Increased Detection of Viruses in Children with Respiratory Tract Infection Using PCR

Chien-Yu Lin, David Hwang, Nan-Chang Chiu, Li-Chuan Weng, Hsin-Fu Liu, Jung-Jung Mu, Chang-Pan Liu, Hsin Chi, Chien-Yu Lin, David Hwang, Nan-Chang Chiu, Li-Chuan Weng, Hsin-Fu Liu, Jung-Jung Mu, Chang-Pan Liu, Hsin Chi

Abstract

Respiratory viruses are a common cause of respiratory tract infection (RTI), particularly in neonates and children. Rapid and accurate diagnosis of viral infections could improve clinical outcomes and reduce the use of antibiotics and treatment sessions. Advances in diagnostic technology contribute to the accurate detection of viruses. We performed a multiplex real-time polymerase chain reaction (PCR) to investigate the viral etiology in pediatric patients and compared the detection rates with those determined using traditional antigen tests and virus cultures. Fifteen respiratory viruses were included in our investigation: respiratory syncytial virus A/B (RSV), influenza virus A (FluA) and influenza virus B (FluB), human metapneumovirus (MPV), enterovirus (EV), human parainfluenza virus (PIV) types 1-4, human rhinovirus (RV), human coronavirus OC43, NL63, and 229E, human adenovirus (ADV), and human bocavirus (Boca). In total, 474 specimens were collected and tested. Respiratory viruses were detected more frequently by PCR (357, 75.3%) than they were by traditional tests (229, 49.3%). The leading pathogens were RSV (113, 23.8%), RV (72, 15.2%), PIV3 (53, 11.2%), FluA (51, 10.8%), and ADV (48, 10.1%). For children younger than 5 years, RSV and RV were most prevalent; for children older than 5 years, FluA and ADV were the most frequently detected. Of the specimens, 25.8% (92/357) were coinfected with two or more viruses. RV, Boca, PIV2, FluB, and PIV4 had higher rates of coinfection; MPV and PIV1 had the lowest rates of coinfection (9.1% and 5.3%). To conclude, the detection power of PCR was better than that of traditional antigen tests and virus cultures when considering the detection of respiratory viruses. RSV and RV were the leading viral pathogens identified in the respiratory specimens. One-quarter of the positive specimens were coinfected with two or more viruses. In the future, further application of PCR may contribute to the rapid and accurate diagnosis of respiratory viruses and could improve patient outcomes.

Keywords: PCR; human metapneumovirus; multiplex quantitative real-time RT-PCR; polymerase chain reaction; respiratory syncytial virus; respiratory virus.

Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Number of respiratory viruses detected by PCR.
Figure 2
Figure 2
Seasonal distribution of respiratory viruses detected by PCR. (Abbreviations: 229E: coronavirus 229E; ADV: human adenovirus; Boca: human bocavirus; EV: human enterovirus; Flu: influenza virus; MPV: human metapneumovirus; NL63: coronavirus NL63; OC43: coronavirus OC43; PIV: human parainfluenza virus; RSV: respiratory syncytial virus; RV: human rhinovirus).
Figure 3
Figure 3
The distribution of respiratory viruses among different age groups. (Abbreviations: 229E: coronavirus 229E; ADV: human adenovirus; Boca: human bocavirus; EV: human enterovirus; Flu: influenza virus; MPV: human metapneumovirus; NL63: coronavirus NL63; OC43: coronavirus OC43; PIV: human parainfluenza virus; RSV: respiratory syncytial virus; RV: human rhinovirus).

References

    1. Lower Respiratory Infections Collaborators Estimates of the global, regional, and national morbidity, mortality, and aetiologies of lower respiratory infections in 195 countries, 1990–2016: A systematic analysis for the global burden of disease study 2016. Lancet Infect. Dis. 2018;18:1191–1210. doi: 10.1016/S1473-3099(18)30310-4.
    1. van den Hoogen B.G., de Jong J.C., Groen J., Kuiken T., de Groot R., Fouchier R.A., Osterhaus A.D. A newly discovered human pneumovirus isolated from young children with respiratory tract disease. Nat. Med. 2001;7:719–724. doi: 10.1038/89098.
