Speaker
Description
Bats have become a focal point in the study of viral dynamics given their role as animal reservoirs for viruses from key families such as Coronaviridae and Paramoxyviridae. In this study, we analyzed RNA-positive samples from bat specimens collected during expeditions to countries in Asia, using primers designed to amplify the RNA-dependent RNA polymerase (RdRp) gene of known and novel paramyxoviruses. Out of 800 museum specimens tested, 23 RdRp sequences were successfully produced. These specimens were obtained from 1993 to 2007 in China (3), Vietnam (16), Indonesia (1) and Malaysia (3), representing bats in families Hipposideridae (12), Pteropodidae (2), Rhinlophidae (5) and Vespertilionidae (4).
We performed a local nucleotide BLAST search against the NCBI virus database, recording the 50 best matches for each sequence. Using the Entrez API, we extracted metadata, including host organism, sample collection date and sampling country, for the non-redundant set of 362 BLAST results. Next, we used MAFFT to generate a multiple sequence alignment and IQ-TREE to reconstruct a maximum likelihood tree. Finally, we used root-to-tip regression to assess support for a molecular clock.
The BLAST results were RdRp sequences predominantly from Jeilongviruses isolated from bats (including Vespertilionidae, n=139; Pteropodidae, n=64 and Molossidae, n=54) with a majority of samples from Africa (n=270, 75%) and only 23 (6%) from Asia. There was no support for a molecular clock; thus, we used two sequences from Orthobulaviruses as an outgroup to root the tree. Museum samples formed several distinct subclades in the phylogeny relative to BLAST sequences. In addition, these subclades were interspersed throughout the tree, implying the repeated migration of virus lineages into Asia. Our results indicate that museum specimens can be an important resource for addressing sampling biases in publicly-available sequence data, improving our understanding of the spread and diversification of viruses in animal hosts.
