Current Topics in Microbiology and Immunology

Volume 331

Series Editors Richard W. Compans Emory University School of Medicine, Department of Microbiology and Immunology, 3001 Rollins Research Center, Atlanta, GA 30322, USA Max D. Cooper Department of Pathology and Laboratory Medicine, Georgia Research Alliance, Emory University, 1462 Clifton Road, Atlanta, GA 30322, USA Tasuku Honjo Department of Medical Chemistry, Kyoto University, Faculty of Medicine, Yoshida, Sakyo-ku, Kyoto 606-8501, Japan Hilary Koprowski Thomas Jefferson University, Department of Cancer Biology, Biotechnology Foundation Laboratories, 1020 Locust Street, Suite M85 JAH, Philadelphia, PA 19107-6799, USA Fritz Melchers Biozentrum, Department of Cell Biology, University of Basel, Klingelbergstr. 50–70, 4056 Basel Switzerland Michael B.A. Oldstone Department of Neuropharmacology, Division of Virology, The Scripps Research Institute, 10550 N. Torrey Pines, La Jolla, CA 92037, USA Sjur Olsnes Department of Biochemistry, Institute for Cancer Research, The Norwegian Radium Hospital, Montebello 0310 Oslo, Norway Peter K. Vogt The Scripps Research Institute, Dept. of Molecular & Exp. Medicine, Division of Oncovirology, 10550 N. Torrey Pines. BCC-239, La Jolla, CA 92037, USA Ethel-Michele de Villiers • Harald zur Hausen Editors

TT Viruses

The Still Elusive Human Pathogens Editor Prof. Dr. Ethel-Michele de Villiers Prof. Dr. mult. Harald zur Hausen Deutsches Krebsforschungszentrum Abt. Deutsches Krebsforschungszentrum (DKFZ) Tumorvirus-Charakterisierung Im Neuenheimer Feld 280 Im Neuenheimer Feld 242 69120 Heidelberg 69120 Heidelberg Germany Germany

ISBN 978-3-540-70971-8 e-ISBN 978-3-540-70972-5

DOI 10.1007/978-3-540-70972-5

Current Topics in Microbiology and Immunology ISSN 0070-217x

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9 8 7 6 5 4 3 2 1 springer.com Preface

Eleven years ago the circular DNA of a novel single-stranded virus was cloned and partially characterized by Nishizawa, Okamoto and their colleagues. According to the initials of the patient from whom the isolate originated, the virus was named TT virus. This name has been subsequently changed by the International Committee on Taxonomy of Viruses (ICTV) into Torque teno virus, permitting the further use of the abbreviation TTV. Although initially suspected to play a role in non-A–E hepatitis, subsequent studies have failed to support this notion. Within a remarkably short period of time it became clear that TT viruses are widely spread globally, infect a large proportion of all human populations studied thus far, and represent an extremely heterogeneous group of viruses, now labelled as Anelloviruses. TT virus-like infections have also been noted in various animal species. The classification of this virus group turns out to be difficult. Their DNA contains between 2,200 and 3,800 nucleotides, while related so-called TT mini- viruses and a substantial proportion of intragenomic recombinants further compli- cate attempts to combine these viruses into a unifying phylogenetic concept. Although studied in many laboratories, the most interesting medical question concerning their possible pathogenic role in humans still remains unanswered today. We know of a substantial number of other infections that persist for life within infected individuals: members of the herpesvirus group, including the Epstein-Barr virus, and also polyomaviruses, such as BK and JC viruses, may serve as examples. In virtually all of these instances these viruses are able to induce human diseases, at least in some patients: e.g. Epstein-Barr virus may cause infectious mononucleosis and in immunosuppressed patients B cell lymphomas. BK and JC virus infections do not seem to cause acute conditions; immunosuppression, how- ever, may result in BK virus-induced haemorrhagic cystitis or, in JC, virus-caused progressive multifocal leukoencephalopathy. Thus, it is not unreasonable to suspect that persistence of at least some specific TT virus genotypes may result in some infected individuals in a definable pathogenicity. We believe that this volume provides the first hints in support of this view. When the editors were approached by Peter Vogt to compile a specific volume of Current Topics in Microbiology and Immunology on TT viruses, they were pleased and quickly agreed. For comparative purposes we also invited contributions on structurally related single-stranded DNA viruses, like chicken anaemia and plant

v vi Preface

Gemini viruses. The response of invited contributors was exceedingly good and all of them delivered their contributions in time. We gratefully appreciate their help in compiling this volume, which seems to represent the first comprehensive documen- tation of this interesting virus group. We are also grateful to Springer, and specifi- cally to Anne Clauss, for gently accompanying the editing and production process of this volume. Heidelberg, 8 June 2008 Ethel-Michele de Villiers Harald zur Hausen Contents