    1. van der Hoek L., Pyrc K., Jebbink M.F., Vermeulen-Oost W., Berkhout R.J., Wolthers K.C., Wertheim-van Dillen P.M., Kaandorp J., Spaargaren J., Berkhout B. Identification of a new human coronavirus. Nat. Med. 2004;10:368–373. doi: 10.1038/nm1024.
    1. Jain S., Williams D.J., Arnold S.R., Ampofo K., Bramley A.M., Reed C., Stockmann C., Anderson E.J., Grijalva C.G., Self W.H., et al. Community-acquired pneumonia requiring hospitalization among US Children. N. Engl. J. Med. 2015;372:835–845. doi: 10.1056/NEJMoa1405870.
    1. Ruuskanen O., Lahti E., Jennings L.C., Murdoch D.R. Viral pneumonia. Lancet. 2011;377:1264–1275. doi: 10.1016/S0140-6736(10)61459-6.
    1. Jain S., Self W.H., Wunderink R.G., Fakhran S., Balk R., Bramley A.M., Reed C., Grijalva C.G., Anderson E.J., Courtney D.M., et al. Community-acquired pneumonia requiring hospitalization among US. Adults. N. Engl. J. Med. 2015;373:415–427. doi: 10.1056/NEJMoa1500245.
    1. Lee J.H., Jang J.H., Lee S.H., Kim Y.J., Yoo K.H., Sung K.W., Lee N.Y., Ki C.S., Koo H.H. Respiratory viral infections during the first 28 days after transplantation in pediatric hematopoietic stem cell transplant recipients. Clin. Transplant. 2012;26:736–740. doi: 10.1111/j.1399-0012.2012.01607.x.
    1. Bennett N.J., Tabarani C.M., Bartholoma N.M., Wang D., Huang D., Riddell S.W., Kiska D.L., Hingre R., Rosenberg H.F., Domachowske J.B. Unrecognized viral respiratory tract infections in premature infants during their birth hospitalization: A prospective surveillance study in two neonatal intensive care units. J. Pediatr. 2012;161:814–818. doi: 10.1016/j.jpeds.2012.05.001.
    1. Minejima E., Wong-Beringer A. Implementation of rapid diagnostics with antimicrobial stewardship. Expert Rev. Anti-Infect. Ther. 2016;14:1065–1075. doi: 10.1080/14787210.2016.1233814.
    1. Krause J.C., Panning M., Hengel H., Henneke P. The role of multiplex pcr in respiratory tract infections in children. Dtsch. Arztebl. Int. 2014;111:639–645. doi: 10.3238/arztebl.2014.0639.
    1. Charles P.G. Early diagnosis of lower respiratory tract infections (point-of-care tests) Curr. Opin. Pulm. Med. 2008;14:176–182. doi: 10.1097/MCP.0b013e3282f7642f.
    1. Ferronato A.E., Gilio A.E., Ferraro A.A., Paulis M., Vieira S.E. Etiological diagnosis reduces the use of antibiotics in infants with bronchiolitis. Clinics Sao Paulo Brazil. 2012;67:1001–1006. doi: 10.6061/clinics/2012(09)03.
    1. Garcia-Garcia M.L., Calvo C., Pozo F., Villadangos P.A., Perez-Brena P., Casas I. Spectrum of respiratory viruses in children with community-acquired pneumonia. Pediatric Infect. Dis. J. 2012;31:808–813. doi: 10.1097/INF.0b013e3182568c67.
    1. Tanday S. Resisting the use of antibiotics for viral infections. Lancet Respir. Med. 2016;4:179. doi: 10.1016/S2213-2600(16)00060-6.
    1. Huijskens E.G., Biesmans R.C., Buiting A.G., Obihara C.C., Rossen J.W. Diagnostic value of respiratory virus detection in symptomatic children using real-time pcr. Virol. J. 2012;9:276. doi: 10.1186/1743-422X-9-276.
    1. Endimiani A., Hujer K.M., Hujer A.M., Kurz S., Jacobs M.R., Perlin D.S., Bonomo R.A. Are we ready for novel detection methods to treat respiratory pathogens in hospital-acquired pneumonia? Clin. Infect. Dis. Off. Publ. Infect. Dis. Soc. Am. 2011;52:S373–S383. doi: 10.1093/cid/cir054.
