Chapter 57 : Immunologic and Molecular Methods for Viral Diagnosis

MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.

Preview this chapter:
Zoom in

Immunologic and Molecular Methods for Viral Diagnosis, Page 1 of 2

| /docserver/preview/fulltext/10.1128/9781555818722/9781555818715_CH57-1.gif /docserver/preview/fulltext/10.1128/9781555818722/9781555818715_CH57-2.gif


Tremendous strides have been made in viral diagnosis in the past decade. Many infections are now treatable and, for optimum effect, antivirals must be started early. For hospitalized patients, rapid and accurate viral diagnosis is essential not only for patient management, but for infection control and prevention of nosocomial transmission. The impact of seasonal and pandemic influenza on morbidity and mortality of all ages has received increasing attention in both the medical literature and the popular press. Emerging, highly virulent viruses such as severe acute respiratory syndrome (SARS) coronavirus (CoV), Middle East respiratory syndrome CoV, and avian influenza H5N1 and H7N9 have also heightened concerns. Lastly, immunosuppressed and other vulnerable populations at risk for serious or life-threatening viral infections continue to increase. In response to these needs, there has been an explosion in viral diagnostic test development.

Citation: Landry M, Tang Y. 2016. Immunologic and Molecular Methods for Viral Diagnosis, p 538-549. In Detrick B, Schmitz J, Hamilton R (ed), Manual of Molecular and Clinical Laboratory Immunology, Eighth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818722.ch57
Highlighted Text: Show | Hide
Loading full text...

Full text loading...


