Phylogenetic analysis of torque teno virus genome from Pakistani isolate and incidence of co-infection among HBV/HCV infected patients
详细信息 查看全文
- 作者：Tabinda Hussain (1)
Sobia Manzoor (1)
Yasir Waheed (1)
Huma Tariq (1)
Khushbakht Hanif (1) - 关键词：Torque teno virus ; TTV prevalence ; Co ; infection in hepatitis ; Pakistani population ; TTV genome
- 刊名：Virology Journal
- 出版年：2012
- 出版时间：December 2012
- 年：2012
- 卷：9
- 期：1
- 全文大小：405KB
- 参考文献：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, 241:92-7. CrossRef
2. Okamoto H, Nishizawa T, Ukita M, Takahashi M, Fukuda M, Iizuka H, Miyakawa Y, Mayumi M: The entire nucleotide sequence of a TT virus isolate from the United States (TUS01): comparison with reported isolates and phylogenetic analysis. / Virology 1999, 259:437-48. CrossRef
3. Mushahwar IK, Erker JC, Muerhoff AS, Leary TP, Simons JN, Birkenmeyer LG, Chalmers ML, Pilot-Matias TJ, Dexai SM: Molecular and biophysical characterization of TT virus: evidence for a new virus family infecting humans. / Proc Natl Acad Sci U S A 1999, 96:3177-182. CrossRef
4. Ninomiya M, Takahashi M, Nishizawa T, Shimosegawa 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, 46:507-14. CrossRef
5. 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):1743-750.
6. Doosti A, Dehkordi PG, Hajimirzaei MR: The prevalence of transfusion-transmitted virus (TTV) infection in patients with chronic hepatitis B and C in southwest of Iran. / Afr J Biotechnol 2011, 10:4954-957.
7. Vasilyev EV, Trofimov DY, Tonevitsky AG, Ilinsky VV, Korostin DO, Rebrikov DV: Torque teno virus (TTV) distribution in healthy Russian population. / Virol J 2009, 6:134. CrossRef
8. Okamoto H, Nishizawa T, Kato N, Ukita M, Ikeda H, Iizuka H, Miyakawa Y, Mayumi M: Molecular cloning and characterization of a novel DNA virus (TTV) associated with post-transfusion hepatitis of unknown etiology. / Hepatol Res 1998, 10:1-6. CrossRef
9. Hino S: TTV, a new human virus with single stranded circular DNA genome. / Rev Med Virol 2002, 12:151-58. CrossRef
10. Bendinelli M, Pistello M, Maggi F, Fornai C, Freer G, Vatteroni ML: Molecular properties, biology, and clinical implications of TT virus, a recently identified widespread infectious agent of humans. / Clin Microbiol Rev 2001, 14:98-13. CrossRef
11. Qiu J, Kakkola L, Cheng F, Ye C, Soderlund-Venermo M, Hedman K, Pintel DJ: Human circovirus TT virus genotype 6 expresses six proteins following transfection of a full-length clone. / J Virol 2005, 79:6505-510. CrossRef
12. Kakkola L, Bondén H, Hedman L, Kivi N, Moisala S, Julin J, Yl?-Liedenpohja J, Miettinen S, Kantola K, Hedman K: Expression of all six human Torque teno virus (TTV) proteins in bacteria and in insect cells, and analysis of their IgG responses. / Virology 2008, 382:182-89. CrossRef
13. Asim M, Singla R, Gupta RK, Kar P: Clinical & molecular characterization of human TT virus in different liver diseases. / Indian J Med Res 2010, 131:545-54.
14. Savas MC, Guney C, Kadayifci A, Balkan A, Koruk M, Kubar A, Uygun A: High prevalence of transfusion-transmitted virus infection in patients with chronic liver diseases in an endemic area of hepatitis B and C virus. / Med Princ Pract 2003, 12:176-79. CrossRef
15. Zehender G, Manzin A, De Maddalena C, Colasante C, Solforosi L, Corsi F, Bianchi-Bosisio A, Girotto M, Schirru I, Russo U, / et al.: Molecular epidemiology of TT virus in Italy and phylogenesis of viral isolates from subjects at different risk for parenteral exposure. / J Med Virol 2001, 63:76-4. CrossRef
16. Abe K, Inami T, Asano K, Miyoshi C, Masaki N, Hayashi S, Ishikawa K, Takebe Y, Win KM, El-Zayadi AR, / et al.: TT virus infection is widespread in the general populations from different geographic regions. / J Clin Microbiol 1999, 37:2703-705.
17. Sampietro M, Tavazzi D, di Martinez Montemuros F, Cerino M, Zatelli S, Lunghi G, Orlandi A, Fargion S, Fiorelli G, Cappellini MD: TT virus infection in adult beta-thalassemia major patients. / Haematologica 2001, 86:39-3.
