Chapter 63 : Respiratory Viruses

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Respiratory viruses are among the most common acute viral infections affecting humans and contribute appreciably to school and to work absenteeism. Globally, acute respiratory tract infections (ARTI) cause frequent morbidity and mortality among children under the age of 5 years, and are a major health care burden (1). Among the very young and the very old, as well as those with chronic medical conditions, respiratory viruses contribute substantially to medical visits, prescription of antibiotics and antivirals, hospitalizations, and deaths.

Citation: Speicher D, Ali M, Smieja M. 2016. Respiratory Viruses, p 598-609. 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.ch63
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1. Fouchier RA, Hartwig NG, Bestebroer TM, Niemeyer B, de Jong JC, Simon JH, Osterhaus AD. 2004. A previously undescribed coronavirus associated with respiratory disease in humans. Proc Natl Acad Sci USA 101 : 6212 6216.[CrossRef].[PubMed]
2. Fine MJ, Stone RA, Singer DE, Coley CM, Marrie TJ, Lave JR, Hough LJ, Obrosky DS, Schulz R, Ricci EM, Rogers JC, Kapoor WN. 1999. Processes and outcomes of care for patients with community-acquired pneumonia: results from the Pneumonia Patient Outcomes Research Team (PORT) cohort study. Arch Intern Med 159 : 970 980.[PubMed].[CrossRef]
3. Arden KE, Nissen MD, Sloots TP, Mackay IM. 2005. New human coronavirus, HCoV-NL63, associated with severe lower respiratory tract disease in Australia. J Med Virol 75 : 455 462.[CrossRef].[PubMed]
4. Mahony JB, Petrich A, Smieja M. 2011. Molecular diagnosis of respiratory virus infections. Crit Rev Clin Lab Sci 48 : 217 249.[CrossRef].[PubMed]
5. Sugrue RJ, Hay AJ. 1991. Structural characteristics of the M2 protein of influenza A viruses: evidence that it forms a tetrameric channel. Virology 180 : 617 624.[PubMed].[CrossRef]
6. Mackay IM, Bialasiewicz S, Jacob KC, McQueen E, Arden KE, Nissen MD, Sloots TP. 2006. Genetic diversity of human metapneumovirus over 4 consecutive years in Australia. J Infect Dis 193 : 1630 1633.[CrossRef].[PubMed]
7. Hamre D, Kindig DA, Mann J. 1967. Growth and intracellular development of a new respiratory virus. J Virol 1 : 810 816.[PubMed]
8. Maertzdorf J, Wang CK, Brown JB, Quinto JD, Chu M, de Graaf M, van den Hoogen BG, Spaete R, Osterhaus AD, Fouchier RA. 2004. Real-time reverse transcriptase PCR assay for detection of human metapneumoviruses from all known genetic lineages. J Clin Microbiol 42 : 981 986.[PubMed].[CrossRef]
9. Tyrrell DA, Bynoe ML. 1965. Cultivation of a novel type of common-cold virus in organ cultures. BMJ 1 : 1467 1470.[PubMed].[CrossRef]
10. Enserink M. 2003. Infectious diseases. Calling all coronavirologists. Science 300 : 413 414.[CrossRef].[PubMed]
11. Vabret A, Mourez T, Gouarin S, Petitjean J, Freymuth F. 2003. An outbreak of coronavirus OC43 respiratory infection in Normandy, France. Clin Infect Dis 36 : 985 989.[CrossRef].[PubMed]
