Screening great ape museum specimens for DNA viruses

Abstract

Natural history museum collections harbour a record of wild species from the past centuries, providing a unique opportunity to study animals as well as their infectious agents. Thousands of great ape specimens are kept in these collections, and could become an important resource for studying the evolution of DNA viruses. Their genetic material is likely to be preserved in dry museum specimens, as reported previously for monkeypox virus genomes from historical orangutan specimens. Here, we screened 209 great ape museum specimens for 99 different DNA viruses, using hybridization capture coupled with short-read high-throughput sequencing. We determined the presence of multiple viruses within this dataset from historical specimens and obtained several near-complete viral genomes. In particular, we report high-coverage (> 18-fold) hepatitis B virus genomes from one gorilla and two chimpanzee individuals, which are phylogenetically placed within clades infecting the respective host species.

Keywords: Great apes; Hepatitis B virus; Museomics; Target-enrichment capture; Viruses.

Fig. 1

Distribution of sequencing reads per library. (A) Numbers of raw reads, reads after trimming and unique reads (after BBmap clumpify) across 214 libraries. (B) Percentage of reads per library assigned to Homo, Bacteria, or Viruses using Kraken2. We note that mapping great ape sequencing data to the human genome is commonly performed in genomic studies to avoid reference bias.

Fig. 2

Summaries of reads assigned to different virus domains and families. (A) Proportion of virus-assigned reads based on kraken2 across 214 libraries, stratified by realm and by family (for DNA viruses and Retroviridae). (B) Number of libraries with any read assigned to virus families. (C) Number of libraries with at least 25 reads assigned to virus families.

Fig. 3

Heatmap of positive reads per viral species. The figure depicts all libraries that have at least 25 hits assigned to one of the 99 viruses in the capture kit (with merged numbers for Cytomegalovirus strains).

Fig. 4

Maximum likelihood phylogeny of hepatitis B virus genomes obtained in this study, in the context of known viral diversity among great apes. The full HBV genomes were used, with a final SNPs alignment length of 4590 bp. The tree was rooted on a human hepatitis B strain, which serves as an outgroup. The colouring of the clades follows Fig. 3 in Locarnini et al., representing the geographical distribution of the great ape species. Samples newly sequenced in this study are marked in red.