Detection of Tioman Virus in Pteropus vampyrus Near Flores, Indonesia

Abstract

Diverse paramyxoviruses have coevolved with their bat hosts, including fruit bats such as flying foxes (Chiroptera: Pteropodidae). Several of these viruses are zoonotic, but the diversity and distribution of Paramyxoviridae are poorly understood. We screened pooled feces samples from three Pteropus vampyrus colonies and assayed tissues, rectal swabs, and oral swabs from 95 individuals of 23 pteropodid species sampled at 17 sites across the Indonesian archipelago with a conventional paramyxovirus PCR; all tested negative. Samples from 43 individuals were screened with next generation sequencing (NGS), and a single Pteropus vampyrus collected near Flores had Tioman virus sequencing reads. Tioman virus is a bat-borne virus in the genus Pararubulavirus with prior evidence of spillover to humans. This work expands the known range of Tioman virus, and it is likely that this isolated colony likely has sustained intergenerational transmission over a long period.

Keywords: Indonesia; Pteropodidae; bat-borne virus; flying foxes; next generation sequencing; paramyxovirus.

Figure 1

Locations of 17 sites across the Indonesian archipelago where tissues from pteropodid bats were sampled for viral screening. Location K is the site of the Pteropus vampyrus positive for Tioman virus.

Figure 2

Coverage of next generation sequencing reads from a Pteropus vampyrus assembled to a reference genome of Tioman virus (Accession number: NC_004074). Coverage ranged from 0–8 nucleotides across the genome, represented in blue above the annotated reference genome.

Figure 3

Maximum likelihood phylogeny of the L (polymerase) gene region of paramyxoviruses. The red box denotes sequences from members of the genus Pararubulavirus and the green box indicates Tioman virus sequences. Bootstrap values > 50% are indicated at branch nodes. The scale bar represents the nucleotide substitutions per site.