence":"additional","affiliation":[{"name":"Vitalant Research Institute, San Francisco, CA 94118, USA"},{"name":"Department of Laboratory Medicine, University of California at San Francisco, San Francisco, CA 94118, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Patricia","family":"Pesavento","sequence":"additional","affiliation":[{"name":"Department of Pathology Microbiology and Immunology, UC Davis, Davis, CA 95616, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Javier","family":"As\u00edn","sequence":"additional","affiliation":[{"name":"Department of Pathology Microbiology and Immunology, UC Davis, Davis, CA 95616, USA"},{"name":"California Animal Health and Food Safety Laboratory System, UC Davis, Davis, CA 95616, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Beate","family":"Crossley","sequence":"additional","affiliation":[{"name":"California Animal Health and Food Safety Laboratory System, UC Davis, Davis, CA 95616, USA"},{"name":"Department of Medicine and Epidemiology, UC Davis, Davis, CA 95616, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xutao","family":"Deng","sequence":"additional","affiliation":[{"name":"Vitalant Research Institute, San Francisco, CA 94118, USA"},{"name":"Department of Laboratory Medicine, University of California at San Francisco, San Francisco, CA 94118, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0681-1878","authenticated-orcid":false,"given":"Francisco A.","family":"Uzal","sequence":"additional","affiliation":[{"name":"Department of Pathology Microbiology and Immunology, UC Davis, Davis, CA 95616, USA"},{"name":"California Animal Health and Food Safety Laboratory System, UC Davis, Davis, CA 95616, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6296-4484","authenticated-orcid":false,"given":"Eric","family":"Delwart","sequence":"additional","affiliation":[{"name":"Vitalant Research Institute, San Francisco, CA 94118, USA"},{"name":"Department of Laboratory Medicine, University of California at San Francisco, San Francisco, CA 94118, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2021,8,14]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1016\/j.cveq.2014.11.007","article-title":"Update on viral diseases of the equine respiratory tract","volume":"31","author":"Gilkerson","year":"2015","journal-title":"Vet. Clin. N. Am. Equine Pract."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"80","DOI":"10.2174\/1874357901812010080","article-title":"Zoonotic Viral Diseases of Equines and Their Impact on Human and Animal Health","volume":"12","author":"Kumar","year":"2018","journal-title":"Open Virol. J."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1111\/avj.12552","article-title":"Experimental Hendra virus infection of dogs: Virus replication, shedding and potential for transmission","volume":"95","author":"Middleton","year":"2017","journal-title":"Aust Vet. J."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1016\/j.tvjl.2017.11.004","article-title":"Enteric coronavirus infection in adult horses","volume":"231","author":"Pusterla","year":"2018","journal-title":"Vet. J."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"102923","DOI":"10.1016\/j.jevs.2020.102923","article-title":"Equine Herpesvirus-I Infection in Horses: Recent Updates on its Pathogenicity, Vaccination, and Preventive Management Strategies","volume":"87","author":"Khusro","year":"2020","journal-title":"J. Equine Vet. Sci."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"123","DOI":"10.1016\/j.vetmic.2013.06.018","article-title":"Equine herpesviruses type 1 (EHV-1) and 4 (EHV-4)--masters of co-evolution and a constant threat to equids and beyond","volume":"167","author":"Ma","year":"2013","journal-title":"Vet. Microbiol."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"86","DOI":"10.1016\/j.vetmic.2013.05.031","article-title":"Equine gammaherpesviruses: Perfect parasites?","volume":"167","author":"Hartley","year":"2013","journal-title":"Vet. Microbiol."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"718","DOI":"10.1111\/evj.13355","article-title":"Acute interstitial pneumonia in foals: A severe, multifactorial syndrome with lung tissue recovery in surviving foals","volume":"53","author":"Punsmann","year":"2021","journal-title":"Equine Vet. J."