Rapid Detection of Human Torque Teno Viruses Using High-Resolution Melting Analysis

Spandole, S; Cimponeriu, D; Toma, M; Radu, I; Ion, D.A.

doi:10.2478/bjmg-2013-0018

Abstract

Torque teno viruses (TTVs) are recently discovered DNA viruses, with heterogeneous genomes, highly prevalent in populations worldwide. The species that infect humans are Torque teno virus (TTV), Torque teno midi virus (TTMDV) and Torque teno mini virus (TTMV). High-resolution melting analysis (HRMA) is a sensitive and effective method for genotyping and mutation scanning. Up to now, HRMA has not been utilized for detection of TTVs.

The aim of this study was to asses if HRMA is suitable for detecting TTVs variants. DNA was extracted from the blood and saliva of 13 healthy subjects for method optimization. Additionally, saliva samples from 100 healthy individuals were collected for estimating the TTVs’ prevalence. Viral DNA was amplified by heminested polymerase chain reaction (PCR). Second round amplicons were used for the HRMA. The samples were analyzed using two fluorescent dyes, SYBR® Green I and EvaGreen®.

The prevalence values for TTV, TTMDV and TTMV were 71.0, 31.0 and 54.0%, respectively. The three major melting curve patterns corresponding to TTV, TTMDV and TTMV on HRMA can be easily distinguished regardless of kit used. Our results showed that HRMA is a rapid and efficient method of detecting human TTVs.

