Recent advances in the detection of respiratory virus infection in humans

Journal of Medical Virology

Volumn 92, Issue 4, 2020, Pages 408-417

  Zhang, Naru ^a   Wang, Lili ^b   Deng, Xiaoqian ^b   Liang, Ruiying ^b   Su, Meng ^b   He, Chen ^b   Hu, Lanfang ^b   Su, Yudan ^b   Ren, Jing ^b   Yu, Fei ^b   Du, Lanying ^c   Jiang, Shibo ^c,d  

^a ZHEJIANG UNIVERSITY CITY COLLEGE   (China)

^b AGRICULTURAL UNIVERSITY OF HEBEI   (China)

^c NEW YORK BLOOD CENTER   (United States)

^d FUDAN UNIVERSITY   (China)

Author keywords

adenovirus; coronavirus; diagnostic methods; influenza virus; respiratory syncytial virus; respiratory viral infection; rhinovirus

Indexed keywords

DNA; QUANTUM DOT;

CORONAVIRINAE; DIAGNOSTIC PROCEDURE; DNA MICROARRAY; ENZYME LINKED IMMUNOSORBENT ASSAY; HIGH THROUGHPUT SEQUENCING; HUMAN; HUMAN ADENOVIRUS C; HUMAN RESPIRATORY SYNCYTIAL VIRUS; HUMAN RHINOVIRUS; IMMUNOASSAY; IMMUNOFLUORESCENCE TEST; INFLUENZA VIRUS; INTERMETHOD COMPARISON; LATERAL FLOW IMMUNOASSAY; LIMIT OF DETECTION; LIMIT OF QUANTITATION; MOLECULAR DIAGNOSIS; MULTIPLEX POLYMERASE CHAIN REACTION; MULTIPLEX REAL TIME POLYMERASE CHAIN REACTION; NONHUMAN; QIAGEN RESPLEX II V2.0; REAL TIME POLYMERASE CHAIN REACTION; REAL TIME REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; REPRODUCIBILITY; REVERSE TRANSCRIPTION LOOP MEDIATED ISOTHERMAL AMPLIFICATION; REVIEW; SEMI-NESTED POLYMERASE CHAIN REACTION; SENSITIVITY AND SPECIFICITY; VIRAL RESPIRATORY TRACT INFECTION; VIRUS DETECTION; VIRUS ISOLATION; CORONAVIRUS INFECTION; GROWTH, DEVELOPMENT AND AGING; HUMAN ADENOVIRUS INFECTION; IMMUNOLOGICAL PROCEDURES; INFLUENZA; ISOLATION AND PURIFICATION; NUCLEIC ACID AMPLIFICATION; PICORNAVIRUS INFECTION; RESPIRATORY SYNCYTIAL VIRUS INFECTION; RESPIRATORY TRACT INFECTION; RHINOVIRUS; VIRUS;

ADENOVIRUS INFECTIONS, HUMAN; CORONAVIRUS INFECTIONS; HUMANS; IMMUNOASSAY; IMMUNOLOGIC TESTS; INFLUENZA, HUMAN; MULTIPLEX POLYMERASE CHAIN REACTION; NUCLEIC ACID AMPLIFICATION TECHNIQUES; PICORNAVIRIDAE INFECTIONS; REAL-TIME POLYMERASE CHAIN REACTION; RESPIRATORY SYNCYTIAL VIRUS INFECTIONS; RESPIRATORY TRACT INFECTIONS; RHINOVIRUS; VIRUSES;

EID: 85078826093     PISSN: 01466615     EISSN: 10969071     Source Type: Journal    
DOI: 10.1002/jmv.25674     Document Type: Review

References (79)

