A diverse group of small circular ssDNA viral genomes in human and non-human primate stools

Virus Evolution

Volumn 1, Issue 1, 2015, Pages

  Ng, Terry Fei Fan ^a,b,f   Zhang, Wen ^a,c   Sachsenrö Der, Jana ^a,d   Kondov, Nikola O ^a   Da Costa, Antonio Charlys ^a,e   Vega, Everardo ^f   Holtz, Lori R ^g   Wu, Guang ^g   Wang, David ^h   Stine, Colin O ⁱ   Antonio, Martin ^j   Mulvaney, Usha S ^a   Muench, Marcus O ^a,b   Deng, Xutao ^a,b   Ambert Balay, Katia ^k   Pothier, Pierre ^k   Vinjé, Jan ^f   Delwart, Eric ^a,b  

^a BLOOD SYSTEMS RESEARCH INSTITUTE   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c JIANGSU UNIVERSITY   (China)

^d FEDERAL INSTITUTE FOR RISK ASSESSMENT   (Germany)

^e UNIVERSITY OF SÃO PAULO   (Brazil)

^f NATIONAL CENTER FOR IMMUNIZATION AND RESPIRATORY DISEASES   (United States)

^g Department of Pediatrics ^*  (United States)

^h WASHINGTON UNIVERSITY   (United States)

ⁱ UNIVERSITY OF MARYLAND SCHOOL OF MEDICINE   (United States)

^j MEDICAL RESEARCH COUNCIL LABORATORIES   (Gambia)

^k DIJON UNIVERSITY HOSPITAL   (France)

more..

Author keywords

Acute gastroenteritis; Deep sequencing; Digital screening; Metagenomics; Smacovirus; SsDNA virus

Indexed keywords

EID: 84962098484     PISSN: None     EISSN: 20571577     Source Type: Journal    
DOI: 10.1093/ve/vev017     Document Type: Article

References (51)