1. Leland DS, Landry ML,. 2010. Virus isolation, p 98112. In Jerome KR (ed), Laboratory Diagnosis of Viral Infections, 4th ed. Informa Press, New York, NY.[CrossRef]
2. Ginocchio CC, Zhang F, Manji R, Arora S, Bornfreund M, Falk L, Lotlikar M, Kowerska M, Becker G, Korologos D, de Geronimo M, Crawford JM. 2009. Evaluation of multiple test methods for the detection of the novel 2009 influenza A (H1N1) during the New York City outbreak. J Clin Virol 45:191195.[CrossRef].[PubMed]
3. Landry ML, Ferguson D, Wlochowski J. 1997. Detection of herpes simplex virus in clinical specimens by cytospin-enhanced direct immunofluorescence. J Clin Microbiol 35:302304.[PubMed]
4. Landry ML, Ferguson D. 2000. SimulFluor respiratory screen for rapid detection of multiple respiratory viruses in clinical specimens by immunofluorescence staining. J Clin Microbiol 38:708711.[PubMed]
5. Gerna G, Revello MG, Percivalle E, Morini F. 1992. Comparison of different immunostaining techniques and monoclonal antibodies to the lower matrix phosphoprotein (pp65) for optimal quantitation of human cytomegalovirus antigenemia. J Clin Microbiol 30:12321237.[PubMed]
6. Landry ML, Ferguson D. 1993. Comparison of quantitative cytomegalovirus antigenemia assay with culture methods and correlation with clinical disease. J Clin Microbiol 31:28512856.[PubMed]
7. Barenfanger J, Drake C, Leon N, Mueller T, Troutt T. 2000. Clinical and financial benefits of rapid detection of respiratory viruses: An outcomes study. J Clin Microbiol 38:28242828.[PubMed]
8. Byington CL, Castillo H, Gerber K, Daly JA, Brimley LA, Adams S, Christenson JC, Pavia AT. 2002. The effect of rapid respiratory viral diagnostic testing on antibiotic use in a children's hospital. Arch Pediatr Adolesc Med 156:12301234.[PubMed].[CrossRef]
9. Couturier MR, Barney T, Alger G, Hymas WC, Stevenson JB, Hillyard D, Daly JA. 2013. Evaluation of the FilmArray® Respiratory Panel for clinical use in a large children's hospital. J Clin Lab Anal 27:148154.[CrossRef].[PubMed]
10. Gautam R, Lyde F, Esona MD, Quaye O, Bowen MD. 2013. Comparison of Premier™ Rotaclone®, ProSpecT™, and RIDASCREEN® rotavirus enzyme immunoassay kits for detection of rotavirus antigen in stool specimens. J Clin Virol 58:292294.[CrossRef].[PubMed]
11. Mitchell EO, Stewart G, Bajzik O, Ferret M, Bentsen C, Shriver MK. 2013. Performance comparison of the 4th generation Bio-Rad Laboratories GS HIV Combo Ag/Ab EIA on the EVOLIS™ automated system versus Abbott ARCHITECT HIV Ag/Ab Combo, Ortho Anti-HIV 1+2 EIA on Vitros ECi and Siemens HIV-1/O/2 enhanced on Advia Centaur. J Clin Virol 58(Suppl 1):e79e84.[CrossRef].[PubMed]
12. Dusetty P, Velázquez FR, Gutiérrez-Escolano AL, Ludert JE. 2013. Evaluation of the second generation of a commercial latex agglutination test for the detection of rotavirus antigens in fecal samples. J Clin Virol 57:8890.[CrossRef].[PubMed]
13. Bonner AB, Monroe KW, Talley LI, Klasner AE, Kimberlin DW. 2003. Impact of the rapid diagnosis of influenza on physician decision-making and patient management in the pediatric emergency department: results of a randomized, prospective, controlled trial. Pediatrics 112:363367.[PubMed].[CrossRef]
14. Dale SE, Mayer C, Mayer MC, Menegus MA. 2008. Analytical and clinical sensitivity of the 3M rapid detection influenza A+B assay. J Clin Microbiol 46:38043807.[CrossRef].[PubMed]
15. Lee CK, Cho CH, Woo MK, Nyeck AE, Lim CS, Kim WJ. 2012. Evaluation of Sofia fluorescent immunoassay analyzer for influenza A/B virus. J Clin Virol 55:239243.[CrossRef].[PubMed]
16. Rath B, Tief F, Obermeier P, Tuerk E, Karsch K, Muehlhans S, Adamou E, Duwe S, Schweiger B. 2012. Early detection of influenza A and B infection in infants and children using conventional and fluorescence-based rapid testing. J Clin Virol 55:329333.[CrossRef].[PubMed]
17. Peters TR, Blakeney E, Vannoy L, Poehling KA. 2013. Evaluation of the limit of detection of the BD Veritor™ system flu A+B test and two rapid influenza detection tests for influenza virus. Diagn Microbiol Infect Dis 75:200202.[CrossRef].[PubMed]
18. Linares EM, Kubota LT, Michaelis J, Thalhammer S. 2012. Enhancement of the detection limit for lateral flow immunoassays: evaluation and comparison of bioconjugates. J Immunol Methods 375:264270.[CrossRef].[PubMed]
19. Blacksell SD, Jarman RG, Bailey MS, Tanganuchitcharnchai A, Jenjaroen K, Gibbons RV, Paris DH, Premaratna R, de Silva HJ, Lalloo DG, Day NP. 2011. Evaluation of six commercial point-of-care tests for diagnosis of acute dengue infections: The need for combining NS1 antigen and IgM/IgG antibody detection to achieve acceptable levels of accuracy. Clin Vaccine Immunol 18:20952101.[CrossRef].[PubMed]
20. Gleaves CA, Smith TF, Shuster EA, Pearson GR. 1984. Rapid detection of cytomegalovirus in MRC-5 cells inoculated with urine specimens by using low-speed centrifugation and monoclonal antibody to an early antigen. J Clin Microbiol 19:917919.[PubMed]
21. Fong CK, Lee MK, Griffith BP. 2000. Evaluation of R-Mix FreshCells in shell vials for detection of respiratory viruses. J Clin Microbiol 38:46604662.[PubMed]