1. Mahony JB, Petrich A, Smieja M. Molecular diagnosis of respiratory virus infections. Crit Rev Clin Lab Sci. 2011;48:217-249.
2. Azar MM, Landry ML. Detection of influenza A and B viruses and respiratory syncytial virus by use of Clinical Laboratory Improvement Amendments of 1988 (CLIA)-waived point-of-care assays: a paradigm shift to molecular tests. J Clin Microbiol. 2018;56:e00367-18.
3. Fendrick AM, Monto AS, Nightengale B, Sarnes M. The economic burden of non-influenza-related viral respiratory tract infection in the United States. Arch Intern Med. 2003;163:487-494.
4. Hu B, Ge X, Wang LF, Shi Z. Bat origin of human coronaviruses. Virol J. 2015;12:221.
5. Vemula SV, Zhao J, Liu J, Wang X, Biswas S, Hewlett I. Current approaches for diagnosis of influenza virus infections in humans. Viruses. 2016;8:96.
6. Zhang P, Vemula SV, Zhao J, et al. A highly sensitive europium nanoparticle-based immunoassay for detection of influenza A/B virus antigen in clinical specimens. J Clin Microbiol. 2014;52:4385-4387.
7. Trombetta VK, Chan YL, Bankowski MJ. Are rapid influenza antigen tests still clinically useful in today's molecular diagnostics world? Hawaii J Med Public Health. 2018;77:226-230.
8. Poon LLM, Leung CSW, Chan KH, et al. Detection of human influenza A viruses by loop-mediated isothermal amplification. J Clin Microbiol. 2005;43:427-430.
9. Kubo T, Agoh M, Mai LQ, et al. Development of a reverse transcription-loop-mediated isothermal amplification assay for detection of pandemic (H1N1) 2009 virus as a novel molecular method for diagnosis of pandemic influenza in resource-limited settings. J Clin Microbiol. 2010;48:728-735.
10. Imai M, Ninomiya A, Minekawa H, et al. Development of H5-RT-LAMP (loop-mediated isothermal amplification) system for rapid diagnosis of H5 avian influenza virus infection. Vaccine. 2006;24:6679-6682.
11. Imai M, Ninomiya A, Minekawa H, et al. Rapid diagnosis of H5N1 avian influenza virus infection by newly developed influenza H5 hemagglutinin gene-specific loop-mediated isothermal amplification method. J Virol Methods. 2007;141:173-180.
12. Nakauchi M, Takayama I, Takahashi H, Tashiro M, Kageyama T. Development of a reverse transcription loop-mediated isothermal amplification assay for the rapid diagnosis of avian influenza A (H7N9) virus infection. J Virol Methods. 2014;204:101-104.
13. Zhao J, Tang S, Storhoff J, et al. Multiplexed, rapid detection of H5N1 using a PCR-free nanoparticle-based genomic microarray assay. BMC Biotechnol. 2010;10:74.
14. Imai K, Tamura K, Tanigaki T, et al. Whole genome sequencing of influenza A and B viruses with the MinION sequencer in the clinical setting: a pilot study. Front Microbiol. 2018;9:2748.
15. Rochelet M, Solanas S, Grossiord C, et al. A thin layer-based amperometric enzyme immunoassay for the rapid and sensitive diagnosis of respiratory syncytial virus infections. Talanta. 2012;100:139-144.
16. Bhandary R, Boloor R. Detection of respiratory syncytial virus using direct fluorescent antibody assay in paediatric patients with acute respiratory tract infection. J Clin Diagn Res. 2016;10:Dc10-Dc12.
17. Tripp RA, Alvarez R, Anderson B, Jones L, Weeks C, Chen W. Bioconjugated nanoparticle detection of respiratory syncytial virus infection. Int J Nanomedicine. 2007;2:117-124.
18. Bentzen EL, House F, Utley TJ, Crowe JE, Wright DW. Progression of respiratory syncytial virus infection monitored by fluorescent quantum dot probes. Nano Lett. 2005;5:591-595.
19. Borek AP, Clemens SH, Gaskins VK, Aird DZ, Valsamakis A. Respiratory syncytial virus detection by remel Xpect, Binax Now RSV, direct immunofluorescent staining, and tissue culture. J Clin Microbiol. 2006;44:1105-1107.
20. Selvarangan R, Abel D, Hamilton M. Comparison of BD Directigen (TM) EZ RSV and Binax NOW (R) RSV tests for rapid detection of respiratory syncytial virus from nasopharyngeal aspirates in a pediatric population. Diagn Microbiol Infec Dis. 2008;62:157-161.