18. Tokita H, Murai S, Kamitsukasa H, Yagura M, Harada H, Takahashi M, Okamoto H: High TT virus load as an independent factor associated with the occurrence of hepatocellular carcinoma among patients with hepatitis C virus-related chronic liver disease. / J Med Virol 2002, 67:501-09. CrossRef
19. Kasirga E, Sanlidag T, Akcali S, Keskin S, Aktas E, Karakoc Z, Helvaci M, Sozen G, Kuzu M: Clinical significance of TT virus infection in children with chronic hepatitis B. / Pediatr Int 2005, 47:300-04. CrossRef
20. Prescott LE, MacDonald DM, Davidson F, Mokili J, Pritchard DI, Arnot DE, Riley EM, Greenwood BM, Hamid S, Saeed AA, / et al.: Sequence diversity of TT virus in geographically dispersed human populations. / J Gen Virol 1999,80(Pt 7):1751-758.
21. / NCBI BLAST. http://blast.ncbi.nlm.nih.gov/
22. Biagini P, Todd D, Bendinelli M, Hino S, Mankertz A, Mishiro S, Niel C, Okamoto H, Radial S, / et al.: Anellovirus. In / Virus taxonomy, eighth report of the International Committee on Taxonomy of Viruses. Edited by: Fauquet CM, Mayo MA, Maniloff J, Desselberger U, Ball LA. Elsevier/Academic Press, California; 2005:335-41.
23. Muljono DH, Nishizawa T, Tsuda F, Takahashi M, Okamoto H: Molecular epidemiology of TT virus (TTV) and characterization of two novel TTV genotypes in Indonesia. / Arch Virol 2001, 146:1249-266. CrossRef
24. Maggi F, Andreoli E, Lanini L, Meschi S, Rocchi J, Fornai C, Vatteroni ML, Pistello M, Bendinelli M: Rapid increase in total torquetenovirus (TTV) plasma viremia load reveals an apparently transient superinfection by a TTV of a novel group 2 genotype. / J Clin Microbiol 2006, 44:2571-574. CrossRef
25. Hallett RL, Clewley JP, Bobet F, McKiernan PJ, Teo CG: Characterization of a highly divergent TT virus genome. / J Gen Virol 2000, 81:2273-279.
26. Heller F, Zachoval R, Koelzer A, Nitschko H, Froesner GG: Isolate KAV: a new genotype of the TT-virus family. / Biochem Biophys Res Commun 2001, 289:937-41. CrossRef
27. Jelcic I, Hotz-Wagenblatt A, Hunziker A, Zur Hausen H, de Villiers EM: Isolation of multiple TT virus genotypes from spleen biopsy tissue from a Hodgkin’s disease patient: genome reorganization and diversity in the hypervariable region. / J Virol 2004, 78:7498-507. CrossRef
28. Peng YH, Nishizawa T, Takahashi M, Ishikawa T, Yoshikawa A, Okamoto H: Analysis of the entire genomes of thirteen TT virus variants classifiable into the fourth and fifth genetic groups, isolated from viremic infants. / Arch Virol 2002, 147:21-1. CrossRef
29. Maggi F, Andreoli E, Lanini L, Fornai C, Vatteroni M, Pistello M, Presciuttini S, Bendinelli M: Relationships between total plasma load of torquetenovirus (TTV) and TTV genogroups carried. / J Clin Microbiol 2005, 43:4807-810. CrossRef
30. Komatsu H, Inui A, Sogo T, Kuroda K, Tanaka T, Fujisawa T: TTV infection in children born to mothers infected with TTV but not with HBV, HCV, or HIV. / J Med Virol 2004, 74:499-06. CrossRef
31. Maggi F, Pifferi M, Fornai C, Andreoli E, Tempestini E, Vatteroni M, Presciuttini S, Marchi S, Pietrobelli A, Boner A, / et al.: TT virus in the nasal secretions of children with acute respiratory diseases: relations to viremia and disease severity. / J Virol 2003, 77:2418-425. CrossRef
32. Yokozaki S, Fukuda Y, Nakano I, Katano Y: TT virus: a mother-to-child transmitted rather than bloodborne virus. / Blood 1999, 93:3569-570.
33. Okamoto H, Takahashi M, Nishizawa T, Ukita M, Fukuda M, Tsuda F, Miyakawa Y, Mayumi M: Marked genomic heterogeneity and frequent mixed infection of TT virus demonstrated by PCR with primers from coding and noncoding regions. / Virology 1999, 259:428-36. CrossRef
34. 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, 12:233-39. CrossRef
35. 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, 260:17-2. CrossRef
36. Hu YW, Al-Moslih MI, Al Ali MT, Khameneh SR, Perkins H, Diaz-Mitoma F, Roy JN, Uzicanin S, Brown EG: Molecular detection method for All known genotypes of TT virus (TTV) and TTV-like viruses in thalassemia patients and healthy individuals. / J Clin Microbiol 2005, 43:3747-754. CrossRef
37. Bouzari M, Baygloo SN: Primers designed for detection of TT virus also detect SEN virus. / Res J of Biol Sci 2008, 3:1063-066.