22. Buck GE, Wiesemann M, Stewart L. 2002. Comparison of mixed cell culture containing genetically engineered BGMK and CaCo-2 cells (Super E-Mix) with RT-PCR and conventional cell culture for the diagnosis of enterovirus meningitis. J Clin Virol 25(Suppl 1):S13S18.[PubMed]
23. Besselaar TG, Blackburn NK, Aldridge N. 1989. Comparison of an antibody-capture IgM enzyme-linked immunosorbent assay with IgM-indirect immunofluorescence for the diagnosis of acute Sindbis and West Nile infections. J Virol Methods 25:337345.[PubMed].[CrossRef]
24. Rawlins ML, Swenson EM, Hill HR, Litwin CM. 2007. Evaluation of an enzyme immunoassay for detection of immunoglobulin M antibodies to West Nile virus and the importance of background subtraction in detecting nonspecific reactivity. Clin Vaccine Immunol 14:665668.[CrossRef].[PubMed]
25. Yan Y, Zhang S, Tang YW. 2011. Molecular assays for the detection and characterization of respiratory viruses. Semin Respir Crit Care Med 32:512526.[CrossRef].[PubMed]
26. Caliendo AM, Valsamakis A, Bremer JW, Ferreira-Gonzalez A, Granger S, Sabatini L, Tsongalis GJ, Wang YF, Yen-Lieberman B, Young S, Lurain NS. 2011. Multilaboratory evaluation of real-time PCR tests for hepatitis B virus DNA quantification. J Clin Microbiol 49:28542858.[CrossRef].[PubMed]
27. Mahony JB. 2008. Detection of respiratory viruses by molecular methods. Clin Microbiol Rev 21:716747.[CrossRef].[PubMed]
28. Rowley AH, Whitley RJ, Lakeman FD, Wolinsky SM. 1990. Rapid detection of herpes-simplex-virus DNA in cerebrospinal fluid of patients with herpes simplex encephalitis. Lancet 335:440441.[PubMed].[CrossRef]
29. Tang YW, Mitchell PS, Espy MJ, Smith TF, Persing DH. 1999. Molecular diagnosis of herpes simplex virus infections in the central nervous system. J Clin Microbiol 37:21272136.[PubMed]
30. Lemieux B, Li Y, Kong H, Tang YW. 2012. Near instrument-free, simple molecular device for rapid detection of herpes simplex viruses. Expert Rev Mol Diagn 12:437443.[CrossRef].[PubMed]
31. Buller RS. 2013. Molecular detection of respiratory viruses. Clin Lab Med 33:439460.[CrossRef].[PubMed]
32. Landry ML. 2011. Diagnostic tests for influenza infection. Curr Opin Pediatr 23:9197.[CrossRef].[PubMed]
33. Emmadi R, Boonyaratanakornkit JB, Selvarangan R, Shyamala V, Zimmer BL, Williams L, Bryant B, Schutzbank T, Schoonmaker MM, Amos Wilson JA, Hall L, Pancholi P, Bernard K. 2011. Molecular methods and platforms for infectious diseases testing a review of FDA-approved and cleared assays. J Mol Diagn 13:583604.[CrossRef].[PubMed]
34. Caliendo AM. 2011. Multiplex PCR and emerging technologies for the detection of respiratory pathogens. Clin Infect Dis 52(Suppl 4):S326S330.[CrossRef].[PubMed]
35. Li H, McCormac MA, Estes RW, Sefers SE, Dare RK, Chappell JD, Erdman DD, Wright PF, Tang YW. 2007. Simultaneous detection and high-throughput identification of a panel of RNA viruses causing respiratory tract infections. J Clin Microbiol 45:21052109.[CrossRef].[PubMed]
36. Mahony J, Chong S, Merante F, Yaghoubian S, Sinha T, Lisle C, Janeczko R. 2007. 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 45:29652970.[CrossRef].[PubMed]
37. Dunbar SA, Zhang H, Tang YW. 2013. Advanced techniques for detection and identification of microbial agents of gastroenteritis. Clin Lab Med 33:527552.[CrossRef].[PubMed]
38. Higgins RR, Beniprashad M, Cardona M, Masney S, Low DE, Gubbay JB. 2011. Evaluation and verification of the Seeplex Diarrhea-V ACE assay for simultaneous detection of adenovirus, rotavirus, and norovirus genogroups I and II in clinical stool specimens. J Clin Microbiol 49:31543162.[CrossRef].[PubMed]
39. Navidad JF, Griswold DJ, Gradus MS, Bhattacharyya S. 2013. Evaluation of Luminex xTAG gastrointestinal pathogen analyte-specific reagents for high-throughput, simultaneous detection of bacteria, viruses, and parasites of clinical and public health importance. J Clin Microbiol 51:30183024.[CrossRef].[PubMed]
40. Schulert GS, Lu Z, Wingo T, Tang YW, Saville BR, Hain PD. 2013. Role of a respiratory viral panel in the clinical management of pediatric inpatients. Pediatr Infect Dis J 32:467472.[CrossRef].[PubMed]
41. Brunstein JD, Cline CL, McKinney S, Thomas E. 2008. Evidence from multiplex molecular assays for complex multipathogen interactions in acute respiratory infections. J Clin Microbiol 46:97102.[CrossRef].[PubMed]
42. Oosterheert JJ, van Loon AM, Schuurman R, Hoepelman AI, Hak E, Thijsen S, Nossent G, Schneider MM, Hustinx WM, Bonten MJ. 2005. Impact of rapid detection of viral and atypical bacterial pathogens by real-time polymerase chain reaction for patients with lower respiratory tract infection. Clin Infect Dis 41:14381444.[CrossRef].[PubMed]
43. Tang YW, Lowery KS, Valsamakis A, Schaefer VC, Chappell JD, White-Abell J, Quinn CD, Li H, Washington CA, Cromwell J, Giamanco CM, Forman M, Holden J, Rothman RE, Parker ML, Ortenberg EV, Zhang L, Lin YL, Gaydos CA. 2013. Clinical accuracy of a PLEX-ID flu device for simultaneous detection and identification of influenza viruses A and B. J Clin Microbiol 51:4045.[CrossRef].[PubMed]
44. Vermehren J, Kau A, Gärtner BC, Göbel R, Zeuzem S, Sarrazin C. 2008. Differences between two real-time PCR-based hepatitis C virus (HCV) assays (RealTime HCV and Cobas AmpliPrep/Cobas TaqMan) and one signal amplification assay (Versant HCV RNA 3.0) for RNA detection and quantification. J Clin Microbiol 46:38803891.[CrossRef].[PubMed]
