The fecal virome of South and Central American children with diarrhea includes small circular DNA viral genomes of unknown origin

详细信息    查看全文

• 作者：Tung Gia Phan ; Antonio Charlys da Costa ; Juana del Valle Mendoza…
• 刊名：Archives of Virology
• 出版年：2016
• 出版时间：April 2016
• 年：2016
• 卷：161
• 期：4
• 页码：959-966
• 全文大小：718 KB
• 参考文献：1.Blinkova O, Victoria J, Li Y, Keele BF, Sanz C, Ndjango JB, 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 91:74–86CrossRef PubMed PubMedCentral
  2.Bucardo F, Nordgren J, Carlsson B, Paniagua M, Lindgren PE, Espinoza F, Svensson L (2008) Pediatric norovirus diarrhea in Nicaragua. J Clin Microbiol 46:2573–2580CrossRef PubMed PubMedCentral
  3.Cheung AK, Ng TF, Lager KM, Bayles DO, Alt DP, Delwart EL, Pogranichniy RM, Kehrli ME Jr (2013) A divergent clade of circular single-stranded DNA viruses from pig feces. Arch Virol 158:2157–2162CrossRef PubMed PubMedCentral
  4.Cheung AK, Ng TF, Lager KM, Alt DP, Delwart EL, Pogranichniy RM (2014) Unique circovirus-like genome detected in pig feces. Genome Announc 2(2):e00251–14. doi:10.​1128/​genomeA.​00251-14 PubMed PubMedCentral
  5.Cheung AK, Ng TF, Lager KM, Alt DP, Delwart E, Pogranichniy RM (2015) Identification of several clades of novel single-stranded circular DNA viruses with conserved stem-loop structures in pig feces. Arch Virol 160:353–358CrossRef PubMed
  6.Dayaram A, Goldstien S, Arguello-Astorga GR, Zawar-Reza P, Gomez C, Harding JS, Varsani A (2015) Diverse small circular DNA viruses circulating amongst estuarine molluscs. Infect Genet Evol J Mol Epidemiol Evol Genet Infect Dis 31:284–295CrossRef
  7.Delwart E, Li L (2012) Rapidly expanding genetic diversity and host range of the Circoviridae viral family and other Rep encoding small circular ssDNA genomes. Virus Res 164:114–121CrossRef PubMed PubMedCentral
  8.Espejo PW, Peralta FO, Pacheres HC, del Valle LJ, Tapia AC, Mayra JB, Ruiz J, Mendoza Jdel V (2014) Diarrhoea caused by rotavirus in a regional Peruvian hospital: determination of circulating genotypes. Trans R Soc Trop Med Hyg 108:425–430CrossRef PubMed
  9.Garigliany MM, Borstler J, Jost H, Badusche M, Desmecht D, Schmidt-Chanasit J, Cadar D (2015) Characterization of a novel circo-like virus in Aedes vexans mosquitoes from Germany: evidence for a new genus within the family Circoviridae. J Gen Virol 96:915–920CrossRef PubMed
  10.Kim HK, Park SJ, Nguyen VG, Song DS, Moon HJ, Kang BK, Park BK (2012) Identification of a novel single-stranded, circular DNA virus from bovine stool. J Gen Virol 93:635–639CrossRef PubMed
  11.Kraberger S, Arguello-Astorga GR, Greenfield LG, Galilee C, Law D, Martin DP, Varsani A (2015) Characterisation of a diverse range of circular replication-associated protein encoding DNA viruses recovered from a sewage treatment oxidation pond. Infect Genet Evol J Mol Epidemiol Evol Genet Infect Dis 31:73–86CrossRef
  12.Labonte JM, Suttle CA (2013) Previously unknown and highly divergent ssDNA viruses populate the oceans. ISME J 7:2169–2177CrossRef PubMed PubMedCentral
  13.Ng TF, Marine R, Wang C, Simmonds P, Kapusinszky B, Bodhidatta L, Oderinde BS, Wommack KE, Delwart E (2012) High variety of known and new RNA and DNA viruses of diverse origins in untreated sewage. J Virol 86:12161–12175CrossRef PubMed PubMedCentral
  14.Ng TFF, Zhang W, Sachsenroder J, Kondov NO, Antonio Charlys da Costa, Vega E, Holtz LR, Wu G, Wang D, Stine CO, Antonio M, Mulvaney US, Muench MO, Deng X, Ambert-Balay K, Pothier P, Vinje J, Delwart E (2015) A diverse group of small circular ssDNA viral genomes in human and non-human primate stools. Virus Evo 1 (1): 1–3. doi:10.​1093/​ve/​vev017 CrossRef
  15.Phan TG, Li L, O’Ryan MG, Cortes H, Mamani N, Bonkoungou IJ, Wang C, Leutenegger CM, Delwart E (2012) A third gyrovirus species in human faeces. J Gen Virol 93:1356–1361CrossRef PubMed PubMedCentral