21. Slinger R, Milk R, Gaboury I, Diaz-Mitoma F. Evaluation of the QuickLab RSV test, a new rapid lateral-flow immunoassay for detection of respiratory syncytial virus antigen. J Clin Microbiol. 2004;42:3731-3733.
22. Falsey AR, Formica MA, Walsh EE. Diagnosis of respiratory syncytial virus infection: Comparison of reverse transcription-PCR to viral culture and serology in adults with respiratory illness. J Clin Microbiol. 2002;40:817-820.
23. Abdel-Moneim AS, Shehab GM, Alsulaimani AA, Al-Malky MIR. Development of TaqMan RT-qPCR for the detection of type A human respiratory syncytial virus. Mol Cell Probes. 2017;33:16-19.
24. Hu AZ, Colella M, Tam JS, Rappaport R, Cheng SM. Simultaneous detection, subgrouping, and quantitation of respiratory syncytial virus A and B by real-time PCR. J Clin Microbiol. 2003;41:149-154.
25. Zhao L, Wang J, Li G, et al. A highly sensitive 1-tube nested real-time RT-PCR assay using LNA-modified primers for detection of respiratory syncytial virus. Diagn Microbiol Infec Dis. 2019;93:101-106.
26. Chen C, Li X, Li G, et al. Use of a rapid reverse-transcription recombinase aided amplification assay for respiratory syncytial virus detection. Diagn Microbiol Infec Dis. 2018;90:90-95.
27. Eboigbodin KE, Moilanen K, Elf S, Hoser M. Rapid and sensitive real-time assay for the detection of respiratory syncytial virus using RT-SIBA((R)). BMC Infec Dis. 2017;17:134.
28. Noh JY, Yoon SW, Kim DJ, et al. Simultaneous detection of severe acute respiratory syndrome, Middle East respiratory syndrome, and related bat coronaviruses by real-time reverse transcription PCR. Arch Virol. 2018;163:819.
29. Go YY, Kim YS, Cheon S, et al. Evaluation and clinical validation of two field-deployable reverse transcription-insulated isothermal PCR assays for the detection of the Middle East respiratory syndrome-coronavirus. J Mol Diagn. 2017;19:817-827.
30. Kim MN, K YJ, Seong MW, Kim JS, Shi BM, Sung H. Analytical and clinical validation of six commercial Middle East respiratory syndrome coronavirus RNA detection kits based on real-time reverse-transcription PCR. Ann Lab Med. 2016;36:450-456.
31. Shirato K, Semba S, El-Kafrawy SA, et al. Development of fluorescent reverse transcription loop-mediated isothermal amplification (RT-LAMP) using quenching probes for the detection of the Middle East respiratory syndrome coronavirus. J Virol Methods. 2018;258:41-48.
32. Koo B, Hong KH, Jin CE, Kim JY, Kim SH, Shin Y. Arch-shaped multiple-target sensing for rapid diagnosis and identification of emerging infectious pathogens. Biosens Bioelectron. 2018;119:79-85.
33. Hashemzadeh MS, Rasouli R, Zahraei B, et al. Development of Dual TaqMan based one-step rRT-PCR assay panel for rapid and accurate diagnostic test of MERS-CoV: a novel human coronavirus, ahead of Hajj Pilgrimage. Iran Red Crescent Med J. 2016;18:e23874.
34. Chen Y, Chan KH, Hong C, et al. A highly specific rapid antigen detection assay for on-site diagnosis of MERS. J Infect. 2016;73:82-84.
35. Zhang Q, Jing S, Cheng Z, et al. Comparative genomic analysis of two emergent human adenovirus type 14 respiratory pathogen isolates in China reveals similar yet divergent genomes. Emerg Microbes Infect. 2017;6:e92.
36. Simpson R, Aliyu S, Iturriza-Gomara M, Desselberger U, Gray J. Infantile viral gastroenteritis: On the way to closing the diagnostic gap. J Med Virol. 2003;70:258-262.
37. Madisch I, Wolfel R, Harste G, Pommer H, Heim A. Molecular identification of adenovirus sequences: a rapid scheme for early typing of human adenoviruses in diagnostic samples of immunocompetent and immunodeficient patients. J Med Virol. 2006;78:1210-1217.
38. Shimada Y, Ariga T, Tagawa Y, Aoki K, Ohno S, Ishiko H. Molecular diagnosis of human adenoviruses D and E by a phylogeny-based classification method using a partial hexon sequence. J Clin Microbiol. 2004;42:1577-1584.