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"750","DOI":"10.1177\/030098588602300614","article-title":"A retrospective study of proliferative interstitial lung disease of horses in Florida","volume":"23","author":"Buergelt","year":"1986","journal-title":"Vet. Pathol."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"20","DOI":"10.1128\/CMR.4.1.20","article-title":"Rhodococcus equi: An animal and human pathogen","volume":"4","author":"Prescott","year":"1991","journal-title":"Clin. Microbiol. Rev."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"277","DOI":"10.1111\/j.1939-1676.1993.tb01020.x","article-title":"Bronchointerstitial pneumonia and respiratory distress in young horses: Clinical, clinicopathologic, radiographic, and pathological findings in 23 cases (1984\u20131989)","volume":"7","author":"Lakritz","year":"1993","journal-title":"J. Vet. Int. Med."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"435","DOI":"10.2746\/042516405774480094","article-title":"Acute lung injury\/acute respiratory distress syndrome in 15 foals","volume":"37","author":"Dunkel","year":"2005","journal-title":"Equine Vet. J."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"151","DOI":"10.1007\/s11262-004-5624-3","article-title":"Analysis of the virus population present in equine faeces indicates the presence of hundreds of uncharacterized virus genomes","volume":"30","author":"Cann","year":"2005","journal-title":"Virus Genes"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"151","DOI":"10.1016\/j.meegid.2016.05.008","article-title":"Circular replication-associated protein encoding DNA viruses identified in the faecal matter of various animals in New Zealand","volume":"43","author":"Steel","year":"2016","journal-title":"Infect. Genet Evol."},{"key":"ref_15","doi-asserted-by":"crossref","unstructured":"Liu, H., Zhang, X., Li, L.X., Shi, N., Sun, X.T., Liu, Q., Jin, N.Y., and Si, X.K. (2019). First isolation and characterization of Getah virus from cattle in northeastern China. BMC Vet. Res., 15.","DOI":"10.1186\/s12917-019-2061-z"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"E1407","DOI":"10.1073\/pnas.1219217110","article-title":"Identification of a previously undescribed divergent virus from the Flaviviridae family in an outbreak of equine serum hepatitis","volume":"110","author":"Chandriani","year":"2013","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"7185","DOI":"10.1128\/JVI.00324-13","article-title":"Identification of a pegivirus (GB virus-like virus) that infects horses","volume":"87","author":"Kapoor","year":"2013","journal-title":"J. Virol."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"1976","DOI":"10.3201\/eid1812.120498","article-title":"Nonprimate hepaciviruses in domestic horses, United kingdom","volume":"18","author":"Lyons","year":"2012","journal-title":"Emerg. Infect. Dis."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"1701","DOI":"10.1099\/vir.0.065094-0","article-title":"Viraemic frequencies and seroprevalence of non-primate hepacivirus and equine pegiviruses in horses and other mammalian species","volume":"95","author":"Lyons","year":"2014","journal-title":"J. Gen. Virol."},{"key":"ref_20","doi-asserted-by":"crossref","unstructured":"Tomlinson, J.E., Wolfisberg, R., Fahnoe, U., Sharma, H., Renshaw, R.W., Nielsen, L., Nishiuchi, E., Holm, C., Dubovi, E., and Rosenberg, B.R. (2020). Equine pegiviruses cause persistent infection of bone marrow and are not associated with hepatitis. PLoS Pathog., 16.","DOI":"10.1371\/journal.ppat.1008677"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"303","DOI":"10.3201\/eid2402.171031","article-title":"New Parvovirus Associated with Serum Hepatitis in Horses after Inoculation of Common Biological Product","volume":"24","author":"Divers","year":"2018","journal-title":"Emerg. Infect. Dis."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"651","DOI":"10.1080\/22221751.2020.1741326","article-title":"Tropism, pathology, and transmission of equine parvovirus-hepatitis","volume":"9","author":"Tomlinson","year":"2020","journal-title":"Emerg. Microbes Infect."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"2721","DOI":"10.1099\/vir.0.000199","article-title":"Exploring the virome of diseased horses","volume":"96","author":"Li","year":"2015","journal-title":"J. Gen. Virol."