45. Madej RM, Davis J, Holden MJ, Kwang S, Labourier E, Schneider GJ. 2010. International standards and reference materials for quantitative molecular infectious disease testing. J Mol Diagn 12:133143.[CrossRef].[PubMed]
46. Kanda T, Yokosuka O, Omata M. 2013. Treatment of hepatitis C virus infection in the future. Clin Transl Med 2:9.[CrossRef].[PubMed]
47. Li H, Dummer JS, Estes WR, Meng S, Wright PF, Tang YW. 2003. Measurement of human cytomegalovirus loads by quantitative real-time PCR for monitoring clinical intervention in transplant recipients. J Clin Microbiol 41:187191.[PubMed].[CrossRef]
48. Razonable RR, Paya CV, Smith TF. 2002. Role of the laboratory in diagnosis and management of cytomegalovirus infection in hematopoietic stem cell and solid-organ transplant recipients. J Clin Microbiol 40:746752.[PubMed].[CrossRef]
49. Espy MJ, Uhl JR, Sloan LM, Buckwalter SP, Jones MF, Vetter EA, Yao JD, Wengenack NL, Rosenblatt JE, Cockerill FR III, Smith TF. 2006. Real-time PCR in clinical microbiology: applications for routine laboratory testing. Clin Microbiol Rev 19:165256.[CrossRef].[PubMed]
50. Caliendo AM, Shahbazian MD, Schaper C, Ingersoll J, Abdul-Ali D, Boonyaratanakornkit J, Pang XL, Fox J, Preiksaitis J, Schönbrunner ER. 2009. A commutable cytomegalovirus calibrator is required to improve the agreement of viral load values between laboratories. Clin Chem 55:17011710.[CrossRef].[PubMed]
51. Pang XL, Fox JD, Fenton JM, Miller GG, Caliendo AM, Preiksaitis JK American Society of Transplantation Infectious Diseases Community of Practice; Canadian Society of Transplantation. 2009. Interlaboratory comparison of cytomegalovirus viral load assays. Am J Transplant 9:258268.[CrossRef].[PubMed]
52. Preiksaitis JK, Pang XL, Fox JD, Fenton JM, Caliendo AM, Miller GG American Society of Transplantation Infectious Diseases Community of Practice. 2009. Interlaboratory comparison of epstein-barr virus viral load assays. Am J Transplant 9:269279.[CrossRef].[PubMed]
53. Boaretti M, Sorrentino A, Zantedeschi C, Forni A, Boschiero L, Fontana R. 2013. Quantification of cytomegalovirus DNA by a fully automated real-time PCR for early diagnosis and monitoring of active viral infection in solid organ transplant recipients. J Clin Virol 56:124128.[CrossRef].[PubMed]
54. Miller MB, Tang YW. 2009. Basic concepts of microarrays and potential applications in clinical microbiology. Clin Microbiol Rev 22:611633.[CrossRef].[PubMed]
55. Stürmer M, Berger A, Preiser W. 2004. HIV-1 genotyping: comparison of two commercially available assays. Expert Rev Mol Diagn 4:281291.[CrossRef]
56. Drew WL. 2010. Cytomegalovirus resistance testing: pitfalls and problems for the clinician. Clin Infect Dis 50:733736.[CrossRef].[PubMed]
57. Moscona A. 2009. Global transmission of oseltamivir-resistant influenza. N Engl J Med 360:953956.[CrossRef].[PubMed]
58. Weck K. 2005. Molecular methods of hepatitis C genotyping. Expert Rev Mol Diagn 5:507520.[CrossRef].[PubMed]
59. Jacka B, Lamoury F, Simmonds P, Dore GJ, Grebely J, Applegate T. 2013. Sequencing of the hepatitis C virus: A systematic review. PLoS One 8:e67073. doi:10.1371/journal.pone.0067073[CrossRef].[PubMed] http://dx.doi.org/doi:10.1371/journal.pone.0067073
60. Pham ST, Bull RA, Bennett JM, Rawlinson WD, Dore GJ, Lloyd AR, White PA. 2010. Frequent multiple hepatitis C virus infections among injection drug users in a prison setting. Hepatology 52:15641572.[CrossRef].[PubMed]
61. González-Candelas F, López-Labrador FX, Bracho MA. 2011. Recombination in hepatitis C virus. Viruses 3:20062024.[CrossRef]
62. Dietz J, Schelhorn SE, Fitting D, Mihm U, Susser S, Welker MW, Füller C, Däumer M, Teuber G, Wedemeyer H, Berg T, Lengauer T, Zeuzem S, Herrmann E, Sarrazin C. 2013. Deep sequencing reveals mutagenic effects of ribavirin during monotherapy of hepatitis C virus genotype 1-infected patients. J Virol 87:61726181.[CrossRef].[PubMed]
63. Shinol RC, Gale HB, Kan VL. 2012. Performance of the Abbott RealTime HCV Genotype II RUO assay. J Clin Microbiol 50:30993101.[CrossRef].[PubMed]
64. Huh W, Einstein MH, Herzog TJ, Franco EL. 2010. What is the role of HPV typing in the United States now and in the next five years in a vaccinated population? Gynecol Oncol 117:481485.[CrossRef].[PubMed]
65. Eide ML, Debaque H. 2012. HPV detection methods and genotyping techniques in screening for cervical cancer. Ann Pathol 32:e1523, 401409.[CrossRef].[PubMed]
66. Honma S, Chizhikov V, Santos N, Tatsumi M, Timenetsky Mdo C, Linhares AC, Mascarenhas JD, Ushijima H, Armah GE, Gentsch JR, Hoshino Y. 2007. Development and validation of DNA microarray for genotyping group A rotavirus VP4 (P[4], P[6], P[8], P[9], and P[14]) and VP7 (G1 to G6, G8 to G10, and G12) genes. J Clin Microbiol 45:26412648.[CrossRef].[PubMed]
67. Pas SD, Tran N, de Man RA, Burghoorn-Maas C, Vernet G, Niesters HG. 2008. Comparison of reverse hybridization, microarray, and sequence analysis for genotyping hepatitis B virus. J Clin Microbiol 46:12681273.[CrossRef].[PubMed]
68. Jääskeläinen AJ, Maunula L. 2006. Applicability of microarray technique for the detection of noro- and astroviruses. J Virol Methods 136:210216.[CrossRef]