12. Peiris JS, Chu CM, Cheng VC, Chan KS, Hung IF, Poon LL, Law KI, Tang BS, Hon TY, Chan CS, Chan KH, Ng JS, Zheng BJ, Ng WL, Lai RW, Guan Y, Yuen KY HKU/UCH SARS Study Group. 2003. Clinical progression and viral load in a community outbreak of coronavirus-associated SARS pneumonia: a prospective study. Lancet 361 : 1767 1772.[PubMed].[CrossRef]
13. Peiris JS, Lai ST, Poon LL, Guan Y, Yam LY, Lim W, Nicholls J, Yee WK, Yan WW, Cheung MT, Cheng VC, Chan KH, Tsang DN, Yung RW, Ng TK, Yuen KY SARS study group. 2003. Coronavirus as a possible cause of severe acute respiratory syndrome. Lancet 361 : 1319 1325.[PubMed].[CrossRef]
14. Garbino J, Gerbase MW, Wunderli W, Deffernez C, Thomas Y, Rochat T, Ninet B, Schrenzel J, Yerly S, Perrin L, Soccal PM, Nicod L, Kaiser L. 2004. Lower respiratory viral illnesses: improved diagnosis by molecular methods and clinical impact. Am J Respir Crit Care Med 170 : 1197 1203.[CrossRef].[PubMed]
15. Mackay IM, Arden KE, Speicher DJ, O'Neil NT, McErlean PK, Greer RM, Nissen MD, Sloots TP. 2012. Co-circulation of four human coronaviruses (HCoVs) in Queensland children with acute respiratory tract illnesses in 2004. Viruses 4 : 637 653.[CrossRef].[PubMed]
16. 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. 2004. Identification of a new human coronavirus. Nat Med 10 : 368 373.[CrossRef].[PubMed]
17. Bastien N, Robinson JL, Tse A, Lee BE, Hart L, Li Y. 2005. Human coronavirus NL-63 infections in children: a 1-year study. J Clin Microbiol 43 : 4567 4573.[CrossRef].[PubMed]
18. Chiu SS, Chan KH, Chu KW, Kwan SW, Guan Y, Poon LL, Peiris JS. 2005. Human coronavirus NL63 infection and other coronavirus infections in children hospitalized with acute respiratory disease in Hong Kong, China. Clin Infect Dis 40 : 1721 1729.[CrossRef].[PubMed]
19. 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. 2005. Characterization and complete genome sequence of a novel coronavirus, coronavirus HKU1, from patients with pneumonia. J Virol 79 : 884 895.[CrossRef].[PubMed]
20. Woo PC, Lau SK, Tsoi HW, Huang Y, Poon RW, Chu CM, Lee RA, Luk WK, Wong GK, Wong BH, Cheng VC, Tang BS, Wu AK, Yung RW, Chen H, Guan Y, Chan KH, Yuen KY. 2005. Clinical and molecular epidemiological features of coronavirus HKU1-associated community-acquired pneumonia. J Infect Dis 192 : 1898 1907.[CrossRef].[PubMed]
21. Sloots TP, McErlean P, Speicher DJ, Arden KE, Nissen MD, Mackay IM. 2006. Evidence of human coronavirus HKU1 and human bocavirus in Australian children. J Clin Virol 35 : 99 102.[CrossRef].[PubMed]
22. Woo PC, Lau SK, Huang Y, Tsoi HW, Chan KH, Yuen KY. 2005. Phylogenetic and recombination analysis of coronavirus HKU1, a novel coronavirus from patients with pneumonia. Arch Virol 150 : 2299 2311.[CrossRef].[PubMed]
23. Allander T, Tammi MT, Eriksson M, Bjerkner A, Tiveljung-Lindell A, Andersson B. 2005. Cloning of a human parvovirus by molecular screening of respiratory tract samples. Proc Natl Acad Sci USA 102 : 12891 12896.[CrossRef].[PubMed]
24. Bialasiewicz S, Whiley DM, Lambert SB, Jacob K, Bletchly C, Wang D, Nissen MD, Sloots TP. 2008. Presence of the newly discovered human polyomaviruses KI and WU in Australian patients with acute respiratory tract infection. J Clin Virol 41 : 63 68.[CrossRef].[PubMed]