    1. Huang H.S., Tsai C.L., Chang J., Hsu T.C., Lin S., Lee C.C. Multiplex pcr system for the rapid diagnosis of respiratory virus infection: Systematic review and meta-analysis. Clin. Microbiol. Infect. Off. Publ. Eur. Soc. Clin. Microbiol. Infect. Dis. 2018;24:1055–1063. doi: 10.1016/j.cmi.2017.11.018.
    1. Chen H., Weng H., Lin M., He P., Li Y., Xie Q., Ke C., Jiao X. The clinical significance of filmarray respiratory panel in diagnosing community-acquired pneumonia. BioMed Res. Int. 2017;2017:7320859. doi: 10.1155/2017/7320859.
    1. Kuypers J., Wright N., Ferrenberg J., Huang M.-L., Cent A., Corey L., Morrow R. Comparison of real-time pcr assays with fluorescent-antibody assays for diagnosis of respiratory virus infections in children. J. Clin. Microbiol. 2006;44:2382–2388. doi: 10.1128/JCM.00216-06.
    1. Templeton K.E., Scheltinga S.A., Beersma M.F., Kroes A.C., Claas E.C. Rapid and sensitive method using multiplex real-time pcr for diagnosis of infections by influenza a and influenza b viruses, respiratory syncytial virus, and parainfluenza viruses 1, 2, 3, and 4. J. Clin. Microbiol. 2004;42:1564–1569. doi: 10.1128/JCM.42.4.1564-1569.2004.
    1. Huang A.S., Chen W.C., Huang W.T., Huang S.T., Lo Y.C., Wei S.H., Kuo H.W., Chan P.C., Hung M.N., Liu Y.L., et al. Public health responses to reemergence of animal rabies, Taiwan, 16 July–28 December, 2013. PLoS ONE. 2015;10:e0132160. doi: 10.1371/journal.pone.0132160.
    1. Bonzel L., Tenenbaum T., Schroten H., Schildgen O., Schweitzer-Krantz S., Adams O. Frequent detection of viral coinfection in children hospitalized with acute respiratory tract infection using a real-time polymerase chain reaction. Pediatr. Infect. Dis. J. 2008;27:589–594. doi: 10.1097/INF.0b013e3181694fb9.
    1. Chidlow G.R., Harnett G.B., Shellam G.R., Smith D.W. An economical tandem multiplex real-time pcr technique for the detection of a comprehensive range of respiratory pathogens. Viruses. 2009;1:42–56. doi: 10.3390/v1010042.
    1. Maertzdorf J., Wang C.K., Brown J.B., Quinto J.D., Chu M., de Graaf M., van den Hoogen B.G., Spaete R., Osterhaus A.D., Fouchier R.A. Real-time reverse transcriptase pcr assay for detection of human metapneumoviruses from all known genetic lineages. J. Clin. Microbiol. 2004;42:981–986. doi: 10.1128/JCM.42.3.981-986.2004.
    1. Ward C.L., Dempsey M.H., Ring C.J., Kempson R.E., Zhang L., Gor D., Snowden B.W., Tisdale M. Design and performance testing of quantitative real time pcr assays for influenza a and b viral load measurement. J. Clin. Virol. Off. Publ. Pan Am. Soc. Clin. Virol. 2004;29:179–188. doi: 10.1016/S1386-6532(03)00122-7.
    1. Chen Y., Cui D., Zheng S., Yang S., Tong J., Yang D., Fan J., Zhang J., Lou B., Li X., et al. Simultaneous detection of influenza a, influenza b, and respiratory syncytial viruses and subtyping of influenza a h3n2 virus and h1n1 (2009) virus by multiplex real-time pcr. J. Clin. Microbiol. 2011;49:1653–1656. doi: 10.1128/JCM.02184-10.
    1. Mills J.M., Harper J., Broomfield D., Templeton K.E. Rapid testing for respiratory syncytial virus in a paediatric emergency department: Benefits for infection control and bed management. J. Hosp. Infect. 2011;77:248–251. doi: 10.1016/j.jhin.2010.11.019.
