Detection and molecular characterization of multiple strains of picobirnavirus causing mixed infection in a diarrhoeic child: Emergence of prototype genogroup ii-like strain in Kolkata, India

International Journal of Molecular Epidemiology and Genetics

Volumn 2, Issue 1, 2011, Pages 61-72

  Ganesh, Balasubramanian ^a   Nagashima, Shigeo ^b   Ghosh, Souvik ^b   Nataraju, Seegekote M ^a   Rajendran, Krishnan ^a   Manna, Byomkesh ^a   Ramamurthy, Thandavarayan ^a   Niyogi, Swapan K ^a   Kanungo, Suman ^a   Sur, Dipika ^a   Kobayashi, Nobumichi ^b   Krishnan, Triveni ^a  

^a NATIONAL INSTITUTE OF CHOLERA AND ENTERIC DISEASES   (India)

^b SAPPORO MEDICAL UNIVERSITY SCHOOL OF MEDICINE   (Japan)

Author keywords

Bisegmented dsrna virus; Genogroup I and II picobirnavirus; Mixed infection; Viral diarrhea

Indexed keywords

AMPLICON; ARTICLE; CASE REPORT; CHILD; DIARRHEA; GENE SEQUENCE; GENETIC VARIABILITY; HUMAN; INDIA; MALE; MIXED INFECTION; MOLECULAR CLONING; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PICOBIRNAVIRUS; POLYACRYLAMIDE GEL ELECTROPHORESIS; PRESCHOOL CHILD; RNA EXTRACTION; SEQUENCE ANALYSIS; UNINDEXED SEQUENCE; VIRUS CHARACTERIZATION; VIRUS DETECTION; VIRUS STRAIN;

ANIMALIA; DSRNA VIRUSES; PICOBIRNAVIRUS; SUS;

EID: 79251571190     PISSN: None     EISSN: 19481756     Source Type: Journal    
DOI: None     Document Type: Article

References (55)

