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Analysis of the entire genomes of fifteen torque teno midi virus variants classifiable into a third group of genus Anellovirus

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Summary

Recently, we identified a novel human virus with a circular DNA genome of 3.2 kb, tentatively designated as torque teno midi virus (TTMDV), with a genomic organization resembling those of torque teno virus (TTV) of 3.8–3.9 kb and torque teno mini virus (TTMV) of 2.8–2.9 kb. To investigate the extent of genomic variability of TTMDV genomes, the full-length sequence was determined for 15 TTMDV isolates obtained from viremic individuals in Japan. The 15 TTMDV isolates comprised 3175–3230 bases and shared 67.0–90.3% identities with each other, and were only 68.4–73.0% identical to the 3 reported TTMDV isolates over the entire genome. TTMDV possessed a genomic organization with four open reading frames (ORF1–ORF4) with characteristic sequence motifs and stem and loop structures with high GC content, similar to TTV and TTMV. The total of 18 TTMDV genomes differed by up to 60.7% from each other in the amino acid sequence of ORF1 (658–677 amino acids), but segregated phylogenetically into the same cluster, which was distantly related to the TTVs and TTMVs. These results indicate that TTMDV with a circular DNA genome of 3.2 kb, has an extremely high degree of genomic variability, and is classifiable into a third group in the genus Anellovirus.

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References

  • E Andreoli F Maggi M Pistello S Meschi M Vatteroni LC Nelli M Bendinelli (2006) ArticleTitleSmall Anellovirus in hepatitis C patients and healthy controls Emerg Infect Dis 12 1175–1176 Occurrence Handle16848049

    PubMed  Google Scholar 

  • MR Bassami D Berryman GE Wilcox SR Raidal (1998) ArticleTitlePsittacine beak and feather disease virus nucleotide sequence analysis and its relationship to porcine circovirus, plant circoviruses, and chicken anaemia virus Virology 249 453–459 Occurrence Handle9791035 Occurrence Handle10.1006/viro.1998.9324 Occurrence Handle1:CAS:528:DyaK1cXmsVymtL4%3D

    Article  PubMed  CAS  Google Scholar 

  • P Biagini P Gallian H Attoui JF Cantaloube M Touinssi P de Micco X de Lamballerie (2001) ArticleTitleComparison of systems performance for TT virus detection using PCR primer sets located in non-coding and coding regions of the viral genome J Clin Virol 22 91–99 Occurrence Handle11418356 Occurrence Handle10.1016/S1386-6532(01)00179-2 Occurrence Handle1:CAS:528:DC%2BD3MXksVGquro%3D

    Article  PubMed  CAS  Google Scholar 

  • P Biagini P Gallian H Attoui M Touinssi JF Cantaloube P de Micco X de Lamballerie (2001) ArticleTitleGenetic analysis of full-length genomes and subgenomic sequences of TT virus-like mini virus human isolates J Gen Virol 82 379–383 Occurrence Handle11161277 Occurrence Handle1:CAS:528:DC%2BD3MXhtFCgsrs%3D

    PubMed  CAS  Google Scholar 

  • Biagini P, Todd D, Bendinelli M, Hino S, Mankertz A, Mishiro S, Niel C, Okamoto H, Radial S, Ritchie BW, Teo GC (2005) Anellovirus. In: Fauquet CM, Mayo MA, Maniloff J, Desselberger U, Ball LA (eds) Virus taxonomy. Eighth Report of the International Committee on Taxonomy of Viruses. Elesevier/Academic Press, San Diego, pp 335–341

  • P Biagini P de Micco X de Lamballerie (2006) ArticleTitleIdentification of a third member of the Anellovirus genus (“small anellovirus”) in French blood donors Arch Virol 151 405–408 Occurrence Handle16328140 Occurrence Handle10.1007/s00705-005-0660-4 Occurrence Handle1:CAS:528:DC%2BD28XmtlOntA%3D%3D

    Article  PubMed  CAS  Google Scholar 

  • P Biagini P Gallian JF Cantaloube H Attoui P de Micco X de Lamballerie (2006) ArticleTitleDistribution and genetic analysis of TTV and TTMV major phylogenetic groups in French blood donors J Med Virol 78 298–304 Occurrence Handle16372292 Occurrence Handle10.1002/jmv.20539 Occurrence Handle1:CAS:528:DC%2BD28XhtVylsbo%3D

    Article  PubMed  CAS  Google Scholar 

  • R Breathnach C Benoist K O’Hare F Gannon P Chambon (1978) ArticleTitleOvalbumin gene: evidence for a leader sequence in mRNA and DNA sequences at the exon-intron boundaries Proc Natl Acad Sci USA 75 4853–4857 Occurrence Handle283395 Occurrence Handle10.1073/pnas.75.10.4853 Occurrence Handle1:CAS:528:DyaE1MXhvFCitg%3D%3D