    1. Sim S.A., Leung V.K.Y., Ritchie D., Slavin M.A., Sullivan S.G., Teh B.W. Viral respiratory tract infections in allogeneic hematopoietic stem cell transplantation recipients in the era of molecular testing. Biol. Blood Marrow Transplant. J. Am. Soc. Blood Marrow Transplant. 2018;24:1490–1496. doi: 10.1016/j.bbmt.2018.03.004.
    1. Shiley K.T., Lautenbach E., Lee I. The use of antimicrobial agents after diagnosis of viral respiratory tract infections in hospitalized adults: Antibiotics or anxiolytics? Infect. Control. Hosp. Epidemiol. Off. J. Soc. Hosp. Epidemiol. Am. 2010;31:1177–1183. doi: 10.1086/656596.
    1. McCaig L.F., Besser R.E., Hughes J.M. Antimicrobial drug prescription in ambulatory care settings, united states, 1992–2000. Emerg. Infect. Dis. 2003;9:432–437. doi: 10.3201/eid0904.020268.
    1. Spurling G.K., Fonseka K., Doust J., Del Mar C. Antibiotics for bronchiolitis in children. Cochrane Database Syst. Rev. 2007:Cd005189. doi: 10.1002/14651858.CD005189.pub3S.
    1. Breakell R., Thorndyke B., Clennett J., Harkensee C. Reducing unnecessary chest x-rays, antibiotics and bronchodilators through implementation of the nice bronchiolitis guideline. Eur. J. Pediatr. 2018;177:47–51. doi: 10.1007/s00431-017-3034-5.
    1. Sung C.C., Chi H., Chiu N.C., Huang D.T., Weng L.C., Wang N.Y., Huang F.Y. Viral etiology of acute lower respiratory tract infections in hospitalized young children in northern Taiwan. J. Microbiol. Immunol. Infect. (Wei Mian Yu Gan Ran Za Zhi) 2011;44:184–190. doi: 10.1016/j.jmii.2011.01.025.
    1. Bharaj P., Sullender W.M., Kabra S.K., Mani K., Cherian J., Tyagi V., Chahar H.S., Kaushik S., Dar L., Broor S. Respiratory viral infections detected by multiplex pcr among pediatric patients with lower respiratory tract infections seen at an urban hospital in delhi from 2005 to 2007. Virol. J. 2009;6:89. doi: 10.1186/1743-422X-6-89.
    1. Jiang W., Wu M., Zhou J., Wang Y., Hao C., Ji W., Zhang X., Gu W., Shao X. Etiologic spectrum and occurrence of coinfections in children hospitalized with community-acquired pneumonia. BMC Infect. Dis. 2017;17:787. doi: 10.1186/s12879-017-2891-x.
    1. Kim H.J., Choi S.M., Lee J., Park Y.S., Lee C.H., Yim J.J., Yoo C.G., Kim Y.W., Han S.K., Lee S.M. Respiratory virus of severe pneumonia in south korea: Prevalence and clinical implications. PLoS ONE. 2018;13:e0198902. doi: 10.1371/journal.pone.0198902.
    1. Ortiz-Hernandez A.A., Nishimura K.K., Noyola D.E., Moreno-Espinosa S., Gamino A., Galindo-Fraga A., Valdez Vazquez R., Magana Aquino M., Ramirez-Venegas A., Valdes Salgado R., et al. Differential risk of hospitalization among single virus infections causing influenza like illnesses. Influenza Respir. Viruses. 2018;13:36–43. doi: 10.1111/irv.12606.
    1. Chi H., Chang I.S., Tsai F.Y., Huang L.M., Shao P.L., Chiu N.C., Chang L.Y., Huang F.Y. Epidemiological study of hospitalization associated with respiratory syncytial virus infection in Taiwanese children between 2004 and 2007. J. Formos. Med Assoc. (Taiwan Yi Zhi) 2011;110:388–396. doi: 10.1016/S0929-6646(11)60057-0.
    1. Hsu C.H., Lin C.Y., Chi H., Chang J.H., Hung H.Y., Kao H.A., Peng C.C., Jim W.T. Prolonged seasonality of respiratory syncytial virus infection among preterm infants in a subtropical climate. PLoS ONE. 2014;9:e110166. doi: 10.1371/journal.pone.0110166.
