pp 1-31 | Cite as

Molecular Virology of Chikungunya Virus

  • I. FrolovEmail author
  • E. I. Frolova
Part of the Current Topics in Microbiology and Immunology book series


Chikungunya virus (CHIKV) was discovered more than six decades ago, but has remained poorly investigated. However, after a recent outbreak of CHIK fever in both hemispheres and viral adaptation to new species of mosquitoes, it has attracted a lot of attention. The currently available experimental data suggest that molecular mechanisms of CHIKV replication in vertebrate and mosquito cells are similar to those of other New and Old World alphaviruses. However, this virus exhibits a number of unique characteristics that distinguish it from the other, better studied members of the alphavirus genus. This review is an attempt to summarize the data accumulated thus far regarding the molecular mechanisms of alphavirus RNA replication and interaction with host cells. Emphasis was placed on demonstrating the distinct features of CHIKV in utilizing host factors to build replication complexes and modify the intracellular environment for efficient viral replication and inhibition of the innate immune response. The available data suggest that our knowledge about alphavirus replication contains numerous gaps that potentially hamper the development of new therapeutic means against CHIKV and other pathogenic alphaviruses.


  1. Abraham R, Hauer D, McPherson RL, Utt A, Kirby IT, Cohen MS, Merits A, Leung AKL, Griffin DE (2018) ADP-ribosyl-binding and hydrolase activities of the alphavirus nsP3 macrodomain are critical for initiation of virus replication. Proc Natl Acad Sci U S A 115 (44):E10457–E10466. Google Scholar
  2. Ahola T, Kaariainen L (1995) Reaction in alphavirus mRNA capping: formation of a covalent complex of nonstructural protein nsP1 with 7-methyl-GMP. Proc Natl Acad Sci U S A 92 (2):507–511Google Scholar
  3. Ahola T, Laakkonen P, Vihinen H, Kaariainen L (1997) Critical residues of Semliki Forest virus RNA capping enzyme involved in methyltransferase and guanylyltransferase-like activities. J Virol 71(1):392–397Google Scholar
  4. Akhrymuk I, Frolov I, Frolova EI (2016) Both RIG-I and MDA5 detect alphavirus replication in concentration-dependent mode. Virology 487:230–241. CrossRefGoogle Scholar
  5. Akhrymuk I, Frolov I, Frolova EI (2018a) Sindbis Virus Infection Causes Cell Death by nsP2-Induced Transcriptional Shutoff or by nsP3-Dependent Translational Shutoff. J Virol 92(23):e01388. CrossRefGoogle Scholar
  6. Akhrymuk I, Kulemzin SV, Frolova EI (2012) Evasion of the innate immune response: the Old World alphavirus nsP2 protein induces rapid degradation of Rpb1, a catalytic subunit of RNA polymerase II. J Virol 86(13):7180–7191. CrossRefGoogle Scholar
  7. Akhrymuk I, Lukash T, Frolov I, Frolova EI (2018b) Novel mutations in nsP2 abolish chikungunya virus-induced transcriptional shutoff and make virus less cytopathic without affecting its replication rates. J Virol.
  8. Atasheva S, Gorchakov R, English R, Frolov I, Frolova E (2007) Development of Sindbis viruses encoding nsP2/GFP chimeric proteins and their application for studying nsP2 functioning. J Virol 81(10):5046–5057. (JVI.02746-06 [pii])CrossRefGoogle Scholar
  9. Blair CD (2011) Mosquito RNAi is the major innate immune pathway controlling arbovirus infection and transmission. Future Microbiol 6(3):265–277. CrossRefGoogle Scholar
  10. Chen R, Wang E, Tsetsarkin KA, Weaver SC (2013) Chikungunya virus 3′ untranslated region: adaptation to mosquitoes and a population bottleneck as major evolutionary forces. PLoS Pathog 9(8):e1003591. (PPATHOGENS-D-13-01023 [pii])CrossRefGoogle Scholar
  11. Cristea IM, Carroll JW, Rout MP, Rice CM, Chait BT, MacDonald MR (2006) Tracking and elucidating alphavirus-host protein interactions. J Biol Chem 281(40):30269–30278. CrossRefGoogle Scholar
  12. Cristea IM, Rozjabek H, Molloy KR, Karki S, White LL, Rice CM, Rout MP, Chait BT, MacDonald MR (2010) Host factors associated with the Sindbis virus RNA-dependent RNA polymerase: role for G3BP1 and G3BP2 in virus replication. J Virol 84(13):6720–6732. CrossRefGoogle Scholar
  13. Das PK, Merits A, Lulla A (2014) Functional cross-talk between distant domains of chikungunya virus non-structural protein 2 is decisive for its RNA-modulating activity. J Biol Chem 289(9):5635–5653. CrossRefGoogle Scholar
