A field guide to eukaryotic circular single-stranded DNA viruses: insights gained from metagenomics (original) (raw)

• Balamurugan V, Kataria JM (2006) Economically important non-oncogenic immunosuppressive viral diseases of chicken—current status. Vet Res Commun 30:541–566
  Article PubMed CAS Google Scholar
• Bassami MR, Berryman D, Wilcox GE, Raidal SR (1998) Psittacine beak and feather disease virus nucleotide sequence analysis and its relationship to porcine circovirus, plant circoviruses, and chicken anaemia virus. Virology 249:453–459
  Article PubMed CAS Google Scholar
• Belyi VA, Levine AJ, Skalka AM (2010) Sequences from ancestral single-stranded DNA viruses in vertebrate genomes: the Parvoviridae and Circoviridae are more than 40 to 50 million years old. J Virol 84:12458–12462
  Article PubMed CAS Google Scholar
• Bergoin M, Tijssen P (2010) Densoviruses: a highly diverse group of arthropod parvoviruses. In: Asgari S, Johnson K (eds) Insect Virology. Caister Academic Press, Great Britain, pp 59–82
  Google Scholar
• Biagini P, Gallian P, Attoui H, Touinssi M, Cantaloube JF, de Micco P, de Lamballerie X (2001) Genetic analysis of full-length genomes and subgenomic sequences of TT virus-like mini virus human isolates. J Gen Virol 82:379–383
  PubMed CAS Google Scholar
• Biagini P (2011) ICTV taxonomy proposal: restructuring and expansion of the family Anelloviridae. http://talk.ictvonline.org/files/proposals/taxonomy_proposals_vertebrate1/m/vert01/3911.aspx
• Biagini P (2011) ICTV taxonomy proposal: restructuring and expansion of the family Circoviridae. http://talk.ictvonline.org/files/proposals/taxonomy_proposals_vertebrate1/m/vert01/3912.aspx
• Binga EK, Lasken RS, Neufeld JD (2008) Something from (almost) nothing: the impact of multiple displacement amplification on microbial ecology. ISME J 2:233–241
  Article PubMed CAS Google Scholar
• Blinkova O, Victoria J, Li Y, Keele BF, Sanz C, Ndjango J-BN, Peeters M, Travis D, Lonsdorf EV, Wilson ML, Pusey AE, Hahn BH, Delwart EL (2010) Novel circular DNA viruses in stool samples of wild-living chimpanzees. J Gen Virol 91:74–86
  Article PubMed CAS Google Scholar
• Breitbart M, Rohwer F (2005) Method for discovering novel DNA viruses in blood using viral particle selection and shotgun sequencing. Biotechniques 39:729–736
  Article PubMed CAS Google Scholar
• Briddon RW, Bull SE, Amin I, Idris AM, Mansoor S, Bedford ID, Dhawan P, Rishi N, Siwatch SS, Abdel-Salam AM, Brown JK, Zafar Y, Markham PG (2003) Diversity of DNA beta, a satellite molecule associated with some monopartite begomoviruses. Virology 312:106–121
  Article PubMed CAS Google Scholar
• Briddon RW, Bull SE, Amin I, Mansoor S, Bedford ID, Rishi N, Siwatch SS, Zafar Y, Abdel-Salam AM, Markham PG (2004) Diversity of DNA 1: a satellite-like molecule associated with monopartite begomovirus-DNA beta complexes. Virology 324:462–474
  Article PubMed CAS Google Scholar
• Briddon RW, Stanley J (2006) Subviral agents associated with plant single-stranded DNA viruses. Virology 344:198–210
  Article PubMed CAS Google Scholar
• Briddon RW, Patil BL, Bagewadi B, Nawaz-ul-Rehman MS, Fauquet CM (2010) Distinct evolutionary histories of the DNA-A and DNA-B components of bipartite begomoviruses. BMC Evol Biol 10:97
