Intra-host variation structure of classical swine fever virus NS5B in relation to antiviral therapy

Antiviral Research

Volumn 98, Issue 2, 2013, Pages 266-272

  Haegeman, Andy ^a   Vrancken, Robert ^b   Neyts, Johan ^c   Koenen, Frank ^a  

^a VETERINARY AND AGROCHEMICAL RESEARCH CENTRE   (Belgium)

^b Okapi Sciences NV   (Belgium)

^c REGA INSTITUTE FOR MEDICAL RESEARCH   (Belgium)

Author keywords

Antiviral; Intra host variation; Sequencing

Indexed keywords

AMINO ACID; NONSTRUCTURAL PROTEIN 5B; RNA DIRECTED RNA POLYMERASE; 5 [(4 BROMOPHENYL)METHYL] 2 PHENYL 5H IMIDAZO[4,5 C]PYRIDINE; ANTIVIRUS AGENT; UNCLASSIFIED DRUG; 5 ((4 BROMOPHENYL)METHYL) 2 PHENYL 5H IMIDAZO(4,5 C)PYRIDINE; 5-((4-BROMOPHENYL)METHYL)-2-PHENYL-5H-IMIDAZO(4,5-C)PYRIDINE; ENZYME INHIBITOR; IMIDAZOLE DERIVATIVE; PYRIDINE DERIVATIVE; VIRUS PROTEIN;

ANTIVIRAL RESISTANCE; ANTIVIRAL THERAPY; ARTICLE; BOVINE DIARRHEA VIRUS; GENETIC VARIABILITY; GENOME; NONHUMAN; NUCLEOTIDE SEQUENCE; PESTIVIRUS; PRIORITY JOURNAL; PROTEIN STRUCTURE; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; VIRUS MUTATION; WILD TYPE; ANIMAL CELL; BOVINE VIRAL DIARRHEA; CLASSICAL SWINE FEVER; CONTROLLED STUDY; GENE SEQUENCE; SEQUENCE ANALYSIS; SWINE; VIRUS GENOME; AMINO ACID SUBSTITUTION; ANIMAL; DRUG ANTAGONISM; DRUG EFFECT; ENZYMOLOGY; GENETICS; METABOLISM; VIROLOGY;

AMINO ACID SUBSTITUTION; ANIMALS; ANTIVIRAL AGENTS; CLASSICAL SWINE FEVER; CLASSICAL SWINE FEVER VIRUS; ENZYME INHIBITORS; GENETIC VARIATION; IMIDAZOLES; PYRIDINES; RNA REPLICASE; SWINE; VIRAL PROTEINS;

EID: 84880561773     PISSN: 01663542     EISSN: 18729096     Source Type: Journal    
DOI: 10.1016/j.antiviral.2013.03.005     Document Type: Article

References (57)