History of Discoveries and Pathogenicity of TT Viruses ...... 1 H. Okamoto

Classifi cation of TTV and Related Viruses (Anelloviruses) ...... 21 P. Biagini

TT Viruses in Animals ...... 35 H. Okamoto

Replication of and Protein Synthesis by TT Viruses ...... 53 L. Kakkola, K. Hedman, J. Qiu, D. Pintel, and M. Söderlund-Venermo

Immunobiology of the Torque Teno Viruses and Other Anelloviruses ...... 65 F. Maggi and M. Bendinelli

Intragenomic Rearrangement in TT Viruses: A Possible Role in the Pathogenesis of Disease ...... 91 E.-M. de Villiers, R. Kimmel, L. Leppik, and K. Gunst

TT Viruses: Oncogenic or Tumor-Suppressive Properties? ...... 109 H. zur Hausen and E.-M. de Villiers

Relationship of Torque Teno Virus to Chicken Anemia Virus ...... 117 S. Hino and A.A. Prasetyo

Apoptosis-Inducing Proteins in Chicken Anemia Virus and TT Virus ...... 131 M.H. de Smit and M.H.M. Noteborn

Chicken Anemia Virus ...... 151 K.A. Schat

vii viii Contents

Geminiviruses ...... 185 H. Jeske

Index ...... 227 List of Contributors

Mauro Bendinelli Retrovirus Center and Department of Experimental Pathology, University of Pisa 37, Via San Zeno I-56127 Pisa, Italy, [email protected] P. Biagini UMR CNRS 6578 Equipe Emergence et co-évolution virale, Etablissement Français du Sang Alpes-Méditerranée et Université de la Méditerranée, 27, Bd. Jean Moulin, 13005 Marseille, France, [email protected], [email protected] Maarten H de Smit Department of Molecular Genetics, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands, [email protected] Ethel-Michele de Villiers Division for the Characterisation of Tumour Viruses, Deutsches Krebsforschungs- zentrum, Im Neuenheimer Feld 242, 69120 Heidelberg, Germany, [email protected] Harald zur Hausen Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany, [email protected] Klaus Hedman Department of Virology, Haartman Institute, University of Helsinki and Helsinki University Central Hospital Laboratory, Finland, klaus.hedman@helsinki.fi Shigeo Hino Medical Scanning, 4-3-1F, Kanda-Surugadai, Chiyoda, Tokyo 101-0062 Japan, [email protected] Holger Jeske Institute of Biology, Department of Molecular Biology and Plant Virology, University of Stuttgart, Pfaffenwaldring 57, 70550 Stuttgart, Germany, [email protected]

ix x List of Contributors

Laura Kakkola Department of Virology, Haartman Institute, University of Helsinki and Helsinki University Central Hospital Laboratory, Finland, laura.kakkola@helsinki.fi Fabrizio Maggi Virology Unit, Pisa University Hospital 35-37, Via San Zeno I-56127 Pisa, Italy, [email protected] Mathieu HM Noteborn Department of Molecular Genetics, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands, [email protected] H. Okamoto Division of Virology, Department of Infection and Immunity, Jichi Medical University School of Medicine, 3311-1 Yakushiji, Shimotsuke-Shi, Tochigi-Ken 329-0498, Japan, [email protected] David Pintel Department of Molecular Microbiology and Immunology, University of Missouri-Columbia, USA, [email protected] Afi ono Agung Prasetyo Division of Virology, Faculty of Medicine, Tottori University, Yonago 683-8503, Japan Jianming Qiu Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, USA, [email protected] Karel A. Schat Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA, [email protected] Maria Söderlund-Venermo Department of Virology, Haartman Institute, University of Helsinki and Helsinki University Central Hospital Laboratory, Finland, maria.soderlund-venermo@helsinki.fi History of Discoveries and Pathogenicity of TT Viruses

H. Okamoto

Contents History of Discoveries ...... 2 Discovery of Original TT Virus ...... 2 Virological Characterization of TTV ...... 3 Discovery of Many TTV-Like Variants in Humans ...... 3 Discovery of Torque Teno Mini Virus ...... 4 Discovery of Torque Teno Midi Virus ...... 6 Multiple Infections of Three Human Anelloviruses (TTV, TTMDV, and TTMV) in Humans ...... 7 PCR Assays for Differential Detection of Three Human Anelloviruses ...... 7 Early Acquisition of Dual or Triple Infection of three Human Anelloviruses During Infancy ...... 9 Pathogenesis and Clinical Manifestations ...... 10 Pathogenesis ...... 10 Host’s Immune Response ...... 10 Disease Associations ...... 11 Conclusions ...... 14 References ...... 15