Generic image for table

Application of various methods for rapid diagnosis of acute or primary viral infections

Citation: Landry M, Tang Y. 2016. Immunologic and Molecular Methods for Viral Diagnosis, p 538-549. In Detrick B, Schmitz J, Hamilton R (ed), Manual of Molecular and Clinical Laboratory Immunology, Eighth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818722.ch57
Generic image for table

Uses and limitations of immunologic detection methods for viral antigens

Citation: Landry M, Tang Y. 2016. Immunologic and Molecular Methods for Viral Diagnosis, p 538-549. In Detrick B, Schmitz J, Hamilton R (ed), Manual of Molecular and Clinical Laboratory Immunology, Eighth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818722.ch57
Generic image for table

Mixed-cell cultures available commercially

Citation: Landry M, Tang Y. 2016. Immunologic and Molecular Methods for Viral Diagnosis, p 538-549. In Detrick B, Schmitz J, Hamilton R (ed), Manual of Molecular and Clinical Laboratory Immunology, Eighth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818722.ch57
Generic image for table

FDA-cleared molecular methods for detection, quantification, and genotyping of viral pathogens

Citation: Landry M, Tang Y. 2016. Immunologic and Molecular Methods for Viral Diagnosis, p 538-549. In Detrick B, Schmitz J, Hamilton R (ed), Manual of Molecular and Clinical Laboratory Immunology, Eighth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818722.ch57

This is a required field
Please enter a valid email address
Please check the format of the address you have entered.
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error