38. Zhong S, Yeo W, Lin CK, Lin XR, Tang MW, Johnson PJ: Quantitative and genotypic analysis of TT virus infection in Chinese blood donors. / Transfusion 2001, 41:1001-007. CrossRef
39. Das K, Kar P, Gupta RK, Das BC: Role of transfusion-transmitted virus in acute viral hepatitis and fulminant hepatic failure of unknown etiology. / J Gastroenterol Hepatol 2004, 19:406-12. CrossRef
40. Al-Moslih MI, Abuodeh RO, Hu Y-W: Detection and genotyping of TT virus in healthy and subjects with HBV or HCV in different populations in the United Arab Emirates. / J Med Virol 2004, 72:502-08. CrossRef
41. Chattopadhyay S, Rao S, Das BC, Singh NP, Kar P: Prevalence of transfusion-transmitted virus infection in patients on maintenance hemodialysis from New Delhi, India. / Hemodial Int 2005, 9:362-66. CrossRef
42. Kakkola L, Bonden H, Hedman L, Kivi N, Moisala S, Julin J, Yla-Liedenpohja J, Miettinen S, Kantola K, Hedman K, Soderlund-Venermo M: Expression of all six human Torque teno virus (TTV) proteins in bacteria and in insect cells, and analysis of their IgG responses. / Virology 2008, 382:182-89. CrossRef
43. Liu Z, Luo K, Zheng R, Hu J, He H: Novel TTV variants isolated in an epidemic of hepatitis of unknown etiology. / J Med Virol 2002, 67:113-17. CrossRef
44. Luo K, He H, Liu Z, Liu D, Xiao H, Jiang X, Liang W, Zhang L: Novel variants related to TT virus distributed widely in China. / J Med Virol 2002, 67:118-26. CrossRef
45. Leppik L, Gunst K, Lehtinen M, Dillner J, Streker K, de Villiers EM: In vivo and in vitro intragenomic rearrangement of TT viruses. / J Virol 2007, 81:9346-356. CrossRef
46. Ukita M, Okamoto H, Nishizawa T, Tawara A, Takahashi M, Iizuka H, Miyakawa Y, Mayumi M: The entire nucleotide sequences of two distinct TT virus (TTV) isolates (TJN01 and TJN02) remotely related to the original TTV isolates. / Arch Virol 2000, 145:1543-559. CrossRef
47. de Villiers EM, Borkosky SS, Kimmel R, Gunst K, Fei JW: The diversity of torque teno viruses: in vitro replication leads to the formation of additional replication-competent subviral molecules. / J Virol 2011, 85:7284-295. CrossRef
48. 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, 43:119-23. CrossRef
49. Biagini P, Attoui H, Gallian P, Touinssi M, Cantaloube JF, de Micco P, de Lamballerie X: Complete sequences of two highly divergent european isolates of TT virus. / Biochem Biophys Res Commun 2000, 271:837-41. CrossRef
50. Okamoto H, Nishizawa T, Tawara A, Takahashi M, Kishimoto J, Sai T, Sugai Y: TT virus mRNAs detected in the bone marrow cells from an infected individual. / Biochem Biophys Res Commun 2000, 279:700-07. CrossRef
51. / CLC workbench. http://www.clcbio.com/
52. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, / et al.: Clustal W and clustal X version 2.0. / Bioinformatics 2007, 23:2947-948. CrossRef
53. / SIAS (sequences identities and similarities). http://imed.med.ucm.es/Tools/sias.html - 作者单位：Tabinda Hussain (1)
Sobia Manzoor (1)
Yasir Waheed (1)
Huma Tariq (1)
Khushbakht Hanif (1)
1. Atta-ur-Rehman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, 44000, Pakistan - ISSN：1743-422X
文摘
Background Torque Teno Virus (TTV) was the first single stranded circular DNA virus to be discovered that infects humans. Although there have been numerous reports regarding the prevalence of TTV from other countries of South Asia, there is severe lack of information regarding its prevalence in Pakistan. Thus the present study compiles the first indigenous report to comprehensively illustrate the incidence of the virus in uninfected and hepatitis infected population from Pakistan. Another aim of the study was to present the sequence of full length TTV genome from a local isolate and compare it with the already reported genome sequences from other parts of the world. Methods TTV DNA was screened in the serum of 116, 100 and 40 HBV infected, HCV infected and uninfected individuals respectively. Nearly full length genome of TTV was cloned from a HBV patient. The genome sequence was subjected to in-silico analysis using CLC Workbench, ClustalW, ClustalX and TreeView. Statistical analysis was carried out in SPSS v17.0. Results Our results report that 89.7%, 90.0% and 92.5% of HBV, HCV patients and healthy control population were positive for TTV infection. TTV genome of 3603 bp was also cloned from a local isolate and given the identity of TPK01. The TTV genome sequence mentioned in this paper is submitted in the GenBank/EMBL/DDBJ under the accession number JN980171. Phylogenetic analysis of TPK01 revealed that the Pakistani isolate has sequence similarities with genotype 23 and 22 (Genogroup 2). Conclusion The results of the current study indicate that the high frequency of TTV viremia in Pakistan conforms to the reports from other areas of the world, wherever screening of TTV DNA was performed against 5-/sup>-UTR of the genome. The high sequence diversity among TTV genome sequences and the high frequency of prevalence makes it harder to study this virus in cellular systems.