25. Gaynor AM, Nissen MD, Whiley DM, Mackay IM, Lambert SB, Wu G, Brennan DC, Storch GA, Sloots TP, Wang D. 2007. Identification of a novel polyomavirus from patients with acute respiratory tract infections. PLoS Pathog 3 : e64.[CrossRef].[PubMed]
26. Sloots TP, Mackay IM, Bialasiewicz S, Jacob KC, McQueen E, Harnett GB, Siebert DJ, Masters BI, Young PR, Nissen MD. 2006. Human metapneumovirus, Australia, 2001–2004. Emerg Infect Dis 12 : 1263 1266.[CrossRef].[PubMed]
27. Granados A, Goodall EC, Luinstra K, Smieja M, Mahony J. 2015. Comparison of asymptomatic and symptomatic rhinovirus infections in university students: incidence, species diversity, and viral load. Diagn Microbiol Infect Dis 82 : 292 296.[CrossRef].[PubMed]
28. Hatchette TF, Drews SJ, Grudeski E, Booth T, Martineau C, Dust K, Garceau R, Gubbay J, Karnauchow T, Krajden M, Levett PN, Mazzulli T, McDonald RR, McNabb A, Mubareka S, Needle R, Petrich A, Richardson S, Rutherford C, Smieja M, Tellier R, Tipples G, LeBlanc JJ. 2015. Detection of enterovirus D68 in Canadian laboratories. J Clin Microbiol 53 : 1748 1751.[CrossRef].[PubMed]
29. Jain S, Self WH, Wunderink RG, Fakhran S, Balk R, Bramley AM, Reed C, Grijalva CG, Anderson EJ, Courtney DM, Chappell JD, Qi C, Hart EM, Carroll F, Trabue C, Donnelly HK, Williams DJ, Zhu Y, Arnold SR, Ampofo K, Waterer GW, Levine M, Lindstrom S, Winchell JM, Katz JM, Erdman D, Schneider E, Hicks LA, McCullers JA, Pavia AT, Edwards KM, Finelli L CDC EPIC Study Team. 2015. Community-acquired pneumonia requiring hospitalization among U.S. adults. N Engl J Med 373 : 415 427.[CrossRef].[PubMed]
30. Jain S, Williams DJ, Arnold SR, Ampofo K, Bramley AM, Reed C, Stockmann C, Anderson EJ, Grijalva CG, Self WH, Zhu Y, Patel A, Hymas W, Chappell JD, Kaufman RA, Kan JH, Dansie D, Lenny N, Hillyard DR, Haynes LM, Levine M, Lindstrom S, Winchell JM, Katz JM, Erdman D, Schneider E, Hicks LA, Wunderink RG, Edwards KM, Pavia AT, McCullers JA, Finelli L CDC EPIC Study Team. 2015. Community-acquired pneumonia requiring hospitalization among U.S. children. N Engl J Med 372 : 835 845.[CrossRef].[PubMed]
31. Centers for Disease Control and Prevention (CDC). 2011. Prevention and control of influenza with vaccines: recommendations of the Advisory Committee on Immunization Practices (ACIP), 2011. MMWR Morb Mortal Wkly Rep 60 : 11281132.[PubMed]
32. Loeb M, Russell ML, Moss L, Fonseca K, Fox J, Earn DJ, Aoki F, Horsman G, Van Caeseele P, Chokani K, Vooght M, Babiuk L, Webby R, Walter SD. 2010. Effect of influenza vaccination of children on infection rates in Hutterite communities: a randomized trial. JAMA 303 : 943 950.[CrossRef].[PubMed]
33. Dobson J, Whitley RJ, Pocock S, Monto AS. 2015. Oseltamivir treatment for influenza in adults: a meta-analysis of randomised controlled trials. Lancet 385 : 1729 1737.[CrossRef].[PubMed]
34. World Health Organization (WHO). 2015. Cumulative number of confirmed human cases for avian influenza A(H5N1) reported to WHO, 2003–2015. http://www.who.int/influenza/human_animal_interface/EN_GIP_20150717cumulativeNumberH5N1cases.pdf?ua=1. Accessed 7 August 2015.