  14. de Groot RJ, Rümenapf T, Kuhn RJ, Strauss EG, Strauss JH (1991) Sindbis virus RNA polymerase is degraded by the N-end rule pathway. Proc Natl Acad Sci USA 88:8967–8971Google Scholar
  15. Dryga SA, Dryga OA, Schlesinger S (1997) Identification of mutations in a Sindbis virus variant able to establish persistent infection in BHK cells: The importance of a mutation in the nsP2 gene. Virology 228:72–83Google Scholar
  16. Eckei L, Krieg S, Butepage M, Lehmann A, Gross A, Lippok B, Grimm AR, Kummerer BM, Rossetti G, Luscher B, Verheugd P (2017) The conserved macrodomains of the non-structural proteins of Chikungunya virus and other pathogenic positive strand RNA viruses function as mono-ADP-ribosylhydrolases. Sci Rep 7:41746. CrossRefGoogle Scholar
  17. Egloff MP, Malet H, Putics A, Heinonen M, Dutartre H, Frangeul A, Gruez A, Campanacci V, Cambillau C, Ziebuhr J, Ahola T, Canard B (2006) Structural and functional basis for ADP-ribose and poly(ADP-ribose) binding by viral macro domains. J Virol 80(17):8493–8502. (80/17/8493 [pii])CrossRefGoogle Scholar
  18. Fayzulin R, Frolov I (2004) Changes of the secondary structure of the 5′ end of the Sindbis virus genome inhibit virus growth in mosquito cells and lead to accumulation of adaptive mutations. J Virol 78(10):4953–4964Google Scholar
  19. Foy NJ, Akhrymuk M, Akhrymuk I, Atasheva S, Bopda-Waffo A, Frolov I, Frolova EI (2013a) Hypervariable domains of nsP3 proteins of New World and Old World alphaviruses mediate formation of distinct, virus-specific protein complexes. J Virol 87(4):1997–2010. CrossRefGoogle Scholar
  20. Foy NJ, Akhrymuk M, Shustov AV, Frolova EI, Frolov I (2013b) Hypervariable domain of nonstructural protein nsP3 of Venezuelan equine encephalitis virus determines cell-specific mode of virus replication. J Virol 87(13):7569–7584. CrossRefGoogle Scholar
  21. Friedman RM, Levin JG, Grimley PM, Berezesky IK (1972) Membrane-associated replication complex in arbovirus infection. J Virol 10(3):504–515Google Scholar
  22. Frolov I, Agapov E, Hoffman TA Jr, Prágai BM, Lippa M, Schlesinger S, Rice CM (1999) Selection of RNA replicons capable of persistent noncytopathic replication in mammalian cells. J Virol 73:3854–3865Google Scholar
  23. Frolov I, Akhrymuk M, Akhrymuk I, Atasheva S, Frolova EI (2012) Early events in alphavirus replication determine the outcome of infection. J Virol 86(9):5055–5066. CrossRefGoogle Scholar
  24. Frolov I, Garmashova N, Atasheva S, Frolova EI (2009) Random insertion mutagenesis of sindbis virus nonstructural protein 2 and selection of variants incapable of downregulating cellular transcription. J Virol 83(18):9031–9044. CrossRefGoogle Scholar
  25. Frolov I, Hardy R, Rice CM (2001) Cis-acting RNA elements at the 5′ end of Sindbis virus genome RNA regulate minus- and plus-strand RNA synthesis. RNA 7(11):1638–1651Google Scholar
  26. Frolov I, Hoffman TA, Prágai BM, Dryga SA, Huang HV, Schlesinger S, Rice CM (1996) Alphavirus-based expression systems: strategies and applications. Proc Natl Acad Sci U S A 93:11371–11377Google Scholar
  27. Frolov I, Kim DY, Akhrymuk M, Mobley JA, Frolova EI (2017) Hypervariable Domain of Eastern Equine Encephalitis Virus nsP3 Redundantly Utilizes Multiple Cellular Proteins for Replication Complex Assembly. J Virol 91(14):e00371–00317.
  28. Frolov I, Schlesinger S (1994) Comparison of the effects of Sindbis virus and Sindbis virus replicons on host cell protein synthesis and cytopathogenicity in BHK cells. J Virol 68:1721–1727Google Scholar
  29. Frolova E, Frolov I, Schlesinger S (1997) Packaging signals in alphaviruses. J Virol 71(1):248–258Google Scholar
  30. Frolova E, Gorchakov R, Garmashova N, Atasheva S, Vergara LA, Frolov I (2006) Formation of nsP3-specific protein complexes during Sindbis virus replication. J Virol 80(8):4122–4134. CrossRefGoogle Scholar
  31. Frolova EI, Fayzulin RZ, Cook SH, Griffin DE, Rice CM, Frolov I (2002) Roles of nonstructural protein nsP2 and Alpha/Beta interferons in determining the outcome of Sindbis virus infection. J Virol 76(22):11254–11264Google Scholar
  32. Frolova EI, Gorchakov R, Pereboeva L, Atasheva S, Frolov I (2010) Functional Sindbis virus replicative complexes are formed at the plasma membrane. J Virol 84(22):11679–11695. CrossRefGoogle Scholar
