Expecting the unexpected: Nucleic acid-based diagnosis and discovery of emerging viruses

Expert Review of Molecular Diagnostics

Volumn 11, Issue 4, 2011, Pages 409-423

  Barnard, Ross Thomas ^a   Hall, Roy A ^a   Gould, Ernest A ^b  

^a UNIVERSITY OF QUEENSLAND   (Australia)

^b Aix Marseille University IRD 190 Inserm 1207   (France)

Author keywords

broad spectrum; emerging viruses; metagenomics; microbead; microsphere; multiplex; nanowire; random PCR; real time PCR

Indexed keywords

BIOINFORMATICS; BIOSENSOR; CLIMATE CHANGE; DIAGNOSTIC TEST; ELECTROSPRAY MASS SPECTROMETRY; ENVIRONMENTAL CHANGE; HUMAN; HYPOTHESIS; METAGENOMICS; MULTIPLEX POLYMERASE CHAIN REACTION; NANOTECHNOLOGY; NONHUMAN; NUCLEIC ACID ANALYSIS; REAL TIME POLYMERASE CHAIN REACTION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; REVIEW; VIRUS DIAGNOSIS; VIRUS MUTATION; VIRUS RECOMBINATION;

ANIMAL MIGRATION; ANIMALS; CLIMATE CHANGE; COMMUNICABLE DISEASES, EMERGING; DISEASE RESERVOIRS; DISEASE VECTORS; EMIGRATION AND IMMIGRATION; ENVIRONMENT; GENETIC VARIATION; HUMANS; MOLECULAR DIAGNOSTIC TECHNIQUES; NUCLEIC ACIDS; VIRUS DISEASES; VIRUSES;

EID: 79955763755     PISSN: 14737159     EISSN: 17448352     Source Type: Journal    
DOI: 10.1586/erm.11.24     Document Type: Review

References (102)