  16.Phan TG, Vo NP, Boros A, Pankovics P, Reuter G, Li OT, Wang C, Deng X, Poon LL, Delwart E (2013) The viruses of wild pigeon droppings. PLoS ONE 8:e72787CrossRef PubMed PubMedCentral
  17.Phan TG, Mori D, Deng X, Rajindrajith S, Ranawaka U, Fan Ng TF, Bucardo-Rivera F, Orlandi P, Ahmed K, Delwart E (2015) Small circular single stranded DNA viral genomes in unexplained cases of human encephalitis, diarrhea, and in untreated sewage. Virology 482:98–104CrossRef PubMed
  18.Reuter G, Boros A, Delwart E, Pankovics P (2014) Novel circular single-stranded DNA virus from turkey faeces. Arch Virol 159:2161–2164CrossRef PubMed
  19.Rosario K, Duffy S, Breitbart M (2012) A field guide to eukaryotic circular single-stranded DNA viruses: insights gained from metagenomics. Arch Virol 157:1851–1871CrossRef PubMed
  20.Rosario K, Schenck RO, Harbeitner RC, Lawler SN, Breitbart M (2015) Novel circular single-stranded DNA viruses identified in marine invertebrates reveal high sequence diversity and consistent predicted intrinsic disorder patterns within putative structural proteins. Front Microbiol 6:696CrossRef PubMed PubMedCentral
  21.Sachsenroder J, Twardziok S, Hammerl JA, Janczyk P, Wrede P, Hertwig S, Johne R (2012) Simultaneous identification of DNA and RNA viruses present in pig faeces using process-controlled deep sequencing. PLoS ONE 7:e34631CrossRef PubMed PubMedCentral
  22.Sachsenroder J, Braun A, Machnowska P, Ng TF, Deng X, Guenther S, Bernstein S, Ulrich RG, Delwart E, Johne R (2014) Metagenomic identification of novel enteric viruses in urban wild rats and genome characterization of a group A rotavirus. J Gen Virol 95:2734–2747CrossRef PubMed
  23.Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425PubMed
  24.Sikorski A, Dayaram A, Varsani A (2013) Identification of a novel circular DNA virus in New Zealand Fur Seal (Arctocephalus forsteri) fecal matter. Genome Announc 1(4):e00558–13. doi:10.​1128/​genomeA.​00558-13 CrossRef PubMed PubMedCentral
  25.Sikorski A, Massaro M, Kraberger S, Young LM, Smalley D, Martin DP, Varsani A (2013) Novel myco-like DNA viruses discovered in the faecal matter of various animals. Virus Res 177:209–216CrossRef PubMed
  26.Smits SL, Raj VS, Oduber MD, Schapendonk CM, Bodewes R, Provacia L, Stittelaar KJ, Osterhaus AD, Haagmans BL (2013) Metagenomic analysis of the ferret fecal viral flora. PLoS ONE 8:e71595CrossRef PubMed PubMedCentral
  27.Smits SL, Schapendonk CM, van Beek J, Vennema H, Schurch AC, Schipper D, Bodewes R, Haagmans BL, Osterhaus AD, Koopmans MP (2014) New viruses in idiopathic human diarrhea cases, the Netherlands. Emerg Infect Dis 20:1218–1222CrossRef PubMed PubMedCentral
  28.Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30:2725–2729CrossRef PubMed PubMedCentral
  29.Vizzi E, Pineros O, Gonzalez GG, Zambrano JL, Ludert JE, Liprandi F (2011) Genotyping of human rotaviruses circulating among children with diarrhea in Valencia, Venezuela. J Med Virol 83:2225–2232CrossRef PubMed
  30.Woo PC, Lau SK, Teng JL, Tsang AK, Joseph M, Wong EY, Tang Y, Sivakumar S, Bai R, Wernery R, Wernery U, Yuen KY (2014) Metagenomic analysis of viromes of dromedary camel fecal samples reveals large number and high diversity of circoviruses and picobirnaviruses. Virology 471–473:117–125CrossRef PubMed
  31.Yu X, Li B, Fu Y, Jiang D, Ghabrial SA, Li G, Peng Y, Xie J, Cheng J, Huang J, Yi X (2010) A geminivirus-related DNA mycovirus that confers hypovirulence to a plant pathogenic fungus. Proc Natl Acad Sci USA 107:8387–8392CrossRef PubMed PubMedCentral
  32.Zawar-Reza P, Arguello-Astorga GR, Kraberger S, Julian L, Stainton D, Broady PA, Varsani A (2014) Diverse small circular single-stranded DNA viruses identified in a freshwater pond on the McMurdo Ice Shelf (Antarctica). Infect Genet Evol J Mol Epidemiol Evol Genet Infect Dis 26:132–138CrossRef
  33.Zuker M (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31:3406–3415CrossRef PubMed PubMedCentral
  
