{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,13]],"date-time":"2026-04-13T11:02:04Z","timestamp":1776078124869,"version":"3.50.1"},"reference-count":49,"publisher":"MDPI AG","issue":"9","license":[{"start":{"date-parts":[[2020,9,6]],"date-time":"2020-09-06T00:00:00Z","timestamp":1599350400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"German Egyptian Mobility Program for Scientific Exchange and Excellence Development (GE-SEED)","award":["project no. 31037"],"award-info":[{"award-number":["project no. 31037"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>In spite of annual mass vaccination programs with polyvalent inactivated vaccines, the incidence and economic impact of foot-and-mouth disease (FMD) in Egypt is high. Viruses of the A, O and SAT 2 serotypes are endemic and repeated incursions of new lineages from other countries lead to an unstable situation that makes the selection of appropriate vaccine antigens very difficult. In this study, whole genome sequencing of a 2016 serotype A isolate from Egypt revealed a recombination event with an African serotype O virus. Based on available vaccine matching data, none of the vaccines currently used in Egypt are expected to sufficiently protect against this virus or other viruses of this lineage (A\/AFRICA\/G-IV) circulating there since 2012. In addition to the risk of vaccine failure caused by strain mismatch, the production of inactivated FMD vaccines is dangerous if adequate biosafety cannot be maintained. Using a high-throughput sequencing protocol optimized for short nucleic acid fragments, the composition of a local inactivated vaccine was analyzed in depth. The serotype O strain identified in the vaccine was genetically identical to viruses found in recent FMD outbreaks in Egypt.<\/jats:p>","DOI":"10.3390\/v12090990","type":"journal-article","created":{"date-parts":[[2020,9,6]],"date-time":"2020-09-06T23:12:49Z","timestamp":1599433969000},"page":"990","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":16,"title":["Sequence Analysis of Egyptian Foot-and-Mouth Disease Virus Field and Vaccine Strains: Intertypic Recombination and Evidence for Accidental Release of Virulent Virus"],"prefix":"10.3390","volume":"12","author":[{"given":"Sahar","family":"Abd El Rahman","sequence":"first","affiliation":[{"name":"Department of Virology, Faculty of Veterinary Medicine, Mansoura University, Mansoura 35516, Egypt"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5358-6445","authenticated-orcid":false,"given":"Bernd","family":"Hoffmann","sequence":"additional","affiliation":[{"name":"Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, 17493 Greifswald-Insel Riems, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Reham","family":"Karam","sequence":"additional","affiliation":[{"name":"Department of Virology, Faculty of Veterinary Medicine, Mansoura University, Mansoura 35516, Egypt"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mohamed","family":"El-Beskawy","sequence":"additional","affiliation":[{"name":"Department of Animal Medicine, Faculty of Veterinary Medicine, Matrouh University, Matrouh 51744, Egypt"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mohammed F.","family":"Hamed","sequence":"additional","affiliation":[{"name":"Department of Pathology, Faculty of Veterinary Medicine, Mansoura University, Mansoura 35516, Egypt"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2708-2515","authenticated-orcid":false,"given":"Leonie F.","family":"Forth","sequence":"additional","affiliation":[{"name":"Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, 17493 Greifswald-Insel Riems, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8408-2274","authenticated-orcid":false,"given":"Dirk","family":"H\u00f6per","sequence":"additional","affiliation":[{"name":"Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, 17493 Greifswald-Insel Riems, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1104-0695","authenticated-orcid":false,"given":"Michael","family":"Eschbaumer","sequence":"additional","affiliation":[{"name":"Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, 17493 Greifswald-Insel Riems, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2020,9,6]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"465","DOI":"10.1128\/CMR.17.2.465-493.2004","article-title":"Foot-and-mouth disease","volume":"17","author":"Grubman","year":"2004","journal-title":"Clin. Microbiol. Rev."