1. Jewish Publication Society. Leviticus, Chapter 13. In: JPS Hebrew-English Tanakh. Jewish Publication Society, PA, USA, 232 (2003).
2. Quiambao BP, Dy-Tioco HZ, Dizon RM, Crisostomo ME, Teuwen DE. Rabies post-exposure prophylaxis with purified equine rabies immunoglobulin: one-year follow-up of patients with laboratory-confirmed category III rabies exposure in the Philippines. Vaccine 27, 7162-7166 (2009).
3. Bossart KN, Zhu Z, Middleton D et al. A neutralizing human monoclonal antibody protects against lethal disease in a new ferret model of acute Nipah virus infection. PLoS Pathog. 5(10), e1000642 (2009).
4. Zhu Z, Bossart KN, Bishop KA et al. Exceptionally potent cross-reactive neutralization of Nipah and Hendra viruses by a human monoclonal antibody. J. Infect. Dis. 197, 846-853 (2008). (Pubitemid 351417007)
5. Davison KL, Crowcroft NS, Ramsay ME, Brown DWG, Andrews NJ. Viral encephalitis in England 1989-1998: what did we miss? Emerg. Infect. Dis. 9, 234-240 (2003). (Pubitemid 36231796)
6. Suttle C. Viruses: a vast reservoir of genetic diversity and driver of global processes. Retrovirology 6(Suppl. 2), 17 (2009).
7. Gubala AJ, Proll DF, Barnard RT et al. Genomic characterisation of Wongabel virus reveals novel genes within the Rhabdoviridae. Virology 376, 13-23 (2008).
8. Gould EA, Higgs S. Impact of climate change and other factors on emerging arbovirus diseases. Trans. R. Soc. Trop. Med. Hyg. 103(2), 109-121 (2009).
9. Ritchie SA. Discovery of a widespread infestation of Aedes albopictus in the torres strait, Australia. J. Am. Mosq. Control Assoc. 22(3), S358-S365 (2006).
10. Hanson SM, Craig GB. Aedes albopictus (Diptera: Culcidae) eggs: field survivorship during Northern Indiana winters. J. Med. Ent. 32(5), S599-S560 (1995).
11. Romi R, Severini F, Toma L. Cold acclimation and overwintering of female Aedes albopictus in Roma. J. Am. Mosq. Control Assoc. 22(1), S149-S151 (2006).
12. Russell RC, Currie BJ, Lindsay MD et al. Dengue and climate change in Australia: prediction for the future should incorporate knowledge from the past. Med. J. Aust. 190, 265-268 (2009).
13. Gould EA, Higgs S, Buckley A, Gritsun TSG. Potential arbovirus emergence and implications for the United Kingdom. Emerg. Infect. Dis. 12(4), 549-555 (2006).
14. Buckley A, Dawson A, Gould EA. Detection of seroconversion to West Nile virus, Usutu virus and Sindbis virus in UK sentinel chickens. Virol. J. 3, 71 (2006).
15. Lounibos LP. Invasions by insect vectors of human disease. Annu. Rev. Entomol. 47, 233-266 (2002). (Pubitemid 34108582)
16. Russell RC, Williams CR, Sutherst RW, Ritchie SA. Aedes (Stegomyia) albopictus - a dengue threat for southern Australia? Commun. Dis. Intell. 29(3), 296-298 (2005).
17. Gould EA, Coutard B, Malet H. Understanding the alphaviruses: recent research on important emerging pathogens and progress towards their control. Antiviral. Res. 87(2), 111-124 (2010).
18. Burke, DS, Monath, TP. Flaviviruses. In:Fields Virology . Straus SE (Ed.). Lippincott Williams & Wilkins, PA, USA, 1043-1125 (2001).
19. De Lamballerie X, Leroy E, Charrel RN, Ttsetsarkin K, Higgs S, Gould EA. Chikungunya virus adapts to tiger mosquito via evolutionary convergence: a sign of things to come? Virol. J. 5, 33 (2008).
20. Reiskind MH, Pesko K,Westbrook CJ, Mores CN. Susceptibility of Florida mosquitoes to Chikungunya virus. Am. J. Trop. Med. Hyg. 78, 422-425 (2008). (Pubitemid 351845192)
21. Beltrame A, Angheben A, Bisoffi Z et al. Imported chikungunya infection, Italy. Emerg. Infect. Dis. 13, 1264-1265 (2007).
22. Hanna JN, Ritchie SA, Richards AR et al. Dengue in north Queensland, 2005-2008. Commun. Dis. Intell. 33, 198-203 (2009).
23. Meijer A, Lackenby A, Hungnes O et al.; on behalf of the European Influenza Surveillance Scheme. Oseltamivir-resistant influenza virus A (H1N1), Europe, 2007-2008 Season. Emerg. Infect. Dis. 15(4), 552-560 (2009).