  33. Fros JJ, Domeradzka NE, Baggen J, Geertsema C, Flipse J, Vlak JM, Pijlman GP (2012) Chikungunya virus nsP3 blocks stress granule assembly by recruitment of G3BP into cytoplasmic foci. J Virol 86(19):10873–10879. CrossRefGoogle Scholar
  34. Fros JJ, Geertsema C, Zouache K, Baggen J, Domeradzka N, van Leeuwen DM, Flipse J, Vlak JM, Failloux AB, Pijlman GP (2015) Mosquito Rasputin interacts with chikungunya virus nsP3 and determines the infection rate in Aedes albopictus. Parasit Vectors 8:464. (1186/s13071-015-1070-4 [pii])CrossRefGoogle Scholar
  35. Fros JJ, Liu WJ, Prow NA, Geertsema C, Ligtenberg M, Vanlandingham DL, Schnettler E, Vlak JM, Suhrbier A, Khromykh AA, Pijlman GP (2010) Chikungunya virus nonstructural protein 2 inhibits type I/II interferon-stimulated JAK-STAT signaling. J Virol 84(20):10877–10887. CrossRefGoogle Scholar
  36. Fros JJ, van der Maten E, Vlak JM, Pijlman GP (2013) The C-terminal domain of chikungunya virus nsP2 independently governs viral RNA replication, cytopathicity, and inhibition of interferon signaling. J Virol 87(18):10394–10400. CrossRefGoogle Scholar
  37. Froshauer S, Kartenbeck J, Helenius A (1988) Alphavirus RNA replicase is located on the cytoplasmic surface of endosomes and lysosomes. J Cell Biol 107(6 Pt 1):2075–2086Google Scholar
  38. Garmashova N, Gorchakov R, Frolova E, Frolov I (2006) Sindbis virus nonstructural protein nsP2 is cytotoxic and inhibits cellular transcription. J Virol 80(12):5686–5696. CrossRefGoogle Scholar
  39. Garmashova N, Gorchakov R, Volkova E, Paessler S, Frolova E, Frolov I (2007) The Old World and New World alphaviruses use different virus-specific proteins for induction of transcriptional shutoff. J Virol 81(5):2472–2484. CrossRefGoogle Scholar
  40. Gomez de Cedron M, Ehsani N, Mikkola ML, Garcia JA, Kaariainen L (1999) RNA helicase activity of Semliki Forest virus replicase protein NSP2. FEBS Lett 448(1):19–22Google Scholar
  41. Gorbalenya AE, Koonin EV, Donchenko AP, Blinov VM (1989) Two related superfamilies of putative helicases involved in replication, recombination, repair and expression of DNA and RNA genomes. Nucleic Acids Res 17(12):4713–4729Google Scholar
  42. Gorchakov R, Frolova E, Sawicki S, Atasheva S, Sawicki D, Frolov I (2008a) A new role for ns polyprotein cleavage in Sindbis virus replication. J Virol 82(13):6218–6231. CrossRefGoogle Scholar
  43. Gorchakov R, Garmashova N, Frolova E, Frolov I (2008b) Different types of nsP3-containing protein complexes in Sindbis virus-infected cells. J Virol 82(20):10088–10101. CrossRefGoogle Scholar
  44. Gorchakov R, Hardy R, Rice CM, Frolov I (2004) Selection of functional 5′ cis-acting elements promoting efficient sindbis virus genome replication. J Virol 78(1):61–75Google Scholar
  45. Grakoui A, Levis R, Raju R, Huang HV, Rice CM (1989) A cis-acting mutation in the Sindbis virus junction region which affects subgenomic RNA synthesis. J Virol 63:5216–5227Google Scholar
  46. Grimley PM, Berezesky IK, Friedman RM (1968) Cytoplasmic structures associated with an arbovirus infection: loci of viral ribonucleic acid synthesis. J Virol 2(11):1326–1338Google Scholar
  47. Grimley PM, Levin JG, Berezesky IK, Friedman RM (1972) Specific membranous structures associated with the replication of Group A arboviruses. J Virol 10:492–503Google Scholar
  48. Hallengard D, Kakoulidou M, Lulla A, Kummerer BM, Johansson DX, Mutso M, Lulla V, Fazakerley JK, Roques P, Le Grand R, Merits A, Liljestrom P (2014) Novel attenuated Chikungunya vaccine candidates elicit protective immunity in C57BL/6 mice. J Virol 88(5):2858–2866. (JVI.03453-13 [pii])CrossRefGoogle Scholar
  49. Hardy WR, Strauss JH (1989) Processing the nonstructural proteins of Sindbis virus: nonstructural proteinase is in the C-terminal half of nsP2 and functions both in cis and trans. J Virol 63:4653–4664Google Scholar
  50. Hyde JL, Gardner CL, Kimura T, White JP, Liu G, Trobaugh DW, Huang C, Tonelli M, Paessler S, Takeda K, Klimstra WB, Amarasinghe GK, Diamond MS (2014) A viral RNA structural element alters host recognition of nonself RNA. Science 343(6172):783–787. CrossRefGoogle Scholar
  51. Jones PH, Maric M, Madison MN, Maury W, Roller RJ, Okeoma CM (2013) BST-2/tetherin-mediated restriction of chikungunya (CHIKV) VLP budding is counteracted by CHIKV non-structural protein 1 (nsP1). Virology 438(1):37–49. CrossRefGoogle Scholar