39. Heim A, Ebnet C, Harste G, Pring-Akerblom P. Rapid and quantitative detection of human adenovirus DNA by real-time PCR. J Med Virol. 2003;70:228-239.
40. Do DH, Laus S, Leber A, et al. A one-step, real-time PCR assay for rapid detection of rhinovirus. J Mol Diagn. 2010;12:102-108.
41. Myatt TA, Johnston SL, Rudnick S, Milton DK. Airborne rhinovirus detection and effect of ultraviolet irradiation on detection by a semi-nested RT-PCR assay. BMC Public Health. 2003;3:5.
42. Schibler M, Yerly S, Vieille G, et al. Critical analysis of rhinovirus RNA load quantification by real-time reverse transcription-PCR. J Clin Microbiol. 2012;50:2868-2872.
43. Huang T, Wang W, Bessaud M, et al. Evidence of recombination and genetic diversity in human rhinoviruses in children with acute respiratory infection. PLoS One. 2009;4:e6355.
44. Zhang N, Zheng BJ, Lu L, Zhou Y, Jiang S, Du L. Advancements in the development of subunit influenza vaccines. Microbes Infect. 2015;17:123-134.
45. BinSaeed AA, Siddiqui AR, Mandil AM, et al. The role of rapid testing and clinical decision in the diagnosis of human influenza A H1N1 infection. Saudi Med J. 2014;35:277-284.
46. Zhao J, Wang X, Ragupathy V, et al. Rapid detection and differentiation of swine-origin influenza A virus (H1N1/2009) from other seasonal influenza A viruses. Viruses. 2012;4:3012-3019.
47. Zhao J, Ragupathy V, Liu J, et al. Nanomicroarray and multiplex next-generation sequencing for simultaneous identification and characterization of influenza viruses. Emerg Infect Dis. 2015;21:400-408.
48. Sato M, Saito R, Sakai T, et al. Molecular epidemiology of respiratory syncytial virus infections among children with acute respiratory symptoms in a community over three seasons. J Clin Microbiol. 2005;43:36-40.
49. Sullender WM. Respiratory syncytial virus genetic and antigenic diversity. Clin Microbiol Rev. 2000;13:1-15.
50. Lim XF, Lee CB, Pascoe SM, et al. Detection and characterization of a novel bat-borne coronavirus in Singapore using multiple molecular approaches. J Gen Virol. 2019;100:1363-1374.
51. Wang N, Luo C, Liu H, et al. Characterization of a new member of alphacoronavirus with unique genomic features in rhinolophus bats. Viruses. 2019;11:E379.
52. Corman VM, Eckerle I, Bleicker T, et al. Detection of a novel human coronavirus by real-time reverse-transcription polymerase chain reaction. Euro Surveill. 2012;17:20185.
53. Huang P, Wang H, Cao Z, et al. A rapid and specific assay for the detection of MERS-CoV. Front Microbiol. 2018;9:1101.
54. Zaki AM, van Boheemen S, Bestebroer TM, Osterhaus AD, Fouchier RA. Isolation of a novel Coronavirus from a man with pneumonia in Saudi Arabia. N Engl J Med. 2012;367:1814-1820.
55. Bhadra S, Jiang YS, Kumar MR, Johnson RF, Hensley LE, Ellington AD. Real-time sequence-validated loop-mediated isothermal amplification assays for detection of Middle East respiratory syndrome coronavirus (MERS-CoV). PLoS One. 2015;10:e0123126.
56. Chan JFW, Choi GKY, Tsang AKL, et al. Development and evaluation of novel real-time reverse transcription-PCR assays with locked nucleic acid probes targeting leader sequences of human-pathogenic coronaviruses. J Clin Microbiol. 2015;53:2722-2726.
57. Lu X, Whitaker B, Sakthivel SKK, et al. Real-time reverse transcription-PCR assay panel for Middle East respiratory syndrome coronavirus. J Clin Microbiol. 2014;52:67-75.
58. Shirato K, Yano T, Senba S, et al. Detection of Middle East respiratory syndrome coronavirus using reverse transcription loop-mediated isothermal amplification (RT-LAMP). Virol J. 2014;11:139.
59. Dou Y, Li Y, Ma C, et al. Rapid diagnosis of human adenovirus B, C and E in the respiratory tract using multiplex quantitative polymerase chain reaction. Mol Med Rep. 2018;18:2889-2897.
