Co-circulation of diverse paramyxoviruses in an urban African fruit bat population

Abstract

Bats constitute a reservoir of zoonotic infections and some bat paramyxoviruses are capable of cross-species transmission, often with fatal consequences. Determining the level of viral diversity in reservoir populations is fundamental to understanding and predicting viral emergence. This is particularly relevant for RNA viruses where the adaptive mutations required for cross-species transmission can be present in the reservoir host. We report the use of non-invasively collected, pooled, neat urine samples as a robust sample type for investigating paramyxoviruses in bat populations. Using consensus PCR assays we have detected a high incidence and genetic diversity of novel paramyxoviruses in an urban fruit bat population over a short period of time. This may suggest a similarly unique relationship between bats and the members of the family Paramyxoviridae as proposed for some other viral families. Additionally, the high rate of bat-human contact at the study site calls for the zoonotic potential of the detected viruses to be investigated further.

Fig. 1.

Diversity of paramyxoviruses in pooled E. helvum urine samples detected by using Paramyxovirinae-targeted PCR. Phylogenetic tree for a 531 bp segment of the polymerase gene of members of the subfamily Paramyxovirinae, including sequences generated in this study and publicly available paramyxovirus sequences (Newcastle disease virus, sendai virus, human parainfluenza virus 3, mossman virus, tupaia paramyxovirus, J virus, beilong virus, canine distemper virus, measles virus, rinderpest, hendra virus, nipah virus (Bangladesh), nipah virus (Malaysia), human parainfluenza virus 4, mumps virus, simian parainfluenza virus 41, human parainfluenza virus 2, simian virus 5, porcine rubulavirus, mapuera virus, tuhoko virus 1, menangle virus, tioman virus, tuhoko virus 3, tuhoko virus 2). Relevant posterior probability values are shown. Bar, 0.3 expected nucleotide substitutions per site. Individual sample IDs are followed by letters denoting the clone and the GenBank accession number for the sequence. Groups containing previously uncharacterized sequences that display a common phylogenetic origin supported by high posterior probability values (≥0.95) are highlighted by numbered grey boxes. Adjacent to each box number is the range of nucleotide identities among sequences in the clade. Clones derived from samples that contained sequences belonging to more than one of these phylogenetically distinct clades were marked with a cross. Sequences derived from samples that were positive only with this PCR (and negative with RMH-PCR) are marked with a dot.

Fig. 2.

Diversity of paramyxoviruses in pooled E. helvum urine samples detected by using RMH-targeted PCR. Phylogenetic tree for a 439 bp gap-stripped alignment of the polymerase gene of members of the subfamily Paramyxovirinae, including sequences generated in this study and publicly available paramyxovirus genome sequences (as per Fig. 1) and partial paramyxovirus sequences available from this species (Ghanaian sequences GH45, GH48 and GH10). Relevant posterior probability values are shown. Bar, 0.4 expected nucleotide substitutions per site. Individual sample IDs are followed by letters denoting the clone and the GenBank accession for the sequence. Groups containing previously uncharacterized sequences that display a common phylogenetic origin supported by high posterior probability values (≥0.95) are highlighted by lettered grey boxes. Adjacent to each box letter is the range of nucleotide identities among sequences in the clade. Clones derived from samples that contained sequences belonging to more than one of these phylogenetically distinct clades were marked with a cross. Sequences derived from samples that were positive only with this PCR (and negative with PMV-PCR) are marked with a dot.