  52. Kallio K, Hellstrom K, Balistreri G, Spuul P, Jokitalo E, Ahola T (2013) Template RNA length determines the size of replication complex spherules for Semliki Forest virus. J Virol 87(16):9125–9134. CrossRefGoogle Scholar
  53. Karpe YA, Aher PP, Lole KS (2011) NTPase and 5′-RNA triphosphatase activities of Chikungunya virus nsP2 protein. PLoS ONE 6(7):e22336. (PONE-D-11-04866 [pii])CrossRefGoogle Scholar
  54. Khan AH, Morita K, Parquet Md Mdel C, Hasebe F, Mathenge EG, Igarashi A (2002) Complete nucleotide sequence of chikungunya virus and evidence for an internal polyadenylation site. J Gen Virol 83(Pt 12):3075–3084. Google Scholar
  55. Kim DY, Atasheva S, Foy NJ, Wang E, Frolova EI, Weaver S, Frolov I (2011a) Design of chimeric alphaviruses with a programmed, attenuated, cell type-restricted phenotype. J Virol 85(9):4363–4376. CrossRefGoogle Scholar
  56. Kim DY, Firth AE, Atasheva S, Frolova EI, Frolov I (2011b) Conservation of a packaging signal and the viral genome RNA packaging mechanism in alphavirus evolution. J Virol 85(16):8022–8036. CrossRefGoogle Scholar
  57. Kim DY, Reynaud JM, Rasalouskaya A, Akhrymuk I, Mobley JA, Frolov I, Frolova EI (2016) New World and old world alphaviruses have evolved to exploit different components of stress granules, FXR and G3BP proteins, for assembly of viral replication complexes. PLoS Pathog 12(8):e1005810. CrossRefGoogle Scholar
  58. Kim KH, Rumenapf T, Strauss EG, Strauss JH (2004) Regulation of Semliki Forest virus RNA replication: a model for the control of alphavirus pathogenesis in invertebrate hosts. Virology 323(1):153–163Google Scholar
  59. Kristensen O (2015) Crystal structure of the G3BP2 NTF2-like domain in complex with a canonical FGDF motif peptide. Biochem Biophys Res Commun 467(1):53–57. (S0006-291X(15)30640-9 [pii])CrossRefGoogle Scholar
  60. Kuhn RJ, Hong Z, Strauss JH (1990) Mutagenesis of 3′ nontranslated region of Sindbis virus RNA. J Virol 64:1465–1476Google Scholar
  61. Kuhn RJ, Niesters HGM, Hong Z, Strauss JH (1991) Infectious RNA transcripts from Ross River virus cDNA clones and the construction and characterization of defined chimeras with Sindbis virus. Virology 182:430–441Google Scholar
  62. Kujala P, Ikaheimonen A, Ehsani N, Vihinen H, Auvinen P, Kaariainen L (2001) Biogenesis of the Semliki Forest virus RNA replication complex. J Virol 75(8):3873–3884Google Scholar
  63. Kujala P, Rikkonen M, Ahola T, Kelve M, Saarma M, Kaariainen L (1997) Monoclonal antibodies specific for Semliki Forest virus replicase protein nsP2. J Gen Virol 78(Pt 2):343–351Google Scholar
  64. Kulasegaran-Shylini R, Atasheva S, Gorenstein DG, Frolov I (2009a) Structural and functional elements of the promoter encoded by the 5′ untranslated region of the Venezuelan equine encephalitis virus genome. J Virol 83(17):8327–8339Google Scholar
  65. Kulasegaran-Shylini R, Thiviyanathan V, Gorenstein DG, Frolov I (2009b) The 5′UTR-specific mutation in VEEV TC-83 genome has a strong effect on RNA replication and subgenomic RNA synthesis, but not on translation of the encoded proteins. Virology 387(1):211–221Google Scholar
  66. Kumar P, Sweeney TR, Skabkin MA, Skabkina OV, Hellen CU, Pestova TV (2014) Inhibition of translation by IFIT family members is determined by their ability to interact selectively with the 5′-terminal regions of cap0-, cap1- and 5′ppp- mRNAs. Nucleic Acids Res 42(5):3228–3245. (gkt1321 [pii])CrossRefGoogle Scholar
  67. Laakkonen P, Auvinen P, Kujala P, Kaariainen L (1998) Alphavirus replicase protein NSP1 induces filopodia and rearrangement of actin filaments. J Virol 72(12):10265–10269Google Scholar
  68. Langsjoen RM, Rubinstein RJ, Kautz TF, Auguste AJ, Erasmus JH, Kiaty-Figueroa L, Gerhardt R, Lin D, Hari KL, Jain R, Ruiz N, Muruato AE, Silfa J, Bido F, Dacso M, Weaver SC (2016) Molecular virologic and clinical characteristics of a Chikungunya Fever Outbreak in La Romana, Dominican Republic, 2014. PLoS Negl Trop Dis 10(12):e0005189. (PNTD-D-16-00891 [pii])CrossRefGoogle Scholar
  69. LaStarza MW, Grakoui A, Rice CM (1994) Deletion and duplication mutations in the C-terminal nonconserved region of Sindbis virus: effects on phosphorylation and on virus replication in vertebrate and invertebrate cells. Virology 202:224–232Google Scholar