Abstract Since 1997, groups of novel nonenveloped DNA viruses with a circular, single-stranded (negative sense) DNA genome of 3.6–3.9 kb, 3.2 kb, or 2.8–2.9 kb in size have been discovered and designated Torque teno virus (TTV), Torque teno midi virus (TTMDV), and Torque teno mini virus (TTMV), respectively, in the floating genus Anellovirus. These three anelloviruses frequently and ubiquitously infect humans, and the infections are characterized by lifelong viremia and great genetic variability. Although TTV infection has been epidemiologically suggested to be associated with many diseases including liver diseases, respiratory disorders, hematological disorders, and cancer, there is no direct causal evidence for links between TTV infection and specific clinical diseases. The pathogenetic role of

H. Okamoto Division of Virology, Department of Infection and Immunity , Jichi Medical University School of Medicine , 3311-1 Yakushiji, Shimotsuke-Shi , Tochigi-Ken , 329-0498 , Japan [email protected]

E.-M. de Villiers, H. zur Hausen (eds.), TT Viruses: The Still Elusive Human Pathogens, 1 © Springer Verlag Berlin Heidelberg 2009 2 H. Okamoto

TTMV and TTMDV infections remains unknown. The changing ratio of the three anelloviruses to each other over time, relative viral load, or combination of different genotype(s) of each anellovirus may be associated with the pathogenicity or the dis- ease-inducing potential of these three human anelloviruses. To clarify their disease association, polymerase chain reaction (PCR) systems for accurately detecting, differentiating, and quantitating all of the genotypes and/or genogroups of TTV, TTMDV, and TTMV should be established and standardized, as should methods to detect past infections and immunological responses to anellovirus infections.

History of Discoveries

Discovery of Original TT Virus

In 1997, while searching for an as-yet-unidentified hepatitis viruses, Nishizawa et al. found a novel DNA virus in a Japanese patient (initials T.T.) with posttransfu- sion hepatitis of unknown etiology (Nishizawa et al. 1997). The patient was 58 years old, and had received 35 units of blood during heart surgery. He had elevated alanine aminotransferase (ALT) levels 9–11 weeks after the surgery (peak, 180 IU/l at 10 weeks after transfusion). Representational difference analysis (RDA) (Lisitsyn et al. 1993) was performed for the specific amplification of nucleic acid sequences present in the serum of the patient during the period of his acute hepatitis, but which were absent before transfusion. After three courses of subtraction, a broad but clear band 0.5 kb in size was visualized on electrophoresis, and subjected to molecular cloning. Among the 36 clones obtained, varying in size from 281 to 564 bp, 9 clones of 500 bp were similar to each other, whose sequence was detectable only during the period of acute hepatitis in the index patient. A representative clone (N22) with the consensus sequence showed poor homology to any of the 1,731,752 sequences deposited in DNA databases as of 2 October 1997 (Nishizawa et al. 1997). The N22 clone was found to originate from the genome of a nonenveloped, single-stranded DNA virus based on data using a PCR method with N22-derived primers RD037 and RD038 in the first round and RD051 and RD052 in the second round. The virus was provisionally named “TT” virus (TTV) after the initials of the index patient (Nishizawa et al. 1997). In brief, since the N22 sequence was not amplified from any of four human genomic DNA samples, a nonhost origin of N22 was attested. Furthermore, since the N22 sequence fractionated in sucrose gradient at 1.26 g/cm3 and was resistant to DNase I, it was concluded to be encapsidated and thereby of viral origin. Furthermore, serum-derived TTV DNA was sensitive to mung bean nuclease but resistant to RNase A and restriction enzymes. Hence, TTV was believed to be a DNA virus that had a single-stranded genome (Nishizawa et al. 1997; Okamoto et al. 1998b). Since the density of Tween 80-treated TTV remained unchanged in sucrose gradient, TTV was understood to be a nonenveloped virus (Okamoto et al. 1998b). History of Discoveries and Pathogenicity of TT Viruses 3

The N22 sequence was extended to 3,739 nt in the prototype TTV isolate (TA278) obtained from a 34-year-old male blood donor with an elevated ALT level of 106 IU/l and containing TTV DNA in high titer (10 5 copies/ml) detectable by PCR with nested N22 primers, but its extreme 5′- and 3′-end sequences remained undetermined at that time (Okamoto et al. 1998b). In 1999, the presence of a GC-rich sequence of approximately 120 nt was reported (Miyata et al. 1999; Mushahwar et al. 1999), leading to the recognition of the circular nature of the TTV genome with negative polarity. The entire genomic length of the TA278 isolate was finally determined to be 3,853 nt, with the unique stem-and-loop structures in the GC-rich region, which would play a pivotal role in viral replication (Okamoto et al. 1999b, c).

