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Virology Journal
Published in: Virology Journal 1/2014

Open Access 01-12-2014 | Research

Identification and characterization of unrecognized viruses in stool samples of non-polio acute flaccid paralysis children by simplified VIDISCA

Authors: Shahzad Shaukat, Mehar Angez, Muhammad Masroor Alam, Maarten F Jebbink, Martin Deijs, Marta Canuti, Salmaan Sharif, Michel de Vries, Adnan Khurshid, Tariq Mahmood, Lia van der Hoek, SyedSohail Zahoor Zaidi

Published in: Virology Journal | Issue 1/2014

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Abstract

Background

The use of sequence independent methods combined with next generation sequencing for identification purposes in clinical samples appears promising and exciting results have been achieved to understand unexplained infections. One sequence independent method, Virus Discovery based on cDNA Amplified Fragment Length Polymorphism (VIDISCA) is capable of identifying viruses that would have remained unidentified in standard diagnostics or cell cultures.

Methods

VIDISCA is normally combined with next generation sequencing, however, we set up a simplified VIDISCA which can be used in case next generation sequencing is not possible. Stool samples of 10 patients with unexplained acute flaccid paralysis showing cytopathic effect in rhabdomyosarcoma cells and/or mouse cells were used to test the efficiency of this method. To further characterize the viruses, VIDISCA-positive samples were amplified and sequenced with gene specific primers.

Results

Simplified VIDISCA detected seven viruses (70%) and the proportion of eukaryotic viral sequences from each sample ranged from 8.3 to 45.8%. Human enterovirus EV-B97, EV-B100, echovirus-9 and echovirus-21, human parechovirus type-3, human astrovirus probably a type-3/5 recombinant, and tetnovirus-1 were identified. Phylogenetic analysis based on the VP1 region demonstrated that the human enteroviruses are more divergent isolates circulating in the community.

