First whole genome sequence of Nipah virus from Pteropus lylei, Thailand

Abstract

Purpose: Nipah virus (NiV), a paramyxovirus, causes febrile encephalitis and severe respiratory disease in humans and animals. Nipah virus outbreaks have been reported from Malaysia, Bangladesh, India and Singapore. The case positive in humans have been attributed to zoonotic transmission from pigs and bats, human-to-human transmission, and eating fruits or juices contaminated with bat secretions. At present no vaccines or drugs are available for those infected with NiV. Fruit bats of family Pteropodidae have been identified as the reservoir for NiV. Whole genome Nipah virus can be help in understanding the epidemiology, evolution and origin of this virus. Methods & Materials: The first whole genome of NiV from pooled urine of Pteropus lylei bat (flying fox in the Pteropodidae family) was sequenced using Next generation sequencing in Thailand. The total read of MiSeq sequencer was 19.8 Gb, where sequences of Pteropus host genome were removed, and NiV was identified using virus sequences from NCBI database. Results: The 4,735 sequences mapped to reference generated 18,236 nucleotides, and average depth of coverage was 41.67% for NiV from Bangladesh 2004 (GenBank accession number: AY988601.1). The genome shared greater than 99% identity (18084/18236 nucleotides) with NiV isolated from a patient in Bangladesh in 2004 (AY988601.1) and 92% identity with NiV Malaysia strain. The phylogenetic tree of whole NiV genome sequenced in Thailand also showed it was closely related to NiV from Bangladesh 2004 (AY988601.1). Conclusion: This finding shows the potential risk of NiV outbreak in Thailand. The preparedness to prevent the potential transmission of NiV from bat to the community or livestock animals, is essential.