{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,27]],"date-time":"2026-02-27T01:31:40Z","timestamp":1772155900949,"version":"3.50.1"},"reference-count":43,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2020,6,19]],"date-time":"2020-06-19T00:00:00Z","timestamp":1592524800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"European Union\u2019s Horizon 2020 Research"},{"DOI":"10.13039\/100010269","name":"Wellcome Trust","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100010269","id-type":"DOI","asserted-by":"publisher"}]},{"name":"ASF-RESIST African Union Commission"},{"DOI":"10.13039\/501100000265","name":"MRC","doi-asserted-by":"publisher","award":["1201412"],"award-info":[{"award-number":["1201412"]}],"id":[{"id":"10.13039\/501100000265","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,7,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>African swine fever virus (ASFV), belonging to the Asfarviridae family, was originally described in Africa almost 100\u2009years ago and is now spreading uncontrolled across Europe and Asia and threatening to destroy the domestic pork industry. Neither effective antiviral drugs nor protective vaccines are currently available. Efforts to understand the basis for viral pathogenicity and the development of attenuated potential vaccine strains are complicated by the large and complex nature of the ASFV genome. We report here a novel alignment-free method of documenting viral diversity based on profile hidden Markov model domains on a genome scale. The method can be used to infer genomic relationships independent of genome alignments and also reveal ASFV genome sequence differences that determine the presence and characteristics of functional protein domains in the virus. We show that the method can quickly identify differences and shared patterns between virulent and attenuated ASFV strains and will be a useful tool for developing much-needed vaccines and antiviral agents to help control this virus. The tool is rapid to run and easy to implement, readily available as a simple Docker image.<\/jats:p>","DOI":"10.1093\/ve\/veaa044","type":"journal-article","created":{"date-parts":[[2020,6,11]],"date-time":"2020-06-11T07:09:27Z","timestamp":1591859367000},"source":"Crossref","is-referenced-by-count":7,"title":["Increased resolution of African swine fever virus genome patterns based on profile HMMs of protein domains"],"prefix":"10.1093","volume":"6","author":[{"given":"Charles","family":"Masembe","sequence":"first","affiliation":[{"name":"College of Natural Sciences, Makerere University, Makerere Hill Road, P. O Box 7062 Kampala, Uganda"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6905-8513","authenticated-orcid":false,"given":"My V T","family":"Phan","sequence":"additional","affiliation":[{"name":"Viral Genomics, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK"},{"name":"Department of Viroscience, Erasmus Medical Centre, Dr. Molewaterplein 40, 3015 GD Rotterdam, The Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"David L","family":"Robertson","sequence":"additional","affiliation":[{"name":"MRC University of Glasgow Centre for Virus Research, 464 Bearsden Rd, Glasgow G61 1QH, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Matthew","family":"Cotten","sequence":"additional","affiliation":[{"name":"Viral Genomics, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK"},{"name":"MRC University of Glasgow Centre for Virus Research, 464 Bearsden Rd, Glasgow G61 1QH, UK"},{"name":"MRC\/UVRI & LSHTM Uganda Research Unit, P.O. Box 49, Plot 51\u201359 Nakiwogo Road, Entebbe, Uganda"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2020,6,19]]},"reference":[{"key":"2020090611234639700_veaa044-B1","doi-asserted-by":"crossref","first-page":"1393","DOI":"10.1111\/tbed.12511","article-title":"Identification of a New Genotype of African Swine Fever Virus in Domestic Pigs from Ethiopia","volume":"64","author":"Achenbach","year":"2017","journal-title":"Transboundary and Emerging Diseases"},{"key":"2020090611234639700_veaa044-B2","doi-asserted-by":"crossref","first-page":"1858","DOI":"10.1128\/JVI.78.4.1858-1864.2004","article-title":"African Swine Fever Virus Multigene Family 360 and 530 Genes Affect Host Interferon Response","volume":"78","author":"Afonso","year":"2004","journal-title":"Journal of Virology"},{"key":"2020090611234639700_veaa044-B3","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1016\/0042-6822(90)90244-L","article-title":"Analysis of Naturally Occurring Deletion Variants of African Swine Fever Virus: Multigene Family 110 is Not Essential for Infectivity or Virulence in Pigs","volume":"176","author":"Aguero","year":"1990","journal-title":"Virology"},{"key":"2020090611234639700_veaa044-B4","doi-asserted-by":"crossref","first-page":"e0192565","DOI":"10.1371\/journal.pone.0192565","article-title":"Phylodynamics and Evolutionary Epidemiology of African Swine Fever P72-CVR Genes in Eurasia and Africa","volume":"13","author":"Alkhamis","year":"2018","journal-title":"PLoS One"},{"key":"2020090611234639700_veaa044-B5","doi-asserted-by":"crossref","first-page":"2064","DOI":"10.1128\/JVI.64.5.2064-2072.1990","article-title":"Multigene Families in African Swine Fever Virus: Family 110","volume":"64","author":"Almendral","year":"1990","journal-title":"Journal of Virology"},{"key":"2020090611234639700_veaa044-B6","doi-asserted-by":"crossref","first-page":"247","DOI":"10.1186\/1743-422X-10-247","article-title":"Molecular 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