Virological Characterization of TTV

Subsequent studies revealed the following characteristics of TTV. The buoyant density in cesium chloride (CsCl) was found to be 1.31–1.33 g/cm3 for TTV in serum and 1.33–1.35 g/cm3 for TTV in feces (Okamoto et al. 1998a). TTV particles in the circulation were bound to immunoglobulin G (IgG), forming immune com- plexes (Itoh et al. 2000). Therefore, TTV-associated particles with a diameter of 30–32 nm recovered from the sera of infected humans were observed as aggregates of various sizes on electron microscopy. In contrast, TTV particles in feces exist as free virions. TTV particles of genotype 1a with a diameter of 30–32 nm and banding at 1.33–1.35 g/cm 3 have been visualized in fecal supernatant by immune electron microscopy using γ-globulins from human plasma containing TTV geno- type 1a-specific antibodies (Itoh et al. 2000; Tsuda et al. 1999). Kamahora et al. (2000) analyzed the messenger RNAs (mRNAs) transcribed from a plasmid containing the whole genome construct of TTV in COS1 cells. They recovered three spliced mRNAs of 3.0 kb, 1.2 kb, and 1.0 kb with common 5′- and 3′-termini, and showed that the splicing sites link distant open reading frames (ORFs) to create two new ORFs capable of encoding 286 amino acids (aa) and 289aa. Such spliced mRNAs of TTV have also been observed in actively replicating cells including bone marrow cells in infected humans (Okamoto et al. 2000d). The proposed genomic organization of the prototype TTV isolate (TA278; Accession No. AB017610) is illustrated in Fig. 1 .

Discovery of Many TTV-Like Variants in Humans

After the discovery of the original TTV isolate, with the use of primers based on a conserved untranslated region, many TTV variants with marked genetic variability were identified (Hallett et al. 2000; Hijikata et al. 1999b; Khudyakov et al. 2000; Muljono et al. 2001; Okamoto et al. 1999a, c, d, 2000d, 2001; Peng et al. 2002; 4 H. Okamoto

TTV TTMDV TTMV

Fig. 1 Genomic organization of the prototype TTV, TTMDV, and TTMV isolates. The circumfer- ence of each circle represents the relative size of the genome. The closed arrows represent ORFs (ORF1 to ORF4). The open boxes located between an upstream closed box and downstream closed arrow in ORF3 and ORF4, which encode joint proteins, represent areas corresponding to introns in the mRNA (Kamahora et al. 2000; Okamoto et al. 2000c). The shaded box indicates the GC-rich stretch and the small closed circle represents the position of the TATA box. (Reproduced from Ninomiya et al. 2007a, with permission)

Takahashi et al. 2000a; Ukita et al. 2000) and segregated into at least 39 genotypes with a difference of greater than 30% or five major genetic groups with a differ- ence of greater than 50% difference (Okamoto et al. 2004; Peng et al. 2002; Fig. 2 ). Independently, the SEN virus (SENV) was discovered by RDA (patent application WO 00/28039, 2000). However, it soon became apparent that it repre- sented different genotypes of TTV (Tanaka et al. 2001). In addition to ubiquitous distribution of many TTV-like variants in various tissues and body fluids of humans, multiple genotypes of TTV may be found within an infected individual, often with different genotype combinations predominating in different tissues (Okamoto et al. 2001). This suggests that certain virus genotypes might be better adapted to particular cell or tissue types.