60. Lion T. Adenovirus infections in immunocompetent and immunocompromised patients. Clin Microbiol Rev. 2014;27:441-462.
61. Nakamura H, Fujisawa T, Suga S, et al. Species differences in circulation and inflammatory responses in children with common respiratory adenovirus infections. J Med Virol. 2018;90:873-880.
62. Wong SSY, Yip CCY, Sridhar S, et al. Comparative evaluation of a laboratory-developed real-time PCR assay and RealStar(R) Adenovirus PCR Kit for quantitative detection of human adenovirus. Virol J. 2018;15:149.
63. Chen M, Zhu Z, Huang F, et al. Adenoviruses associated with acute respiratory diseases reported in Beijing from 2011 to 2013. PLoS One. 2015;10:e0121375.
64. Bochkov YA, Grindle K, Vang F, Evans MD, Gern JE. Improved molecular typing assay for rhinovirus species A, B, and C. J Clin Microbiol. 2014;52:2461-2471.
65. McIntyre CL, Knowles NJ, Simmonds P. Proposals for the classification of human rhinovirus species A, B and C into genotypically assigned types. J Gen Virol. 2013;94:1791-1806.
66. Simmonds P, McIntyre C, Savolainen-Kopra C, Tapparel C, Mackay IM, Hovi T. Proposals for the classification of human rhinovirus species C into genotypically assigned types. J Gen Virol. 2010;91:2409-2419.
67. Turunen R, Jartti T, Bochkov YA, Germ JE, Vuorinen T. Rhinovirus species and clinical characteristics in the first wheezing episode in children. J Med Virol. 2016;88:2059-2068.
68. Hung HM, Yang SL, Chen CJ, et al. Molecular epidemiology and clinical features of rhinovirus infections among hospitalized patients in a medical center in Taiwan. J Microbiol Immunol Infect. 2018;52:233-241.
69. Sears MR. Epidemiology of asthma exacerbations. J Allergy Clin Immunol. 2008;122:662-668.
70. Canela LNP, Magalhães-Barbosa MC, Raymundo CE, et al. Viral detection profile in children with severe acute respiratory infection. Braz J Infect Dis. 2018;22:402-411.
71. Echenique IA, Chan PA, Chapin KC, Andrea SB, Fava JL, Mermel LA. Clinical characteristics and outcomes in hospitalized patients with respiratory viral co-infection during the 2009 H1N1 influenza pandemic. PLoS One. 2013;8:e60845.
72. Nascimento MS, Souza AV, Ferreira AV, Rodrigues JC, Abramovici S, Silva Filho LV. High rate of viral identification and coinfections in infants with acute bronchiolitis. Clinics. 2010;65:1133-1137.
73. Chen JHK, Lam HY, Yip CCY, et al. Clinical evaluation of the new high-throughput Luminex NxTAG Respiratory Pathogen Panel assay for multiplex respiratory pathogen detection. J Clin Microbiol. 2016;54:1820-1825.
74. Feng Z, Zhao L, Wang J, et al. A multiplex one-tube nested real time RT-PCR assay for simultaneous detection of respiratory syncytial virus, human rhinovirus and human metapneumovirus. Virol J. 2018;15:167.
75. Sam SS, Caliendo AM, Ingersoll J, Abdul-Ali D, Hill CE, Kraft CS. Evaluation of performance characteristics of Panther Fusion assays for detection of respiratory viruses from nasopharyngeal and lower respiratory tract specimens. J Clin Microbiol. 2018;56:e00787-18.
76. Huzly D, Korn K, Bierbaum S, et al. Influenza A virus drift variants reduced the detection sensitivity of a commercial multiplex nucleic acid amplification assay in the season 2014/15. Arch Virol. 2016;161:2417-2423.
77. Li J, Mao NY, Zhang C, et al. The development of a GeXP-based multiplex reverse transcription-PCR assay for simultaneous detection of sixteen human respiratory virus types/subtypes. BMC Infect Dis. 2012;12:189.
78. Deng J, Ma Z, Huang W, et al. Respiratory virus multiplex RT-PCR assay sensitivities and influence factors in hospitalized children with lower respiratory tract infections. Virol Sin. 2013;28:97-102.
79. Loeffelholz MJ, Pong DL, Pyles RB, et al. Comparison of the FilmArray Respiratory Panel and Prodesse real-time PCR assays for detection of respiratory pathogens. J Clin Microbiol. 2011;49:4083-4088.