Historical perspectives on great ape RNA viruses

In this project, we want to discover if RNA viruses were preserved in great ape specimens from museums. Great apes are our closest living relatives, but difficult to study in the wild. However, as our closest living relatives they are very interesting species to study, and they also did interact with humans in various ways over the past millions of years. One particular type of interactions was the exchange of germs, which is and has been a threat to both humans and other great ape species. Because of the close relationship and the fact that evolution of these pathogens happens in parallel to the evolution of their host species, germs that infect one species may easily infect another - they jump between host species. RNA viruses are a group of viruses to which the recently important virus SARS-CoV2 belongs. But also other viruses from mild to dangerous, like Influenza or Ebola, are RNA viruses. These viruses evolve quickly, much more so than other types of germs. As a consequence, even within the past 100 years some of them might have changed, some even disappearing, while others appeared more recently. Here, we want to find out if we can detect such viruses in museum specimens of great apes from the past 100 years. This is difficult, because these viruses use RNA for their genome, while other viruses and all other organisms (like bacteria, animals or plants) use the much more stable DNA. RNA decays much more rapidly than DNA, and it will be much more difficult to find in museum specimens. We want to try museum specimens of different sources and types, from different great ape species, and apply novel methods for RNA extraction and also for computational processing of the data. We want to either find old versions of the genomes of virus types that still exist, or new genomes of extinct virus types, and first of all, find out if any RNA viruses are preserved.

In this project, we aimed to discover if and how RNA viruses were preserved in great ape specimens from museums. Great apes are our closest living relatives and very interesting species to study, but difficult to study in the wild. An aspect which interested us in this project was one of the various ways of interaction with humans: the exchange of germs between species. We first analysed a dataset of more than 200 historical great ape specimens, stored in natural history collections, from which we extracted DNA. Sequencing the short and damaged molecules, we were able to reconstruct multiple virus genomes, in particular monkeypox and hepatitis viruses. Based on this experience, we designed experiments to find RNA viruses, which evolve quickly compared to other types of germs. Also, the RNA they use for their genome decays much more rapidly than DNA makes them much more difficult to study than DNA viruses. We collected historical specimens from great apes preserved in liquids such as alcohol, pieces of skin from pelts and other dry-preserved specimens, such as teeth. With laboratory protocols for RNA extraction, but in the more challenging setting of an ancient DNA laboratory, we searched for traces of RNA. As expected, many of these specimens did not have RNA preserved, but we still successfully found primate-like RNA in several of them. Although this is encouraging, the amount of virus RNA - if at all present, because it is not known if the individuals had any infections - is of course a small fraction of all molecules. Because virus genomes are very small, we could only find few RNA virus molecules in our dataset. Still, this means that even though the chances are small, such viruses can be studied from historical great apes. In a final step, we are trying to enrich for these virus fragments, with the hope to also find whole virus genomes.