1. Ahrens, U.,Kaden,V.,Drexler,C.,Visser,N.,2000.Efficacy of the classical swine fever (CSF) marker vaccine Porcilis pesti in pregnant sows.Vet.Microbiol.77, 83-97.
2. Bartels, D.J.,Zhou,Y.,Zhang,E.Z.,Marcial,M.,Byrn,R.A.,Pfeiffer,T.,Tigges,A.M., Adiwijaya, B.S.,Lin,C.,Kwong,A.D.,Kieffer,T.L.,2008.Natural prevalence of hepatitis C virus variants with decreased sensitivity toNS3.4A protease in hibito Rs in treatment-naive subjects.J.Infect.Dis.198 (6),800-807.
3. Beer, M.,Reimann,I.,Hoffmann,B.,Depner,K.,2007.Novel marker vaccines against classical swine fever.Vaccine 25(30),5665-5670.
4. Bracho, M.A.,Moya,A.,Barrio,E.,1998.Contribution of Taq polymerase-induced errors to the estimation of RNA virus diversity.J.Gen.Virol.79(Pt12),2921-2928.
5. Charpentier, C.,Dwyer,D.E.,Mammano,F.,Lecossier,D.,Clavel,F.,Hance,A.J.,2004. Role of minority populations of human immunodeficiency virus type 1 in the evolution of viral resistance to protease in hibito Rs.J.Virol.78(8),4234-4247.
6. Choi, K.H.,Gallei,A.,Becher,P.,Rossmann,M.G.,2006.Hestructure of bovine viral diarrhea virus RNA-dependent RNA polymerase and its amino-terminal domain. Structure 4(7),1107-1113.
7. Collett, M.,2005.Role for antiviral drugs in response to virus disease out breaks.In: Proceedings of the 6th Pestiviruses Symposium.Thun,Switzerland,p.16.
8. Comas, I.,Moya,A.,Gonzalez-Candelas,F.,2005.Validating viral quasispecies with digital organisms: areexamination of the critical mutation rate.BMC Evol.Biol. 5, 5.
9. De Smit,A.J.,Bouma,A.,deKluijver,E.P.,Terpstr,C.,Moormann,R.J.,2001. Prevention of transplacental transmission of moderate-virulent classical swine fever virus after single ordouble vaccination with an E2 subunit vaccine.Vet.Q 22, 150-153.
10. Depner, K.R.,Bouma,A.,Koenen,F.,Klinkenberg,D.,Lange,E.,DeSmit,H., Vanderhallen, H.,2001.Classical swine fever (CSF)marker vaccine.Trial II. Challenge study in pregnant sows.Vet.Microbiol.83,107-120.
11. Domingo, E.,Gomez,J.,2007.Quasispecies and its impact on viral hepatitis. Virus Res. 127 (2),131-150.
12. Drake, J.W.,Holland,J.J.,1999.Mutation rates among RNA viruses.Proc.Natl.Acad. Sci. USA 96,13910-13913.
13. Eigen, M.,1971.Selorganisation of matter and the evolution ofbiological macromolecules. Naturwissenschaften 58,465-523.
14. Fanning, L.J.,2008.Practical consequences of hepatitis Cvirus quasispecies for target-specific antivirals.J.Infect.Dis.198 (6),797-799.
15. Ferrer-Orta, C.,Arias,A.,Escarmis,C.,Verdaguer,N.,2006.Acomparison of viral RNA-dependent RNA polymerases.Curr.Opin.Struct.Biol.16(1),27-34.
16. Floegel-Niesmann, G.,2001.Classical swine fever (CSF)marker vaccine.Trial III. Evaluation of discriminato Ry ELISAs.Vet.Microbiol.83(2),121-136.
17. Friedberg, E.C.,Walker,G.C.,Siede,W.,Wood,R.D.,Schultz,R.A.,Ellenberger,T., 2006. DNA Repair and Mutagenesis.American Society for Microbiology, Washington, DC.
