Redondoviridae, a Family of Small, Circular DNA Viruses of the Human Oro-Respiratory Tract Associated with Periodontitis and Critical Illness

Abbas, 2017, The perioperative lung transplant virome: torque Teno viruses are elevated in donor lungs and show divergent dynamics in primary graft dysfunction, Am. J. Transplant., 17, 1313, 10.1111/ajt.14076 Abbas, 2019, Bidirectional transfer of Anelloviridae lineages between graft and host during lung transplantation, Am. J. Transplant., 19, 1086, 10.1111/ajt.15116 Abeles, 2015, Effects of long term antibiotic therapy on human oral and fecal viromes, PLoS One, 10, e0134941, 10.1371/journal.pone.0134941 Aggarwala, 2017, Viral communities of the human gut: metagenomic analysis of composition and dynamics, Mob. DNA, 8, 12, 10.1186/s13100-017-0095-y Altschul, 1990, Basic local alignment search tool, J. Mol. Biol., 215, 403, 10.1016/S0022-2836(05)80360-2 Anisimova, 2006, Approximate likelihood-ratio test for branches: a fast, accurate, and powerful alternative, Syst. Biol., 55, 539, 10.1080/10635150600755453 Breitbart, 2017, ICTV virus taxonomy profile: Circoviridae, J. Gen. Virol., 98, 1997, 10.1099/jgv.0.000871 Califf, 2017, Multi-omics analysis of periodontal pocket microbial communities pre- and posttreatment, mSystems, 2, 10.1128/mSystems.00016-17 Cappuyns, 2005, Viruses in periodontal disease - a review, Oral Dis., 11, 219, 10.1111/j.1601-0825.2005.01123.x Charlson, 2011, Topographical continuity of bacterial populations in the healthy human respiratory tract, Am. J. Respir. Crit. Care Med., 184, 957, 10.1164/rccm.201104-0655OC Charlson, 2010, Disordered microbial communities in the upper respiratory tract of cigarette smokers, PLoS One, 5, e15216, 10.1371/journal.pone.0015216 Cheung, 2014, Identification of a novel single-stranded circular DNA virus in pig feces, Genome Announc., 2, 10.1128/genomeA.00347-14 Clarke, 2018, Microbial lineages in sarcoidosis. A metagenomic analysis tailored for low microbial content samples, Am. J. Respir. Crit. Care Med., 197, 225, 10.1164/rccm.201705-0891OC Clarke, 2017, Swga: a primer design toolkit for selective whole genome amplification, Bioinformatics, 33, 2071, 10.1093/bioinformatics/btx118 Clarke, 2019, Sunbeam: an extensible pipeline for analyzing metagenomic sequencing experiments, Microbiome, 7, 46, 10.1186/s40168-019-0658-x Costalonga, 2014, The oral microbiome and the immunobiology of periodontal disease and caries, Immunol. Lett., 162, 22, 10.1016/j.imlet.2014.08.017 Crooks, 2004, WebLogo: a sequence logo generator, Genome Res., 14, 1188, 10.1101/gr.849004 Cui, 2017, Identification and genetic characterization of a novel circular single-stranded DNA virus in a human upper respiratory tract sample, Arch. Virol., 162, 3305, 10.1007/s00705-017-3481-3 Edgar, 2004, Muscle: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Res., 32, 1792, 10.1093/nar/gkh340 Edlund, 2015, Bacteriophage and their potential roles in the human oral cavity, J. Oral Microbiol., 7, 27423, 10.3402/jom.v7.27423 Ellis, 2014, Porcine circovirus: a historical perspective, Vet. Pathol., 51, 315, 10.1177/0300985814521245 Fahsbender, 2017, Diverse and highly recombinant anelloviruses associated with Weddell seals in Antarctica, Virus Evol., 3, vex017, 10.1093/ve/vex017 Fauquet, 2005 Gorbalenya, 1990, A new superfamily of putative NTP-binding domains encoded by genomes of small DNA and RNA viruses, FEBS Lett., 262, 145, 10.1016/0014-5793(90)80175-I Grabundzija, 2016, A Helitron transposon reconstructed from bats reveals a novel mechanism of genome shuffling in eukaryotes, Nat. Commun., 7, 10716, 10.1038/ncomms10716 Guindon, 2010, New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0, Syst. Biol., 59, 307, 10.1093/sysbio/syq010 Harrison, 1977, Plant viruses with circular single-stranded DNA, Nature, 270, 760, 10.1038/270760a0 Huang, 1999, CAP3: a DNA sequence assembly program, Genome Res., 9, 868, 10.1101/gr.9.9.868 Ihaka, 1996, R: a language for data analysis and graphics, J. Comp. Graph. Stat., 5, 299 Ilyina, 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, 10.1093/nar/20.13.3279 Kelley, 2015, The Phyre2 web portal for protein modeling, prediction and analysis, Nat. Protoc., 10, 845, 10.1038/nprot.2015.053 