AG Jones - Computational virology, ancient viruses, virus evolution, virus discovery, virus ecology, computational virus diagnostics

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Research focus

Our overall aim is to help to make computational analysis an everyday part of virus research. A good historical analogue is the history of the development and use of the microscope. The microscopic world was unknown and unsuspected prior to the invention of the microscope in the 17th century. The microscope opened a vast realm of biology to human enquiry, though of course access to the technology and technical expertise developed only gradually. With the rise of both increasingly inexpensive genetic sequencing and computational power we are in a similar position today. Computer algorithms can be used as a kind of microscope for data. The amount of data available and becoming available far exceeds the number of people with computational expertise working in the biological sciences. It is still early days, but this situation has begun to change and we can anticipate a future in which virologists are as well trained computationally as they are in the laboratory. Our group is focussed on applying computational tools to virology and also on the broader issue of helping the Institute of Virology and also the wider virology community to become more computational.

Our recent research has primarily been in the area of examining ancient DNA data for viruses, resulting in finds of hepatitis B virus and human parvovirus B19. We have also analyzed many next-generation datasets both for the purpose of general virus screening and with specific hypotheses. We have begun the process of sequencing and analyzing the large (about half a million) collection of frozen samples that institute researchers and collaborators have gathered in the field over the last 15 years. We are also involved in the analysis of human diagnostic cases from the Charité hospital when viral infections are suspected. We have also worked on the design and development of an algorithm for Virus discovery based on predicted secondary structure. This is an attempt to identify so-called genetic “dark matter”, i.e., sequencing data from viruses with conserved structural elements but whose genomes are too different at the nucleotide or amino acid levels to match databases of known viruses.

Collaborations

  • Prof. Derek Smith, University of Cambridge.
  • Prof. Eske Willerslev, Lundbeck Centre for GeoGenetics in Copenhagen and the University of Cambridge.
  • Prof. Ron Fouchier, Erasmus Medical Centre, Rotterdam.
  • Prof. Peter Simmonds, Nuffield Department of Medicine, University of Oxford.
  • Prof. Dieter Glebe, Justus-Liebig University of Giessen.
  • Berlin Museum of Medical History at Charité.

Significant publications

A complete list of publications can be found at Google Scholar.   

Selected publications:

Ancient hepatitis B viruses from the Bronze Age to the Medieval period. https://www.nature.com/articles/s41586-018-0097-z

Ancient human parvovirus B19 in Eurasia reveals its long-term association with humans. https://www.pnas.org/content/115/29/7557.short