    Article  PubMed  CAS  Google Scholar 

  • PL Collins YT Huang GW Wertz (1984) ArticleTitleNucleotide sequence of the gene encoding the fusion (F) glycoprotein of human respiratory syncytial virus Proc Natl Acad Sci USA 81 7683–7687 Occurrence Handle6096849 Occurrence Handle10.1073/pnas.81.24.7683 Occurrence Handle1:CAS:528:DyaL2MXht1Knsrk%3D

    Article  PubMed  CAS  Google Scholar 

  • J Felsenstein (1985) ArticleTitleConfidence limits on phylogenies: an approach using the bootstrap Evolution 39 783–791 Occurrence Handle10.2307/2408678

    Article  Google Scholar 

  • M Hijikata K Takahashi S Mishiro (1999) ArticleTitleComplete 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 260 17–22 Occurrence Handle10405352 Occurrence Handle10.1006/viro.1999.9797 Occurrence Handle1:CAS:528:DyaK1MXktlynsL4%3D

    Article  PubMed  CAS  Google Scholar 

  • Y Ina (1994) ArticleTitleODEN: a program package for molecular evolutionary analysis and database search of DNA and amino acid sequences Comput Appl Biosci 10 11–12 Occurrence Handle8193950 Occurrence Handle1:CAS:528:DyaK2cXksFKls7s%3D

    PubMed  CAS  Google Scholar 

  • T Inami T Obara M Moriyama Y Arakawa K Abe (2000) ArticleTitleFull-length nucleotide sequence of a simian TT virus isolate obtained from a chimpanzee: evidence for a new TT virus-like species Virology 277 330–335 Occurrence Handle11080480 Occurrence Handle10.1006/viro.2000.0621 Occurrence Handle1:CAS:528:DC%2BD3cXotVOgsLk%3D

    Article  PubMed  CAS  Google Scholar 

  • WL Irving JK Ball S Berridge R Curran AM Grabowska CL Jameson KR Neal SD Ryder BJ Thomson (1999) ArticleTitleTT virus infection in patients with hepatitis C: frequency, persistence, and sequence heterogeneity J Infect Dis 180 27–34 Occurrence Handle10353857 Occurrence Handle10.1086/314825 Occurrence Handle1:CAS:528:DyaK1MXktlequrg%3D

    Article  PubMed  CAS  Google Scholar 

  • MS Jones A Kapoor VV Lukashov P Simmonds F Hecht E Delwart (2005) ArticleTitleNew DNA viruses identified in patients with acute viral infection syndrome J Virol 79 8230–8236 Occurrence Handle15956568 Occurrence Handle10.1128/JVI.79.13.8230-8236.2005 Occurrence Handle1:CAS:528:DC%2BD2MXlslGjtbk%3D

    Article  PubMed  CAS  Google Scholar 

  • K Kamada T Kamahora P Kabat S Hino (2004) ArticleTitleTranscriptional regulation of TT virus: promoter and enhancer regions in the 1.2-kb noncoding region Virology 321 341–348 Occurrence Handle15051393 Occurrence Handle10.1016/j.virol.2003.12.024 Occurrence Handle1:CAS:528:DC%2BD2cXis1Wgu7s%3D

    Article  PubMed  CAS  Google Scholar 

  • T Kamahora S Hino H Miyata (2000) ArticleTitleThree spliced mRNAs of TT virus transcribed from a plasmid containing the entire genome in COS1 cells J Virol 74 9980–9986 Occurrence Handle11024126 Occurrence Handle10.1128/JVI.74.21.9980-9986.2000 Occurrence Handle1:CAS:528:DC%2BD3cXnsFOlt7g%3D

    Article  PubMed  CAS  Google Scholar 

  • A Matsumoto AE Yeo JW Shih E Tanaka K Kiyosawa HJ Alter (1999) ArticleTitleTransfusion-associated TT virus infection and its relationship to liver disease Hepatology 30 283–288 Occurrence Handle10385668 Occurrence Handle10.1002/hep.510300118 Occurrence Handle1:STN:280:DyaK1MzhsFOltA%3D%3D

    Article  PubMed  CAS  Google Scholar 

  • T Miyata S Miyazawa T Yasunaga (1979) ArticleTitleTwo types of amino acid substitutions in protein evolution J Mol Evol 12 219–236 Occurrence Handle439147 Occurrence Handle10.1007/BF01732340 Occurrence Handle1:CAS:528:DyaE1MXhvVWrtLk%3D