  Article PubMed CAS Google Scholar
• Carstens E (2010) Ratification vote on taxonomic proposals to the International Committee on Taxonomy of Viruses (2009). Arch Virol 155:133–146
  Article PubMed CAS Google Scholar
• Cheung AK (2004) Identification of an octanucleotide motif sequence essential for viral protein, DNA, and progeny virus biosynthesis at the origin of DNA replication of porcine circovirus type 2. Virology 324:28–36
  Article PubMed CAS Google Scholar
• Cheung AK (2004) Detection of template strand switching during initiation and termination of DNA replication of porcine circovirus. J Virol 78:4268–4277
  Article PubMed CAS Google Scholar
• Choudhury NR, Malik PS, Singh DK, Islam MN, Kaliappan K, Mukherjee SK (2006) The oligomeric Rep protein of Mungbean yellow mosaic India virus (MYMIV) is a likely replicative helicase. Nucl Acids Res 34:6362–6377
  Article PubMed CAS Google Scholar
• Clerot D, Bernardi F (2006) DNA helicase activity is associated with the replication initiator protein Rep of Tomato yellow leaf curl geminivirus. J Virol 80:11322–11330
  Article PubMed CAS Google Scholar
• Culley AI, Lang AS, Suttle CA (2006) Metagenomic analysis of coastal RNA virus communities. Science 312:1795–1798
  Article PubMed CAS Google Scholar
• Davidson I, Shulman LM (2008) Unraveling the puzzle of human anellovirus infections by comparison with avian infections with the chicken anemia virus. Virus Res 137:1–15
  Article PubMed CAS Google Scholar
• Day JM, Ballard LL, Duke MV, Scheffler BE, Zsak L (2010) Metagenomic analysis of the turkey gut RNA virus community. Virol J 7:313
  Article PubMed CAS Google Scholar
• de Villiers E-M, zur Hausen H (2009) TT viruses—the still elusive human pathogens. Springer, Berlin
  Google Scholar
• de Villiers EM, Borkosky SS, Kimmel R, Gunst K, Fei JW (2011) The diversity of torque teno viruses: In vitro replication leads to the formation of additional replication-competent subviral molecules. J Virol 85:7284–7295
  Article PubMed CAS Google Scholar
• del Solar G, Giraldo R, Ruiz-Echevarria MJ, Espinosa M, Diaz-Orejas R (1998) Replication and control of circular bacterial plasmids. Microbiol Mol Biol Rev 62:434–464
  PubMed Google Scholar
• Desbiez C, David C, Mettouchi A, Laufs J, Gronenborn B (1995) Rep protein of tomato yellow leaf curl geminivirus has an ATPase activity required for viral DNA replication. Proc Natl Acad Sci USA 92:5640–5644
  Article PubMed CAS Google Scholar
• Djikeng A, Kuzmickas R, Anderson NG, Spiro DJ (2009) Metagenomic analysis of RNA viruses in a fresh water lake. PLoS ONE 4:e7264
  Article PubMed CAS Google Scholar
• Dry IB, Krake LR, Rigden JE, Rezaian MA (1997) A novel subviral agent associated with a geminivirus: The first report of a DNA satellite. Proc Natl Acad Sci USA 94:7088–7093
  Article PubMed CAS Google Scholar
• Duffy S, Shackelton LA, Holmes EC (2008) Rates of evolutionary change in viruses: patterns and determinants. Nat Rev Genet 9:267–276
  Article PubMed CAS Google Scholar
• Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32:1792–1797
  Article PubMed CAS Google Scholar
• Fauquet C, Briddon R, Brown J, Moriones E, Stanley J, Zerbini M, Zhou X (2008) Geminivirus strain demarcation and nomenclature. Arch Virol 153:783–821