Conclusion

Our data support that a simplified VIDISCA protocol can efficiently identify unrecognized viruses grown in cell culture with low cost, limited time without need of advanced technical expertise. Also complex data interpretation is avoided thus the method can be used as a powerful diagnostic tool in limited resources. Redesigning the routine diagnostics might lead to additional detection of previously undiagnosed viruses in clinical samples of patients.
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Literature
1.
Nichol ST, Spiropoulou CF, Morzunov S, Rollin PE, Ksiazek TG, Feldmann H, Sanchez A, Childs J, Zaki S, Peters CJ: Genetic identification of a hantavirus associated with an outbreak of acute respiratory illness. Science 1993,262(5135):914-917.PubMedCrossRef
2.
Scaramozzino N, Crance JM, Jouan A, DeBriel DA, Stoll F, Garin D: Comparison of flavivirus universal primer pairs and development of a rapid, highly sensitive heminested reverse transcription-PCR assay for detection of flaviviruses targeted to a conserved region of the NS5 gene sequences. J Clin Microbiol 2001,39(5):1922-1927.PubMedPubMedCentralCrossRef
3.
Adachi D, Johnson G, Draker R, Ayers M, Mazzulli T, Talbot PJ, Tellier R: Comprehensive detection and identification of human coronaviruses, including the SARS-associated coronavirus, with a single RT-PCR assay. J Virol Methods 2004,122(1):29-36.PubMedCrossRef
4.
Woo PC, Lau SK, Chu CM, Chan KH, Tsoi HW, Huang Y, Wong BH, Poon RW, Cai JJ, Luk WK, Poon LL, Wong SS, Guan Y, Peiris JS, Yuen KY: Characterization and complete genome sequence of a novel coronavirus, coronavirus HKU1, from patients with pneumonia. J Virol 2005,79(2):884-895.PubMedPubMedCentralCrossRef
5.
Choo QL, Kuo G, Weiner AJ, Overby LR, Bradley DW, Houghton M: Isolation of a cDNA clone derived from a blood-borne non-A, non-B viral hepatitis genome. Science 1989,244(4902):359-362.PubMedCrossRef
6.
Chang Y, Cesarman E, Pessin MS, Lee F, Culpepper J, Knowles DM, Moore PS: Identification of herpesvirus-like DNA sequences in AIDS-associated Kaposi’s sarcoma. Science 1994,266(5192):1865-1869.PubMedCrossRef
7.
Karst SM, Wobus CE, Lay M, Davidson J, Virgin HW: STAT1-dependent innate immunity to a Norwalk-like virus. Science 2003,299(5612):1575-1578.PubMedCrossRef
8.
Lisitsyn N, Wigler M: Cloning the differences between two complex genomes. Science 1993,259(5097):946-951.PubMedCrossRef
9.
Canuti M, Eis-Huebinger AM, Deijs M, de Vries M, Drexler JF, Oppong SK, Muller MA, Klose SM, Wellinghausen N, Cottontail VM, Kalko EK, Drosten C, van der Hoek L: Two novel parvoviruses in frugivorous new and old world bats. PLoS One 2011,6(12):e29140.PubMedPubMedCentralCrossRef
10.
van der Hoek L, Pyrc K, Jebbink MF, Vermeulen-Oost W, Berkhout RJ, Wolthers KC, Wertheim-van Dillen PM, Kaandorp J, Spaargaren J, Berkhout B: Identification of a new human coronavirus. Nat Med 2004,10(4):368-373.PubMedCrossRef
11.
de Vries M, Pyrc K, Berkhout R, Vermeulen-Oost W, Dijkman R, Jebbink MF, Bruisten S, Berkhout B, van der Hoek L: Human parechovirus type 1, 3, 4, 5, and 6 detection in picornavirus cultures. J Clin Microbiol 2008,46(2):759-762.PubMedPubMedCentralCrossRef
12.
de Souza Luna LK, Baumgarte S, Grywna K, Panning M, Drexler JF, Drosten C: Identification of a contemporary human parechovirus type 1 by VIDISCA and characterisation of its full genome. Virol J 2008, 5: 26.PubMedPubMedCentralCrossRef
13.
de Vries M, Deijs M, Canuti M, van Schaik BD, Faria NR, van de Garde MD, Jachimowski LC, Jebbink MF, Jakobs M, Luyf AC, Coenjaerts FE, Claas EC, Molenkamp R, Koekkoek SM, Lammens C, Leus F, Goossens H, Ieven M, Baas F, van der Hoek L: A sensitive assay for virus discovery in respiratory clinical samples. PLoS One 2011,6(1):e16118.PubMedPubMedCentralCrossRef
14.
Harvala H, McIntyre CL, McLeish NJ, Kondracka J, Palmer J, Molyneaux P, Gunson R, Bennett S, Templeton K, Simmonds P: High detection frequency and viral loads of human rhinovirus species A to C in fecal samples; diagnostic and clinical implications. J Med Virol 2012,84(3):536-542.PubMedCrossRef