    Article  PubMed  CAS  Google Scholar 

  • SM Mount (1982) ArticleTitleA catalogue of splice junction sequences Nucleic Acids Res 10 459–472 Occurrence Handle7063411 Occurrence Handle10.1093/nar/10.2.459 Occurrence Handle1:CAS:528:DyaL38XhtFKrurw%3D

    Article  PubMed  CAS  Google Scholar 

  • IK Mushahwar (2000) ArticleTitleRecently discovered blood–borne viruses: are they hepatitis viruses or merely endosymbionts? J Med Virol 62 399–404 Occurrence Handle11074465 Occurrence Handle10.1002/1096-9071(200012)62:4<399::AID-JMV1>3.0.CO;2-U Occurrence Handle1:STN:280:DC%2BD3M%2FovF2lsg%3D%3D

    Article  PubMed  CAS  Google Scholar 

  • FD Niagro AN Forsthoefel RP Lawther L Kamalanathan BW Ritchie KS Latimer PD Lukert (1998) ArticleTitleBeak and feather disease virus and porcine circovirus genomes: intermediates between the geminiviruses and plant circoviruses Arch Virol 143 1723–1744 Occurrence Handle9787657 Occurrence Handle10.1007/s007050050412 Occurrence Handle1:CAS:528:DyaK1cXms1Ggsrw%3D

    Article  PubMed  CAS  Google Scholar 

  • M Ninomiya T Nishizawa M Takahashi FR Lorenzo T Shimosegawa H Okamoto (2007) ArticleTitleIdentification and genomic characterization of a novel human torque teno virus of 3.2 kb J Gen Virol 88 1939–1944 Occurrence Handle17554026 Occurrence Handle10.1099/vir.0.82895-0 Occurrence Handle1:CAS:528:DC%2BD2sXns1OqtL0%3D

    Article  PubMed  CAS  Google Scholar 

  • T Nishizawa H Okamoto K Konishi H Yoshizawa Y Miyakawa M Mayumi (1997) ArticleTitleA novel DNA virus (TTV) associated with elevated transaminase levels in posttransfusion hepatitis of unknown etiology Biochem Biophys Res Commun 241 92–97 Occurrence Handle9405239 Occurrence Handle10.1006/bbrc.1997.7765 Occurrence Handle1:CAS:528:DyaK2sXotVWitLo%3D

    Article  PubMed  CAS  Google Scholar 

  • H Okamoto T Nishizawa N Kato M Ukita H Ikeda H Iizuka Y Miyakawa M Mayumi (1998) ArticleTitleMolecular cloning and characterization of a novel DNA virus (TTV) associated with posttransfusion hepatitis of unknown etiology Hepatol Res 10 1–16 Occurrence Handle10.1016/S1386-6346(97)00123-X

    Article  Google Scholar 

  • H Okamoto T Nishizawa M Ukita M Takahashi M Fukuda H Iizuka Y Miyakawa M Mayumi (1999) ArticleTitleThe entire nucleotide sequence of a TT virus isolate from the United States (TUS01): comparison with reported isolates and phylogenetic analysis Virology 259 437–448 Occurrence Handle10388667 Occurrence Handle10.1006/viro.1999.9769 Occurrence Handle1:CAS:528:DyaK1MXktV2rsbw%3D

    Article  PubMed  CAS  Google Scholar 

  • H Okamoto M Takahashi T Nishizawa M Ukita M Fukuda F Tsuda Y Miyakawa M Mayumi (1999) ArticleTitleMarked genomic heterogeneity and frequent mixed infection of TT virus demonstrated by PCR with primers from coding and noncoding regions Virology 259 428–436 Occurrence Handle10388666 Occurrence Handle10.1006/viro.1999.9770 Occurrence Handle1:CAS:528:DyaK1MXktV2rsb0%3D

    Article  PubMed  CAS  Google Scholar 

  • H Okamoto M Fukuda A Tawara T Nishizawa Y Itoh I Hayasaka F Tsuda T Tanaka Y Miyakawa M Mayumi (2000) ArticleTitleSpecies-specific TT viruses and cross-species infection in nonhuman primates J Virol 74 1132–1139 Occurrence Handle10627523 Occurrence Handle10.1128/JVI.74.3.1132-1139.2000 Occurrence Handle1:CAS:528:DC%2BD3cXmtFyjuw%3D%3D