  Article PubMed CAS Google Scholar
• Fauquet CM, Mayo MA, Maniloff J, Desselberger U, Ball LA (2005) Virus Taxonomy: eighth report of the international committee on Taxonomy of Viruses. Academic Press, San Diego
  Google Scholar
• Faurez F, Dory D, Grasland B, Jestin A (2009) Replication of porcine circoviruses. Virol J 6:60
  Article PubMed CAS Google Scholar
• Finn RD, Tate J, Mistry J, Coggill PC, Sammut SJ, Hotz H-R, Ceric G, Forslund K, Eddy SR, Sonnhammer ELL, Bateman A (2008) The Pfam protein families database. Nucleic Acids Res 36:D281–D288
  Article PubMed CAS Google Scholar
• Firth C, Charleston MA, Duffy S, Shapiro B, Holmes EC (2009) Insights into the evolutionary history of an emerging livestock pathogen: porcine circovirus 2. J Virol 83:12813–12821
  Article PubMed CAS Google Scholar
• Ge XY, Li JL, Peng C, Wu LJ, Yang XL, Wu YQ, Zhang YZ, Shi ZL (2011) Genetic diversity of novel circular ssDNA viruses in bats in China. J Gen Virol 92:2646–2653
  Article PubMed CAS Google Scholar
• Gibbs MJ, Weiller GF (1999) Evidence that a plant virus switched hosts to infect a vertebrate and then recombined with a vertebrate-infecting virus. Proc Natl Acad Sci USA 96:8022–8027
  Article PubMed CAS Google Scholar
• Gibbs MJ, Smeianov VV, Steele JL, Upcroft P, Efimov BA (2006) Two families of Rep-like genes that probably originated by interspecies recombination are represented in viral, plasmid, bacterial, and parasitic protozoan genomes. Mol Biol Evol 23:1097–1100
  Article PubMed CAS Google Scholar
• Gorbalenya AE, Koonin EV, Wolf YI (1990) A new superfamily of putative NTP-binding domains encoded by genomes of small DNA and RNA viruses. FEBS Lett 262:145–148
  Article PubMed CAS Google Scholar
• Gorbalenya AE, Koonin EV (1993) Helicases: amino acid sequence comparisons and structure-function relationships. Curr Opin Struct Biol 3:419–429
  Article CAS Google Scholar
• Grigoras I, Timchenko T, Grande-Perez A, Katul L, Vetten HJ, Gronenborn B (2010) High variability and rapid evolution of a nanovirus. J Virol 84:9105–9117
  Article PubMed CAS Google Scholar
• Gutierrez C (1999) Geminivirus DNA replication. Cell Mol Life Sci 56:313–329
  Article PubMed CAS Google Scholar
• Hafner GJ, Stafford MR, Wolter LC, Harding RM, Dale JL (1997) Nicking and joining activity of banana bunchy top virus replication protein in vitro. J Gen Virol 78:1795–1799
  PubMed CAS Google Scholar
• Hanley-Bowdoin L, Settlage SB, Orozco BM, Nagar S, Robertson D (1999) Geminiviruses: Models for plant DNA replication, transcription, and cell cycle regulation. Crit Rev Plant Sci 18:71–106
  Article CAS Google Scholar
• Heyraud-Nitschke F, Schumacher S, Laufs J, Schaefer S, Schell J, Gronenborn B (1995) Determination of the origin cleavage and joining domain of geminivirus Rep proteins. Nucleic Acids Res 23:910–916
  Article PubMed CAS Google Scholar
• Heyraud F, Matzeit V, Kammann M, Schaefer S, Schell J, Gronenborn B (1993) Identification of the initiation sequence for viral-strand DNA synthesis of wheat dwarf virus. EMBO J 12:4445–4452
  PubMed CAS Google Scholar