• 作者单位：Tung Gia Phan (1) (2)
  Antonio Charlys da Costa (1) (3)
  Juana del Valle Mendoza (4) (5)
  Filemon Bucardo-Rivera (6)
  Johan Nordgren (7)
  Miguel O’Ryan (8)
  Xutao Deng (1)
  Eric Delwart (1) (2)
  
  1. Blood Systems Research Institute, San Francisco, CA, 94118, USA
  2. Department of Laboratory Medicine, University of California at San Francisco, San Francisco, CA, 94118, USA
  3. Institute of Tropical Medicine, School of Medicine, University of São Paulo, São Paulo, Brazil
  4. Faculty of Health Sciences, School of Medicine, Universidad Peruana de Ciencias Aplicadas-UPC, Lima, Peru
  5. Instituto de Investigación Nutricional, Lima, Peru
  6. Department of Microbiology, University of León, León, Nicaragua
  7. Division of Molecular Virology, Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
  8. Microbiology and Mycology Program, Faculty of Medicine, University of Chile, Santiago, Chile
  
• 刊物类别：Biomedical and Life Sciences
• 刊物主题：Biomedicine
  Virology
  Medical Microbiology
  Infectious Diseases
  
• 出版者：Springer Wien
• ISSN：1432-8798

文摘

Viral metagenomics of feces collected from 58 Peruvian children with unexplained diarrhea revealed several small circular ssDNA genomes. Two genomes related to sequences previously reported in feces from chimpanzees and other mammals and recently named smacoviruses were characterized and then detected by PCR in 1.7 % (1/58) and 19 % (11/58) of diarrheal samples, respectively. Another three genomes from a distinct small circular ssDNA viral group provisionally called pecoviruses encoded Cap and Rep proteins with <35 % identity to those in related genomes reported in human, seal, porcine and dromedary feces. Pecovirus DNA was detected in 15.5 % (9/58), 5.9 % (3/51) and 3 % (3/100) of fecal samples from unexplained diarrhea in Peru, Nicaragua and Chile, respectively. Feces containing these ssDNA genomes also contained known human enteric viral pathogens. The cellular origins of these circular ssDNA viruses, whether human cells, ingested plants, animals or fungal foods, or residents of the gut microbiome, are currently unknown.