Bioinformatics and virus evolution

Principal investigator(s)

Prof. Dr. Alexander E. Gorbalenya

Sequence alignmentDescription of the research

Humans suffer from different diseases caused by viruses that range from common cold to fatal. However, virus infection may also go silent or be beneficial to host. The ability to evolve very fast is the key to both the pathogenicity and the remarkable adaptability of viruses to different hosts. Enormous scale of the natural virus diversity is the biggest challenge in our quest for understanding of how the virus universe evolved and how viruses adapt, and to control virus infections. We pursue these goals by applying bioinformatics to genomic sequences which are the most reliable, comprehensive, and up-to-the-date source of information about viruses. We develop and employ genomics-based computational approaches to differentiate and classify viruses, and to gain insight into function, structure, and evolution of viruses. Results of these analyses guide experimental studies and facilitate development of virus diagnostics and antivirals, often conducted through fruitful collaboration.

Research topics

  • Origin, evolution and adaptation of RNA and DNA viruses
  • Evolution and molecular mechanisms of genome replication and expression
  • Classification of viruses
  • Hunting for new human and other animal RNA and DNA viruses
  • Software developing for virus genome data management, analysis and integration

Key publications

  • A planarian nidovirus expands the limits of RNA genome size. Saberi A, Gulyaeva AA, Brubacher JL, Newmark PA, Gorbalenya AE. PLoS Pathogens 2018, 14: e1007314.
  • Domain organization and evolution of the highly divergent 5’ coding region of genomes of arteriviruses including the novel possum nidovirus. Gulyaeva AA, Dunowska M, Hoogendoorn E, Giles J, Samborskiy DV, Gorbalenya AE. J. Virol. 2017; 91 (6): e02096-16.
  • Discovery of an essential nucleotidylating activity associated with a newly delineated conserved domain in the RNA polymerase-containing protein of all nidoviruses. Lehmann KC, Gulyaeva A, Zevenhoven-Dobbe JC, Janssen GM, Ruben M, Overkleeft HS, van Veelen PA, Samborskiy DV, Kravchenko AA, Leontovich AM, Sidorov IA, Snijder EJ, Posthuma CC, Gorbalenya AE. Nucleic Acids Res. 2015; 43:8416-34
  • Interspecific adaptation by binary choice at de novo polyomavirus T antigen site through accelerated codon-constrained Val-Ala toggling within an intrinsically disordered region. Lauber C, Kazem S, Kravchenko AA, Feltkamp MC, Gorbalenya AE. Nucleic Acids Res. 2015 May 26;43(10):4800-13.
  • The footprint of genome architecture in the largest genome expansion in RNA viruses. Lauber C, Goeman JJ, Parquet Mdel C, Thi Nga P, Snijder EJ, Morita K, Gorbalenya AE. PLoS Pathog. 2013; 9(7):e1003500.
  • Toward genetics-based virus taxonomy: comparative analysis of a genetics-based classification and the taxonomy of picornaviruses. Lauber C, Gorbalenya AE. J Virol. 2012; 86(7):3905-15.
  • Practical application of bioinformatics by the multidisciplinary VIZIER consortium. Gorbalenya AE, Lieutaud P, Harris MR, Coutard B, Canard B, Kleywegt GJ, Kravchenko AA, Samborskiy DV, Sidorov IA, Leontovich AM, Jones TA. Antiviral Res. 2010; 87:95-110.
  • Evidence for emergence of diverse polioviruses from C-cluster coxsackie A viruses and implications for global poliovirus eradication. Jiang P, Faase JA, Toyoda H, Paul A, Wimmer E, Gorbalenya AE. Proc Natl Acad Sci USA. 2007; 104:9457-62.

naar boven

Research team

  • Prof. dr. Alexander Gorbalenya - PI
  • Dr. Igor Sidorov - Senior researcher 
  • Anastasia Gulyaeva – PhD student

External Funding

  • EU H2020 project EVAg (project 653316)
  • EU H2020 project ZIKAlliance (project 734548)

     Completed

  • EU FP7 project SILVER (project 260644)
  • EU FP7-Marie Curie Initial Training Network EUVIRNA (project 264286)
  • EU FP6 project VIZIER (project 511960)
  • EU FP6 project GRACE (project 518226)
  • EU FP6 project SARS-DTV (project 511064)
  • NBIC BioRange

PhD Theses

Awards