  70. Lehtovaara P, Söderlund H, Keränen S, Pettersson RF, Kääriäinen L (1981) 18S defective interfering RNA of Semliki Forest virus contains a triplicated linear repeat. Proc Natl Acad Sci USA 78:5353-5357Google Scholar
  71. Lemm JA, Rice CM (1993a) Assembly of functional Sindbis virus RNA replication complexes: requirement for coexpression of P123 and P34. J Virol 67:1905–1915Google Scholar
  72. Lemm JA, Rice CM (1993b) Roles of nonstructural polyproteins and cleavage products in regulating Sindbis virus RNA replication and transcription. J Virol 67:1916–1926Google Scholar
  73. Lemm JA, Rümenapf T, Strauss EG, Strauss JH, Rice CM (1994) Polypeptide requirements for assembly of functional Sindbis virus replication complexes: a model for the temporal regulation of minus and plus-strand RNA synthesis. EMBO J 13:2925–2934Google Scholar
  74. Liljestrom P (1994) Alphavirus expression systems. Curr Opin Biotechnol 5(5):495–500Google Scholar
  75. Liljeström P, Garoff H (1991) A new generation of animal cell expression vectors based on the Semliki Forest virus replicon. Biotechnology 9:1356–1361Google Scholar
  76. Lulla A, Lulla V, Merits A (2012) Macromolecular assembly-driven processing of the 2/3 cleavage site in the alphavirus replicase polyprotein. J Virol 86(1):553–565. CrossRefGoogle Scholar
  77. Lulla V, Karo-Astover L, Rausalu K, Merits A, Lulla A (2013) Presentation overrides specificity: probing the plasticity of alphaviral proteolytic activity through mutational analysis. J Virol 87(18):10207–10220. CrossRefGoogle Scholar
  78. Lulla V, Merits A, Sarin P, Kaariainen L, Keranen S, Ahola T (2006) Identification of mutations causing temperature-sensitive defects in Semliki Forest virus RNA synthesis. J Virol 80(6):3108–3111. (80/6/3108 [pii])CrossRefGoogle Scholar
  79. Mai J, Sawicki SG, Sawicki DL (2009) Fate of minus-strand templates and replication complexes produced by a p23-cleavage-defective mutant of Sindbis virus. J Virol 83(17):8553–8564. CrossRefGoogle Scholar
  80. Malet H, Coutard B, Jamal S, Dutartre H, Papageorgiou N, Neuvonen M, Ahola T, Forrester N, Gould EA, Lafitte D, Ferron F, Lescar J, Gorbalenya AE, de Lamballerie X, Canard B (2009) The crystal structures of Chikungunya and Venezuelan equine encephalitis virus nsP3 macro domains define a conserved adenosine binding pocket. J Virol 83(13):6534–6545. (JVI.00189-09 [pii])CrossRefGoogle Scholar
  81. Mayuri Geders TW, Smith JL, Kuhn RJ (2008) Role for conserved residues of sindbis virus nonstructural protein 2 methyltransferase-like domain in regulation of minus-strand synthesis and development of cytopathic infection. J Virol 82(15):7284–7297Google Scholar
  82. McInerney GM, Kedersha NL, Kaufman RJ, Anderson P, Liljestrom P (2005) Importance of eIF2alpha phosphorylation and stress granule assembly in alphavirus translation regulation. Mol Biol Cell 16(8):3753–3763. CrossRefGoogle Scholar
  83. McPherson RL, Abraham R, Sreekumar E, Ong SE, Cheng SJ, Baxter VK, Kistemaker HA, Filippov DV, Griffin DE, Leung AK (2017) ADP-ribosylhydrolase activity of Chikungunya virus macrodomain is critical for virus replication and virulence. Proc Natl Acad Sci U S A 114(7):1666–1671. Google Scholar
  84. McSweegan E, Weaver SC, Lecuit M, Frieman M, Morrison TE, Hrynkow S (2015) The global virus network: challenging chikungunya. Antiviral Res 120:147–152. (S0166-3542(15)00134-5 [pii])CrossRefGoogle Scholar
  85. Meshram CD, Agback P, Shiliaev N, Urakova N, Mobley JA, Agback T, Frolova EI, Frolov I (2018) Multiple host factors interact with hypervariable domain of Chikungunya Virus nsP3 and Determine Viral Replication in Cell-Specific Mode. J Virol.
  86. Michel G, Petrakova O, Atasheva S, Frolov I (2007) Adaptation of Venezuelan equine encephalitis virus lacking 51-nt conserved sequence element to replication in mammalian and mosquito cells. Virology 362(2):475–487. CrossRefGoogle Scholar
  87. Monroe SS, Schlesinger S (1983) RNAs from two independently isolated defective interfering particles of Sindbis virus contain a cellular tRNA sequence at their 5′ ends. Proc Natl Acad Sci USA 80(11):3279-3283Google Scholar
  88. Mounce BC, Cesaro T, Vlajnic L, Vidina A, Vallet T, Weger-Lucarelli J, Passoni G, Stapleford KA, Levraud JP, Vignuzzi M (2017) Chikungunya Virus Overcomes Polyamine Depletion by Mutation of nsP1 and the Opal Stop Codon To Confer Enhanced Replication and Fitness. J Virol 91(15).