• Ilyina TV, Koonin EV (1992) Conserved sequence motifs in the initiator proteins for rolling circle DNA replication encoded by diverse replicons from eubacteria, eucaryotes and archaebacteria. Nucleic Acids Res 20:3279–3285
  Article PubMed CAS Google Scholar
• Iyer LM, Balaji S, Koonin EV, Aravind L (2006) Evolutionary genomics of nucleo-cytoplasmic large DNA viruses. Virus Res 117:156–184
  Article PubMed CAS Google Scholar
• Jeske H, Lutgemeier M, Preiss W (2001) DNA forms indicate rolling circle and recombination-dependent replication of Abutilon mosaic virus. EMBO J 20:6158–6167
  Article PubMed CAS Google Scholar
• Kapitonov VV, Jurka J (2001) Rolling-circle transposons in eukaryotes. Proc Natl Acad Sci USA 98:8714–8719
  Article PubMed CAS Google Scholar
• Katzourakis A, Gifford RJ (2010) Endogenous viral elements in animal genomes. PLoS Genet 6:e1001191
  Article PubMed CAS Google Scholar
• Khan SA (1997) Rolling-circle replication of bacterial plasmids. Microbiol Mol Biol Rev 61:442–455
  PubMed CAS Google Scholar
• Kim KH, Chang HW, Nam YD, Roh SW, Kim MS, Sung Y, Jeon CO, Oh HM, Bae JW (2008) Amplification of uncultured single-stranded DNA viruses from rice paddy soil. Appl Environ Microbiol 74:5975–5985
  Article PubMed CAS Google Scholar
• Kim KH, Bae JW (2011) Amplification methods bias metagenomic libraries of uncultured single-stranded and double-stranded DNA viruses. Appl Environ Microbiol 77:7663–7668
  Article PubMed CAS Google Scholar
• Koonin EV, Ilyina TV (1992) Geminivirus replication proteins are related to prokaryotic plasmid rolling circle DNA-replication initiator proteins. J Gen Virol 73:2763–2766
  Article PubMed CAS Google Scholar
• Krupovic M, Ravantti JJ, Bamford DH (2009) Geminiviruses: a tale of a plasmid becoming a virus. BMC Evol Biol 9:112
  Article PubMed CAS Google Scholar
• Latham G (2001) DNase I demystified (Ambion, Inc.). http://www.invitrogen.com/site/us/en/home/References/Ambion-Tech-Support/nuclease-enzymes/general-articles/dnase-i-demystified.html
• Laufs J, Jupin I, David C, Schumacher S, HeyraudNitschke F, Gronenborn B (1995) Geminivirus replication: Genetic and biochemical characterization of Rep protein function, a review. Biochimie 77:765–773
  Article PubMed CAS Google Scholar
• Laufs J, Schumacher S, Geisler N, Jupin I, Gronenborn B (1995) Identification of the nicking tyrosine of geminivirus Rep protein. FEBS Lett 377:258–262
  Article PubMed CAS Google Scholar
• Laufs J, Traut W, Heyraud F, Matzeit V, Rogers SG, Schell J, Gronenborn B (1995) In vitro cleavage and joining at the viral origin of replication by the replication initiator protein of tomato yellow leaf curl virus. Proc Natl Acad Sci USA 92:3879–3883
  Article PubMed CAS Google Scholar
• Lefeuvre P, Lett JM, Varsani A, Martin DP (2009) Widely conserved recombination patterns among single-stranded DNA viruses. J Virol 83:2697–2707
  Article PubMed CAS Google Scholar
• Lefeuvre P, Harkins GW, Lett JM, Briddon RW, Chase MW, Moury B, Martin DP (2011) Evolutionary time-scale of the begomoviruses: Evidence from integrated sequences in the Nicotiana genome. PLoS ONE 6:e19193
  Article PubMed CAS Google Scholar
• Leppik L, Gunst K, Lehtinen M, Dillner J, Streker K, de Villiers E-M (2007) In vivo and in vitro intragenomic rearrangement of TT viruses. J Virol 81:9346–9356
  Article PubMed CAS Google Scholar
