Molecular biology of +RNA virus replication

Principal Investigator(s)

Dr. Martijn J. van HemertProf. Dr. Alexander E. Gorbalenya, Prof. Dr. Eric J. Snijder

SARS-CoV RdRpDescription of research

Positive-stranded RNA (+RNA) viruses, the largest group of viruses, are important pathogens of humans and animals. Their unconventional molecular biology includes an RNA genome that also serves as the mRNA for the expression of the viral replicative enzymes. The cytoplasmic replication of +RNA viruses can be explosive, with dramatic consequences for the architecture and functioning of the infected cell. Due to the relatively low fidelity of their RNA polymerase, +RNA viruses exhibit genetic variation and rapid evolution, allowing them to readily adapt to new circumstances and – for example - emerge as human pathogens. The MERS- and SARS-coronaviruses, the alphavirus Chikungunya virus, and the flavivirus Zika virus are prominent examples of such (re)emerging +RNA viruses with a serious impact on human health and society.
Our research focuses on the in-depth molecular biological and biochemical dissection of +RNA virus replication, and on the functional characterization of viral enzymes in particular. Using biochemical and molecular biological approaches, bioinformatics, and advanced electron microscopy, we aim to increase our understanding of +RNA virus replication and evolution. This will facilitate the development of strategies to combat these pathogens, for example by identifying inhibitors of virus replication or improving the technology  to develop +RNA virus-based vaccine vectors.

Research Topics

  • +RNA virus replication and evolution
  • Structure and function of +RNA virus enzymes
  • Host factors involved in +RNA virus replication
  • +RNA virus reverse genetics and expression vectors

Key publications

  • The enzymatic activity of the nsp14 exoribonuclease is critical for replication of MERS-CoV and SARS-CoV-2. Natacha S. Ogando, Jessika C. Zevenhoven-Dobbe, Yvonne van der Meer, Peter J. Bredenbeek, Clara C. Posthuma, Eric J. Snijder. Online 16 September 2020 J. Virol. doi:10.1128/JVI.01246-20
  • SARS-coronavirus-2 replication in Vero E6 cells: replication kinetics, rapid adaptation and cytopathology. Ogando NS, Dalebout TJ, Zevenhoven-Dobbe JC, Limpens RWAL, van der Meer Y, Caly L, Druce J, de Vries JJC, Kikkert M, Bárcena M, Sidorov I, Snijder EJ. J Gen Virol. 2020 Jun 22. doi: 10.1099/jgv.0.001453.