    1. Scheltema N.M., Gentile A., Lucion F., Nokes D.J., Munywoki P.K., Madhi S.A., Groome M.J., Cohen C., Moyes J., Thorburn K., et al. Global respiratory syncytial virus-associated mortality in young children (rsv gold): A retrospective case series. Lancet Global Health. 2017;5:e984–e991. doi: 10.1016/S2214-109X(17)30344-3.
    1. Michelow I.C., Olsen K., Lozano J., Rollins N.K., Duffy L.B., Ziegler T., Kauppila J., Leinonen M., McCracken G.H., Jr. Epidemiology and clinical characteristics of community-acquired pneumonia in hospitalized children. Pediatrics. 2004;113:701–707. doi: 10.1542/peds.113.4.701.
    1. Nolan V.G., Arnold S.R., Bramley A.M., Ampofo K., Williams D.J., Grijalva C.G., Self W.H., Anderson E.J., Wunderink R.G., Edwards K.M., et al. Etiology and impact of coinfections in children hospitalized with community-acquired pneumonia. J. Infect. Dis. 2018;218:179–188. doi: 10.1093/infdis/jix641.
    1. Debiaggi M., Canducci F., Ceresola E.R., Clementi M. The role of infections and coinfections with newly identified and emerging respiratory viruses in children. Virol. J. 2012;9:247. doi: 10.1186/1743-422X-9-247.
    1. Stefanska I., Romanowska M., Donevski S., Gawryluk D., Brydak L.B. Co-infections with influenza and other respiratory viruses. Adv. Exp. Med. Biol. 2013;756:291–301.
    1. Yoshida L.M., Suzuki M., Nguyen H.A., Le M.N., Dinh Vu T., Yoshino H., Schmidt W.P., Nguyen T.T., Le H.T., Morimoto K., et al. Respiratory syncytial virus: Co-infection and paediatric lower respiratory tract infections. Eur. Respir. J. 2013;42:461–469. doi: 10.1183/09031936.00101812.
    1. Semple M.G., Cowell A., Dove W., Greensill J., McNamara P.S., Halfhide C., Shears P., Smyth R.L., Hart C.A. Dual infection of infants by human metapneumovirus and human respiratory syncytial virus is strongly associated with severe bronchiolitis. J. Infect. Dis. 2005;191:382–386. doi: 10.1086/426457.
    1. Xepapadaki P., Psarras S., Bossios A., Tsolia M., Gourgiotis D., Liapi-Adamidou G., Constantopoulos A.G., Kafetzis D., Papadopoulos N.G. Human metapneumovirus as a causative agent of acute bronchiolitis in infants. J. Clin. Virol. Off. Publ. Pan Am. Soc. Clin. Virol. 2004;30:267–270. doi: 10.1016/j.jcv.2003.12.012.
    1. Lau S.K., Yip C.C., Tsoi H.W., Lee R.A., So L.Y., Lau Y.L., Chan K.H., Woo P.C., Yuen K.Y. Clinical features and complete genome characterization of a distinct human rhinovirus (HRV) genetic cluster, probably representing a previously undetected hrv species, hrv-c, associated with acute respiratory illness in children. J. Clin. Microbiol. 2007;45:3655–3664. doi: 10.1128/JCM.01254-07.
    1. Ma Y.J., Wang S.M., Cho Y.H., Shen C.F., Liu C.C., Chi H., Huang Y.C., Huang L.M., Huang Y.C., Lin H.C., et al. Clinical and epidemiological characteristics in children with community-acquired mycoplasma pneumonia in Taiwan: A nationwide surveillance. J. Microbiol. Immunol. Infect. (Wei Mian Yu Gan Ran Za Zhi) 2015;48:632–638. doi: 10.1016/j.jmii.2014.08.003.
    1. Babakir-Mina M., Ciccozzi M., Perno C.F., Ciotti M. The human polyomaviruses ki and wu: Virological background and clinical implications. APMIS Acta Pathol. Microbiol. et Immunol. Scand. 2013;121:746–754. doi: 10.1111/apm.12091.

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