• Li L, Kapoor A, Slikas B, Bamidele OS, Wang C, Shaukat S, Masroor MA, Wilson ML, Ndjango J-BN, Peeters M, Gross-Camp ND, Muller MN, Hahn BH, Wolfe ND, Triki H, Bartkus J, Zaidi SZ, Delwart E (2010) Multiple diverse circoviruses infect farm animals and are commonly found in human and chimpanzee feces. J Virol 84:1674–1682
  Article PubMed CAS Google Scholar
• Li L, Victoria JG, Wang C, Jones M, Fellers GM, Kunz TH, Delwart E (2010) Bat guano virome: predominance of dietary viruses from insects and plants plus novel mammalian viruses. J Virol 84:6955–6965
  Article PubMed CAS Google Scholar
• Li LL, Shan TL, Soji OB, Alam MM, Kunz TH, Zaidi SZ, Delwart E (2011) Possible cross-species transmission of circoviruses and cycloviruses among farm animals. J Gen Virol 92:768–772
  Article PubMed CAS Google Scholar
• Liu HQ, Fu YP, Li B, Yu X, Xie JT, Cheng JS, Ghabrial SA, Li GQ, Yi XH, Jiang DH (2011) Widespread horizontal gene transfer from circular single-stranded DNA viruses to eukaryotic genomes. BMC Evol Biol 11:276
  Article PubMed CAS Google Scholar
• Londono A, Riego-Ruiz L, Arguello-Astorga GR (2010) DNA-binding specificity determinants of replication proteins encoded by eukaryotic ssDNA viruses are adjacent to widely separated RCR conserved motifs. Arch Virol 155:1033–1046
  Article PubMed CAS Google Scholar
• Lopez-Bueno A, Tamames J, Velazquez D, Moya A, Quesada A, Alcami A (2009) High diversity of the viral community from an Antarctic lake. Science 326:858–861
  Article PubMed CAS Google Scholar
• Lorinez M, Csagola A, Farkas SL, Szekely C, Tuboly T (2011) First detection and analysis of a fish circovirus. J Gen Virol 92:1817–1821
  Article CAS Google Scholar
• Ma Y, Paulsen IT, Palenik B (2011) Analysis of two marine metagenomes reveals the diversity of plasmids in oceanic environments. Environ Microbiol 14:453–466
  Article PubMed CAS Google Scholar
• Mandal B (2010) Advances in small isometric multicomponent ssDNA viruses infecting plants. Indian J Virol 21:18–30
  Article Google Scholar
• Mansoor S, Zafar Y, Briddon RW (2006) Geminivirus disease complexes: the threat is spreading. Trends Plant Sci 11:209–212
  Article PubMed CAS Google Scholar
• Martin D, Shepherd D (2009) The epidemiology, economic impact and control of maize streak disease. Food Secur 1:305–315
  Article Google Scholar
• Martin DP, Biagini P, Lefeuvre P, Golden M, Roumagnac P, Varsani A (2011) Recombination in eukaryotic single stranded DNA viruses. Viruses 3:1699–1738
  Article PubMed CAS Google Scholar
• McDaniel L, Breitbart M, Mobberley J, Long A, Haynes M, Rohwer F, Paul JH (2008) Metagenomic analysis of lysogeny in Tampa Bay: implications for prophage gene expression. PLoS ONE 3:e3263
  Article PubMed CAS Google Scholar
• Merits A, Fedorkin ON, Guo D, Kalinina NO, Morozov SY (2000) Activities associated with the putative replication initiation protein of Coconut foliar decay virus, a tentative member of the genus Nanovirus. J Gen Virol 81:3099–3106
  PubMed CAS Google Scholar
• Nash TE, Dallas MB, Reyes MI, Buhrman GK, Ascencio-Ibanez JT, Hanley-Bowdoin L (2011) Functional analysis of a novel motif conserved across geminivirus Rep proteins. J Virol 85:1182–1192
  Article PubMed CAS Google Scholar