35. Müller MA, Meyer B, Corman VM, Al-Masri M, Turkestani A, Ritz D, Sieberg A, Aldabbagh S, Bosch BJ, Lattwein E, Alhakeem RF, Assiri AM, Albarrak AM, Al-Shangiti AM, Al-Tawfiq JA, Wikramaratna P, Alrabeeah AA, Drosten C, Memish ZA. 2015. Presence of Middle East respiratory syndrome coronavirus antibodies in Saudi Arabia: a nationwide, cross-sectional, serological study. Lancet Infect Dis 15 : 559 564.[CrossRef]
36. World Health Organization. 2015. Middle East respiratory syndrome coronavirus (MERS-CoV)–Republic of Korea. Disease outbreak news. WHO, Geneva, Switzerland. http://www.who.int/csr/don/03-july-2015-mers-korea/en/
37. Khan F. 2015. Enterovirus D68: acute respiratory illness and the 2014 outbreak. Emerg Med Clin North Am 33 : e19 e32.[PubMed].[CrossRef]
38. Smieja M, Castriciano S, Carruthers S, So G, Chong S, Luinstra K, Mahony JB, Petrich A, Chernesky M, Savarese M, Triva D. 2010. Development and evaluation of a flocked nasal midturbinate swab for self-collection in respiratory virus infection diagnostic testing. J Clin Microbiol 48 : 3340 3342.[CrossRef].[PubMed]
39. Wurzel DF, Marchant JM, Clark JE, Mackay IM, Wang CY, Sloots TP, Upham JW, Yerkovich ST, Masters IB, Baker PJ, Anderson-James S, Chang AB. 2013. Respiratory virus detection in nasopharyngeal aspirate versus bronchoalveolar lavage is dependent on virus type in children with chronic respiratory symptoms. J Clin Virol 58 : 683 688.[CrossRef].[PubMed]
40. Daley P, Castriciano S, Chernesky M, Smieja M. 2006. Comparison of flocked and rayon swabs for collection of respiratory epithelial cells from uninfected volunteers and symptomatic patients. J Clin Microbiol 44 : 2265 2267.[CrossRef].[PubMed]
41. Luinstra K, Petrich A, Castriciano S, Ackerman M, Chong S, Carruthers S, Ammons B, Mahony JB, Smieja M. 2011. Evaluation and clinical validation of an alcohol-based transport medium for preservation and inactivation of respiratory viruses. J Clin Microbiol 49 : 2138 2142.[CrossRef].[PubMed]
42. Mahony JB, Blackhouse G, Babwah J, Smieja M, Buracond S, Chong S, Ciccotelli W, O'Shea T, Alnakhli D, Griffiths-Turner M, Goeree R. 2009. Cost analysis of multiplex PCR testing for diagnosing respiratory virus infections. J Clin Microbiol 47 : 2812 2817.[CrossRef].[PubMed]
43. Herman M, Smieja M, Carruthers S, Loeb M. 2014. Oseltamivir use amongst hospitalized patients infected with influenza. Influenza Other Respi Viruses 8 : 547 548.[CrossRef]
44. Chartrand C, Leeflang MM, Minion J, Brewer T, Pai M. 2012. Accuracy of rapid influenza diagnostic tests: a meta-analysis. Ann Intern Med 156 : 500 511.[CrossRef].[PubMed]
45. Hatchette TF, Bastien N, Berry J, Booth TF, Chernesky M, Couillard M, Drews S, Ebsworth A, Fearon M, Fonseca K, Fox J, Gagnon JN, Guercio S, Horsman G, Jorowski C, Kuschak T, Li Y, Majury A, Petric M, Ratnam S, Smieja M, Van Caeseele P Pandemic Influenza Laboratory Preparedness Network. 2009. The limitations of point of care testing for pandemic influenza: what clinicians and public health professionals need to know. Can J Public Health 100 : 204 207.[PubMed]
46. 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 : 329 333.[CrossRef].[PubMed]
