{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,16]],"date-time":"2026-10-16T06:54:31Z","timestamp":1792133671622,"version":"4.4.0"},"reference-count":14,"publisher":"MDPI AG","issue":"8","license":[{"start":{"date-parts":[[2024,7,23]],"date-time":"2024-07-23T00:00:00Z","timestamp":1721692800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"USDA internal funding","award":["CRIS 301-3022-505-63"],"award-info":[{"award-number":["CRIS 301-3022-505-63"]}]},{"name":"USDA internal funding","award":["BIO-2018-0029"],"award-info":[{"award-number":["BIO-2018-0029"]}]},{"name":"NBAF partnership funding","award":["CRIS 301-3022-505-63"],"award-info":[{"award-number":["CRIS 301-3022-505-63"]}]},{"name":"NBAF partnership funding","award":["BIO-2018-0029"],"award-info":[{"award-number":["BIO-2018-0029"]}]},{"name":"Canadian Food Inspection Agency\u2014Global Affairs Canada Project","award":["CRIS 301-3022-505-63"],"award-info":[{"award-number":["CRIS 301-3022-505-63"]}]},{"name":"Canadian Food Inspection Agency\u2014Global Affairs Canada Project","award":["BIO-2018-0029"],"award-info":[{"award-number":["BIO-2018-0029"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>African swine fever (ASF) is a deadly hemorrhagic disease of domestic and wild swine that was first described in the early 20th century after the introduction of European pigs to Kenya. The etiological agent, the African swine fever virus (ASFV), is a large DNA virus within the Asfarviridae family that is broadly categorized epidemiologically into genotypes based on the nucleotide sequence of B646L, the gene encoding the major capsid protein p72. ASF outbreaks in Africa have been linked historically to 25 genotypes by p72 nucleotide analysis and, recently, to 6 genotypes by amino acid comparison, whereas global outbreaks of ASF outside of Africa have only been linked to 2 genotypes: genotype I, which led to an outbreak in Europe during the 1960s that later spread to South America, and genotype II, responsible for the current pandemic that began in Georgia in 2007 and has since spread to Europe, Asia, and Hispaniola. Here, we present an analysis of the genome of ASFV Spencer, an isolate that was collected in 1951 near Johannesburg, South Africa. While nucleotide analysis of Spencer indicates the p72 coding sequence is unique, differentiating from the closest reference by five nucleotides, the predicted amino acid sequence indicates that it is 100% homologous to contemporary genotype 1. Full genome analysis reveals it is more similar to Mkuzi1979 and encodes genes that share similarity with either genotype 1 or genotype 2 outbreak strains.<\/jats:p>","DOI":"10.3390\/v16081175","type":"journal-article","created":{"date-parts":[[2024,7,23]],"date-time":"2024-07-23T07:57:23Z","timestamp":1721721443000},"page":"1175","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["Analysis of the Unique Historical Isolate of African Swine Fever Virus Isolate Spencer from Outbreaks in 1951"],"prefix":"10.3390","volume":"16","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-7268-6580","authenticated-orcid":false,"given":"Edward","family":"Spinard","sequence":"first","affiliation":[{"name":"Plum Island Animal Disease Center (PIADC), ARS, USDA, P.O. Box 848, Greenport, NY 11944, USA"},{"name":"National Bio and Agro-Defense Facility, Foreign Animal Disease Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Manhattan, KS 66502, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mark","family":"Dinhobl","sequence":"additional","affiliation":[{"name":"Plum Island Animal Disease Center (PIADC), ARS, USDA, P.O. Box 848, Greenport, NY 11944, USA"},{"name":"National Bio and Agro-Defense Facility, Foreign Animal Disease Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Manhattan, KS 66502, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jacob","family":"Fenster","sequence":"additional","affiliation":[{"name":"Plum Island Animal Disease Center (PIADC), ARS, USDA, P.O. Box 848, Greenport, NY 11944, USA"},{"name":"Oak Ridge Institute for Science and Education (ORISE), Oak Ridge, TN 37830, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Charronne","family":"Davis","sequence":"additional","affiliation":[{"name":"American Type Culture Collection, 0801 University Blvd, Manassas, VA 20108, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Manuel V.","family":"Borca","sequence":"additional","affiliation":[{"name":"Plum Island Animal Disease Center (PIADC), ARS, USDA, P.O. Box 848, Greenport, NY 11944, USA"},{"name":"National Bio and Agro-Defense Facility, Foreign Animal Disease Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Manhattan, KS 66502, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7894-0233","authenticated-orcid":false,"given":"Douglas P.","family":"Gladue","sequence":"additional","affiliation":[{"name":"Plum Island Animal Disease