24. Epstein JH, Quan P-L, Briese T et al. Identification of GBV-D, a Novel GB-like flavivirus from old world frugivorous bats (Pteropus giganteus) in Bangladesh. PLoS Pathog. 6(7), e1000972 (2010).
25. Breed AC, Field HE, Smith CS et al. Bats without borders: long-distance movements and implications for disease risk management. EcoHealth DOI: 10.1007/ s10393-010-0332-z (2010) (Epub ahead of print).
26. Weissenböck H, Kolodziejek J, Url A, Lussy H, Rebel-Bauder B, Nowotny N. Emergence of Usutu virus, an African mosquito-borne Flavivirus of the Japanese encephalitis virus group, Central Europe. Emerg. Infect. Dis. 8(7), 652-656 (2002). (Pubitemid 34764727)
27. Nanda M, Curtin VT, Hilliard JK, Bernstein ND, Dix RD. Ocular histopathologic findings in a case of human herpes B virus infection. Arch. Opthalmol. 108, 713-716 (1990). (Pubitemid 20168833)
28. Sugita S, Shimizu N, Watanabe K et al. Use of multiplex PCR and real-time PCR to detect human herpes virus genome in ocular fluids of patients with uveitis. Br. J. Opthalmol. 92, 928-932 (2008). (Pubitemid 351969672)
29. Switzer WM, Garcia AD, Yang C et al. Coinfection with HIV-1 and simian foamy virus in West Central Africans. J. Infect. Dis. 197(10), 1389-1393 (2008). (Pubitemid 351706462)
30. Zheng H, Wolfe ND, Sintasath DM et al. Emergence of a novel and highly divergent HTLV-3 in a primate hunter in Cameroon. Virology 401(2), 137-145 (2010).
31. Heneine W. Emergence of novel retroviruses. Retrovirology 6(Suppl. 2), 15 (2009).
32. Eigen M, Winkler-Oswatitsch R. Steps Towards Life: A Perspective on Evolution. Oxford University Press, Oxford, UK, (1996).
33. Holland J, Spindler K, Horodyski F, Grabau E, Nichol S, VandePol S. Rapid evolution of RNA genomes. Science 215, 1577-1585 (1982). (Pubitemid 12102984)
34. Sanjuán R, Nebot MR, Chirico N, Mansky LM, Belshaw R. Viral mutation rates. J. Virol. 84(19), 9733-9748 (2010).
35. Whiley DM, Lambert SB, Bialasiewicz S, Goire N, Nissen MD, Sloots TP. False-negative results in nucleic acid amplification tests - do we need to routinely use two genetic targets in all assays to overcome problems caused by sequence variation? Crit. Rev. Microbiol. 34(2), 71-76 (2008). (Pubitemid 351878990)
36. Whiley DM, Crisante ME, Syrmis MW, Mackay IM, Sloots TP. Detection of Neisseria meningitidis in clinical samples by a duplex real-time PCR targeting the porA and ctrA genes. Mol. Diagn. 7(3), 141-145 (2003). (Pubitemid 38533780)
37. Whiley DM, Bialasiewicz S, Bletchly C et al. Detection of novel influenza A(H1N1) virus by real-time RT-PCR. J. Clin. Virol. 45, 203-204 (2009).
38. Barzon L, Franchin E, Squarzon L et al. Epidemiology and molecular characterization of west nile virus infection in north-eastern Italy. Presented at: 4th European Congress of Virology. Cernobbio, Lake Como, Italy, 7-11 April 2010.
39. Simmonds P. Recombination and selection in the evolution of picornaviruses and other Mammalian positive-stranded RNA viruses. J. Virol. 80(22), 11124-11140 (2006). (Pubitemid 44706553)
40. Levinson RS, Strauss JH, Strauss EG. Complete sequence of the genomic RNA of O'nyong-nyong virus and its use in the construction of alphavirus phylogenetic trees. Virology 175, 110-123 (1990). (Pubitemid 20093066)
41. Worobey M, Holmes EC. Homologous recombination in GB virus C/hepatitis G virus. Mol. Biol. Evol. 18, 254-261 (2001). (Pubitemid 32118870)
42. Legrand-Abravanel F, Claudinon J, Nicot F et al. New natural intergenotypic (2/5) recombinant of hepatitis C virus. J. Virol. 81(8), 4357-4362 (2007). (Pubitemid 46586931)
43. Chuang CK, Chen WJ. Experimental evidence that RNA recombination occurs in the Japanese encephalitis virus. Virology 394, 286-297 (2009).
44. Yun S-M, Cho J E, Ju Y-R et al. Molecular epidemiology of Japanese encephalitis virus circulating in South Korea, 1983-2005. Virol. J. 7, 127 (2010).