• Ng TF, Duffy S, Polston JE, Bixby E, Vallad GE, Breitbart M (2011) Exploring the diversity of plant DNA viruses and their satellites using vector-enabled metagenomics on whiteflies. PLoS One 6:e19050
  Article PubMed CAS Google Scholar
• Ng TF, Wheeler E, Greig D, Waltzek TB, Gulland F, Breitbart M (2011) Metagenomic identification of a novel anellovirus in Pacific harbor seal (Phoca vitulina richardsii) lung samples and its detection in samples from multiple years. J Gen Virol 92:1318–1323
  Article PubMed CAS Google Scholar
• Ng TFF, Manire C, Borrowman K, Langer T, Ehrhart L, Breitbart M (2009) Discovery of a novel single-stranded DNA virus from a sea turtle fibropapilloma by using viral metagenomics. J Virol 83:2500–2509
  Article PubMed CAS Google Scholar
• Ng TFF, Suedmeyer WK, Wheeler E, Gulland F, Breitbart M (2009) Novel anellovirus discovered from a mortality event of captive California sea lions. J Gen Virol 90:1256–1261
  Article PubMed CAS Google Scholar
• Ng TFF, Willner DL, Lim YW, Schmieder R, Chau B, Nilsson C, Anthony S, Ruan YJ, Rohwer F, Breitbart M (2011) Broad surveys of DNA viral diversity obtained through viral metagenomics of mosquitoes. PLoS ONE 6:e20579
  Article PubMed CAS Google Scholar
• Niagro FD, Forsthoefel AN, Lawther RP, Kamalanathan L, Ritchie BW, Latimer KS, Lukert PD (1998) Beak and feather disease virus and porcine circovirus genomes: intermediates between the geminiviruses and plant circoviruses. Arch Virol 143:1723–1744
  Article PubMed CAS Google Scholar
• Niel C, Diniz-Mendes L, Devalle S (2005) Rolling-circle amplification of Torque teno virus (TTV) complete genomes from human and swine sera and identification of a novel swine TTV genogroup. J Gen Virol 86:1343–1347
  Article PubMed CAS Google Scholar
• Novick RP (1998) Contrasting lifestyles of rolling-circle phages and plasmids. Trends Biochem Sci 23:434–438
  Article PubMed CAS Google Scholar
• Orozco BM, Kong LJ, Batts LA, Elledge S, Hanley-Bowdoin L (2000) The multifunctional character of a geminivirus replication protein is reflected by its complex oligomerization properties. J Biol Chem 275:6114–6122
  Article PubMed CAS Google Scholar
• Oshima K, Kakizawa S, Nishigawa H, Kuboyama T, Miyata S, Ugaki M, Namba S (2001) A plasmid of phytoplasma encodes a unique replication protein having both plasmid- and virus-like domains: Clue to viral ancestry or result of virus/plasmid recombination? Virology 285:270–277
  Article PubMed CAS Google Scholar
• Park EJ, Kim KH, Abell GC, Kim MS, Roh SW, Bae JW (2011) Metagenomic analysis of the viral communities in fermented foods. Appl Environ Microbiol 77:1284–1291
  Article PubMed CAS Google Scholar
• Phan TG, Kapusinszky B, Wang CL, Rose RK, Lipton HL, Delwart EL (2011) The fecal viral flora of wild rodents. PLoS Pathogens 7:e1002218
  Article PubMed CAS Google Scholar
• Pietila MK, Roine E, Paulin L, Kalkkinen N, Bamford DH (2009) An ssDNA virus infecting archaea: a new lineage of viruses with a membrane envelope. Mol Microbiol 72:307–319
  Article PubMed CAS Google Scholar
• Prasetyo AA, Kamahora T, Kuroishi A, Murakami K, Hino S (2009) Replication of chicken anemia virus (CAV) requires apoptin and is complemented by VP3 of human torque teno virus (TTV). Virology 385:85–92