47. Leonardi GP, Wilson AM, Zuretti AR. 2013. Comparison of conventional lateral-flow assays and a new fluorescent immunoassay to detect influenza viruses. J Virol Methods 189 : 379 382.[CrossRef].[PubMed]
48. Hassan F, Nguyen A, Formanek A, Bell JJ, Selvarangan R. 2014. Comparison of the BD Veritor system for Flu A+B with the Alere BinaxNOW influenza A&B card for detection of influenza A and B viruses in respiratory specimens from pediatric patients. J Clin Microbiol 52 : 906 910.[CrossRef].[PubMed]
49. Nam MH, Jang JW, Lee JH, Cho CH, Lim CS, Kim WJ. 2014. Clinical performance evaluation of the BD Veritor system Flu A+B assay. J Virol Methods 204 : 86 90.[CrossRef].[PubMed]
50. Dunn JJ, Ginocchio CC. 2015. Can newly developed, rapid immunochromatographic antigen detection tests be reliably used for the laboratory diagnosis of influenza virus infections? J Clin Microbiol 53 : 1790 1796.[CrossRef].[PubMed]
51. Khanom AB, Velvin C, Hawrami K, Schutten M, Patel M, Holmes MV, Atkinson C, Breuer J, Fitzsimons J, Geretti AM. 2011. Performance of a nurse-led paediatric point of care service for respiratory syncytial virus testing in secondary care. J Infect 62 : 52 58.[CrossRef].[PubMed]
52. Ratcliff RM, Chang G, Kok T, Sloots TP. 2007. Molecular diagnosis of medical viruses. Curr Issues Mol Biol 9 : 87 102.[PubMed]
53. Centers for Disease Control and Prevention. Table 1. FDA-cleared RT-PCR Assays and Other Molecular Assays for Influenza Viruses. http://www.cdc.gov/flu/pdf/professionals/diagnosis/table1-molecular-assays.pdf. Accessed 7 August 2015.
54. Hazelton B, Gray T, Ho J, Ratnamohan VM, Dwyer DE, Kok J. 2015. Detection of influenza A and B with the Alere i Influenza A & B: a novel isothermal nucleic acid amplification assay. Influenza Other Respi Viruses 9 : 151 154.[CrossRef]
55. 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 : 2965 2970.[CrossRef].[PubMed]
56. Popowitch EB, O'Neill SS, Miller MB. 2013. Comparison of the Biofire FilmArray RP, Genmark eSensor RVP, Luminex xTAG RVPv1, and Luminex xTAG RVP fast multiplex assays for detection of respiratory viruses. J Clin Microbiol 51 : 1528 1533.[CrossRef].[PubMed]
57. Hurt AC, Chotpitayasunondh T, Cox NJ, Daniels R, Fry AM, Gubareva LV, Hayden FG, Hui DS, Hungnes O, Lackenby A, Lim W, Meijer A, Penn C, Tashiro M, Uyeki TM, Zambon M WHO Consultation on Pandemic Influenza A (H1N1) 2009 Virus Resistance to Antivirals. 2012. Antiviral resistance during the 2009 influenza A H1N1 pandemic: public health, laboratory, and clinical perspectives. Lancet Infect Dis 12 : 240 248.[CrossRef].[PubMed]


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Reported ranges of sensitivity and specificity of a representative selection of influenza rapid antigen detection kits

Citation: Speicher D, Ali M, Smieja M. 2016. Respiratory Viruses, p 598-609. 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.ch63
Generic image for table

Representative molecular assays for influenza cleared by the U.S. FDA

Citation: Speicher D, Ali M, Smieja M. 2016. Respiratory Viruses, p 598-609. 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.ch63

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