  89. Mutso M, Morro AM, Smedberg C, Kasvandik S, Aquilimeba M, Teppor M, Tarve L, Lulla A, Lulla V, Saul S, Thaa B, McInerney GM, Merits A, Varjak M (2018) Mutation of CD2AP and SH3KBP1 Binding Motif in Alphavirus nsP3 Hypervariable Domain Results in Attenuated Virus. Viruses 10(5). Google Scholar
  90. Myles KM, Kelly CL, Ledermann JP, Powers AM (2006) Effects of an opal termination codon preceding the nsP4 gene sequence in the O’Nyong-Nyong virus genome on Anopheles gambiae infectivity. J Virol 80(10):4992–4997. CrossRefGoogle Scholar
  91. Nappe TM, Chuhran CM, Johnson SA (2016) The Chikungunya virus: an emerging US pathogen. World J Emerg Med 7(1):65–67. (WJEM-7-65 [pii])CrossRefGoogle Scholar
  92. Nasar F, Palacios G, Gorchakov RV, Guzman H, Da Rosa AP, Savji N, Popov VL, Sherman MB, Lipkin WI, Tesh RB, Weaver SC (2012) Eilat virus, a unique alphavirus with host range restricted to insects by RNA replication. Proc Natl Acad Sci U S A 109(36):14622–14627. Google Scholar
  93. Neuvonen M, Ahola T (2009) Differential activities of cellular and viral macro domain proteins in binding of ADP-ribose metabolites. J Mol Biol 385(1):212–225. (S0022-2836(08)01334-X [pii])CrossRefGoogle Scholar
  94. Neuvonen M, Kazlauskas A, Martikainen M, Hinkkanen A, Ahola T, Saksela K (2011) SH3 domain-mediated recruitment of host cell amphiphysins by alphavirus nsP3 promotes viral RNA replication. PLoS Pathog 7(11):e1002383. (PPATHOGENS-D-11-01401 [pii])CrossRefGoogle Scholar
  95. Niesters HGM, Strauss JH (1990) Defined mutations in the 5′ nontranslated sequence of Sindbis virus RNA. J Virol 64:4162–4168Google Scholar
  96. Nikonov A, Molder T, Sikut R, Kiiver K, Mannik A, Toots U, Lulla A, Lulla V, Utt A, Merits A, Ustav M (2013) RIG-I and MDA-5 detection of viral RNA-dependent RNA polymerase activity restricts positive-strand RNA virus replication. PLoS Pathog 9(9):e1003610. CrossRefGoogle Scholar
  97. Ou JH, Trent DW, Strauss JH (1982) The 3′-non-coding regions of alphavirus RNAs contain repeating sequences. J Mol Biol 156(4):719–730Google Scholar
  98. Panas MD, Ahola T, McInerney GM (2014) The C-terminal repeat domains of nsP3 from the Old World alphaviruses bind directly to G3BP. J Virol 88(10):5888–5893. CrossRefGoogle Scholar
  99. Panas MD, Varjak M, Lulla A, Eng KE, Merits A, Karlsson Hedestam GB, McInerney GM (2012) Sequestration of G3BP coupled with efficient translation inhibits stress granules in Semliki Forest virus infection. Mol Biol Cell 23(24):4701–4712. CrossRefGoogle Scholar
  100. Park E, Griffin DE (2009) The nsP3 macro domain is important for Sindbis virus replication in neurons and neurovirulence in mice. Virology 388(2):305–314. (S0042-6822(09)00209-8 [pii])CrossRefGoogle Scholar
  101. Peranen J, Rikkonen M, Liljestrom P, Kaariainen L (1990) Nuclear localization of Semliki Forest virus-specific nonstructural protein nsP2. J Virol 64(5):1888–1896Google Scholar
  102. Perri S, Driver DA, Gardner JP, Sherrill S, Belli BA, Dubensky TW Jr, Polo JM (2000) Replicon vectors derived from Sindbis virus and Semliki forest virus that establish persistent replication in host cells. J Virol 74(20):9802–9807Google Scholar
  103. Plante K, Wang E, Partidos CD, Weger J, Gorchakov R, Tsetsarkin K, Borland EM, Powers AM, Seymour R, Stinchcomb DT, Osorio JE, Frolov I, Weaver SC (2011) Novel chikungunya vaccine candidate with an IRES-based attenuation and host range alteration mechanism. PLoS Pathog 7(7):e1002142. CrossRefGoogle Scholar
  104. Rack JG, Perina D, Ahel I (2016) Macrodomains: structure, function, evolution, and catalytic activities. Annu Rev Biochem 85:431–454. CrossRefGoogle Scholar
  105. Raju R, Hajjou M, Hill KR, Botta V, Botta S (1999) In vivo addition of poly(A) tail and AU-rich sequences to the 3′ terminus of the Sindbis virus RNA genome: a novel 3′-end repair pathway. J Virol 73(3):2410–2419Google Scholar
  106. Rausalu K, Utt A, Quirin T, Varghese FS, Zusinaite E, Das PK, Ahola T, Merits A (2016) Chikungunya virus infectivity, RNA replication and non-structural polyprotein processing depend on the nsP2 protease’s active site cysteine residue. Sci Rep 6:37124. (srep37124 [pii])CrossRefGoogle Scholar
  107. Reynaud JM, Kim DY, Atasheva S, Rasalouskaya A, White JP, Diamond MS, Weaver SC, Frolova EI, Frolov I (2015) IFIT1 differentially interferes with translation and replication of alphavirus genomes and promotes induction of type I interferon. PLoS Pathog 11(4):e1004863. CrossRefGoogle Scholar
  108. Rikkonen M, Peranen J, Kaariainen L (1992) Nuclear and nucleolar targeting signals of Semliki Forest virus nonstructural protein nsP2. Virology 189(2):462–473Google Scholar
  109. Rikkonen M, Peranen J, Kaariainen L (1994) ATPase and GTPase activities associated with Semliki Forest virus nonstructural protein nsP2. J Virol 68(9):5804–5810Google Scholar