  Article PubMed CAS Google Scholar
• Rijsewijk FAM, dos Santos HF, Teixeira TF, Cibulski SP, Varela APM, Dezen D, Franco AC, Roehe PM (2011) Discovery of a genome of a distant relative of chicken anemia virus reveals a new member of the genus Gyrovirus. Arch Virol 156:1097–1100
  Article PubMed CAS Google Scholar
• Rojas MR, Hagen C, Lucas WJ, Gilbertson RL (2005) Exploiting chinks in the plant’s armor: Evolution and emergence of geminiviruses. Annu Rev Phytopathol 43:361–394
  Article PubMed CAS Google Scholar
• Rosario K, Duffy S, Breitbart M (2009) Diverse circovirus-like genome architectures revealed by environmental metagenomics. J Gen Virol 90:2418–2424
  Article PubMed CAS Google Scholar
• Rosario K, Nilsson C, Lim YW, Yijun R, Breitbart M (2009) Metagenomic analysis of viruses in reclaimed water. Environ Microbiol 11:2806–2820
  Article PubMed CAS Google Scholar
• Rosario K, Breitbart M (2011) Exploring the viral world through metagenomics. Curr Opin Virol 1:289–297
  Article PubMed CAS Google Scholar
• Rosario K, Marinov M, Stainton D, Kraberger S, Wiltshire EJ, Collings DA, Walters M, Martin DP, Breitbart M, Varsani A (2011) Dragonfly cyclovirus, a novel single-stranded DNA virus discovered in dragonflies (Odonata: Anisoptera). J Gen Virol 92:1302–1308
  Article PubMed CAS Google Scholar
• Saccardo F, Cettul E, Palmano S, Noris E, Firrao G (2011) On the alleged origin of geminiviruses from extrachromosomal DNAs of phytoplasmas. BMC Evol Biol 11:185
  Article PubMed CAS Google Scholar
• Sauvage V, Cheval J, Foulongne V, Gouilh MA, Pariente K, Manuguerra JC, Richardson J, Dereure O, Lecuit M, Burguiere A, Caro V, Eloit M (2011) Identification of the first human Gyrovirus, a virus related to chicken anemia virus. J Virol 85:7948–7950
  Article PubMed CAS Google Scholar
• Segales J, Allan GM, Domingo M (2005) Porcine circovirus diseases. Anim Health Res Rev/Conf Res Workers Anim Dis 6:119–142
  Article Google Scholar
• Shan TL, Li LL, Simmonds P, Wang CL, Moeser A, Delwart E (2011) The fecal virome of pigs on a high-density farm. J Virol 85:11697–11708
  Article PubMed CAS Google Scholar
• Steinfeldt T, Finsterbusch T, Mankertz A (2001) Rep and Rep ‘ protein of Porcine circovirus type 1 bind to the origin of replication in vitro. Virology 291:152–160
  Article PubMed CAS Google Scholar
• Steinfeldt T, Finsterbusch T, Mankertz A (2006) Demonstration of nicking/joining activity at the origin of DNA replication associated with the Rep and Rep’ proteins of porcine circovirus type 1. J Virol 80:6225–6234
  Article PubMed CAS Google Scholar
• Steinfeldt T, Finsterbusch T, Mankertz A (2007) Functional analysis of cis- and trans-acting replication factors of porcine circovirus type 1. J Virol 81:5696–5704
  Article PubMed CAS Google Scholar
• Stenlund A (2003) Initiation of DNA replication: Lessons from viral initiator proteins. Nat Rev Mol Cell Biol 4:777–785
  PubMed CAS Google Scholar
• Streck AF, Bonatto SL, Homeier T, Souza CK, Gonçalves KR, Gava D, Canal CW, Truyen U (2011) High rate of viral evolution in the capsid protein of porcine parvovirus. J Gen Virol 92:2628–2636
  Article PubMed CAS Google Scholar
• Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods. Mol Biol Evol 28:2731–2739