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"316","DOI":"10.1111\/tbed.12373","article-title":"Review of the Global Distribution of Foot-and-Mouth Disease Virus from 2007 to 2014","volume":"64","author":"Brito","year":"2017","journal-title":"Transbound. Emerg. Dis."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"6487","DOI":"10.1128\/JVI.79.10.6487-6504.2005","article-title":"Comparative genomics of foot-and-mouth disease virus","volume":"79","author":"Carrillo","year":"2005","journal-title":"J. Virol."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"291","DOI":"10.1111\/j.1865-1682.2011.01204.x","article-title":"The pathogenesis of foot-and-mouth disease I: Viral pathways in cattle","volume":"58","author":"Arzt","year":"2011","journal-title":"Transbound. Emerg. Dis."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"102","DOI":"10.1016\/j.vetmic.2016.12.018","article-title":"Foot-and-mouth disease vaccines","volume":"206","author":"Medina","year":"2017","journal-title":"Vet. Microbiol."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"979","DOI":"10.1111\/tbed.13433","article-title":"Evidence for multiple recombination events within foot-and-mouth disease viruses circulating in West Eurasia","volume":"67","author":"Jamal","year":"2020","journal-title":"Transbound. Emerg. Dis."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1111\/tbed.13017","article-title":"Foot-and-mouth disease outbreaks due to an exotic virus serotype A lineage (A\/AFRICA\/G-IV) in Algeria in 2017","volume":"66","author":"Pezzoni","year":"2019","journal-title":"Transbound. Emerg. Dis."},{"key":"ref_8","doi-asserted-by":"crossref","unstructured":"Forth, L.F., H\u00f6per, D., Beer, M., and Eschbaumer, M. (2020). High-Resolution Composition Analysis of an Inactivated Polyvalent Foot-and-Mouth Disease Vaccine. Pathogens, 9.","DOI":"10.3390\/pathogens9010063"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"1636","DOI":"10.2460\/javma.2002.220.1636","article-title":"Use of a portable real-time reverse transcriptase-polymerase chain reaction assay for rapid detection of foot-and-mouth disease virus","volume":"220","author":"Callahan","year":"2002","journal-title":"J. Am. Vet. Med. Assoc."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"778","DOI":"10.1177\/1040638719870859","article-title":"Reliable detection, sequencing, and transfection of foot-and-mouth disease virus RNA from badly preserved vesicular epithelium","volume":"31","author":"Dill","year":"2019","journal-title":"J. Vet. Diagn. Investig."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"1714","DOI":"10.1128\/JCM.03370-12","article-title":"A continuous bovine kidney cell line constitutively expressing bovine alphavbeta6 integrin has increased susceptibility to foot-and-mouth disease virus","volume":"51","author":"LaRocco","year":"2013","journal-title":"J. Clin. Microbiol."},{"key":"ref_12","doi-asserted-by":"crossref","unstructured":"Dill, V., Beer, M., and Hoffmann, B. (2017). Simple, quick and cost-efficient: A universal RT-PCR and sequencing strategy for genomic characterisation of foot-and-mouth disease viruses. J. Virol. Methods.","DOI":"10.1016\/j.jviromet.2017.04.007"},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"159","DOI":"10.1016\/j.virol.2017.06.019","article-title":"Use of Sequence-Independent, Single-Primer-Amplification (SISPA) for rapid detection, identification, and characterization of avian RNA viruses","volume":"509","author":"Chrzastek","year":"2017","journal-title":"Virology"},{"key":"ref_14","doi-asserted-by":"crossref","unstructured":"Scheuch, M., H\u00f6per, D., and Beer, M. (2015). RIEMS: A software pipeline for sensitive and comprehensive taxonomic classification of reads from metagenomics datasets. BMC Bioinform., 16.","DOI":"10.1186\/s12859-015-0503-6"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"1792","DOI":"10.1093\/nar\/gkh340","article-title":"MUSCLE: Multiple sequence alignment with high accuracy and high throughput","volume":"32","author":"Edgar","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"ref_16","doi-asserted-by":"crossref","unstructured":"Price, M.N., Dehal, P.S., and Arkin, A.P. (2010). FastTree 2\u2014Approximately maximum-likelihood trees for large alignments. PLoS ONE, 5.","DOI":"10.1371\/journal.pone.0009490"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"vev003","DOI":"10.1093\/ve\/vev003","article-title":"RDP4: Detection and analysis of recombination patterns in virus genomes","volume":"1","author":"Martin","year":"2015","journal-title":"Virus Evol."