18. Gao, G.,Stuver,S.O.,Okayama,A.,Tsubouchi,H.,Mueller,N.E.,Tabor,E.,2005.The minimum number of clones necessary to sequence inorder toobtain the maximum information about hepatitis Cvirus quasispecies: a comparison of subjects with and without liver cancer.J.Viral Hepat.12(1),46-50.
19. Gerrish, P.J.,García-Lerma,J.G.,2003.Mutation rate and the efficacy of antimicrobial drug treatment. Lancet Infect.Dis.(1),28-32.
20. Greiser-Wilke, I.,Fritzemeier,J.,Koenen,F.,Vanderhallen,H.,Rutili,D.,DeMia,G.M., Romero, L.,Rosel,R.,Sanchez-Vizcaino,J.M.,San Gabriel,A.,2000.Molecular epidemiology of alarge classical swine fever epi demic in the European Union in 1997-1998. Vet.Microbiol.77(1-2),17-27.
21. Gretch, D.R.,Polyak,S.J.,1997.The Quasisepcies Nature of hepatitis CVirus: Research Methods and Biological Implications,pp.57-69.
22. Hedskog, C.,Mild,M.,Jernberg,J.,Sherwood,E.,Bratt,G.,Leitner,T.,Lundeberg,J., Andersson, B.,Albert,J.,2010.Dynamics of hIV-1 quasispecies during antiviral treatment dissected using ultra-deep pyrosequencing.PLoS One 5(7),7.
23. Holmes, E.C.,2003.Error thresholds and the constraints to RNA virus evolution. Trends Microbiol. 11,543-546.
24. Holmes, E.C.,2010.The RNA virus quasispecies: fact or Fiction? J.Mol.Biol.400, 271-273.
25. Holmes, E.C.,Moya,A.,2002. Is the quasispecies concept relevant to RNA viruses? J. Virol. 76,460-465.
26. Huang, X.,1992.Acontig assembly program based on sensitive detection of fragment overlaps. Genomics 14(1),18-25.
27. Jenkins, G.M.,Worobey,M.,Woelk,C.H.,Holmes,E.C.,2001.Evidence for the non- quasispecies evolution of RNA viruses [corrected].Mol.Biol.Evol.18,987-994.
28. Kiss, I.,Ros,C.,Kecskeméti,S.,Tanyi,J.,Klingeborn,S.B.,Belák,S., 1999.Observations on the quasispecies composition of Three animal pathogenic RNA viruses.Acta Vet. Hung.47(4),471-480.
29. Koenen, F.,Lefebvre,J.,1995.Kinetics ofanexperimental infection with aclassical swine fever (CSF) fieldisolate.In:Proceedings of the 3rd Congress European Society of Vet.Virology,pp.322-326.
30. Kulldorff M. and Information Management Services,Inc.SaTScanTM:Sof Tware for the spatial and space-time scan statistics.http://www.satscan.org/, 2006).
31. Kuntzen, T.,Timm,J.,Berical,A.,Lennon,N.,Berlin,A.M.,Young,S.K.,Lee,B., Heckerman, D.,Carlson,J.,Reyor,L.L.,Kleyman,M.,McMahon,C.M.,Birch,C., Schulze Zur Wiesch,J.,Ledlie,T.,Koehrsen,M.,Kodira,C.,Roberts,A.D.,Lauer, G.M., Rosen,H.R.,Bihl,F.,Cerny,A.,Spengler,U.,Liu,Z.,Kim,A.Y.,Xing,Y., Schneidewind, A.,Madey,M.A.,Fleckenstein,J.F.,Park,V.M.,Galagan,J.E., Nusbaum, C.,Walker,B.D.,Lake-Bakaar,G.V.,Daar,E.S.,Jacobson,I.M., Gomperts, E.D.,Edlin,B.R.,Donfield,S.M.,Chung,R.T.,Talal,A.H.,Marion,T., Birren, B.W.,Henn,M.R.,Allen,T.M.,2008.Naturally occurring dominant resistance mutations to hepatitis Cvirus protease and polymerase in hibito Rs in treatment-naïve patients.Hepatology 48(6),1769-1778.
32. Kurbanov, F.,Tanaka,Y.,Matsuura,K.,Sugauchi,F.,Elkady,A.,Khan,A.,Hasegawa,I., Ohno, T.,Tokuda,H.,Mizokami,M.,2010.Positive selection of core 70Q variant genotype 1b hepatitis Cvirus strains induced bypegylated interferon and ribavirin. J.Infect.Dis.201 (11),1663-1671.