  110. Robinson MC (1955) An epidemic of virus disease in Southern Province, Tanganyika Territory, in 1952-53. Trans Roy S Trop Med Hyg 49:28Google Scholar
  111. Rubach JK, Wasik BR, Rupp JC, Kuhn RJ, Hardy RW, Smith JL (2009) Characterization of purified Sindbis virus nsP4 RNA-dependent RNA polymerase activity in vitro. Virology 384(1):201–208Google Scholar
  112. Rupp JC, Jundt N, Hardy RW (2011) Requirement for the amino-terminal domain of sindbis virus nsP4 during virus infection. J Virol 85(7):3449–3460. CrossRefGoogle Scholar
  113. Rupp JC, Sokoloski KJ, Gebhart NN, Hardy RW (2015) Alphavirus RNA synthesis and non-structural protein functions. J Gen Virol 96(9):2483–2500. CrossRefGoogle Scholar
  114. Russo AT, White MA, Watowich SJ (2006) The crystal structure of the Venezuelan equine encephalitis alphavirus nsP2 protease. Structure 14(9):1449–1458. (S0969-2126(06)00333-9 [pii])CrossRefGoogle Scholar
  115. Sawicki DL, Gomatos PJ (1976) Replication of semliki forest virus: polyadenylate in plus-strand RNA and polyuridylate in minus-strand RNA. J Virol 20(2):446–464Google Scholar
  116. Scholte FE, Tas A, Albulescu IC, Zusinaite E, Merits A, Snijder EJ, van Hemert MJ (2015) Stress granule components G3BP1 and G3BP2 play a proviral role early in Chikungunya virus replication. J Virol 89(8):4457–4469. CrossRefGoogle Scholar
  117. Scholte FE, Tas A, Martina BE, Cordioli P, Narayanan K, Makino S, Snijder EJ, van Hemert MJ (2013) Characterization of synthetic Chikungunya viruses based on the consensus sequence of recent E1-226 V isolates. PLoS ONE 8(8):e71047. CrossRefGoogle Scholar
  118. Shin G, Yost SA, Miller MT, Elrod EJ, Grakoui A, Marcotrigiano J (2012) Structural and functional insights into alphavirus polyprotein processing and pathogenesis. Proc Natl Acad Sci U S A 109(41):16534–16539. Google Scholar
  119. Shirako Y, Strauss JH (1990) Cleavage between nsP1 and nsP2 initiates the processing pathway of Sindbis virus nonstructural polyprotein P123. Virology 177:54–64Google Scholar
  120. Shirako Y, Strauss JH (1994) Regulation of Sindbis virus RNA replication: uncleaved P123 and nsP4 function in minus strand RNA synthesis whereas cleaved products from P123 are required for efficient plus strand RNA synthesis. J Virol 185:1874–1885Google Scholar
  121. Siomi MC, Eder PS, Kataoka N, Wan L, Liu Q, Dreyfuss G (1997) Transportin-mediated nuclear import of heterogeneous nuclear RNP proteins. J Cell Biol 138(6):1181–1192Google Scholar
  122. Sokoloski KJ, Dickson AM, Chaskey EL, Garneau NL, Wilusz CJ, Wilusz J (2010) Sindbis virus usurps the cellular HuR protein to stabilize its transcripts and promote productive infections in mammalian and mosquito cells. Cell Host Microbe 8(2):196–207. (S1931-3128(10)00242-8 [pii])CrossRefGoogle Scholar
  123. Sokoloski KJ, Haist KC, Morrison TE, Mukhopadhyay S, Hardy RW (2015) Noncapped alphavirus genomic RNAs and their role during infection. J Virol 89(11):6080–6092. CrossRefGoogle Scholar
  124. Sokoloski KJ, Nease LM, May NA, Gebhart NN, Jones CE, Morrison TE, Hardy RW (2017) Identification of interactions between Sindbis virus capsid protein and cytoplasmic vRNA as novel virulence determinants. PLoS Pathog 13(6):e1006473. (PPATHOGENS-D-16-02887 [pii])CrossRefGoogle Scholar
  125. Spuul P, Balistreri G, Kaariainen L, Ahola T (2010) Phosphatidylinositol 3-kinase-, actin-, and microtubule-dependent transport of Semliki Forest Virus replication complexes from the plasma membrane to modified lysosomes. J Virol 84(15):7543–7557. (JVI.00477-10 [pii])CrossRefGoogle Scholar
  126. Strauss EG, deGroot RJ, Levinson R, Strauss JH (1992) Identification of the active site residues in the nsP2 proteinase of Sindbis virus. Virology 191:932–940Google Scholar
  127. Strauss EG, Rice CM, Strauss JH (1983) Sequence coding for the alphavirus nonstructural proteins is interrupted by an opal termination codon. Proc Natl Acad Sci U S A 80(17):5271–5275Google Scholar
  128. Strauss JH, Strauss EG (1994) The alphaviruses: gene expression, replication, evolution. Microbiol Rev 58:491–562Google Scholar
  129. Sun C, Gardner CL, Watson AM, Ryman KD, Klimstra WB (2014) Stable, high-level expression of reporter proteins from improved alphavirus expression vectors to track replication and dissemination during encephalitic and arthritogenic disease. J Virol 88(4):2035–2046. CrossRefGoogle Scholar
  130. Svejstrup JQ (2003) Rescue of arrested RNA polymerase II complexes. J Cell Sci 116(Pt 3):447–451Google Scholar
  131. Takkinen K (1986) Complete nucleotide sequence of the nonstructural protein genes of Semliki Forest virus. Nucleic Acids Res 14(14):5667–5682Google Scholar
