Project Reference: TRG27-ZOO-CS1

Project title: Ancient Viral Genomics and Human Adaptation: Reconstructing Host–Pathogen Co-evolution in Medieval Britain

Project outline

Ancient DNA research has transformed our understanding of past human infectious diseases; however, viruses are poorly understood compared to bacteria. This project will investigate co-evolution of humans and viruses in Britain by analysing ancient DNA and proteins recovered from archaeological human remains.

The aim is to understand how viruses have changed through time and whether they have left detectable selection signatures in the human genome. The student will also explore how past disease exposure may have influenced the evolution of immune-related genes in human populations.

The project has three main objectives. First, the student will identify and characterise ancient viral DNA from archaeological samples dating from the early medieval through post-medieval periods. Second, they will reconstruct viral genomes and compare them with modern viral diversity to investigate how viruses have evolved through time. Third, they will analyse human genomic data from the same individuals to test whether genetic variants involved in immune function show evidence of adaptation associated with historical viral exposure.

The research will involve laboratory-based ancient DNA extraction, capture and sequencing, followed by computational analyses of both human and viral genomes. The student will use bioinformatic and statistical approaches to identify viral sequences, reconstruct evolutionary relationships, and investigate patterns of genetic variation in human immune genes. Archaeological and historical information will be integrated to place the genomic findings in their broader social and environmental context. Palaeoproteomic analyses offer the possibility of detecting RNA viruses in ancient remains, a significant but almost entirely unstudied class of human and animal pathogens. This interdisciplinary project will provide training in molecular biology, genomics, bioinformatics, evolutionary biology, and infectious disease research.

Principal Supervisor

Dr Christiana Scheib

Email address: cls83@cam.ac.uk

Department / Partner Institute: Zoology

Website: https://www.zoo.cam.ac.uk/people/christiana-scheib

BBSRC strategic theme

Bioscience for an integrated understanding of health