1. Blinkova, O. et al. (2010) 'Novel Circular DNA Viruses in Stool Samples of Wild-Living Chimpanzees', Journal of General Virology, 91: 74-86.
2. Boni, M. F., Posada, D., and Feldman, M. W. (2007) 'An Exact Nonparametric Method for Inferring mosaic Structure in Sequence Triplets', Genetics, 176: 1035-47.
3. Cheung, A. K. et al. (2013) 'A Divergent Clade of Circular Single-Stranded DNA Viruses from Pig Feces', Archives of Virology, 158: 2157-62.
4. Cheung, A. K. et al. (2014) 'Unique Circovirus-Like Genome Detected in Pig feces', Genome Announcements 2.
5. Cheung, A. K. et al. (2014) 'Identification of Several Clades of Novel Single-Stranded Circular DNA Viruses with Conserved Stem-Loop Structures in Pig Feces', Archives of Virology, 160: 353-8.
6. Dayaram, A. et al. (2013) 'High Global Diversity of Cycloviruses Amongst Dragonflies', The Journal of General Virology, 94: 1827-40.
7. Dayaram, A. et al. (2014) 'Novel Circular DNA Viruses Identified in Procordulia grayi and Xanthocnemis zealandica Larvae Using Metagenomic Approaches', Infection, Genetics and Evolution, 22: 134-41.
8. Delwart, E., and Li, L. (2012) 'Rapidly Expanding Genetic Diversity and Host Range of the Circoviridae Viral Family and Other Rep Encoding Small Circular ssDNA Genomes', Virus Research, 164: 114-21.
9. Deng, X. et al. (2015) 'An Ensemble Strategy that Significantly Improves De Novo Assembly of Microbial Genomes from Metagenomic Next-Generation Sequencing Data', Nucleic Acids Research, 43: e46.
10. Duffy, S., Shackelton, L. A., and Holmes, E. C. (2008) 'Rates of Evolutionary Change in Viruses: Patterns and Determinants', Nature Reviews. Genetics, 9: 267-76.
11. Dunlap, D. S. et al. (2013) 'Molecular and Microscopic Evidence of Viruses in Marine Copepods', Proceedings of the National Academy of Sciences of the United States of America, 110: 1375-80.
12. Dutilh, B. E. et al. (2014) 'A Highly Abundant Bacteriophage Discovered in the Unknown Sequences of Human Faecal Metagenomes', Nature Communications, 5: 4498.
13. Fontes, E. P. et al. (1994) 'Geminivirus Replication Origins have a Modular Organization'. The Plant Cell, 6: 405-16.
14. Grard, G. et al. (2012) 'A Novel Rhabdovirus Associated with Acute Hemorrhagic Fever in Central Africa', PLoS Pathogens, 8: e1002924.
15. Huelsenbeck, J. P., and Ronquist, F. (2001) 'MRBAYES: Bayesian Inference of Phylogenetic Trees', Bioinformatics, 17: 754-5.
16. Kaplan, J. E., et al. (1982) 'Epidemiology of Norwalk Gastroenteritis and the Role of Norwalk Virus in Outbreaks of Acute Nonbacterial Gastroenteritis', Annals of Internal Medicine, 96: 756-61.
17. Katoh, K. et al. (2005) 'MAFFT Version 5: Improvement in Accuracy of Multiple Sequence Alignment', Nucleic Acids Research, 33: 511-8.
18. Kim, H. K. et al. (2012), 'Identification of a Novel Single-Stranded, Circular DNA Virus from Bovine Stool', The Journal of General Virology, 93: 635-9.
19. Kotloff, K. L. et al. (2013) 'Burden and Aetiology of Diarrhoeal Disease in Infants and Young Children in Developing Countries (the Global Enteric Multicenter Study, GEMS): a Prospective, Case-Control Study', Lancet (London, England), 382: 209-22.
20. Kraberger, S. et al. (2015) 'Characterisation of a Diverse Range of Circular Rep-Encoding DNA Viruses Recovered from a Sewage Treatment Oxidation Pond', Infection, Genetics and Evolution, 31: 73-86.
21. Lefeuvre, P. et al. (2009) 'Widely Conserved Recombination Patterns Among Single-Stranded DNA Viruses', Journal of Virology, 83: 2697-707.
22. Li, L. et al. (2010) 'Multiple Diverse Circoviruses Infect Farm Animals and are Commonly Found in Human and Chimpanzee Feces', Journal of Virology, 91: 74-86.
23. Martin, D. P. et al. (2005) 'A Modified Bootscan Algorithm for Automated Identification of Recombinant Sequences and Recombination Breakpoints', AIDS Research and Human Retroviruses, 21: 98-102.
24. Martin, D. P. et al. (2011) 'Recombination in Eukaryotic Single Stranded DNA Viruses', Viruses, 3: 1699-738.
25. Martin, D. P. et al. (2015) 'RDP4: Detection and Analysis of Recombination Patterns in Virus Genomes' Virus Evolution, 1: vev003.
26. Meyer, C. T. et al. (2015) 'Prevalence of Classic, MLB-Clade and VA-Clade Astroviruses in Kenya and The Gambia', Virology Journal, 12: 78.
