Apurahat ja residenssipaikat

Tiede

Persistence and evolution of ancient DNA viruses in the Americas

Hakemuksen tiivistelmä

It is known that several DNA viruses persist in the body years or even decades after primary infection. Although this finding is of great relevance to explore the record of viral infections in an individual, it was not until recently that studies of viral evolution acquired a whole new dimension by incorporating ancient viral genomes of great antiquity. In a global context, novel DNA viral sequences from the Americas are non-existent, which does not allow to obtain a comprehensive picture of the whole diversity and handicaps the interpretation of the directionality of the viral infections. For instance, one interesting hypothesis to evaluate is whether certain viruses, e.g. variola, existed in the Americas prior to European colonization and the evolutionary trajectories of viruses before and after transatlantic contact. We aim to understand the origin, adaptation and evolution of DNA viruses by analyzing ancient genomes from a 900-year transect (700 – 1600 CE) which includes ~100 samples from both pre- and post-Columbian Peru, while including also worldwide reference datasets from published sources. We will utilize cutting-edge NGS technologies and computational methods to assure the authenticity of the ancient genetic material. Phylogenetic reconstructions of novel and published viral strains will be carried out with various tools freely available online. During this two-year project we aim to produce at least two scientific articles related to topics on ancient virus persistence and virus evolution. Since no ancient viral genomes from the Americas exist in the literature, this research also aims to fill in this gap and as such it is a bold initiative that will draw great interest from the scientific community and the general public alike. Our local and international collaborators are top scientists in the fields of ancient human DNA and ancient viruses, which will guarantee the success of the project and the quality of the results.

During the past few years, the study of persistent human DNA viruses from both soft and hard tissues has gained great importance. The identification and abundance assessment of these viruses facilitate the investigation of viral tissue tropism, evolution, fitness and also disease association. In this context, our research focuses on the persistence and evolution of DNA viruses in humans. This rich information allows us to evaluate relevant questions about the origin, evolution and spread of viruses and other microbes across the globe.

It is known that several human DNA viruses persist in the body years or even decades after primary infection, enabling the study of ancient substrates from different time and population cohorts. For this research, we assembled a collection of over 200 human samples from a ~3400-year transect with the aim to recover genomic traces from these viruses and other ancient pathogens. The questions we address are numerous, including how these microbes emerged and colonized certain regions of the world as well as how they evolved in certain environmental settings. To date we have been able to produce two scientific articles, one focusing on the evolution of Plasmodium vivax on a global scale, where data from our native American samples provide support for the introduction of this particular pathogen into the Americas at the time of European contact (~1532 CE). Our second publication highlights the evolution of Treponema pallidum in the Americas, where it likely originated. In addition to these publications, we have also detected 42 different viral genomes (including e.g. B19V, polyoma viruses, hepatitis B, herpes virus, variola virus) in a subset of our samples. Currently, we are preparing a third publication with focus only on Merkel polyoma virus (MCPyV) evolution, a virus implicated in a rare but aggressive skin cancer known as Merkel cell Carcinoma (MCC). Even though our research has advanced substantially, our work is still ongoing.

Takaisin apurahalistaukseen