  • Alisporivir inhibits MERS- and SARS-coronavirus replication in cell culture, but not SARS-coronavirus infection in a mouse model. de Wilde AH, Falzarano D, Zevenhoven-Dobbe JC, Beugeling C, Fett C, Martellaro C, Posthuma CC, Feldmann H, Perlman S, Snijder EJ. Virus Res. 2017 Jan 15;228:7-13. doi: 10.1016/j.virusres.2016.11.011.
  • Host Factors in Coronavirus Replication. de Wilde AH, Snijder EJ, Kikkert M, van Hemert MJ. Curr Top Microbiol Immunol. 2018;419:1-42. doi: 10.1007/82_2017_25.
  • Coronaviruses and arteriviruses display striking differences in their cyclophilin A-dependence during replication in cell culture. de Wilde AH, Zevenhoven-Dobbe JC, Beugeling C, Chatterji U, de Jong D, Gallay P, Szuhai K, Posthuma CC, Snijder EJ. Virology. 2018 Apr;517:148-156. doi: 10.1016/j.virol.2017.11.022.
  • Mechanism and structural diversity of exoribonuclease-resistant RNA structures in flaviviral RNAs. MacFadden A, O'Donoghue Z, Silva PAGC, Chapman EG, Olsthoorn RC, Sterken MG, Pijlman GP, Bredenbeek PJ, Kieft JS. Nat Commun. 2018 Jan 9;9(1):119.
  • Purification of highly active alphavirus replication complexes demonstrates altered fractionation of multiple cellular membranes. Pietilä MK, van Hemert MJ, Ahola T. J Virol. 2018 Jan 24. pii: JVI.01852-17. 
  • Suramin inhibits Zika virus replication by interfering with virus attachment and release of infectious particles. Albulescu IC, Kovacikova K, Tas A, Snijder EJ, van Hemert MJ. Antiviral Res. 2017 Jul;143:230-236. 
  • Domain Organization and evolution of the highly divergent 5' coding region of genomes of arteriviruses, including the novel possum nidovirus. Gulyaeva A, Dunowska M, Hoogendoorn E, Giles J, Samborskiy D, Gorbalenya AE. J Virol. 2017 Feb 28;91(6).  
  • Nidovirus RNA polymerases: Complex enzymes handling exceptional RNA genomes. Posthuma CC, Te Velthuis AJW, Snijder EJ. Virus Res. 2017 Apr 15;234:58-73.  
  • Mutations in encephalomyocarditis virus 3A protein uncouple the dependency of genome replication on host factors phosphatidylinositol 4-kinase IIIα and oxysterol-binding protein. Dorobantu CM, Albulescu L, Lyoo H, van Kampen M, De Francesco R, Lohmann V, Harak C, van der Schaar HM, Strating JR, Gorbalenya AE, van Kuppeveld FJ. mSphere. 2016 May 11;1(3)
  • A novel role for poly(C) binding proteins in programmed ribosomal frameshifting. Napthine S, Treffers EE, Bell S, Goodfellow I, Fang Y, Firth AE, Snijder EJ, Brierley I. Nucleic Acids Res. 2016 Jul 8;44(12):5491-503
  • 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 Sep 30;43(17):8416-34.  
  • A Kinome-Wide small Interfering RNA screen identifies proviral and antiviral host factors in Severe Acute Respiratory Syndrome coronavirus replication, including double-stranded RNA-activated protein kinase and early secretory pathway proteins. de Wilde AH, Wannee KF, Scholte FE, Goeman JJ, Ten Dijke P, Snijder EJ, Kikkert M, van Hemert MJ. J Virol. 2015 Aug;89(16):8318-33.  
  • Stress granule components G3BP1 and G3BP2 play a proviral role early in Chikungunya virus replication. Scholte FE, Tas A, Albulescu IC, Žusinaite E, Merits A, Snijder EJ, van Hemert MJ. J Virol. 2015 Apr;89(8):4457-69
  • One severe acute respiratory syndrome coronavirus protein complex integrates processive RNA polymerase and exonuclease activities. Subissi L, Posthuma CC, Collet A, Zevenhoven-Dobbe JC, Gorbalenya AE, Decroly E, Snijder EJ, Canard B, Imbert I. Proc Natl Acad Sci U S A. 2014 Sep 16;111(37):E3900-9.
  • Transactivation of programmed ribosomal frameshifting by a viral protein. Li Y, Treffers EE, Napthine S, Tas A, Zhu L, Sun Z, Bell S, Mark BL, van Veelen PA, van Hemert MJ, Firth AE, Brierley I, Snijder EJ, Fang Y. Proc Natl Acad Sci U S A. 2014 May 27;111(21):E2172-81.
  • Structural basis for the regulatory function of a complex zinc-binding domain in a replicative arterivirus helicase resembling a nonsense-mediated mRNA decay helicase. Deng Z, Lehmann KC, Li X, Feng C, Wang G, Zhang Q, Qi X, Yu L, Zhang X, Feng W, Wu W, Gong P, Tao Y, Posthuma CC, Snijder EJ, Gorbalenya AE, Chen Z. Nucleic Acids Res. 2014; 42:3464-77.
  • MERS-coronavirus replication induces severe in vitro cytopathology and is strongly inhibited by cyclosporin A or interferon-a treatment. de Wilde AH, Raj VS, Oudshoorn D, Bestebroer TM, van Nieuwkoop S, Limpens RW, Posthuma CC, van der Meer Y, Bárcena M, Haagmans BL, Snijder EJ, van den Hoogen BG. J Gen Virol. 2013; 94:1749-60.
  • Genomic characterization of a newly discovered coronavirus associated with acute respiratory distress syndrome in humans. van Boheemen S, de Graaf M, Lauber C, Bestebroer TM, Raj VS, Zaki AM, Osterhaus AD, Haagmans BL, Gorbalenya AE, Snijder EJ, Fouchier RA. mBio. 2012; 3:e00473-12