Whole-genome Sequencing and Phylogenetic Analysis of Rabies Viruses from Jordan

Overview

Journal PLoS Negl Trop Dis

Specialties Infectious Diseases
Tropical Medicine

Date 2021 May 20

PMID 34014930

Citations 4

Authors

Laith N Al-Eitan

Guanghui Wu

Megan Golding

Yue Tang

Hooman Goharriz

Denise A Marston

Anthony R Fooks

Lorraine M McElhinney

Affiliations

Soon will be listed here.

Abstract

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.

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References

Letunic I, Bork P . Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees. Nucleic Acids Res. 2016; 44(W1):W242-5. PMC: 4987883. DOI: 10.1093/nar/gkw290. View

McElhinney L, Marston D, Brookes S, Fooks A . Effects of carcase decomposition on rabies virus infectivity and detection. J Virol Methods. 2014; 207:110-3. DOI: 10.1016/j.jviromet.2014.06.024. View

Leung A, Davies H, Hon K . Rabies: epidemiology, pathogenesis, and prophylaxis. Adv Ther. 2008; 24(6):1340-7. DOI: 10.1007/BF02877781. View

Li H, Durbin R . Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics. 2010; 26(5):589-95. PMC: 2828108. DOI: 10.1093/bioinformatics/btp698. View

Troupin C, Dacheux L, Tanguy M, Sabeta C, Blanc H, Bouchier C . Large-Scale Phylogenomic Analysis Reveals the Complex Evolutionary History of Rabies Virus in Multiple Carnivore Hosts. PLoS Pathog. 2016; 12(12):e1006041. PMC: 5158080. DOI: 10.1371/journal.ppat.1006041. View

McElhinney L, Marston D, Freuling C, Cragg W, Stankov S, Lalosevic D . Molecular diversity and evolutionary history of rabies virus strains circulating in the Balkans. J Gen Virol. 2011; 92(Pt 9):2171-2180. DOI: 10.1099/vir.0.032748-0. View

David D, Hughes G, Yakobson B, Davidson I, Un H, Aylan O . Identification of novel canine rabies virus clades in the Middle East and North Africa. J Gen Virol. 2007; 88(Pt 3):967-980. DOI: 10.1099/vir.0.82352-0. View

Fooks A, Cliquet F, Finke S, Freuling C, Hemachudha T, Mani R . Rabies. Nat Rev Dis Primers. 2017; 3:17091. DOI: 10.1038/nrdp.2017.91. View

Vega S, Lorenzo-Rebenaque L, Marin C, Domingo R, Farinas F . Tackling the Threat of Rabies Reintroduction in Europe. Front Vet Sci. 2021; 7:613712. PMC: 7843519. DOI: 10.3389/fvets.2020.613712. View

10.

Hampson K, Coudeville L, Lembo T, Sambo M, Kieffer A, Attlan M . Estimating the global burden of endemic canine rabies. PLoS Negl Trop Dis. 2015; 9(4):e0003709. PMC: 4400070. DOI: 10.1371/journal.pntd.0003709. View

11.

Singh R, Singh K, Cherian S, Saminathan M, Kapoor S, Manjunatha Reddy G . Rabies - epidemiology, pathogenesis, public health concerns and advances in diagnosis and control: a comprehensive review. Vet Q. 2017; 37(1):212-251. DOI: 10.1080/01652176.2017.1343516. View

12.

Dellicour S, Troupin C, Jahanbakhsh F, Salama A, Massoudi S, Moghaddam M . Using phylogeographic approaches to analyse the dispersal history, velocity and direction of viral lineages - Application to rabies virus spread in Iran. Mol Ecol. 2019; 28(18):4335-4350. DOI: 10.1111/mec.15222. View

13.

Crowcroft N, Thampi N . The prevention and management of rabies. BMJ. 2015; 350:g7827. DOI: 10.1136/bmj.g7827. View

14.

Horton D, McElhinney L, Freuling C, Marston D, Banyard A, Goharrriz H . Complex epidemiology of a zoonotic disease in a culturally diverse region: phylogeography of rabies virus in the Middle East. PLoS Negl Trop Dis. 2015; 9(3):e0003569. PMC: 4374968. DOI: 10.1371/journal.pntd.0003569. View

15.

Marston D, Horton D, Nunez J, Ellis R, Orton R, Johnson N . Genetic analysis of a rabies virus host shift event reveals within-host viral dynamics in a new host. Virus Evol. 2017; 3(2):vex038. PMC: 5729694. DOI: 10.1093/ve/vex038. View

16.

Stamatakis A . RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 2014; 30(9):1312-3. PMC: 3998144. DOI: 10.1093/bioinformatics/btu033. View

17.

David D, Yakobson B, Smith J, Stram Y . Molecular epidemiology of rabies virus isolates from Israel and other middle- and Near-Eastern countries. J Clin Microbiol. 2000; 38(2):755-62. PMC: 86197. DOI: 10.1128/JCM.38.2.755-762.2000. View

18.

Nathwani D, McIntyre P, White K, Shearer A, Reynolds N, Walker D . Fatal human rabies caused by European bat Lyssavirus type 2a infection in Scotland. Clin Infect Dis. 2003; 37(4):598-601. DOI: 10.1086/376641. View

19.

Faizee N, Hailat N, Ababneh M, Hananeh W, Muhaidat A . Pathological, immunological and molecular diagnosis of rabies in clinically suspected animals of different species using four detection techniques in Jordan. Transbound Emerg Dis. 2012; 59(2):154-64. DOI: 10.1111/j.1865-1682.2011.01255.x. View

20.

Nigg A, Walker P . Overview, prevention, and treatment of rabies. Pharmacotherapy. 2009; 29(10):1182-95. DOI: 10.1592/phco.29.10.1182. View