Full-Length Genome of an Africa-4 Lineage Wild-Type Lyssavirus rabies from a Stray Dog in Egypt, 2019
Full-Length Genome of an Africa-4 Lineage Wild-Type Lyssavirus rabies from a Stray Dog in Egypt, 2019
Amthal Ahmed Fouad1, Basem Mohamed Ahmed2, Momtaz Abdelhady Shahein1, Hussein Aly Hussein2*
ABSTRACT
Background: Lyssavirus rabies is a major global zoonosis and is endemic in Egypt. Rabid dogs are the prime source for human and livestock Lyssavirus rabies (RABV) exposure with almost 100% case fatality. While all lyssavirus rabies genetic data -including whole genomes- from Egypt are clustered within a unique lineage (Africa-4 lineage of the cosmopolitan clade), no report provided detailed description of this lineage genome and the last published whole genome dates back to 2009. In this context, a complete RABV genome (5EG-QH19) was obtained from a stray dog, analyzed, and compared to other RABV sequences to update the present knowledge. Methods: Rapid immune-chromatography and direct fluorescent antibody test (DFAT) were applied to detect RABV antigens in the brain of rabid dog. Relevant reads from the Ion S5 sequencing system were assembled into a draft genome. The draft genome was analyzed, re-assembled, and compared to representative RABV genomes from Africa and the Middle East region. Results: The complete genome of 5EG-QH19 strain extends for 11919 nt including the standard RABV protein genes in the correct order. Twenty-nine synonymous and five non-synonymous mutations were evident in the protein genes. Deletions and insertions were observed in the intergenic spaces. It was highly similar to Egyptian RABV genomes and clustered within the Africa-4 (AF4) lineage of the cosmopolitan clade. It was submitted to NCBI GenBank under the access number OL314495. Conclusion: The study provides analysis for the 5EG-QH19 wild-type RABV genome, elucidates some key structural features of the AF4 lineage dominant in Egypt and supports the recently proposed division of AF4 lineage into two sub-lineages (AF4a and AF4b). Divergence from SAD B19 vaccine strain sequence was also reported but the exact effect of the observed genetic changes in an infectious RABV particle dictates in-vivo studies.
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