45. Twiddy SS, Holmes EC. The extent of homologous recombination in members of the genus flavivirus. J. Gen. Virol. 84, 429-440 (2003). (Pubitemid 36175718)
46. May FJ, Li L, Zhang S et al. Genetic variation of St. Louis encephalitis virus. J. Gen. Virol. 89(8), 1901-1910 (2008).
47. Seligman SJ, Gould EA. Live flavivirus vaccines: reasons for caution. Lancet 363, 2073-2075 (2004). (Pubitemid 38781111)
48. Nowotny N. Emergence and dispersal of West Nile and Usutu virus infections in Europe. Presented at: 4th European Congress of Virology. Cernobbio, Lake Como, Italy, 7-11 April 2010.
49. Hochedez P, Jaureguiberry S, Debruyne M et al. Chikungunya onfection in travelers. Emerg. Infect. Dis. 12(10), 1565-1567 (2006).
50. Hochedez P, Hausfater P, Jaureguiberry S et al. Cases of chikungunya fever imported from the islands of the South West Indian Ocean to Paris. Euro Surveill. 12(1), 679 (2007).
51. Pecorari M, Longo G, Gennari W et al. First human case of Usutu virus neuroinvasive infection, Italy, August- September 2009. Euro Surveill. 14(50), pii: 19446 (2009).
52. Gould EA, Gallian P, De Lamballerie X, Charrel RN. First cases of autochthonous dengue fever and chikungunya fever in France: from bad dream to reality! Clin. Microbiol. Infect. 16, 1702-1704 (2010).
53. Barlow KL, Tosswill JH, Parry JV, Clewley JP. Performance of the Amplicor human immunodeficiency virus type 1 PCR and analysis of specimens with false-negative results. J. Clin. Microbiol. 35(11), 2846-2853 (1997). (Pubitemid 27452421)
54. Cohen BJ, Gandhi J, Clewley JP. Genetic variants of parvovirus B19 identified in the United Kingdom: implications for diagnostic testing. J. Clin. Virol. 36(2), 152-155 (2006).
55. Vandenbussche F, Vandemeulebrouke E, De Clercq K. Simultaneous detection of bluetongue virus RNA, internal control GAPDH mRNA, and external control synthetic RNA by multiplex real-time PCR. In:RT-PCR Protocols (2nd Edition) . Methods in Molecular Biology (Volume 630). King N (Ed.). Springer Verlag, NY, USA, 97-108 (2010).
56. González-Reiche AS, Monzón-Pineda MDL, Johnson BW, Morales-Betoulle ME. Detection of West Nile viral RNA from field-collected mosquitoes in tropical regions by conventional and real-time RT-PCR. In:RT-PCR Protocols (2nd Edition) . Methods in Molecular Biology (Volume 630). King N (Ed.). Springer Verlag, NY, USA, 109-124 (2010).
57. Lo CL, Yip SP, Cheng PK, To TS, Lim WW, Leung PH. One-step rapid reverse transcription-PCR assay for detecting and typing dengue viruses with GC tail and induced fluorescence resonance energy transfer techniques for melting temperature and color multiplexing. Clin. Chem. 53(4), 594-599 (2007). (Pubitemid 46580227)
58. Balada-Llasat J-M, LaRue H, Kelly C, Rigali L, Pancholi P. Evaluation of commercial ResPlex II v2.0, MultiCode® - PLx, and xTAG® respiratory viral panels for the diagnosis of respiratory viral infections in adults. J. Clin. Virol. 50(1), 42-45 (2011).
59. Mahony J, Chong S, Merante F et al. Development of a respiratory virus panel test for detection of twenty human respiratory viruses by use of multiplex PCR and a fluid microbead-based assay. J. Clin. Microbiol. 45(9), 2965-2970 (2007). (Pubitemid 47417341)
60. Nolte FS, Marshall DJ, Rasberry C et al. MultiCode-PLx system for multiplexed detection of seventeen respiratory viruses. J. Clin Microbiol. 45(9), 2779-2786 (2007). (Pubitemid 47417314)
61. Ginocchio CC, St George K. Likelihood that an unsubtypeable influenza A result in the Luminex xTAG respiratory virus panel is indicative of novel H1N1 (swinelike) influenza. J. Clin. Microbiol. 47, 2347-2348 (2009).
62. Ginocchio CC, Zhang F, Manji R. Evaluation of multiple test methods for the detection of the novel 2009 influenza A (H1N1) during the New York City outbreak. J. Clin. Virol. 45, 191-195 (2009).
63. Gould EA, Buckley A, Cammack N et al. Examination of the immunological relationships between flaviviruses using yellow fever virus monoclonal antibodies. J. Gen. Virol. 66, 1369-1382 (1985). (Pubitemid 15070379)