1. Carstens EB, Ball LA. Ratification vote on taxo-nomic proposals to the International Committee on Taxonomy of Viruses. Arch Virol 2009;154: 1181-1188.
2. Rosen BI, Fang ZY, Glass RI, Monroe SS. Cloning of human picobirnavirus genomic segments and development of an RT-PCR detection assay. Virology 2000;277:316-329.
3. Wakuda M, Pongsuwanna Y, Taniguchi K. Complete nucleotide sequences of two RNA segments of human picobirnavirus. J Virol Methods 2005;126:165-169.
4. Bhattacharya R, Sahoo GC, Nayak MK, Saha DR, Sur D, Naik TN, Bhattacharya SK, Krishnan T. Molecular epidemiology of human picobirnaviruses among children of a slum community in Kolkata, India. Infect Genet Evol 2006;6:453-458.
5. Ganesh B, Nataraju SM, Rajendran K, Ramamurthy T, Kanungo S, Manna B, Nagashima S, Sur D, Kobayashi N, and Krishnan T. Detection of closely related Picobirnaviruses among diarrhoeic children in Kolkata: Evidence of zoonoses? Infect Genet Evol 2010;10:511-16.
6. Gallimore CI, Appleton H, Lewis D, Green J, Brown DW. Detection and characterisation of bisegmented double-stranded RNA viruses (picobirnaviruses) in human faecal specimens. J Med Virol 1995;45:135-40.
7. Gallimore CI, Green J, Casemore DP, Brown DW. Detection of a picobirnavirus associated with Cryptosporidium positive stools from humans. Arch Virol 1995;140:1275-78.
8. Bhattacharya R, Sahoo GC, Nayak MK, Rajen-dran K, Dutta P, Mitra, U, Bhattacharya, MK, Naik TN, Bhattacharya SK, Krishnan T. Detection of Genogroup I and II human picobirnavi-ruses showing small genomic RNA profile causing acute watery diarrhoea among children in Kolkata, India Infect Genet Evol 2007;7:229-38.
9. Duquerroy S, Da Costa B, Henry C, Vigouroux A, Libersou S, Lepault J, Navaza J, Delmas B, Rey FA. The picobirnavirus crystal structure provides functional insights into virion assembly and cell entry. EMBO J 2009;28: 1655-65.
10. Pongsuwanna Y, Taniguchi K, Chiwakul M, Urasawa T, Wakasugi F, Jayavasu C, Urasawa S. Serological and genomic characterization of porcine rotaviruses in Thailand: detection of a G10 porcine rotavirus. J Clin Microbiol 1996;34:1050-57.
11. Muñoz M, Alvarez M, Lanza I, Cármenes P. Role of enteric pathogens in the aetiology of neonatal diarrhoea in lambs and goat kids in Spain. Epidemiol Infect 1996;117:203-11.
12. Ludert JE, Abdul-Latiff L, Liprandi A, Liprandi, F. Identification of picobirnavirus, viruses with bisegmented double stranded RNA, in rabbit faeces. Res Vet Sci 1995;59:222-25.
13. Grohmann GS, Glass RI, Pereira HG, Monroe SS, Hightower AW, Weber R, Bryan RT. Enteric viruses and diarrhea in HIV-infected patients. Enteric Opportunistic Infections Working Group. N Engl J. Med 1993;329:14-20.
14. Cascio A, Bosco M, Vizzi E, Giammanco A, Ferraro D, Arista S. Identification of picobirnavirus from faeces of Italian children suffering from acute diarrhea. Eur J Epidemiol 1996;12:545-47.
15. Giordano MO, Martinez LC, Rinaldi D, Espul C, Martinez N, Isa MB, Depetris AR, Medeot SI, Nates SV. Diarrhea and enteric emerging viruses in HIV-infected patients. AIDS Res Hum Retroviruses 1999;15:1427-32.
16. Pereira HG, Fialho AM, Flewett TH, Teixeira JM, Andrade ZP. Novel viruses in human faeces. Lancet 1988;2:103-4.
17. Pereira HG, Flewett TH, Candeias JA, Barth OM, 1988b. A virus with a bisegmented double-stranded RNA genome in rat (Oryzomys ni-gripes) intestines. J Gen Virol 1988;69 (Pt 11):2749-54.
18. Martínez LC, Giordano MO, Isa MB, Alvarado LF, Paván JV, Rinaldi D, Nates SV Molecular diversity of partial-length genomic segment 2 of human picobirnavirus. Intervirology 2003;46: 207-13.
19. Bányai K, Jakab F, Reuter G, Bene J, Uj M, Me-legh B, Szücs G. Sequence heterogeneity among human picobirnaviruses detected in a gastroenteritis outbreak. Arch. Virol. 2003; 148:2281-91.
20. Ludert JE, Liprandi F. Identification of viruses with bi- and trisegmented double-stranded RNA genome in faeces of children with gastroenteritis. Res Virol 1993;144:219-24.
21. Novikova NA, Epifanova NV, Fedorova OF, Golitsyna LN., Kupriianova NV. Detection of picobirnaviruses by electrophoresis of RNA in polyacrylamide gel. Vopr Virusol 2003;48:41-43.
22. Finkbeiner SR, Allred AF, Tarr PI, Klein EJ, Kirk-wood CD, Wang D. Metagenomic analysis of human diarrhea: viral detection and discovery. PLoS Pathog 2008;4:e1000011.
23. Gatti MS, de Castro AF, Ferraz MM., Fialho AM., Pereira HG. Viruses with bisegmented double-stranded RNA in pig faeces. Res Vet Sci 1989;47:397-98.
24. Chasey D. Porcine picobirnavirus in UK? Vet Rec 1990;126:465.
25. Ludert JE, Hidalgo M, Gil F, Liprandi F. Identification in porcine faeces of a novel virus with a bisegmented double stranded RNA genome. Arch Virol 1991;117: 97-107.
26. Bányai K, Martella V, Bogdán A, Forgách P, Jakab F, Meleg E, Bíró H, Melegh B, Szucs G. Genogroup I picobirnaviruses in pigs: evidence for genetic diversity and relatedness to human strains. J Gen Virol 2008;89(Pt 2):534-39.
27. Vanopdenbosch E, Wellemans G. Bovine birna-type virus: a new etiological agent of neonatal calf diarrhoea? Laams Dierg Tijdsch 1990;59:222-25.
28. Chandra R. Picobirnavirus, a novel group of undescribed viruses of mammals and birds: a minireview. Acta Virol 1997;41:59-62.