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1007\/s11262-019-01714-7","article-title":"Cell culture propagation of foot-and-mouth disease virus: Adaptive amino acid substitutions in structural proteins and their functional implications","volume":"56","author":"Dill","year":"2020","journal-title":"Virus Genes"},{"key":"ref_19","unstructured":"WRLFMD (2020, July 21). Genotyping Report WRLFMD\/2017\/00014. Available online: https:\/\/perma.cc\/5M8F-9MUS."},{"key":"ref_20","unstructured":"WRLFMD (2020, July 21). FMD Vaccine Matching Strain Differentiation Report WRLFMD\/2016\/00024. Available online: https:\/\/perma.cc\/T468-FUD4."},{"key":"ref_21","unstructured":"WRLFMD (2020, July 21). FMD Vaccine Matching Strain Differentiation Report WRLFMD\/2017\/00014. Available online: https:\/\/perma.cc\/JB26-FWVQ."},{"key":"ref_22","first-page":"33","article-title":"Efficacy of a Commercial Local Trivalent Foot and Mouth Disease (FMD) Vaccine against Recently Isolated O-EA3","volume":"8","author":"Shafik","year":"2019","journal-title":"Int. J. Vet. Sci."},{"key":"ref_23","unstructured":"MEVAC (2020, July 21). Ruminants Vaccines. Available online: https:\/\/perma.cc\/BZ4T-HZ8W."},{"key":"ref_24","unstructured":"WRLFMD (2020, July 22). Quarterly Report 2020 Quarter 1 (Jan\u2013Mar). Available online: https:\/\/perma.cc\/J4BF-LPH3."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"384","DOI":"10.1099\/vir.0.057521-0","article-title":"Antigenic variation of foot-and-mouth disease virus serotype A","volume":"95","author":"Ludi","year":"2014","journal-title":"J. Gen. Virol."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"1681","DOI":"10.1016\/j.vaccine.2008.01.038","article-title":"High potency vaccines induce protection against heterologous challenge with foot-and-mouth disease virus","volume":"26","author":"Brehm","year":"2008","journal-title":"Vaccine"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"241","DOI":"10.21608\/bvmj.2015.32757","article-title":"Evaluation of cross-protection between FMD serotypes O and A local Egyptian isolate with vaccinal strains in the local commercial and imported vaccines by challenge test","volume":"28","author":"Sharawi","year":"2015","journal-title":"Benha Vet. Med. J."},{"key":"ref_28","unstructured":"OIE (2020, August 27). Manual of Diagnostic Tests and Vaccines for Terrestrial Animals, Chapter 3.1.8. Foot and Mouth Disease., Available online: https:\/\/perma.cc\/EG94-MX4N."},{"key":"ref_29","unstructured":"VSVRI (2020, July 22). Bivalent Inactivated Foot and Mouth Disease Oil Vaccine (Types O1&A). Available online: https:\/\/perma.cc\/D4NQ-R3JN."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"1593","DOI":"10.3201\/eid1310.070252","article-title":"Foot-and-mouth disease virus serotype A in Egypt","volume":"13","author":"Knowles","year":"2007","journal-title":"Emerg. Infect. Dis."},{"key":"ref_31","first-page":"16","article-title":"Comparative Study on the Hemato-Biochemical and Immunological Effects of the Hexavalent FMD Vaccine Alone or in Combination with Trivalent FMD Vaccine in Cattle","volume":"4","author":"Shawky","year":"2016","journal-title":"J. Biosci. Med."},{"key":"ref_32","unstructured":"WRLFMD (2020, July 22). Genotyping Report WRLFMD\/2019\/00005. Available online: https:\/\/perma.cc\/V6HM-9CP9."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"22","DOI":"10.1016\/j.ijvsm.2018.02.001","article-title":"Outbreaks of foot and mouth disease in Egypt: Molecular epidemiology, evolution and cardiac biomarkers prognostic significance","volume":"6","author":"Sobhy","year":"2018","journal-title":"Int. J. Vet. Sci. Med."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"14693","DOI":"10.1038\/s41598-018-32693-8","article-title":"Reconstructing the evolutionary history of pandemic foot-and-mouth disease viruses: The impact of recombination within the emerging O\/ME-SA\/Ind-2001 lineage","volume":"8","author":"Wadsworth","year":"2018","journal-title":"Sci. Rep."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"11827","DOI":"10.1128\/JVI.01100-06","article-title":"Recombination patterns in aphthoviruses mirror those found in other picornaviruses","volume":"80","author":"Heath","year":"2006","journal-title":"J. Virol."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"2011","DOI":"10.1111\/tbed.13249","article-title":"Serological and phylogenetic characterization of foot and mouth disease viruses from Uganda during cross-sectional surveillance study in cattle between 2014 and 2017","volume":"66","author":"Mwiine","year":"2019","journal-title":"Transbound. Emerg. Dis."