  132. Tamberg N, Lulla V, Fragkoudis R, Lulla A, Fazakerley JK, Merits A (2007) Insertion of EGFP into the replicase gene of Semliki Forest virus results in a novel, genetically stable marker virus. J Gen Virol 88(Pt 4):1225–1230Google Scholar
  133. Thaa B, Biasiotto R, Eng K, Neuvonen M, Gotte B, Rheinemann L, Mutso M, Utt A, Varghese F, Balistreri G, Merits A, Ahola T, McInerney GM (2015) Differential Phosphatidylinositol-3-Kinase-Akt-mTOR Activation by Semliki Forest and chikungunya viruses is dependent on nsP3 and connected to replication complex internalization. J Virol 89(22):11420–11437. CrossRefGoogle Scholar
  134. Tomar S, Hardy RW, Smith JL, Kuhn RJ (2006) Catalytic core of alphavirus nonstructural protein nsP4 possesses terminal adenylyltransferase activity. J Virol 80(20):9962–9969Google Scholar
  135. Tossavainen H, Aitio O, Hellman M, Saksela K, Permi P (2016) Structural basis of the high affinity interaction between the Alphavirus Nonstructural Protein-3 (nsP3) and the SH3 domain of Amphiphysin-2. J Biol Chem 291(31):16307–16317. CrossRefGoogle Scholar
  136. Trobaugh DW, Gardner CL, Sun C, Haddow AD, Wang E, Chapnik E, Mildner A, Weaver SC, Ryman KD, Klimstra WB (2014) RNA viruses can hijack vertebrate microRNAs to suppress innate immunity. Nature 506(7487):245–248. CrossRefGoogle Scholar
  137. Tsetsarkin KA, Vanlandingham DL, McGee CE, Higgs S (2007) A single mutation in chikungunya virus affects vector specificity and epidemic potential. PLoS Pathog 3(12):e201. CrossRefGoogle Scholar
  138. Utt A, Das PK, Varjak M, Lulla V, Lulla A, Merits A (2015) Mutations conferring a noncytotoxic phenotype on chikungunya virus replicons compromise enzymatic properties of nonstructural protein 2. J Virol 89(6):3145–3162. CrossRefGoogle Scholar
  139. Vasiljeva L, Merits A, Auvinen P, Kaariainen L (2000) Identification of a novel function of the alphavirus capping apparatus. RNA 5′-triphosphatase activity of Nsp2. J Biol Chem 275(23):17281–17287. (M910340199 [pii])CrossRefGoogle Scholar
  140. Vasiljeva L, Merits A, Golubtsov A, Sizemskaja V, Kaariainen L, Ahola T (2003) Regulation of the sequential processing of Semliki Forest virus replicase polyprotein. J Biol Chem 278(43):41636–41645Google Scholar
  141. Vihinen H, Ahola T, Tuittila M, Merits A, Kaariainen L (2001) Elimination of phosphorylation sites of Semliki Forest virus replicase protein nsP3. J Biol Chem 276(8):5745–5752Google Scholar
  142. Volkova E, Frolova E, Darwin JR, Forrester NL, Weaver SC, Frolov I (2008) IRES-dependent replication of Venezuelan equine encephalitis virus makes it highly attenuated and incapable of replicating in mosquito cells. Virology 377(1):160–169. CrossRefGoogle Scholar
  143. Wang E, Kim DY, Weaver SC, Frolov I (2011) Chimeric Chikungunya viruses are nonpathogenic in highly sensitive mouse models but efficiently induce a protective immune response. J Virol 85(17):9249–9252. CrossRefGoogle Scholar
  144. Wang E, Volkova E, Adams AP, Forrester N, Xiao SY, Frolov I, Weaver SC (2008) Chimeric alphavirus vaccine candidates for chikungunya. Vaccine 26(39):5030–5039Google Scholar
  145. Weaver SC, Forrester NL (2015) Chikungunya: evolutionary history and recent epidemic spread. Antiviral Res 120:32–39. CrossRefGoogle Scholar
  146. Weaver SC, Lecuit M (2015a) Chikungunya virus and the global spread of a mosquito-borne disease. N Engl J Med 372(13):1231–1239. CrossRefGoogle Scholar
  147. Weaver SC, Lecuit M (2015b) Chikungunya virus infections. N Engl J Med 373(1):94–95. CrossRefGoogle Scholar
  148. Weiss B, Geigenmuller-Gnirke U, Schlesinger S (1994) Interactions between Sindbis virus RNAs and a 68 amino acid derivative of the viral capsid protein further defines the capsid binding site. Nucleic Acids Res 22(5):780–786Google Scholar
  149. Weiss B, Nitschko H, Ghattas I, Wright R, Schlesinger S (1989) Evidence for specificity in the encapsidation of Sindbis virus RNAs. J Virol 63:5310–5318Google Scholar
  150. White CL, Thomson M, Dimmock NJ (1998) Deletion analysis of a defective interfering Semliki Forest virus RNA genome defines a region in the nsP2 sequence that is required for efficient packaging of the genome into virus particles. J Virol 72(5):4320–4326Google Scholar
  151. White LK, Sali T, Alvarado D, Gatti E, Pierre P, Streblow D, Defilippis VR (2011) Chikungunya virus induces IPS-1-dependent innate immune activation and protein kinase R-independent translational shutoff. J Virol 85(1):606–620. (JVI.00767-10 [pii])CrossRefGoogle Scholar

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© Springer Nature Switzerland AG 2018

Authors and Affiliations

  1. 1.Department of MicrobiologyUniversity of Alabama at BirminghamBirminghamUSA

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