Kerpedjiev, 2015, Forna (force-directed RNA): simple and effective online RNA secondary structure diagrams, Bioinformatics, 31, 3377, 10.1093/bioinformatics/btv372 Kim, 2011, Amplification methods bias metagenomic libraries of uncultured single-stranded and double-stranded DNA viruses, Appl. Environ. Microbiol., 77, 7663, 10.1128/AEM.00289-11 Kim, 2008, Amplification of uncultured single-stranded DNA viruses from rice paddy soil, Appl. Environ. Microbiol., 74, 5975, 10.1128/AEM.01275-08 Köster, 2012, Snakemake—a scalable bioinformatics workflow engine, Bioinformatics, 28, 2520, 10.1093/bioinformatics/bts480 Krishnamurthy, 2017, Origins and challenges of viral dark matter, Virus Res., 239, 136, 10.1016/j.virusres.2017.02.002 Krishnamurthy, 2018, Extensive conservation of prokaryotic ribosomal binding sites in known and novel picobirnaviruses, Virology, 516, 108, 10.1016/j.virol.2018.01.006 Krupovic, 2016, Genomoviridae: a new family of widespread single-stranded DNA viruses, Arch. Virol., 161, 2633, 10.1007/s00705-016-2943-3 Kumar, 2018, Metagenomic analysis uncovers strong relationship between periodontal pathogens and vascular dysfunction in American Indian population, bioRxiv Labonté, 2013, Previously unknown and highly divergent ssDNA viruses populate the oceans, ISME J., 7, 2169, 10.1038/ismej.2013.110 Langmead, 2012, Fast gapped-read alignment with Bowtie 2, Nat. Methods, 9, 357, 10.1038/nmeth.1923 Le, 2008, An improved general amino acid replacement matrix, Mol. Biol. Evol., 25, 1307, 10.1093/molbev/msn067 Lefeuvre, 2009, Widely conserved recombination patterns among single-stranded DNA viruses, J. Virol., 83, 2697, 10.1128/JVI.02152-08 Leinonen, 2011, The sequence read archive, Nucleic Acids Res., 39, D19, 10.1093/nar/gkq1019 Leppik, 2007, In vivo and in vitro intragenomic rearrangement of TT viruses, J. Virol., 81, 9346, 10.1128/JVI.00781-07 Li, 2015, MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph, Bioinformatics, 31, 1674, 10.1093/bioinformatics/btv033 Li, 2017, Herpesviruses in etiopathogenesis of aggressive periodontitis: a meta-analysis based on case-control studies, PLoS One, 12, e0186373, 10.1371/journal.pone.0186373 Li, 2009, The Sequence Alignment/Map format and SAMtools, Bioinformatics, 25, 2078, 10.1093/bioinformatics/btp352 Li, 2010, Multiple diverse circoviruses infect farm animals and are commonly found in human and chimpanzee feces, J. Virol., 84, 1674, 10.1128/JVI.02109-09 Ly, 2014, Altered oral viral ecology in association with periodontal disease, mBio, 5, 10.1128/mBio.01133-14 Ma, 2007, Evidence for recombination in natural populations of porcine circovirus type 2 in Hong Kong and mainland China, J. Gen. Virol., 88, 1733, 10.1099/vir.0.82629-0 Maggi, 2001, TT virus (TTV) loads associated with different peripheral blood cell types and evidence for TTV replication in activated mononuclear cells, J. Med. Virol., 64, 190, 10.1002/jmv.1035 Mankertz, 1997, Mapping and characterization of the origin of DNA replication of porcine circovirus, J. Virol., 71, 2562, 10.1128/JVI.71.3.2562-2566.1997 Mariscal, 2002, TT virus replicates in stimulated but not in nonstimulated peripheral blood mononuclear cells, Virology, 301, 121, 10.1006/viro.2002.1545 Minot, 2013, Rapid evolution of the human gut virome, Proc. Natl. Acad. Sci. USA, 110, 12450, 10.1073/pnas.1300833110 Minot, 2011, The human gut virome: inter-individual variation and dynamic response to diet, Genome Res., 21, 1616, 10.1101/gr.122705.111 Mokili, 2013, Identification of a novel human papillomavirus by metagenomic analysis of samples from patients with febrile respiratory illness, PLoS One, 8, e58404, 10.1371/journal.pone.0058404 Monaco, 2016, Altered virome and bacterial microbiome in human immunodeficiency virus-associated acquired immunodeficiency syndrome, Cell Host Microbe, 19, 311, 10.1016/j.chom.2016.02.011 Muhire, 2014, Evidence of pervasive biologically functional secondary structures within the genomes of eukaryotic single-stranded DNA viruses, J. Virol., 88, 1972, 10.1128/JVI.03031-13 Murrell, 2013, Fubar: a fast, unconstrained bayesian approximation for inferring selection, Mol. Biol. Evol., 30, 1196, 10.1093/molbev/mst030 Naccache, 2013, The perils of pathogen discovery: