{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,25]],"date-time":"2026-03-25T05:34:47Z","timestamp":1774416887760,"version":"3.50.1"},"update-to":[{"DOI":"10.1371\/journal.pntd.0009431","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2021,6,2]],"date-time":"2021-06-02T00:00:00Z","timestamp":1622592000000}}],"reference-count":37,"publisher":"Public Library of Science (PLoS)","issue":"5","license":[{"start":{"date-parts":[[2021,5,20]],"date-time":"2021-05-20T00:00:00Z","timestamp":1621468800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000277","name":"Department for Environment, Food & Rural Affairs","doi-asserted-by":"crossref","award":["SE0431\/SE0433"],"award-info":[{"award-number":["SE0431\/SE0433"]}],"id":[{"id":"10.13039\/501100000277","id-type":"DOI","asserted-by":"crossref"}]},{"name":"The European Union's Horizon 2020 research and innovation programme","award":["871029 EVA-GLOBAL"],"award-info":[{"award-number":["871029 EVA-GLOBAL"]}]}],"content-domain":{"domain":["www.plosntds.org"],"crossmark-restriction":false},"short-container-title":["PLoS Negl Trop Dis"],"abstract":"<jats:p>Human fatalities caused by rabies are rarely reported in Jordan; however, domestic animals are more likely to fall victim to rabies compared to wild animals, at least this is the case in Jordan due to the presence of canine rabies. In this study, twelve brain samples from domestic and wild animals suspected of being infected with rabies virus from different regions of Jordan were collected during 2019. Seven of them tested positive using the fluorescent antibody test and real-time SYBR RT-PCR assay. Five specimens were from stray dogs and two from foxes. The whole genome sequences were obtained from the positive samples. Sequence analysis showed that one dog virus from Al Quwaysimah city located in Amman governorate, was closely related to an Israeli strain belonging to a Cosmopolitan ME1a clade. The genomes of the remaining six viruses (four from dogs and two from foxes) collected from different areas of Jordan were genetically-related to each other and clustered together with sequences from Iran and Turkey; all belong to Cosmopolitan ME2 clade. These sequences were analyzed with six other Jordanian rabies virus nucleoprotein (N) gene sequences available in the public database, five of them belong to ME1a clade and one belongs to ME1b clade. Rabies virus whole genome data is scarce across the Middle East. This study provides a better understanding of the molecular epidemiology of rabies virus in the region.<\/jats:p>","DOI":"10.1371\/journal.pntd.0009431","type":"journal-article","created":{"date-parts":[[2021,5,20]],"date-time":"2021-05-20T18:05:52Z","timestamp":1621533952000},"page":"e0009431","update-policy":"https:\/\/doi.org\/10.1371\/journal.pntd.corrections_policy","source":"Crossref","is-referenced-by-count":14,"title":["Whole-genome sequencing and phylogenetic analysis of rabies viruses from Jordan"],"prefix":"10.1371","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0064-0190","authenticated-orcid":true,"given":"Laith N.","family":"AL-Eitan","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Guanghui","family":"Wu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Megan","family":"Golding","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9638-8270","authenticated-orcid":true,"given":"Yue","family":"Tang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hooman","family":"Goharriz","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9215-088X","authenticated-orcid":true,"given":"Denise A.","family":"Marston","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3243-6154","authenticated-orcid":true,"given":"Anthony R.","family":"Fooks","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6022-348X","authenticated-orcid":true,"given":"Lorraine M.","family":"McElhinney","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2021,5,20]]},"reference":[{"issue":"4","key":"pntd.0009431.ref001","doi-asserted-by":"crossref","first-page":"e0003709","DOI":"10.1371\/journal.pntd.0003709","article-title":"Estimating the global burden of endemic canine rabies","volume":"9","author":"K Hampson","year":"2015","journal-title":"PLoS Negl Trop Dis"},{"key":"pntd.0009431.ref002","doi-asserted-by":"crossref","first-page":"219","DOI":"10.3389\/fpubh.2015.00219","article-title":"Mapping of Networks to Detect Priority Zoonoses in Jordan","volume":"3","author":"EM Sorrell","year":"2015","journal-title":"Front Public Health"},{"issue":"3","key":"pntd.0009431.ref003","doi-asserted-by":"crossref","first-page":"967","DOI":"10.1099\/vir.0.82352-0","article-title":"Identification of novel canine rabies virus clades in the Middle East and North Africa","volume":"88","author":"D David","year":"2007","journal-title":"J Gen Virol"},{"issue":"2\/3","key":"pntd.0009431.ref004","first-page":"129","article-title":"An epidemiological investigation of rabies in Jordan","volume":"47","author":"KM Al-Qudah","year":"1997","journal-title":"Acta Vet"},{"key":"pntd.0009431.ref005","unstructured":"Su A. 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Available online: https:\/\/www.ktb.gov.tr\/EN-249299\/yearly-bulletins.html [Accessed March, 31 2021]."},{"key":"pntd.0009431.ref032","doi-asserted-by":"crossref","first-page":"175","DOI":"10.1017\/S0950268899004306","article-title":"Human rabies in Lebanon: lessons for control","volume":"125","author":"AR Bizri","year":"2000","journal-title":"Epidemiology & Infection"},{"key":"pntd.0009431.ref033","first-page":"171","volume-title":"Historical Perspective of Rabies in Europe and the Mediterranean Basin","author":"BA Yakobson","year":"2004"},{"key":"pntd.0009431.ref034","doi-asserted-by":"crossref","first-page":"1196","DOI":"10.3389\/fvets.2020.613712","article-title":"Tackling the Threat of Rabies Reintroduction in Europe","volume":"7","author":"S Vega","year":"2021","journal-title":"Frontiers in Veterinary Science"},{"issue":"6","key":"pntd.0009431.ref035","doi-asserted-by":"crossref","first-page":"260","DOI":"10.17221\/67\/2018-VETMED","article-title":"Seroprevalence of Brucella canis in dogs and at-risk humans in Jordan","volume":"64","author":"M Alshehabat","year":"2019","journal-title":"Veterin\u00e1rn\u00ed medic\u00edna"},{"key":"pntd.0009431.ref036","unstructured":"Hashemite Kingdome of Jordan, Official Gazette, rule no. 138 and 145\/2016. 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