    Article  PubMed  CAS  Google Scholar 

  • H Okamoto T Nishizawa A Tawara Y Peng M Takahashi J Kishimoto T Tanaka Y Miyakawa M Mayumi (2000) ArticleTitleSpecies-specific TT viruses in humans and nonhuman primates and their phylogenetic relatedness Virology 277 368–378 Occurrence Handle11080484 Occurrence Handle10.1006/viro.2000.0588 Occurrence Handle1:CAS:528:DC%2BD3cXotVOhu70%3D

    Article  PubMed  CAS  Google Scholar 

  • H Okamoto T Nishizawa A Tawara M Takahashi J Kishimoto T Sai Y Sugai (2000) ArticleTitleTT virus mRNAs detected in the bone marrow cells from an infected individual Biochem Biophys Res Commun 279 700–707 Occurrence Handle11118348 Occurrence Handle10.1006/bbrc.2000.4012 Occurrence Handle1:CAS:528:DC%2BD3cXovVCmsrg%3D

    Article  PubMed  CAS  Google Scholar 

  • H Okamoto M Takahashi N Kato M Fukuda A Tawara S Fukuda T Tanaka Y Miyakawa M Mayumi (2000) ArticleTitleSequestration of TT virus of restricted genotypes in peripheral blood mononuclear cells J Virol 74 10236–10239 Occurrence Handle11024155 Occurrence Handle10.1128/JVI.74.21.10236-10239.2000 Occurrence Handle1:CAS:528:DC%2BD3cXnsFOlurs%3D

    Article  PubMed  CAS  Google Scholar 

  • H Okamoto M Mayumi (2001) ArticleTitleTT virus: virological and genomic characteristics and disease associations J Gastroenterol 36 519–529 Occurrence Handle11519830 Occurrence Handle10.1007/s005350170054 Occurrence Handle1:CAS:528:DC%2BD3MXmsVOgtrs%3D

    Article  PubMed  CAS  Google Scholar 

  • H Okamoto T Nishizawa M Takahashi S Asabe F Tsuda A Yoshikawa (2001) ArticleTitleHeterogeneous distribution of TT virus of distinct genotypes in multiple tissues from infected humans Virology 288 358–368 Occurrence Handle11601907 Occurrence Handle10.1006/viro.2001.1097 Occurrence Handle1:CAS:528:DC%2BD3MXnsFGjtbY%3D

    Article  PubMed  CAS  Google Scholar 

  • H Okamoto T Nishizawa M Takahashi A Tawara Y Peng J Kishimoto Y Wang (2001) ArticleTitleGenomic and evolutionary characterization of TT virus (TTV) in tupaias and comparison with species-specific TTVs in humans and non-human primates J Gen Virol 82 2041–2050 Occurrence Handle11514713 Occurrence Handle1:CAS:528:DC%2BD3MXmslSkt7k%3D

    PubMed  CAS  Google Scholar 

  • H Okamoto M Takahashi T Nishizawa A Tawara K Fukai U Muramatsu Y Naito A Yoshikawa (2002) ArticleTitleGenomic characterization of TT viruses (TTVs) in pigs, cats and dogs and their relatedness with species-specific TTVs in primates and tupaias J Gen Virol 83 1291–1297 Occurrence Handle12029143 Occurrence Handle1:CAS:528:DC%2BD38XktlGitrc%3D

    PubMed  CAS  Google Scholar 

  • H Okamoto T Nishizawa M Takahashi (2004) Torque teno virus (TTV): molecular virology and clinical implications IK Mushahwar (Eds) Viral hepatitis: molecular biology, diagnosis, epidemiology and control Elsevier Amsterdam 241–254

    Google Scholar 

  • RDM Page (1996) ArticleTitleTreeView: an application to display phylogenetic trees on personal computers Comput Appl Biosci 12 357–358 Occurrence Handle8902363 Occurrence Handle1:STN:280:ByiD2MfgtlA%3D

    PubMed  CAS  Google Scholar 

  • YH Peng T Nishizawa M Takahashi T Ishikawa A Yoshikawa H Okamoto (2002) ArticleTitleAnalysis of the entire genomes of thirteen TT virus variants classifiable into the fourth and fifth genetic groups, isolated from viremic infants Arch Virol 147 21–41 Occurrence Handle11855633 Occurrence Handle10.1007/s705-002-8301-7 Occurrence Handle1:CAS:528:DC%2BD38XitFSrs78%3D

    Article  PubMed  CAS  Google Scholar 

  • MA Peters DC Jackson BS Crabb GF Browning (2002) ArticleTitleChicken anemia virus VP2 is a novel dual specificity protein phosphatase J Biol Chem 277 39566–39573 Occurrence Handle12151384 Occurrence Handle10.1074/jbc.M201752200 Occurrence Handle1:CAS:528:DC%2BD38XnvVeitbs%3D