References

1. Nishizawa T, Okamoto H, Konishi K, Yoshizawa H, Miyakawa Y, Mayumi M. A novel DNA virus (TTV) associated with elevated transaminase levels in posttransfusion hepatitis of unknown etiology. Biochem Biophys Res Commun. 1997; 241(1): 92-97.10.1006/bbrc.1997.77659405239
Search in Google Scholar
2. Takahashi K, Hijikata M, Samokhvalov EI, Mishiro S. Full or near full length nucleotide sequences of TT virus variants (Types SANBAN and YONBAN) and the TT virus-like mini virus. Intervirology. 2000; 43(2): 119-123.10.1159/00002503410971131
Search in Google Scholar
3. Ninomiya M, Nishizawa T, Takahashi M, Lorenzo FR, Shimosegawa T, Okamoto H. Identification and genomic characterization of a novel human torque teno virus of 3.2 kb. J Gen Virol. 2007; 88(Pt 7): 1939-1944.10.1099/vir.0.82895-017554026
Search in Google Scholar
4. Ninomiya M, Takahashi M, Nishizawa T, Shimose-gawa T, Okamoto H. Development of PCR assays with nested primers specific for differential detection of three human anelloviruses and early acquisition of dual or triple infection during infancy. J Clin Microbiol. 2008; 46(2): 507-514.10.1128/JCM.01703-07223809518094127
Search in Google Scholar
5. Okamoto H, Nishizawa T, Ukita M, Takahashi M, Fukuda M, Iizuka H, et al. The entire nucleotide sequence of a TT virus isolate from the United States (TUS01): comparison with reported isolates and phylogenetic analysis. Virology. 1999; 259(2): 437-448.10.1006/viro.1999.976910388667
Search in Google Scholar
6. Biagini P, Todd D, Bendinelli M, Hino S, Mankertz A, Mishiro S, et al. Anellovirus in virus taxonomy. In: Fauquet CM, Mayo MA, Maniloff J, Desselberger U, Ball LA, Eds. Eighth Report of the International Committee on Taxonomy of Viruses. London: Elsevier/Academic Press. 2004: 335-341.
Search in Google Scholar
7. Khudyakov YE, Cong ME, Nichols B, Reed D, Dou XG, Viazov SO, et al. Sequence heterogeneity of TT virus and closely related viruses. J Virol. 2000; 74(7): 2990-3000.10.1128/JVI.74.7.2990-3000.200011179710708413
Search in Google Scholar
8. Hijikata M, Takahashi K, Mishiro S. Complete circular DNA genome of a TT virus variant (isolate name SANBAN) and 44 partial ORF2 sequences implicating a great degree of diversity beyond genotypes. Virology. 1999; 260(1): 17-22.10.1006/viro.1999.979710405352
Search in Google Scholar
9. Erker JC, Leary TP, Desai SM, Chalmers ML, Mushahwar IK. Analyses of TT virus full-length genomic sequences. J Gen Virol. 1999; 80(Pt 7): 1743-1750.10.1099/0022-1317-80-7-174310423143
Search in Google Scholar
10. Rocchi J, Ricci V, Albani M, Lanini L, Andreoli E, Macera L, et al. Torquetenovirus DNA drives proinflammatory cytokines production and secretion by immune cells via toll-like receptor 9. Virology. 2009; 394(2): 235-242.10.1016/j.virol.2009.08.03619765789
Search in Google Scholar
11. Devalle S, Niel C. A multiplex PCR assay able to simultaneously detect Torque teno virus isolates from phylogenetic groups 1 to 5. Braz J Med Biol Res. 2005; 38(6): 853-860.10.1590/S0100-879X2005000600006
Search in Google Scholar
12. Takahashi K, Hoshino H, Ohta Y, Yoshida N, Mishiro S. Very high prevalence of TT virus (TTV) infection in general population of Japan revealed by a new set of PCR primers. Hepatol Res. 1998; 12(3): 233-239.10.1016/S1386-6346(98)00068-0
Search in Google Scholar
13. Leary TP, Erker JC, Chalmers ML, Desai SM, Mushahwar IK. Optimized PCR assay for the detection of TT virus. J Virol Meth. 1999; 82(2): 109-112.10.1016/S0166-0934(99)00100-7
Search in Google Scholar
14. Wittwer CT, Reed GH, Gundry CN, Vandersteen JG, Pryor RJ. High-resolution genotyping by amplicon melting analysis using LCGreen. Clin Chem. 2003; 49(6 Pt 1): 853-860.10.1373/49.6.85312765979
Search in Google Scholar
15. Toi CS, Dwyer DE. Prevalence of varicella-zoster virus genotypes in Australia characterized by highresolution melt analysis and ORF22 gene analyses. J Med Microbiol. 2010; 59(Pt 8): 935-940.10.1099/jmm.0.019547-020466839
Search in Google Scholar
16. Matsuda Y, Qazi Y, Iwaki Y. A rapid and efficient method BK polyomavirus genotyping by highresolution melting analysis. J Med Virol. 2011; 83(12): 2128-2134.10.1002/jmv.2223922012720
Search in Google Scholar
17. Steer PA, O’Rourke D, Ghorashi SA, Noormohammadi AH. Application of high-resolution melting curve analysis for typing of fowl adenoviruses in field cases of inclusion body hepatitis. Aust Vet J. 2011; 89(5): 184-192.10.1111/j.1751-0813.2011.00695.x21495991
Search in Google Scholar
18. Zhao XT, Zhou DQ, Wu S, Chen YW, Shao Y, Zhang J, et al. Genotyping cytomegalovirus UL97 muta-tions by high-resolution melting analysis with unlabeled probe. Arch Virol. 2012; 157(3): 475-481.10.1007/s00705-011-1173-y22205145
Search in Google Scholar
19. Robertson T, Bibby S, O’Rourke D, Belfiore T, Lambie H, Noormohammadi A. Characterization of Chlamydiaceae species using PCR and high resolution melt curve analysis of the 16S rRNA gene. J Appl Microbiol. 2009; 107(6): 2017-2028.10.1111/j.1365-2672.2009.04388.x19583801
Search in Google Scholar
20. Li JH, Yin YP, Zheng HP, Zhong MY, Peng RR, Wang B, et al. A high-resolution melting analysis for genotyping urogenital Chlamydia trachomatis. Diagn Microbiol Infect Dis. 2010; 68(4): 366-374.10.1016/j.diagmicrobio.2010.07.01320889277
Search in Google Scholar
21. Devalle S, Niel C. Distribution of TT virus genomic groups 1-5 in Brazilian blood donors, HBV car-riers, and HIV-1-infected patients. J Med Virol. 2004; 72(1): 166-173.10.1002/jmv.1056414635027
Search in Google Scholar
22. Niel C, de Oliveira JM, Ross RS, Gomes SA, Roggendorf M, Viazov S. High prevalence of TT virus infection in Brazilian blood donors. J Med Virol. 1999; 57(3): 259-263.10.1002/(SICI)1096-9071(199903)57:3<;259::AID-JMV8>3.0.CO;2-2
Search in Google Scholar
23. Vasilyev EV, Trofimov DY, Tonevitsky AG, Ilinsky VV, Korostin DO, Rebrikov DV. Torque Teno Virus (TTV) distribution in healthy Russian population. Virol J. 2009; 6(9): 134-138.10.1186/1743-422X-6-134
Search in Google Scholar
24. Moen EM, Huang L, Grinde B. Molecular epidemiology of TTV-like mini virus in Norway. Arch Virol. 2002; 147(1): 181-185.10.1007/s705-002-8310-6
Search in Google Scholar
25. Ninomiya M, Takahashi M, Shimosegawa T, Okamoto H. Analysis of the entire genomes of fifteen torque teno midi virus variants classifiable into a third group of genus Anellovirus. Arch Virol. 2007; 152(11): 1961-1975.10.1007/s00705-007-1046-6
Search in Google Scholar
26. Markham NR, Zuker M. DINAMelt web server for nucleic acid melting prediction. Nucleic Acids Res. 2005; 33(Web server issue): W577-W581.10.1093/nar/gki591
Search in Google Scholar
27. Introduction to High Resolution Melt Analysis (http://www.kapabiosystems.com/public/pdfs/kapa-hrm-fast-pcr-kits/Introduction_to_High_Resolution_Melt_Analysis_Guide.pdf; accessed June 11 2012).
Search in Google Scholar
28. Ruskova L, Raclavsky V. The potential of high resolution melting analysis (hrma) to streamline, facilitate and enrich routine diagnostics in medical microbiology. Biomed Pap Med Fac Univ Palacky Olomouc Czech Repub. 2011; 155(3): 239-252.10.5507/bp.2011.045
Search in Google Scholar
29. Farrar JS, Reed GH, Wittwer CT. High-resolution melting curve analysis for molecular diagnostics. In: Patrinos GP, Ansorge W, Eds. Molecular Diagnostics, 2nd ed. Amsterdam; Boston: Elsevier/Academic Press. 2010: 229-245.10.1016/B978-0-12-374537-8.00015-8
Search in Google Scholar
30. Ririe KM, Rasmussen RP, Wittwer CT. Product differentiation by analysis of DNA melting curves during the polymerase chain reaction. Anal Biochem.1997; 245(2): 154-160.10.1006/abio.1996.9916
Search in Google Scholar
31. Herrmann MG, Durtschi JD, Wittwer CT, Voelkerding KV. Expanded instrument comparison of amplicon DNA melting analysis for mutation scanning and genotyping. Clin Chem. 2007; 53(8): 1544-1548. 10.1373/clinchem.2007.088120
Search in Google Scholar

Rapid Detection of Human Torque Teno Viruses Using High-Resolution Melting Analysis

Abstract

Paradigm

My account