  Article PubMed CAS Google Scholar
• Thurber RV (2011) Methods in Viral Metagenomics. In: de Bruijn FJ (ed) Handbook of molecular microbial ecology II. Wiley, New York, pp 15–24
  Chapter Google Scholar
• Timchenko T, de Kouchkovsky F, Katul L, David C, Vetten HJ, Gronenborn B (1999) A single Rep protein initiates replication of multiple genome components of faba bean necrotic yellows virus, a single-stranded DNA virus of plants. J Virol 73:10173–10182
  PubMed CAS Google Scholar
• Todd D, Hino S, Mankertz A, Mishiro S, Raidal S, Ritchie BW, Biagini P, Okamoto H, Niel C, Bendinelli M, Teo CG (2005) Family Circoviridae. In: Fauquet CM, Mayo MA, Maniloff J, Desselberger U, Ball LA (eds) Virus taxonomy: eighth report of the international committee on taxonomy of viruses. Academic Press, San Diego, pp 327–341
  Google Scholar
• Varsani A, Shepherd D, Dent K, Monjane A, Rybicki E, Martin D (2009) A highly divergent South African geminivirus species illuminates the ancient evolutionary history of this family. Virol J 6:36
  Article PubMed CAS Google Scholar
• Vega-Rocha S, Gronenborn B, Gronenborn AM, Campos-Olivas R (2007) Solution structure of the endonuclease domain from the master replication initiator protein of the nanovirus Faba bean necrotic yellows virus and comparison with the corresponding geminivirus and circovirus structures. Biochemistry 46:6201–6212
  Article PubMed CAS Google Scholar
• Vega Thurber RL, Barott KL, Hall D, Liu H, Rodriguez-Mueller B, Desnues C, Edwards RA, Haynes M, Angly FE, Wegley L, Rohwer FL (2008) Metagenomic analysis indicates that stressors induce production of herpes-like viruses in the coral Porites compressa. Proc Natl Acad Sci USA 105:18413–18418
  Article PubMed CAS Google Scholar
• Wen LB, He KW, Yang HC, Ni YX, Zhang XH, Guo RL, Pan QX (2008) Complete nucleotide sequence of a novel porcine circo-virus-like agent and its infectivity in vitro. Sci China Ser C 51:453–458
  Article CAS Google Scholar
• Wen LB, He KW, Yu ZY, Mao AH, Ni YX, Zhang XH, Guo RL, Li B, Wang XM, Zhou JM, Lv LX (2012) Complete genome sequence of a novel porcine circovirus-like agent. J Virol 86:639
  Article PubMed CAS Google Scholar
• Willner D, Furlan M, Haynes M, Schmieder R, Angly FE, Silva J, Tammadoni S, Nosrat B, Conrad D, Rohwer F (2009) Metagenomic analysis of respiratory tract DNA viral communities in cystic fibrosis and non-cystic fibrosis individuals. PLoS ONE 4:e7370
  Article PubMed CAS Google Scholar
• Yazdi HRB, Heydarnejad J, Massumi H (2008) Genome characterization and genetic diversity of beet curly top Iran virus: a geminivirus with a novel nonanucleotide. Virus Genes 36:539–545
  Article PubMed CAS Google Scholar
• Yoon HS, Price DC, Stepanauskas R, Rajah VD, Sieracki ME, Wilson WH, Yang EC, Duffy S, Bhattacharya D (2011) Single-cell genomics reveals organismal interactions in uncultivated marine protists. Science 332:714–717
  Article PubMed CAS Google Scholar
• Yu X, Li B, Fu YP, Jiang DH, Ghabrial SA, Li GQ, Peng YL, Xie JT, Cheng JS, Huang JB, Yi XH (2010) A geminivirus-related DNA mycovirus that confers hypovirulence to a plant pathogenic fungus. Proc Natl Acad Sci USA 107:8387–8392
  Article PubMed CAS Google Scholar