33. Le Potier,M.F.,Mesplede,A.,Vannier,P.,2006.Classical swine fever and other pestiviruses. In:Straw,B.E.,Zimmerman,J.J.,D'Allaire,S.,Taylor,D.J.(Eds.), Diseases of Swine,9th ed.Blackwell Publishing,pp.309-323.
34. Leifer, I.,Hoffmann,B.,Höper,D.,Bruun Rasmussen,T.,Blome,S.,Strebelow,G., Höreth-Böntgen, D.,Staubach,C.,Beer,M.,2010.Molecular epidemiology of current classical swine fever virus isolates ofwild boar inGermany.J.Gen.Virol. 91, 2687-2697.
35. Malet, I.,Belnard,M.,Agut,H.,Cahour,A.,2003.From RNA toquasispecies: a DNA polymerase with proof Reading activity ishighly recommended for accurate assessment of viral diversity.J.Virol.Methods 109 (2),161-170. Más, A.,López-Galíndez,C.,Cacho,I.,Gómez,J.,Martí nez,M.A.,2010.Unfinished sto Ries on viral quasispecies and Darwinian views ofevolution.J.Mol.Biol.397 (4), 865-877.
36. Meuwissen, M.P.M.,Horst,S.H.,Huirne,R.B.M.,Dijkhuizen,A.A.,1999.Amodel to estimate the financialconsequences of classical swine fever outbreaks: principles and outcomes. Prev.Vet.Med.42,249-270.
37. Mullan, B.,Sheehy,P.,Shanahan,F.,Fanning,L.,2004.DoTaq-generated RT-PCR products from RNA viruses accurately reflectviral genetic heterogeneity J. Viral Hepat. 11(2),108-114.
38. Nájera, I.,Richman,D.D.,Olivares,I.,Rojas,J.M.,Peinado,M.A.,Perucho,M.,Ná jera, R., López-Galíndez,C.,1994.Natural occurrence of drug resistance mutations in the reverse transcriptase of human immunodeficiencyvirus type 1isolates. AIDS Res. Hum.Retroviruses 10(11),1479-1488.
39. Paeshuyse, J.,Leyssen,P.,Mabery,E.,Boddeker,N.,Vrancken,R.,Froeyen,M.,Ansari, I.H., Dutartre,H.,Rozenski,J.,Gil,L.H.V.G.,Letellier,C.,Lanford,R.,Canard,B., Koenen, F.,Kerkhofs,P.,Donis,R.O.,Herdewijn,P.,Watson,J.,DeClercq,E., Puerstinger, G.,Neyts,J.,2006.Anovel,highly selective inhibito R ofpestivirus replication that targets the viral RNA-dependent RNA polymerase.J.Virol.80, 149-160.
40. Paeshuyse, J.,Chezal,J.M.,Froeyen,M.,Leyssen,P.,Dutartre,H.,Vrancken,R., Canard, B.,Letellier,C.,Li,T.,Mittendorfer,H.,Koenen,F.,Kerkhofs,P.,DeClercq, E., Herdewijn,P.,Puerstinger,G.,Gueiffier,A.,Chavignon,O.,Teulade,J.C.,Neyts , J., 2007.The imidazopyrrolopyridine analogue AG110 isanovel,highly selective inhibito R ofpestiviruses that targets the viral RNA-dependent RNA polymerase at ahot spot for inhibition of viral replication.J.Virol.81(20), 11046-11053.
41. Paeshuyse, J.,Letellier,C.,Froeyen,M.,Dutartre,H.,Vrancken,R.,Canard,B.,De Clercq, E.,Gueiffier,A.,Teulade,J.C.,Herdewijn,P.,Puerstinger,G.,Koenen,F., Kerkhofs, P.,Baraldi,P.G.,Neyts,J.,2009.Apyrazolotriazolopyrimidinamine inhibito R of bovine viral diarrhea virus replication that targets the viral RNA- dependent RNA polymerase.Antiviral Res.82(3),141-147.
42. Prosperi, M.C.,Prosperi,L.,Bruselles,A.,Abbate,I.,Rozera,G.,Vincenti,D.,Solmone, M.C., Capobianchi,M.R.,Ulivi,G.,2011.Combinato Rial analysis and algorithms for quasispecies reconstruction using next-generation sequencing. BMC Bioinformatics 12, 5.