15.
McLeish NJ, Witteveldt J, Clasper L, McIntyre C, McWilliam Leitch EC, Hardie A, Bennett S, Gunson R, Carman WF, Feeney SA, Coyle PV, Vipond B, Muir P, Benschop K, Wolthers K, Waris M, Osterback R, Johannessen I, Templeton K, Harvala H, Simmonds P: Development and assay of RNA transcripts of enterovirus species A to D, rhinovirus species a to C, and human parechovirus: assessment of assay sensitivity and specificity of real-time screening and typing methods. J Clin Microbiol 2012,50(9):2910-2917.PubMedPubMedCentralCrossRef
16.
Hu YF, Zhao R, Xue Y, Yang F, Jin Q: Full genome sequence of a novel coxsackievirus B5 strain isolated from neurological hand, foot, and mouth disease patients in China. J Virol 2012,86(20):11408-11409.PubMedPubMedCentralCrossRef
17.
Laxmivandana R, Yergolkar P, Gopalkrishna V, Chitambar SD: Characterization of the non-polio enterovirus infections associated with acute flaccid paralysis in South-Western India. PLoS One 2013,8(4):e61650.PubMedPubMedCentralCrossRef
18.
Roth B, Enders M, Arents A, Pfitzner A, Terletskaia-Ladwig E: Epidemiologic aspects and laboratory features of enterovirus infections in Western Germany, 2000–2005. J Med Virol 2007,79(7):956-962.PubMedCrossRef
19.
Cabrerizo M, Echevarria J, Gonzalez I, de Miguel T, Trallero G: Molecular epidemiological study of human EV-B enteroviruses involved in the increase in meningitis cases occurred in Spain during 2006. J Med Virol 2008, 80: 1018-1024.PubMedCrossRef
20.
21.
Rico-Hesse R, Pallansch MA, Nottay BK, Kew OM: Geographic distribution of wild poliovirus type 1 genotypes. Virology 1987,160(2):311-322.PubMedCrossRef
22.
Ito M, Yamashita T, Tsuzuki H, Takeda N, Sakae K: Isolation and identification of a novel human parechovirus. J Gen Virol 2004,85(Pt 2):391-398.PubMedCrossRef
23.
Legay V, Chomel JJ, Fernandez E, Lina B, Aymard M, Khalfan S: Encephalomyelitis due to human parechovirus type 1. J Clin Virol 2002,25(2):193-195.PubMedCrossRef
24.
Li L, Kapoor A, Slikas B, Bamidele OS, Wang C, Shaukat S, Masroor MA, Wilson ML, Ndjango JB, Peeters M, Gross-Camp ND, Muller MN, Hahn BH, Wolfe ND, Triki H, Bartkus J, Zaidi SZ, Delwart E: Multiple diverse circoviruses infect farm animals and are commonly found in human and chimpanzee feces. J Virol 2010,84(4):1674-1682.PubMedPubMedCentralCrossRef
25.
Watanabe K, Oie M, Higuchi M, Nishikawa M, Fujii M: Isolation and characterization of novel human parechovirus from clinical samples. Emerg Infect Dis 2007,13(6):889-895.PubMedPubMedCentralCrossRef
26.
Alam MM, Khurshid A, Shaukat S, Sharif S, Rana MS, Angez M, Naeem M, Zaidi SS: Identification of human parechovirus genotype, HPeV-12, in a paralytic child with diarrhea. J Clin Virol 2012,55(4):339-342.PubMedCrossRef
27.
28.
Victoria JG, Kapoor A, Li L, Blinkova O, Slikas B, Wang C, Naeem A, Zaidi S, Delwart E: Metagenomic analyses of viruses in stool samples from children with acute flaccid paralysis. J Virol 2009,83(9):4642-4651.PubMedPubMedCentralCrossRef
29.
Belliot G, Laveran H, Monroe SS: Detection and genetic differentiation of human astroviruses: phylogenetic grouping varies by coding region. Arch Virol 1997,142(7):1323-1334.PubMedCrossRef
30.
Walter J, Mitchell D, Guerrero M, Berke T, Matson D, Monroe S, Pickering L, R-P G: Molecular epidemiology of human astrovirus diarrhea among children from a periurban community of Mexico City. J Infect Dis 2001,183(5):681-686.PubMedCrossRef
31.
Wolfaardt M, Kiulia NM, Mwenda JM, Taylor MB: Evidence of a recombinant wild-type human astrovirus strain from a Kenyan child with gastroenteritis. J Clin Microbiol 2011,49(2):728-731.PubMedPubMedCentralCrossRef
32.
Pativada MS, Chatterjee D, Mariyappa NS, Rajendran K, Bhattacharya MK, Ghosh M, Kobayashi N, Krishnan T: Emergence of unique variants and inter-genotype recombinants of human astroviruses infecting infants, children and adults in Kolkata, India. International journal of molecular epidemiology and genetics 2011,2(3):228-235.PubMedPubMedCentral