Center (PIADC), ARS, USDA, P.O. Box 848, Greenport, NY 11944, USA"},{"name":"National Bio and Agro-Defense Facility, Foreign Animal Disease Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Manhattan, KS 66502, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2024,7,23]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"Spinard, E., Dinhobl, M., Tesler, N., Birtley, H., Signore, A.V., Ambagala, A., Masembe, C., Borca, M.V., and Gladue, D.P. (2023). A Re-Evaluation of African Swine Fever Genotypes Based on p72 Sequences Reveals the Existence of Only Six Distinct p72 Groups. Viruses, 15.","DOI":"10.3390\/v15112246"},{"key":"ref_2","doi-asserted-by":"crossref","unstructured":"Dinhobl, M., Spinard, E., Tesler, N., Birtley, H., Signore, A., Ambagala, A., Masembe, C., Borca, M.V., and Gladue, D.P. (2023). Reclassification of ASFV into 7 Biotypes Using Unsupervised Machine Learning. Viruses, 16.","DOI":"10.3390\/v16010067"},{"key":"ref_3","doi-asserted-by":"crossref","unstructured":"Mthombeni, R.F., Bastos, A.D., van Schalkwyk, A., van Emmenes, J., and Heath, L. (2023). Phylogenomic Comparison of Seven African Swine Fever Genotype II Outbreak Viruses (1998-2019) Reveals the Likely African Origin of Georgia 2007\/1. Pathogens, 12.","DOI":"10.3390\/pathogens12091129"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"2377","DOI":"10.1007\/s00705-022-05543-2","article-title":"Complete genome sequence of virulent genotype I African swine fever virus strain K49 from the Democratic Republic of the Congo, isolated from a domestic pig (Sus scrofa domesticus)","volume":"167","author":"Koltsov","year":"2022","journal-title":"Arch. Virol."},{"key":"ref_5","first-page":"24","article-title":"African swine fever. V. Cultivation of the virus in primary pig kidney cells","volume":"31","author":"Greig","year":"1967","journal-title":"Can. J. Comp. Med. Vet. Sci."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"i884","DOI":"10.1093\/bioinformatics\/bty560","article-title":"fastp: An ultra-fast all-in-one FASTQ preprocessor","volume":"34","author":"Chen","year":"2018","journal-title":"Bioinformatics"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"599","DOI":"10.3201\/eid1704.101283","article-title":"Genomic analysis of highly virulent Georgia 2007\/1 isolate of African swine fever virus","volume":"17","author":"Chapman","year":"2011","journal-title":"Emerg. Infect. Dis."},{"key":"ref_8","doi-asserted-by":"crossref","unstructured":"MVasimuddin, S.M., Li, H., and Aluru, S. (2019, January 20\u201324). Efficient Architecture-Aware Acceleration of BWA-MEM for Multicore Systems. Proceedings of the IEEE International Parallel and Distributed Processing Symposium (IPDPS), Rio de Janeiro, Brazil.","DOI":"10.1109\/IPDPS.2019.00041"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"giaa051","DOI":"10.1093\/gigascience\/giaa051","article-title":"An improved pig reference genome sequence to enable pig genetics and genomics research","volume":"9","author":"Warr","year":"2020","journal-title":"Gigascience"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1089\/cmb.2012.0021","article-title":"SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing","volume":"19","author":"Bankevich","year":"2012","journal-title":"J. Comput. Biol."},{"key":"ref_11","unstructured":"Ribeca, P. (2024, January 15). The Transporter. Available online: http:\/\/github.com\/PaoloRibeca\/TheTransporter."},{"key":"ref_12","doi-asserted-by":"crossref","unstructured":"Edgar, R.C. (2004). MUSCLE: A multiple sequence alignment method with reduced time and space complexity. BMC Bioinform., 5.","DOI":"10.1186\/1471-2105-5-113"},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"2446","DOI":"10.1111\/tbed.13582","article-title":"Development of a real-time PCR assay for detection of African swine fever virus with an endogenous internal control","volume":"67","author":"Wang","year":"2020","journal-title":"Transbound. Emerg. Dis."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"408","DOI":"10.1099\/vir.0.070508-0","article-title":"Related strains of African swine fever virus with different virulence: Genome comparison and analysis","volume":"96","author":"Portugal","year":"2015","journal-title":"J. Gen. Virol."}],"container-title":["Viruses"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1999-4915\/16\/8\/1175\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T15:21:25Z","timestamp":1760109685000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1999-4915\/16\/8\/1175"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,7,23]]},"references-count":14,"journal-issue":{"issue":"8","published-online":{"date-parts":[[2024,8]]}},"alternative-id":["v16081175"],"URL":"https:\/\/doi.org\/10.3390\/v16081175","relation":{},"ISSN":["1999-4915"],"issn-type":[{"value":"1999-4915","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,7,23]]}}}