},{"key":"ref_24","doi-asserted-by":"crossref","unstructured":"Altan, E., Li, Y., Sabino-Santos, G., Sawaswong, V., Barnum, S., Pusterla, N., Deng, X., and Delwart, E. (2019). Viruses in Horses with Neurologic and Respiratory Diseases. Viruses, 11.","DOI":"10.3390\/v11100942"},{"key":"ref_25","doi-asserted-by":"crossref","unstructured":"Hui, A., Altan, E., Slovis, N., Fletcher, C., Deng, X., and Delwart, E. (2021). Circovirus in Blood of a Febrile Horse with Hepatitis. Viruses, 13.","DOI":"10.3390\/v13050944"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"1981","DOI":"10.1128\/JCM.00135-12","article-title":"New real-time PCR assay using allelic discrimination for detection and differentiation of equine herpesvirus-1 strains with A2254 and G2254 polymorphisms","volume":"50","author":"Smith","year":"2012","journal-title":"J. Clin. Microbiol."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"924","DOI":"10.1177\/1040638718799388","article-title":"Development and evaluation of a multiplex reverse-transcription real-time PCR assay for detection of equine respiratory disease viruses","volume":"30","author":"Ghoniem","year":"2018","journal-title":"J. Vet. Diagn. Invest."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"3256","DOI":"10.1128\/JCM.40.9.3256-3260.2002","article-title":"Development of a real-time reverse transcriptase PCR assay for type A influenza virus and the avian H5 and H7 hemagglutinin subtypes","volume":"40","author":"Spackman","year":"2002","journal-title":"J. Clin. Microbiol."},{"key":"ref_29","doi-asserted-by":"crossref","unstructured":"Altan, E., Delaney, M.A., Colegrove, K.M., Spraker, T.R., Wheeler, E.A., Deng, X., Li, Y., Gulland, F.M.D., and Delwart, E. (2020). Complex Virome in a Mesenteric Lymph Node from a Californian Sea Lion (Zalophus Californianus) with Polyserositis and Steatitis. Viruses, 12.","DOI":"10.3390\/v12080793"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1016\/j.jviromet.2014.12.002","article-title":"Comparing viral metagenomics methods using a highly multiplexed human viral pathogens reagent","volume":"213","author":"Li","year":"2015","journal-title":"J. Virol. Methods"},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"49","DOI":"10.1016\/0022-2836(91)90380-O","article-title":"Prediction of human mRNA donor and acceptor sites from the DNA sequence","volume":"220","author":"Brunak","year":"1991","journal-title":"J. Mol. Biol."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"1547","DOI":"10.1093\/molbev\/msy096","article-title":"MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms","volume":"35","author":"Kumar","year":"2018","journal-title":"Mol. Biol. Evol."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"1307","DOI":"10.1093\/molbev\/msn067","article-title":"An improved general amino acid replacement matrix","volume":"25","author":"Le","year":"2008","journal-title":"Mol. Biol. Evol."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"1349","DOI":"10.1099\/jgv.0.000775","article-title":"Two novel dromedary camel bocaparvoviruses from dromedaries in the Middle East with unique genomic features","volume":"98","author":"Woo","year":"2017","journal-title":"J. Gen. Virol."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"14","DOI":"10.1016\/j.tvjl.2004.04.018","article-title":"Equine herpesviruses 1 (EHV-1) and 4 (EHV-4)--epidemiology, disease and immunoprophylaxis: A brief review","volume":"170","author":"Patel","year":"2005","journal-title":"Vet. J."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"1941","DOI":"10.3389\/fmicb.2018.01941","article-title":"A Comprehensive Review on Equine Influenza Virus: Etiology, Epidemiology, Pathobiology, Advances in Developing Diagnostics, Vaccines, and Control Strategies","volume":"9","author":"Singh","year":"2018","journal-title":"Front. Microbiol."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"355","DOI":"10.1007\/978-1-0716-0346-8_26","article-title":"A Brief Introduction to Equine Influenza and Equine Influenza Viruses","volume":"2123","author":"Chambers","year":"2020","journal-title":"Methods Mol. Biol."},{"key":"ref_38","first-page":"58","article-title":"Equine herpesvirus 1 and 4 infections: An update","volume":"24","year":"2002","journal-title":"Vet. Q."