Genetic characterization of Nipah virus from Thai fruit bats (Pteropus lylei)

Background: Nipah virus (NiV) is an emerging zoonosis of paramyxovirus that causes febrile encephalitis with high death rates in humans. It has been successfully isolated and genetically characterized in three species of fruit bats including Pteropus hypomelanus, P. vampyrus in Malaysia, and P. lylei (Lyle’s fruit bat) in Cambodia. Little is still known about NiV genetic information in Lyle’s fruit bats in Thailand.

Objective: Partial NiV sequences obtained from 61 isolates from nine bat roosting sites, in Central Thailand during 2002-2008 were genetically characterized to determine the diversity of NiV found in Thai bats.

Methods: All samples were collected from Lyle’s fruit bats, except for two from insectivorous bats. NiV RNA was extracted directly from the bat urine, saliva or serum specimens, and a fragment of the nucleoprotein (N) gene was amplified by hemi-nested RT-PCR and 357 base pairs were sequenced for phylogenetic analysis.

Results: The NiV isolates from bats found in Thailand form a monophyletic group with those from Malaysia, Bangladesh and Cambodia. It is divided into two closely related lineages: Clade A and B. Clade A represents the majority of those found in Thailand (52/61).

Conclusion: The genetic divergence of NiV isolates obtained from Lyle’s fruit bats in a small geographic region might indicate that the ancestor of this group of virus has circulated in Pteropus fruit bats for a long time. More viral surveillance studies in Pteropus bat populations in this region might help to clarify the genetic distribution of bat-NiV in Pteropus and allow risk assessment in NiV outbreaks from fruit bats.