64. Gaunt MW, Gould EA. Rapid subgroup identification of the flaviviruses using degenerate primer E-gene RT-PCR and site specific restriction enzyme analysis. J. Virol. Methods 128(1-2), 113-127 (2005). (Pubitemid 40980217)
65. Moureau G, Temmam S, Gonzalez JP, Charrel RN, Grard G, De Lamballerie X. A real-time RT-PCR method for the universal detection and identification of flaviviruses. Vector Borne Zoonotic Dis. 7(4), 467-477 (2007).
66. Maher-Sturgess SL, Forrester, NL, Wayper PJ et al. Universal primers that amplify RNA from all three flavivirus subgroups Virol. J. 5, 16-30 (2008).
67. Fischer V, Smith G, Hall R, van den Hurk A, Smith I. Development of a multiplexed Luminex based approach for the diagnosis of arboviral infections of public health importance in Australia. Arbovirus Res. Aust. 10, 39-45 (2008).
68. Zheng L, Wayper PJ, Gibbs AJ, Fourment M, Rodoni BC, Gibbs MJ. Accumulating variation at conserved sites in potyvirus genomes is driven by species discovery and affects degenerate primer design. PLoS ONE 3(2), 1-8 (2008).
69. Macdonald J, Poidinger M, Mackenzie JS et al. Molecular phylogeny of Edge Hill virus supports its position in the Yellow Fever virus group and identifies a new genetic variant. Evol. Intell. 6, 91-96 (2010).
70. Gibbs MJ, Armstrong JS, Gibbs AJ. Individual sequences in large sets of gene sequences may be distinguished efficiently by combinations of shared sub-sequences. BMC Bioinformatics 6, 90 (2005).
71. Wang D, Urisman A, Liu Y-T Yu et al. Viral discovery and sequence recovery using DNA microarrays. PLoS Biol. 1(2), 257-260 (2003).
72. Cook S, Bennett SN, Holmes EC, De Chesse R, Moureau G, De Lamballerie X. Isolation of a new strain of the flavivirus cell fusing agent virus in a natural mosquito population from Puerto Rico. J. Gen. Virol. 87(4), 735-748 (2006).
73. Crochu S, Cook S, Attoui H et al. Sequences of flavivirus-related RNA viruses persist in DNA form integrated in the genome of Aedes spp. mosquitoes. J. Gen. Virol. 85(7), 1971-1980 (2004). (Pubitemid 39023276)
74. Grard G, Lemasson JJ, Sylla M et al. Ngoye virus: a novel evolutionary lineage within the genus Flavivirus. J. Gen. Virol. 87, 3273-3277 (2006). (Pubitemid 44608362)
75. 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. 39(5), 1922-1927 (2001). (Pubitemid 32417044)
76. Lynn T, Marano N, Treadwell T, Bokma B. Linking human and animal health surveillance for emerging diseases in the United States: achievements and challenge. Ann. NY Acad. Sci. 1081, 108-111 (2006). (Pubitemid 44968761)
77. Alvarez AC, Brunck MEG, Boyd V et al. A broad spectrum, one-step reverse-transcription PCR amplification of the neuraminidase gene from multiple subtypes of influenza A virus. Virol. J. 5, 77 (2008).
78. Alvarez AC, Boyd V, Lai R et al. Detection of influenza A virus neuraminidase and PB2 gene segments by one step reverse transcription polymerase chain reaction. In:RT-PCR Protocols (2nd Edition). Methods in Molecular Biology (Volume 630). King N (Ed.). Springer, NY, USA, 65-81 (2010).
79. Eshoo MW, Chris A, Whitehouse CA et al. Direct broad-range detection of alphaviruses in mosquito extracts. Virology 368(2), 286-295 (2007). (Pubitemid 350016217)
80. Petrosino JF, Highlander S, Luna RA, Gibbs RA, Versalovic J. Metagenomic pyrosequencing and microbial identification. Clin. Chem. 55(5), 856-866 (2009).
81. Van Den Hoogen BG, De Jong JC, Groen J. A newly discovered human pneumovirus isolated from young children with respiratory tract disease. Nat. Med. 7(6), 719-724 (2001). (Pubitemid 32588029)
82. Allander T, Tammi MT, Eriksson M et al. Cloning of a human parvovirus by molecular screening of respiratory tract samples. Proc. Natl Acad. Sci. USA 102, 12891-12896 (2005). (Pubitemid 41279460)