Discovery of Torque Teno Mini Virus

In 2000, a small virus that was distantly related to TTV was accidentally discovered by PCR of human plasma samples using TTV-specific primers that partially matched homologous sequences but generated a noticeably shorter amplicon than expected for TTV, and was provisionally named as TTV-like mini virus (TLMV) (Takahashi et al. 2000b). The genome of TLMV consists of a circular, single-stranded DNA of approximately 2,800–2,900 nt with negative polarity (Fig. 1). The size of a TLMV virion has been estimated to be less than 30 nm in diameter (Takahashi et al. 2000b). TLMV resembles TTV in genomic structure, and also contains an arginine- rich N-terminus as well as Rep-motifs in the ORF1 region and a chicken anemia virus (CAV)-like motif in the ORF2 region (Biagini et al. 2001b, 2007; Okamoto History of Discoveries and Pathogenicity of TT Viruses 5 -joining method scale bar represents the he TTMDV MDJHem3-2 (AB303554) MDJHem5 (AB303555) MD1-073 (AB290918) MD1-032 (AB290917) MDJN51 (AB303582) TTV group 4 MDJN1 (AB303558) MDJN97 (AB303566) MDJHem3-1 (AB303553) MDJN52 (AB303563) MDJHem8-1 (AB303556) MDJHem2 (AB303552) MDJN2 (AB303559) MDJHem8-2 (AB303557) PB4TL MDJN47 (AB303561) TTMV CLC062 (AF291073) MD2-013 (AB290919) (AB038625) MDJN69 (AB303564) MDJN14 (AB303560) MDJN91 (AB303565) (AB038631) NLC030 yonKC009 (AB038621) JT19F (AB064602) yonLC011 (AB038622) JT03F (AB064599) yonKC197 (AB038624) CT25F (AB064596) CBD203 CT30F (AB064597) CT43F (AB064598) yonKC186 (AB038623) JT14F (AB064601) JT41F (AB064603) CT23F (AB064595) (AB026929) JT05F (AB064600) 96 CLC156 (AB038627)

53 100 97

Pt-TTV8-II

) (AB041963)

2913) 8) TTV group 1 TGP96 (AB041962)

21 (AF254410) 21 100

98 91 30) 2916)

AF079173) NLC026 (AB0386

TTV0 94

66)

100 92 )

GH1 (AF12 GH1 57 NLC023

CHN1 ( CHN1 629)

TWH (AF351132) TWH (AB038 JA20 (AF122914 JA20

(AB026345)

JA2B (AF12291 JA2B

JA1 (AF12 JA1 31

(AY0264 TRM1 CBD2 CHN2 (AF129887) CHN2

US32 (AF122921) US32

(AB021877) 100 100 (AB026930) 4)

US35 (AF122920) US35

L02 L02

100

7138)

(AF116842) CBD279

BDH1

0 (AF122919) 0 (AB026931)

JA4 (AF122917 JA4

(AB00839 CLC138

JA1

620218)

69 TA278 (AB038626)

BM1B-05 (DQ186999) tth5 (AJ620227)

100 CLC205

T3PB (AF24 T3PB (AB038628) 8) tth3 (AJ tth3

JT33F (AB064606)

100

JA9 (AF122915) TK16 (AB026346) P/1C1 (AF298585) (AF298585) P/1C1

TP1-3 (AB026347)

) L01

58

HEL32 (AY666122) HEL32 64 (AY026465) 100

100 JT34F (AB064607)

(AB041957

s-TTV.CH71 (AB04960 s-TTV.CH71

33

100 (DQ187004)

BM1C-16 BM1C-16

Pt-TTV6

38

(AB037926) 65

)

96

TTV group 5 23989)

(AJ620231) s-TTV.CH65-1 s-TTV.CH65-1

5014 12)

tth8 tth8 )

3h (AY8 3h

100

0) F43

TUS01

tth6 tth6 (AB017613

80

100

(AJ6202 F247137) 39F (AB064604) 39F

64

94 (AB064605) F KAV (A KAV

TUPB (A TUPB

99 CT 99

TJN01 (AB028668) TJN01 CT44

68)

61)

SENV-D (AX02573 SENV-D 98 0.1

99

SENV-F

4647)

)

(AX025822) (AF2617 PMV

ViPi04 (DQ3612 ViPi04 )

100 607

TTV group 2

08F (AB05 08F

(AB054648

597) Kt- (AX025830)

SAa-38 (AB060593)

-2 (AB049 -2

SENV-G Kt-10F SENV-H (AX025838) P601

SANBAN (AB025946) 01 (AB060 01 SENV-C (AX025718) (AB028669) TJN02

SAf-09 (AB060596)

(AX025761) SAa-

(DQ186994) SAa-10 (AB060594) s-TTV.CH65 2h (AY823988) SAj-30 (AB060595) tth4 (AJ620226) BM1A-02 SAa-39 (AB060592) TYM9 (AB050448) SENV-E (AB038620) (DQ186996) sanS039 TTV group 3 (AB038619) sanIR1031 Phylogenetic tree based on the entire nucleotide sequence of ORF1 81 TTV, 18 TTMDV, and 13 TTMV isolates by neighbor

Fig. 2 Fig. number of nucleotide substitutions per position. (Reproduced from Ninomiya et al. 2008, with permission) (Saitou and Nei 1987). The percentage of bootstrap values generated from 1,000 samplings the data is shown near nodes. T