33.
Kapoor A, Simmonds P, Lipkin W, Zaidi S, Delwart E: Use of nucleotide composition analysis to infer hosts for three novel picorna-like viruses. J Virol 2010,84(19):10322-10328.PubMedPubMedCentralCrossRef
34.
Palacios G, Druce J, Du L, Tran T, Birch C, Briese T, Conlan S, Quan PL, Hui J, Marshall J, Simons JF, Egholm M, Paddock CD, Shieh WJ, Goldsmith CS, Zaki SR, Catton M, Lipkin WI: A new arenavirus in a cluster of fatal transplant-associated diseases. N Engl J Med 2008,358(10):991-998.PubMedCrossRef
35.
Finkbeiner SR, Allred AF, Tarr PI, Klein EJ, Kirkwood CD, Wang D: Metagenomic analysis of human diarrhea: viral detection and discovery. PLoS Pathog 2008,4(2):e1000011.PubMedPubMedCentralCrossRef
36.
Barzon L, Lavezzo E, Militello V, Toppo S, Palu G: Applications of next-generation sequencing technologies to diagnostic virology. Int J Mol Sci 2011,12(11):7861-7884.PubMedPubMedCentralCrossRef
37.
Shaukat S, Angez M, Alam MM, Sharif S, Khurshid A, Malik F, Rana MS, Mahmood T, Zaidi SS: Molecular identification and characterization of a new type of Bovine Enterovirus. Appl Environ Microbiol 2012,78(12):4497-4500.PubMedPubMedCentralCrossRef
38.
Kapoor A, Slikas E, Simmonds P, Chieochansin T, Naeem A, Shaukat S, Alam MM, Sharif S, Angez M, Zaidi S, Delwart E: A newly identified bocavirus species in human stool. J Infect Dis 2009,199(2):196-200.PubMedPubMedCentralCrossRef
39.
Kapoor A, Victoria J, Simmonds P, Slikas E, Chieochansin T, Naeem A, Shaukat S, Sharif S, Alam MM, Angez M, Wang C, Shafer RW, Zaidi S, Delwart E: A highly prevalent and genetically diversified Picornaviridae genus in South Asian children. Proc Natl Acad Sci U S A 2008,105(51):20482-20487.PubMedPubMedCentralCrossRef
40.
Kilpatrick DR, Yang CF, Ching K, Vincent A, Iber J, Campagnoli R, Mandelbaum M, De L, Yang SJ, Nix A, Kew OM: Rapid group-, serotype-, and vaccine strain-specific identification of poliovirus isolates by real-time reverse transcription-PCR using degenerate primers and probes containing deoxyinosine residues. J Clin Microbiol 2009,47(6):1939-1941.PubMedPubMedCentralCrossRef
41.
Boom R, Sol CJ, Salimans MM, Jansen CL, Wertheim-van Dillen PM, van der Noordaa J: Rapid and simple method for purification of nucleic acids. J Clin Microbiol 1990,28(3):495-503.PubMedPubMedCentral
42.
Endoh D, Mizutani T, Kirisawa R, Maki Y, Saito H, Kon Y, Morikawa S, Hayashi M: Species-independent detection of RNA virus by representational difference analysis using non-ribosomal hexanucleotides for reverse transcription. Nucleic Acids Res 2005,33(6):e65.PubMedPubMedCentralCrossRef
43.
Oberste MS, Maher K, Williams AJ, Dybdahl-Sissoko N, Brown BA, Gookin MS, Penaranda S, Mishrik N, Uddin M, Pallansch MA: Species-specific RT-PCR amplification of human enteroviruses: a tool for rapid species identification of uncharacterized enteroviruses. J Gen Virol 2006,87(Pt 1):119-128.PubMedCrossRef
44.
Benschop KS, Schinkel J, Minnaar RP, Pajkrt D, Spanjerberg L, Kraakman HC, Berkhout B, Zaaijer HL, Beld MG, Wolthers KC: Human parechovirus infections in Dutch children and the association between serotype and disease severity. Clin Infect Dis 2006,42(2):204-210.PubMedCrossRef
45.
Tamura K, Dudley J, Nei M, Kumar S: MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 2007,24(8):1596-1599.PubMedCrossRef
46.
Kimura M: A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980,16(2):111-120.PubMedCrossRef
Metadata
Title
Identification and characterization of unrecognized viruses in stool samples of non-polio acute flaccid paralysis children by simplified VIDISCA
Authors
Shahzad Shaukat
Mehar Angez
Muhammad Masroor Alam
Maarten F Jebbink
Martin Deijs
Marta Canuti
Salmaan Sharif
Michel de Vries
Adnan Khurshid
Tariq Mahmood
Lia van der Hoek
SyedSohail Zahoor Zaidi
Publication date
01-12-2014
Publisher
BioMed Central
Published in
Virology Journal / Issue 1/2014
Electronic ISSN: 1743-422X
DOI
https://doi.org/10.1186/1743-422X-11-146

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