Persistence of Multiple Paramyxoviruses in a Closed Captive Colony of Fruit Bats (Eidolon helvum)

Abstract

Bats have been identified as the natural hosts of several emerging zoonotic viruses, including paramyxoviruses, such as Hendra and Nipah viruses, that can cause fatal disease in humans. Recently, African fruit bats with populations that roost in or near urban areas have been shown to harbour a great diversity of paramyxoviruses, posing potential spillover risks to public health. Understanding the circulation of these viruses in their reservoir populations is essential to predict and prevent future emerging diseases. Here, we identify a high incidence of multiple paramyxoviruses in urine samples collected from a closed captive colony of circa 115 straw-coloured fruit bats (Eidolon helvum). The sequences detected have high nucleotide identities with those derived from free ranging African fruit bats and form phylogenetic clusters with the Henipavirus genus, Pararubulavirus genus and other unclassified paramyxoviruses. As this colony had been closed for 5 years prior to this study, these results indicate that within-host paramyxoviral persistence underlies the role of bats as reservoirs of these viruses.

Keywords: Henipavirus; Pararubulavirus; Pteropodidae; chiroptera; longitudinal study.

Figure 1

Cage housing the Eidolon helvum bat colony. The mesh double-walls, ground-level cladding and outer solid roof are clearly visible. Note, the bat colony can be seen roosting while hanging from the inner mesh roof towards the left side of this photograph.

Figure 2

Timeline of amplicon sequences detected using the PAR-PCR (lower panel) and RMH-PCR assays (upper panel). The red dot denotes the positive amplicon sequence and the grey dot denotes the negative amplicon sequence detected at each time point.

Figure 3

Phylogenetic analysis of partial L gene sequences obtained after PAR-PCR on E. helvum urine samples (red arrows). Maximum likelihood tree with bootstrapping (1000 iterations) generated in MEGA X, using 530 bp alignment against publicly available paramyxovirus sequences (NCBI Genbank) and outgroup Newcastle disease virus. Bootstrap values for 1000 replicates are indicated as percentages (where >50%) and the number of nucleotide substitutions per site is to scale as indicated by the scale bar.

Figure 4

Phylogenetic analysis of partial L gene sequences obtained after RMH-PCR on E. helvum urine samples (red arrows). Maximum likelihood tree with bootstrapping (1000 iterations) generated in MEGA X, using 439 bp alignment against publicly available paramyxovirus sequences (NCBI Genbank) and outgroup Newcastle disease virus. Bootstrap values for 1000 replicates are indicated as percentages (where >50%) and the number of nucleotide substitutions per site is to scale as indicated by the scale bar.