origin of a novel parvovirus-like hybrid genome traced to nucleic acid extraction spin columns, J. Virol., 87, 11966, 10.1128/JVI.02323-13 Norman, 2015, Disease-specific alterations in the enteric virome in inflammatory bowel disease, Cell, 160, 447, 10.1016/j.cell.2015.01.002 Norrander, 1983, Construction of improved M13 vectors using oligodeoxynucleotide-directed mutagenesis, Gene, 26, 101, 10.1016/0378-1119(83)90040-9 Paez-Espino, 2016, Uncovering Earth's virome, Nature, 536, 425, 10.1038/nature19094 Pérez-Brocal, 2018, The analysis of the oral DNA virome reveals which viruses are widespread and rare among healthy young adults in Valencia (Spain), PLoS One, 13, e0191867, 10.1371/journal.pone.0191867 Phan, 2014, Cyclovirus in nasopharyngeal aspirates of Chilean children with respiratory infections, J. Gen. Virol., 95, 922, 10.1099/vir.0.061143-0 Pond, 2005, HyPhy: hypothesis testing using phylogenies, Bioinformatics, 21, 676, 10.1093/bioinformatics/bti079 Quinlan, 2010, BEDTools: a flexible suite of utilities for comparing genomic features, Bioinformatics, 26, 841, 10.1093/bioinformatics/btq033 Rice, 2000, EMBOSS: the European molecular biology open software suite, Trends Genet., 16, 276, 10.1016/S0168-9525(00)02024-2 Rosario, 2011, Exploring the viral world through metagenomics, Curr. Opin. Virol., 1, 289, 10.1016/j.coviro.2011.06.004 Rosario, 2012, A field guide to eukaryotic circular single-stranded DNA viruses: insights gained from metagenomics, Arch. Virol., 157, 1851, 10.1007/s00705-012-1391-y Salter, 2014, Reagent and laboratory contamination can critically impact sequence-based microbiome analyses, BMC Biol., 12, 87, 10.1186/s12915-014-0087-z Shi, 2015, Dynamic changes in the subgingival microbiome and their potential for diagnosis and prognosis of periodontitis, mBio, 6, 10.1128/mBio.01926-14 Simmonds, 2017, Virus taxonomy in the age of metagenomics, Nat. Rev. Microbiol., 15, 161, 10.1038/nrmicro.2016.177 Smits, 2014, New viruses in idiopathic human diarrhea cases, the Netherlands, Emerg. Infect. Dis., 20, 1218, 10.3201/eid2007.140190 Spandole, 2015, Human anelloviruses: an update of molecular, epidemiological and clinical aspects, Arch. Virol., 160, 893, 10.1007/s00705-015-2363-9 Suyama, 2006, PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments, Nucleic Acids Res., 34, W609, 10.1093/nar/gkl315 Taylor, 2017, Pyviko: an automated Python tool to design gene knockouts in complex viruses with overlapping genes, BMC Microbiol., 17, 12, 10.1186/s12866-016-0920-3 Todd, 2000, Circoviruses: immunosuppressive threats to avian species: a review, Avian Pathol., 29, 373, 10.1080/030794500750047126 Varsani, 2017, Sequence-based taxonomic framework for the classification of uncultured single-stranded DNA viruses of the family Genomoviridae, Virus Evol., 3, vew037, 10.1093/ve/vew037 Varsani, 2018, Smacoviridae: a new family of animal-associated single-stranded DNA viruses, Arch. Virol., 163, 2005, 10.1007/s00705-018-3820-z Wang, 2013, Metagenomic sequencing reveals microbiota and its functional potential associated with periodontal disease, Sci. Rep., 3, 1843, 10.1038/srep01843 Wang, 2016, Metagenomic analysis of viral genetic diversity in respiratory samples from children with severe acute respiratory infection in China, Clin. Microbiol. Infect., 22, 4580, 10.1016/j.cmi.2016.01.006 Willner, 2009, Metagenomic analysis of respiratory tract DNA viral communities in cystic fibrosis and non-cystic fibrosis individuals, PLoS One, 4, e7370, 10.1371/journal.pone.0007370 Wylie, 2012, Sequence analysis of the human virome in febrile and afebrile children, PLoS One, 7, e27735, 10.1371/journal.pone.0027735 Young, 2015, Viral metagenomics reveal blooms of anelloviruses in the respiratory tract of lung transplant recipients, Am. J. Transplant., 15, 200, 10.1111/ajt.13031 Zanini, 2013, Quantifying selection against synonymous mutations in HIV-1 env evolution, J. Virol., 87, 11843, 10.1128/JVI.01529-13 Zhang, 2015, The oral and gut microbiomes are perturbed in rheumatoid arthritis and partly normalized after treatment, Nat. Med., 21, 895, 10.1038/nm.3914 Zuker, 2003, Mfold web server for nucleic acid folding and hybridization prediction, Nucleic Acids Res., 31, 3406, 10.1093/nar/gkg595