43. Puerstinger, G.,Paeshuyse,J.,Herdewijn,P.,Rozenski,J.,DeClercq,E.,Neyts,J.,2006. Substituted 5-benzyl-2-phenyl-5Himidazo[4,5-c]pyridines: anew class of pestivirus in hibito Rs. Bioorg.Med.Chem.Lett.16,5345-5349.
44. Reed, L.J.,Muench,H.,1938.Asimple method ofestimating fiftypercent endpoints. Am. J.Hyg.27,493-497.
45. Rozera, G.,Abbate,I.,Bruselles,A.,Vlassi,C.,D'Offizi,G.,Narciso,P.,Chillemi,G., Prosperi, M.,Ippolito,G.,Capobianchi,M.R.,2009.Massively parallel pyrosequencing highlights minority variants in the HIV-1 env quasispecies deriving from lymphomonocyte sub-populations.Retrovirology 6,15.
46. Sanjuán, R.,Nebot,M.R.,Chirico,N.,Mansky,L.M.,Belshaw,R.,2010.Viral mutation rates. J.Virol.84(19),9733-9748.
47. Tatusova, T.A.,Madden,T.L.,1999.Blast 2sequences-anew tool for comparing protein and nucleotide sequences.FEMS Microbiol.Lett.174,247-250.
48. Thompson, J.D.,Higgins,D.G.,Gibson,T.J.,1994.CLUSTAL W:improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position specificgap penalties and weight matrix choice.Nucleic Acids Res. 22(22),4673-4680.
49. Uttenthal, A.,LePotier,M.F.,Romero,L.,DeMia,G.M.,Floegel-Niesmann,G.,2001. Classical swine fever (CSF)marker vaccine.Trial I.Challenge studies inweaner pigs. Vet.Microbiol.83(2),85-106.
50. van Oirschot, J.T.,2003.Vaccinology of classical swine fever:from lab tofield.Vet. Microbiol. 96,367-384.
51. Van Regenmortel, M.H.V.,Fauquet,C.M.,Bishop,D.H.L.,Carstens,E.B.,Estes,M.K., Lemon, S.M.,Maniloff,J.,Mayo,M.A.,McGeoch,D.J.,Pringle,C.R.,Wickner,R.B., 2000. Virus Taxonomy Seventh Report of the International Committee on Taxonomy of Viruses.Academic Press,San Diego.
52. Vanderhallen, H.,Mittelholzer,C.,Hof mann,M.A.,Koenen,F.,Mittelhozer,C.,1999. Classical swine fever virus isgenetically stable invitro and invivo.Arch.Virol. 144 (9), 1669-1677.
53. Vrancken, R.,Paeshuyse,J.,Haegeman,A.,Puerstinger,G.,Froeyen,M.,Herdewijn,P., Kerkhofs, P.,Neyts,J.,Koenen,F.,2008.Imidazo[4,5-c]pyridines inhibit the in vitro replication of the classical swine fever virus and target the viral polymerase. Antiviral Res.77(2),114-119.
54. Más, A.,López-Galíndez,C.,Cacho,I.,Gómez,J.,Martí nez,M.A.,2010.Unfinished sto Ries on viral quasispecies and Darwinian views ofevolution.J.Mol.Biol.397 (4), 865-877.
55. Vrancken, R.,Haegeman,A.,Dewulf,J.,Paeshuyse,J.,Puerstinger,G.,Tignon,M.,Le Potier, M.F.,Neyts,J.,Koenen,F.,2009a.The reduction of cSFV transmission to untreated pigs bythe pestivirus inhibito R BPIP: a proof of concept.Vet. Microbiol. 139 (3-4),365-368.
56. Vrancken, R.,Haegeman,A.,Paeshuyse,J.,Puerstinger,G.,Rozenski,J.,Wright,M., Tignon, M.,LePotier,M.F.,Neyts,J.,Koenen,F.,2009b.Proof of concept for the reduction of classical swine fever infection inpigs byanovel viral polymerase inhibito R. J.Gen.Virol.90(Pt6),1335-13342.
57. Wilke, C.O.,2005.Quasispecies theory in the context ofpopulation genetics.BMC Evol. Biol.5,44.