    Article  PubMed  CAS  Google Scholar 

  • N Saitou M Nei (1987) ArticleTitleThe neighbor-joining method: a new method for reconstructing phylogenetic trees Mol Biol Evol 4 406–425 Occurrence Handle3447015 Occurrence Handle1:STN:280:BieC1cbgtVY%3D

    PubMed  CAS  Google Scholar 

  • T Suzuki R Suzuki J Li M Hijikata M Matsuda TC Li Y Matsuura S Mishiro T Miyamura (2004) ArticleTitleIdentification of basal promoter and enhancer elements in an untranslated region of the TT virus genome J Virol 78 10820–10824 Occurrence Handle15367649 Occurrence Handle10.1128/JVI.78.19.10820-10824.2004 Occurrence Handle1:CAS:528:DC%2BD2cXotVemtLY%3D

    Article  PubMed  CAS  Google Scholar 

  • K Takahashi Y Iwasa M Hijikata S Mishiro (2000) ArticleTitleIdentification of a new human DNA virus (TTV-like mini virus, TLMV) intermediately related to TT virus and chicken anemia virus Arch Virol 145 979–993 Occurrence Handle10881684 Occurrence Handle10.1007/s007050050689 Occurrence Handle1:CAS:528:DC%2BD3cXksVeksL8%3D

    Article  PubMed  CAS  Google Scholar 

  • K Takahashi M Hijikata EI Samokhvalov S Mishiro (2000) ArticleTitleFull or near full length nucleotide sequences of TT virus variants (Types SANBAN and YONBAN) and the TT virus-like mini virus Intervirology 43 119–123 Occurrence Handle10971131 Occurrence Handle10.1159/000025034 Occurrence Handle1:CAS:528:DC%2BD3cXntFGisro%3D

    Article  PubMed  CAS  Google Scholar 

  • Y Tanaka D Primi RY Wang T Umemura AE Yeo M Mizokami HJ Alter JW Shih (2001) ArticleTitleGenomic and molecular evolutionary analysis of a newly identified infectious agent (SEN virus) and its relationship to the TT virus family J Infect Dis 183 359–367 Occurrence Handle11133366 Occurrence Handle10.1086/318091 Occurrence Handle1:CAS:528:DC%2BD3MXhtVarsLw%3D

    Article  PubMed  CAS  Google Scholar 

  • K Thom C Morrison JC Lewis P Simmonds (2003) ArticleTitleDistribution of TT virus (TTV), TTV-like minivirus, and related viruses in humans and nonhuman primates Virology 306 324–333 Occurrence Handle12642105 Occurrence Handle10.1016/S0042-6822(02)00049-1 Occurrence Handle1:CAS:528:DC%2BD3sXitVKmt7s%3D

    Article  PubMed  CAS  Google Scholar 

  • JD Thompson DG Higgins TJ Gibson (1994) ArticleTitleCLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice Nucleic Acids Res 22 4673–4680 Occurrence Handle7984417 Occurrence Handle10.1093/nar/22.22.4673 Occurrence Handle1:CAS:528:DyaK2MXitlSgu74%3D

    Article  PubMed  CAS  Google Scholar 

  • H Tokita S Murai H Kamitsukasa M Yagura H Harada M Takahashi H Okamoto (2002) ArticleTitleHigh 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 67 501–509 Occurrence Handle12115995 Occurrence Handle10.1002/jmv.10129

    Article  PubMed  Google Scholar 

  • M Ukita H Okamoto T Nishizawa A Tawara M Takahashi H Iizuka Y Miyakawa M Mayumi (2000) ArticleTitleThe entire nucleotide sequences of two distinct TT virus (TTV) isolates (TJN01 and TJN02) remotely related to the original TTV isolates Arch Virol 145 1543–1559 Occurrence Handle11003468 Occurrence Handle10.1007/s007050070075 Occurrence Handle1:CAS:528:DC%2BD3cXnt1Whtrk%3D

    Article  PubMed  CAS  Google Scholar 

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  1. Division of Virology, Department of Infection and Immunity, Jichi Medical University School of Medicine, Tochigi, Japan

    M. Ninomiya, M. Takahashi & H. Okamoto

  2. Department of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan

    M. Ninomiya & T. Shimosegawa

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  1. M. Ninomiya
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Ninomiya, M., Takahashi, M., Shimosegawa, T. et al. Analysis of the entire genomes of fifteen torque teno midi virus variants classifiable into a third group of genus Anellovirus. Arch Virol 152, 1961–1975 (2007). https://doi.org/10.1007/s00705-007-1046-6

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