Whole-genome sequencing and phylogenetic analysis of rabies viruses from Jordan.

Laith N Al-Eitan,Hooman Goharriz,Denise A Marston,Yue Tang,Guanghui Wu,Megan Golding,Lorraine M Mcelhinney,Anthony R Fooks,Daniel G Streicker

doi:10.1371/journal.pntd.0009431

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.

Highlights

Canine rabies death tolls estimated by 59,000 human deaths worldwide and over 3.7 million disability-adjusted life years (DALYs) [1]
We performed whole genome sequencing (WGS) for rabies virus (RABV) isolates from seven samples, five of which were of stray dogs, and the other two were from foxes
Six out of the seven isolates were belonging to the Cosmopolitan ME2 clade, which related to the Iranian and Turkish sequences

Summary

Introduction

Canine rabies death tolls estimated by 59,000 human deaths worldwide and over 3.7 million disability-adjusted life years (DALYs) [1]. Human rabies is a rare occurrence in Jordan, and the Ministry of Health (MOH) provides post-exposure prophylaxis for any individual afflicted by a stray or owned dog bite and is responsible for investigating rabies virus infection. In an epidemiological study of 419 brain samples from animals suspected of rabies collected by Jordan’s MOH, among the 164 positive animals, the majority were from stray dogs (45.1%) and cattle (19.5%) [4]. Due to the lack of national surveillance of rabies and insufficiency in animal screening, prevalence in animals is not fully understood or reported, which is a major health issue. A recent study reported that the primary diagnostic test for rabies in Jordan, the fluorescent antibody test (FAT), was not conclusive when used on its own, as it resulted in false positive results for some samples [6].

Methods

Results

Conclusion