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1007\/s11262-011-0599-3","article-title":"Comparative sequence analysis of representative foot-and-mouth disease virus genomes from Southeast Asia","volume":"43","author":"Radford","year":"2011","journal-title":"Virus Genes"},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"2049","DOI":"10.1016\/j.meegid.2011.09.015","article-title":"Molecular characterization of serotype Asia-1 foot-and-mouth disease viruses in Pakistan and Afghanistan; emergence of a new genetic Group and evidence for a novel recombinant virus","volume":"11","author":"Jamal","year":"2011","journal-title":"Infect. Genet. Evol."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"87","DOI":"10.1016\/0168-1702(85)90044-9","article-title":"Isolation and biochemical characterization of intertypic recombinants of foot-and-mouth disease virus","volume":"3","author":"McCahon","year":"1985","journal-title":"Virus Res."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"230","DOI":"10.1016\/j.meegid.2013.09.009","article-title":"Reconstructing the origin and transmission dynamics of the 1967-68 foot-and-mouth disease epidemic in the United Kingdom","volume":"20","author":"Wright","year":"2013","journal-title":"Infect. Genet. Evol."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"190","DOI":"10.14202\/vetworld.2019.190-197","article-title":"Foot-and-mouth disease outbreaks in Egypt during 2013-2014: Molecular characterization of serotypes A, O, and SAT2","volume":"12","author":"Diab","year":"2019","journal-title":"Vet. World"},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"529","DOI":"10.1017\/S0950268899002265","article-title":"Genetic analysis of type O viruses responsible for epidemics of foot-and-mouth disease in North Africa","volume":"122","author":"Samuel","year":"1999","journal-title":"Epidemiol. Infect."},{"key":"ref_43","unstructured":"VSVRI (2020, July 22). Polyvalent Inactivated Foot and Mouth Disease Oil Vaccine (Types O1,A&SAT2). Available online: https:\/\/perma.cc\/A3NC-8V7Y."},{"key":"ref_44","unstructured":"WRLFMD (2020, July 22). Country Reports: Egypt, Samples Tested. Available online: https:\/\/perma.cc\/KDK8-CQ9F."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"1887","DOI":"10.3201\/eid1112.050908","article-title":"Pandemic strain of foot-and-mouth disease virus serotype O","volume":"11","author":"Knowles","year":"2005","journal-title":"Emerg. Infect. Dis."},{"key":"ref_46","doi-asserted-by":"crossref","unstructured":"Abu-Elnaga, H.I., Rizk, S.A., Daoud, H.M., Mohamed, A.A., Mossad, W., Gamil, M.A., Soudy, A.F., and El-Shehawy, L.I. (2020). Comparative nucleotide sequencing of the VP1 capsid gene of recent isolates of foot-and-mouth disease virus serotype O from Egypt. Arch. Virol.","DOI":"10.1007\/s00705-020-04708-1"},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"1621","DOI":"10.1128\/jvi.61.5.1621-1629.1987","article-title":"Subtyping of European foot-and-mouth disease virus strains by nucleotide sequence determination","volume":"61","author":"Beck","year":"1987","journal-title":"J. Virol."},{"key":"ref_48","doi-asserted-by":"crossref","unstructured":"Cottam, E.M., Wadsworth, J., Shaw, A.E., Rowlands, R.J., Goatley, L., Maan, S., Maan, N.S., Mertens, P.P., Ebert, K., and Li, Y. (2008). Transmission pathways of foot-and-mouth disease virus in the United Kingdom in 2007. PLoS Pathog., 4.","DOI":"10.1371\/journal.ppat.1000050"},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1016\/0168-1702(90)90012-Z","article-title":"Comparison of vaccine strains and the virus causing the 1986 foot-and-mouth disease outbreak in Spain: Epizootiological analysis","volume":"15","author":"Carrillo","year":"1990","journal-title":"Virus Res."}],"container-title":["Viruses"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1999-4915\/12\/9\/990\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T10:07:17Z","timestamp":1760177237000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1999-4915\/12\/9\/990"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,9,6]]},"references-count":49,"journal-issue":{"issue":"9","published-online":{"date-parts":[[2020,9]]}},"alternative-id":["v12090990"],"URL":"https:\/\/doi.org\/10.3390\/v12090990","relation":{"has-preprint":[{"id-type":"doi","id":"10.20944\/preprints202008.0285.v1","asserted-by":"object"}]},"ISSN":["1999-4915"],"issn-type":[{"value":"1999-4915","type":"electronic"}],"subject":[],"published":{"date-parts":[[2020,9,6]]}}}