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"519","DOI":"10.1038\/195519a0","article-title":"An equine respiratory virus with enterovirus properties","volume":"195","author":"Plummer","year":"1962","journal-title":"Nature"},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"225","DOI":"10.1111\/j.1439-0450.1978.tb01180.x","article-title":"Isolation and characterisation of an equine rhinovirus","volume":"25","author":"Studdert","year":"1978","journal-title":"Zent. Vet. B"},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"1719","DOI":"10.1099\/0022-1317-77-8-1719","article-title":"Equine rhinovirus serotypes 1 and 2: Relationship to each other and to aphthoviruses and cardioviruses","volume":"77","author":"Wutz","year":"1996","journal-title":"J. Gen. Virol."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"65","DOI":"10.1016\/j.vetmic.2006.08.031","article-title":"Prevalence of serum neutralising antibody to equine rhinitis A virus (ERAV), equine rhinitis B virus 1 (ERBV1) and ERBV2","volume":"119","author":"Black","year":"2007","journal-title":"Vet. Microbiol."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"78","DOI":"10.1016\/j.vetmic.2013.05.012","article-title":"Equine picornaviruses: Well known but poorly understood","volume":"167","author":"Horsington","year":"2013","journal-title":"Vet. Microbiol."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"2421","DOI":"10.1099\/jgv.0.000911","article-title":"ICTV Virus Taxonomy Profile: Picornaviridae","volume":"98","author":"Zell","year":"2017","journal-title":"J. Gen. Virol."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"367","DOI":"10.1099\/jgv.0.001212","article-title":"ICTV Virus Taxonomy Profile: Parvoviridae","volume":"100","author":"Cotmore","year":"2019","journal-title":"J. Gen. Virol."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"2133","DOI":"10.1007\/s00705-020-04632-4","article-title":"Reorganizing the family Parvoviridae: A revised taxonomy independent of the canonical approach based on host association","volume":"165","author":"Penzes","year":"2020","journal-title":"Arch. Virol."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"418","DOI":"10.1016\/S2352-4642(19)30057-4","article-title":"Human bocaviruses and paediatric infections","volume":"3","author":"Christensen","year":"2019","journal-title":"Lancet Child Adolesc. Health"},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1128\/CMR.00040-16","article-title":"Human Parvoviruses","volume":"30","author":"Qiu","year":"2017","journal-title":"Clin. Microbiol. Rev."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1016\/j.jcv.2015.11.027","article-title":"Human bocavirus in stool: A true pathogen or an innocent bystander?","volume":"74","author":"Ong","year":"2016","journal-title":"J. Clin. Virol."},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"328","DOI":"10.1159\/000173734","article-title":"Animal bocaviruses: A brief review","volume":"51","author":"Manteufel","year":"2008","journal-title":"Intervirology"},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"121","DOI":"10.3389\/fvets.2020.00121","article-title":"Equine Parvovirus-Hepatitis in China: Characterization of Its Genetic Diversity and Evidence for Natural Recombination Events Between the Chinese and American Strains","volume":"7","author":"Lu","year":"2020","journal-title":"Front. Vet. Sci."},{"key":"ref_52","doi-asserted-by":"crossref","unstructured":"Badenhorst, M., de Heus, P., Auer, A., Tegtmeyer, B., Stang, A., Dimmel, K., Tichy, A., Kubacki, J., Bachofen, C., and Steinmann, E. (2021). Active equine parvovirus-hepatitis infection is most frequently detected in Austrian horses of advanced age. Equine Vet. J.","DOI":"10.1111\/evj.13444"},{"key":"ref_53","doi-asserted-by":"crossref","unstructured":"Meister, T.L., Tegtmeyer, B., Bruggemann, Y., Sieme, H., Feige, K., Todt, D., Stang, A., Cavalleri, J.V., and Steinmann, E. (2019). Characterization of Equine Parvovirus in Thoroughbred Breeding Horses from Germany. Viruses, 11.","DOI":"10.3390\/v11100965"}],"container-title":["Viruses"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1999-4915\/13\/8\/1612\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T06:46:06Z","timestamp":1760165166000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1999-4915\/13\/8\/1612"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,8,14]]},"references-count":53,"journal-issue":{"issue":"8","published-online":{"date-parts":[[2021,8]]}},"alternative-id":["v13081612"],"URL":"https:\/\/doi.org\/10.3390\/v13081612","relation":{},"ISSN":["1999-4915"],"issn-type":[{"value":"1999-4915","type":"electronic"}],"subject":[],"published":{"date-parts":[[2021,8,14]]}}}