83. Gaynor AM, Nissen MD, Whiley DM et al. Identification of a novel polyomavirus from patients with acute respiratory tract infections. PLoS Pathogens 3(5), 595-564 (2007).
84. Finkbeiner SR, Allred AF, Tarr PI, Klein EJ, Kirkwood CD, Wang D. Metagenomic analysis of human diarrhea: viral detection and discovery. PLoS Pathog. 4(2), e1000011 (2008).
85. Nanda S, Jayan G, Voulgaropoulou F et al. Universal virus detection by degenerate-oligonucleotide primed polymerase chain reaction of purified viral nucleic acids. J. Virol. Methods 152, 18-24 (2008).
86. Uhlenhaut C, Cohen JI, Fedorko D, Nanda S, Krause PR. Use of a universal virus detection assay to identify human metapneumovirus in a hematopoietic stem cell transplant recipient with pneumonia of unknown origin. J. Clin. Virol. 44, 337-339 (2009).
87. Uhlenhaut C, McClenahan S, Scherba G et al. A universal virus detection assay - innovative molecular tools for identification of new viruses. Presented at: 4th European Congress of Virology. Cernobbio, Lake Como, Italy, 7-11 April 2010.
88. Luna RA, Fasciano LR, Jones SC, Boyanton BL Jr, Ton TT, Versalovic J. DNA pyrosequencing-based bacterial pathogen identification in a pediatric hospital setting. J. Clin. Microbiol. 45, 2985-2992 (2007). (Pubitemid 47417344)
89. Wong CW, Heng CLW, Leong WL et al. Optimization and clinical validation of a pathogen detection microarray. Genome Biol. 8, R93 (2007).
90. Lee WH, Wong CW, Leong WY, Miller LD, Sung WK. LOMA: a fast method to generate efficient tagged-random primers despite amplification bias of random PCR on pathogens. BMC Bioinformatics 9, 368 (2008).
91. Lodes MJ, Suciu D, Elliott M et al. Use of semiconductor-based oligonucleotide microarrays for influenza A virus subtype identification and sequencing. J. Clin. Microbiol. 44(4) 1209-1218 (2006).
92. Bolotin S, Lombos E, Yeung R, Eshaghi A, Blair J, Drews SJ. Verification of the Combimatrix influenza detection assay for the detection of influenza A subtype during the 2007-2008 influenza season in Toronto, Canada. Virol. J. 6, 37-39 (2009).
93. Azzazy HME, Mansour MMH, Kazmierczak SC. Nanodiagnostics: a new frontier for clinical laboratory medicine. Clin. Chem. 52(7), 1238-1246 (2006). (Pubitemid 43956012)
94. Margulies M, Egholm M, Altman WE et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature 437, 376-380 (2005). (Pubitemid 41613494)
95. Barnard R, Lai R, Corrie S et al. Integration of a novel real-time PCR detection system onto Luminex beads in a PCR reaction. Presented at: 5th International qPCR Symposium: Molecular Diagnostics from Single Cells to Next Generation Sequencing. Freising- Weihenstephan, Germany, 28 March-1 April 2011.
96. Sambol AR, Iwen PC, Pieretti M et al. Validation of the Cepheid Xpert Flu A real time RT-PCR detection panel for emergency use authorization. J. Clin. Virol. 48(4), 234-238 (2010).
97. Stern E, Klemic JF, Routenberg DA et al. Label-free immunodetection with CMOS-compatible semiconducting nanowires Nature 445, 519-522 (2007). (Pubitemid 46197629)
98. Gao Z, Agarwal A, Trigg AD et al. Silicon nanowire arrays for ultrasensitive label-free detection of DNA. Anal. Chem. 79, 3291-3297 (2007). (Pubitemid 46717159)
99. Zhang G, Chua J, Chee RE et al. DNA sensing by silicon nanowire: charge layer distance dependence. Nano Lett. 8, 1066-1070 (2008).
100. Bunimovich YL, Shin YS, Yeo W-S, Amori M, Kwoong G, Heath JR. Quantitative real-time measurements of DNA hybridization with alkylated nonoxidised silicon nanowires in electrolyte solution. J. Am. Chem. Soc. 128, 16323-16331 (2006). (Pubitemid 44936627)
101. Neuzil P, Zhang C, Pipper J, Oh S, Zhuo L. Ultrafast miniaturized real-time PCR: 40 cycles in less than 6 minutes. Nucleic Acids Res. 34 (11), 277 (2006).
102. Barnard R. A new diagnostic paradigm. Presented at: 36th Annual Conference of the Association of Clinical Biochemists of India. Kochi, India, 5-7 November 2009.