27. Muhire, B. M., Varsani, A., and Martin, D. P. (2014) 'SDT: a Virus Classification Tool Based on Pairwise Sequence Alignment and Identity Calculation', PLoS One 9: e108277.
28. Naccache, S. N. et al. (2013) 'The Perils of Pathogen Discovery: Origin of a Novel Parvovirus-Like Hybrid Genome Traced to Nucleic Acid Extraction Spin Columns', Journal of Virology, 87: 11966-77.
29. Ng, T. F. et al. (2012) 'High Variety of Known and New RNA and DNA Viruses of Diverse Origins in Untreated Sewage', Journal of Virology, 86: 12161-75.
30. Ng, T. F. et al. (2013) 'Metagenomic Identification of a Nodavirus and a Circular ssDNA Virus in Semi-Purified Viral Nucleic Acids from the Hepatopancreas of Healthy Farfantepenaeus Duorarum Shrimp', Diseases of Aquatic Organisms, 105: 237-42.
31. Ng, T. F. et al. (2013) 'Identification of an Astrovirus Commonly Infecting Laboratory Mice in the US and Japan', PLoS One, 8: e66937.
32. Ng, T. F. et al. (2013) 'Distinct Lineage of Vesiculovirus from Big Brown Bats, United States', Emerging Infectious Diseases, 19: 1978-80.
33. Ng, T. F. et al. (2014) 'Divergent Picobirnaviruses in Human Feces', Genome Announcements 2.
34. Padidam, M., Sawyer, S., and Fauquet, C. M. (1999) 'Possible Emergence of New Geminiviruses by Frequent Recombination', Virology, 265: 218-25.
35. Posada, D., and Crandall, K. A. (2001) 'Evaluation of Methods for Detecting Recombination from DNA Sequences: Computer Simulations', Proceedings of the National Academy of Sciences of the United States of America, 98: 13757-62.
36. Reuter, G. et al. (2014) 'Novel Circular Single-Stranded DNA Virus from Turkey Faeces', Archives of Virology, 159: 2161-4.
37. Rosario, K., Duffy, S., and Breitbart, M. (2012) 'A Field Guide to Eukaryotic Circular Single-Stranded DNA Viruses: Insights Gained from Metagenomics', Archives of Virology, 157: 1851-71.
38. Rosario, K., Duffy, S., and Breitbart, M. (2012) 'Diverse Circular ssDNA Viruses Discovered in Dragonflies (Odonata: Epiprocta)', The Journal of General Virology, 93: 2668-81.
39. Sachsenröder, J. et al. (2012) 'Simultaneous Identification of DNA and RNA Viruses Present in Pig Faeces Using Process-Controlled Deep Sequencing', PLoS One, 7: e34631.
40. Sachsenröder, J. et al. (2014) 'Metagenomic Identification of Novel Enteric Viruses in Urban Wild Rats and Genome Characterization of a Group A Rotavirus', The Journal of General Virology, 95: 2734-47.
41. Sikorski, A. et al. (2013), 'Novel Myco-Like DNA Viruses Discovered in the Faecal Matter of Various Animals', Virus Research, 177: 209-16.
42. Smith, J. M. (1992) 'Analyzing the Mosaic Structure of Genes', Journal of Molecular Evolution, 34: 126-9.
43. Smits, S. L. et al. (2013) 'Metagenomic Analysis of the Ferret Fecal Viral Flora', PLoS One, 8: e71595.
44. Stenger, D. C. et al. (1991) 'Replicational Release of Geminivirus Genomes from Tandemly Repeated Copies: Evidence for Rolling-Circle Replication of a Plant Viral DNA', Proceedings of the National Academy of Sciences of the United States of America, 88: 8029-33.
45. van Leeuwen, M. et al. (2010) 'Human Picobirnaviruses Identified by Molecular Screening of Diarrhea Samples', Journal of Clinical Microbiology, 48: 1787-94.
46. Victoria, J. G. et al. (2008) 'Rapid Identification of Known and New RNA Viruses from Animal Tissues', PLoS Pathogens, 4: e1000163.
47. Victoria, J. G. et al. (2009) 'Metagenomic Analyses of Viruses in Stool Samples from Children with Acute Flaccid Paralysis', Journal of Virology, 83: 4642-51.
48. Yu, X. et al. (2010) 'A Geminivirus-Related DNA Mycovirus that Confers Hypovirulence to a Plant Pathogenic Fungus', Proceedings of the National Academy of Sciences of the United States of America, 107: 8387-92.
49. Zawar-Reza, P. et al. (2014) 'Diverse Small Circular Single-Stranded DNA Viruses Identified in a Freshwater Pond on the McMurdo Ice Shelf (Antarctica)', Infection, Genetics and Evolution, 26: 132-8.
50. Zhang, T. et al. (2006) 'RNA Viral Community in Human Feces: Prevalence of Plant Pathogenic Viruses', PLoS Biology, 4: 108-18.
51. Zuker, M. (2003) 'Mfold Web Server for Nucleic Acid Folding and Hybridization Prediction', Nucleic Acids Research, 31: 3406-15.