29. Buzinaro MG, Freitas PP, Kisiellius JJ, Ueda M, Jerez JA. Identification of a bisegmented double -stranded RNA virus (picobirnavirus) in calf faeces. Vet J 2003;166:185-87.
30. Ghosh S, Kobayashi N, Nagashima S, Naik TN. Molecular characterization of full-length genomic segment 2 of a bovine picobirnavirus strain: Evidence for high genetic diversity with genogroup I picobirnaviruses. J Gen Virol 2009;90:2519-24.
31. Browning GF, Chalmers RM, Snodgrass DR, Batt RM, Hart CA, Ormarod SE, Leadon D, Stoneham SJ, Rossdale PD. The prevalence of enteric pathogens in diarrhoeic thoroughbred foals in Britain and Ireland. Equine Vet J 1991;23:405-9.
32. Gallimore C, Lewis D, Brown D. Detection and characterization of a novel bisegmented double -stranded RNA virus (picobirnavirus) from rabbit faeces. Arch Virol 1993;133:63-73.
33. Green J, Gallimore CI, Clewley JP, Brown DW. Genomic characterisation of the large segment of a rabbit picobirnavirus and comparison with the atypical picobirnavirus of Cryptosporidium parvum. Arch. Virol. 1999;144:2457-65.
34. Pereira HG, de Araujo HP, Fialho AM, de Castro L, Monteiro SP. A virus with bi-segmented double-stranded RNA genome in guinea pig intestines. Mem. Inst. Oswaldo Cruz 1989;84:137-40.
35. Leite JP, Monteiro SP, Fialho, AM, Pereira HG. A novel avian virus with trisegmented double-stranded RNA and further observations on previously described similar viruses with bisegmented genome. Virus Res 1990;16:119-26.
36. Haga IR, Martins, SS, Hosomi ST, Vicentini F, Tanaka H, Gatti MS. Identification of a bisegmented double-stranded RNA virus (Picobirnavirus) in faeces of giant anteaters (Myrmecophaga tridactyla). Vet J 1999;158: 234-36.
37. Masachessi G, Martínez LC, Giordano MO, Barril PA, Isa BM, Ferreyra L, Villareal D, Carello M, Asis C, Nates SV. Picobirnavirus (PBV) natural hosts in captivity and virus excretion pattern in infected animals. Arch Virol 2007;152:989-98.
38. Wang Y, Tu X, Humphrey C, McClure H, Jiang X, Qin C, Glass RI, Jiang B. Detection of viral agents in fecal specimens of monkeys with diarrhea. J Med Primatol 2007;36:101-7.
39. Fregolente MC, de Castro-Dias E, Martins SS, Spilki FR, Allegretti SM, Gatti MS. Molecular characterization of picobirnaviruses from new hosts. Virus Res 2009;143:134-36.
40. González GG, Pujol FH, Liprandi F, Deibis L, Ludert JE. Prevalence of enteric viruses in human immunodeficiency virus seropositive patients in Venezuela. J Med Virol 1998;55:288-92.
41. Giordano MO, Martinez LC, Rinaldi D, Gúinard S, Naretto E, Casero R, Yacci MR, Depetris AR, Medeot SI, Nates SV. Detection of picobirnavirus in HIV-infected patients with diarrhea in Argentina. J. Acquir. Immune. Defic. Syndr. Hum Retrovirol 1998;18:380-83.
42. Zhang T, Breitbart M, Lee WH, Run JQ, Wei CL, Soh SW, Hibberd ML, Liu ET, Rohwer F, Ruan Y. RNA viral community in human feces: prevalence of plant pathogenic viruses. PLoS Biol 2006;4:e3.
43. Herring AJ, Inglis NF, Ojeh CK, Snodgrass DR, Menzies JD. Rapid diagnosis of rotavirus infection by direct detection of viral nucleic acid in silver-stained polyacrylamide gels. J Clin Micro-biol 1982;16:473-77.
44. Victoria JG, Kapoor A, Li L, Blinkova O, Slikas B, Wang C, Naeem A, Zaidi S, Delwart E. Metage-nomic analyses of viruses in stool samples from children with acute flaccid paralysis. J Virol 2009; 83:4642-4651.
45. Nair GB, Ramamurthy T, Bhattacharya MK, Krishnan T, Ganguly S, Saha DR, Rajendran K, Manna B, Ghosh M, Okamoto K, Takeda Y. Emerging trends in the etiology of enteric pathogens as evidenced from an active surveillance of hospitalized diarrhoeal patients in Kolkata, India Gut Pathog 2010;2:4. doi: 10.1186/1757-4749-2-4.
46. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997;25:3389-402.
47. Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994;22:4673-80.
48. Huang X, Miller W. A time-efficient, linear-space local similarity algorithm. Adv Appl Math 1991;12:337-57.
49. Tamura K, Dudley J, Nei M, Kumar S. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol 2007;24:1596-99.
50. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987;4:406-25.
51. Fregolente MC, Gatti MS. Nomenclature proposal for picobirnavirus. Arch Virol 2009; 154:1953-54.
52. Carruyo GM., Mateu G, Martínez LC, Pujol FH, Nates SV, Liprandi F, Ludert JE. Molecular characterization of porcine picobirnaviruses and development of a specific reverse transcription-PCR assay. J Clin Microbiol 2008;46:2402-05.
53. Giordano MO, Masachessi G, Martinez LC, Barril PA, Ferreyra LJ, Isa MB, Nates SV. Two instances of large genome profile picobirnavirus occurrence in Argentinian infants with diarrhea over a 26-year period (1977-2002). J Infect 2008;56:371-75.
54. Parrish CR, Holmes EC, Morens DM, Park EC, Burke DS, Calisher CH, Laughlin CA, Saif LJ, Daszak P. Cross-species virus transmission and the emergence of new epidemic diseases. Mi-crobiol Mol Biol Rev 2008;72:457-70.
55. van Leeuwen M, Williams MM, Koraka P, Simon JH, Smits SL, Osterhaus AD. Human pico-birnaviruses identified by molecular screening of diarrhea samples. J Clin Microbiol 2010;48: 1787-94.