Missed detections of influenza A(H1)pdm09 by real-time RT–PCR assay due to haemagglutinin sequence mutation, December 2017 to March 2018, northern Viet Nam
DOI:
https://doi.org/10.5365/wpsar.2018.9.3.003Abstract
Introduction: There are two methods of reverse transcription polymerase chain reaction (RT–PCR) that have been the common methods to detect influenza infections: conventional and real-time RT–PCR. From December 2017 to March 2018, several missed diagnoses of influenza A(H1)pdm09 using real-time RT–PCR were reported in northern Viet Nam. This study investigated how these missed detections occurred to determine their effect on the surveillance of influenza.
Methods: The haemagglutinin (HA) segments of A(H1N1)pdm09 from both real-time RT–PCR positive and negative samples were isolated and sequenced. The primer and probe sets in the HA gene were checked for mismatches, and phylogenetic analyses were performed to determine the molecular epidemiology of these viruses.
Results: There were 86 positive influenza A samples; 32 were A(H1)pdm09 positive by conventional RT–PCR but were negative by real-time RT–PCR. Sequencing was conducted on 23 influenza (H1N1)pdm09 isolates that were recovered from positive samples. Eight of these were negative for A(H1)pdm09 by real-time RT–PCR. There were two different mismatches in the probe target sites of the HA gene sequences of all isolates (n = 23) with additional mismatches only at position 7 (template binding site) identified for all eight negative real-time RT–PCR isolates. The prime target sites had no mismatches. Phylogenetic analysis of the HA gene showed that both the positive and negative real-time RT–PCR isolates were grouped in clade 6B.1; however, the real-time RT–PCR negative viruses were located in a subgroup that referred to substitution I295V.
Conclusion: Constant monitoring of genetic changes in the circulating influenza A(H1N1)pdm09 viruses is important for maintaining the sensitivity of molecular detection assays.
References
Refference
WHO. Evolution of a pandemic. 2010.
European Centre for Disease Prevention and Control (ECDC) - Health Comunication Unit -. SURVEILLANCE SURVEILLANCE REPORT Influenza virus Influenza virus characterisation. 2014;1–10.
Nguyen HKL, Nguyen PTK, Nguyen TC, Hoang PVM, Le TT, Vuong CD, et al. Virological characterization of influenza H1N1pdm09 in Vietnam, 2010-2013. Influenza Other Respi Viruses. 2015;9(4):216–24.
Nguyen YT, Graitcer SB, Nguyen TH, Tran DN, Pham TD, Le MTQ, et al. National surveillance for influenza and influenza-like illness in Vietnam, 2006-2010. Vaccine [Internet]. Elsevier Ltd; 2013 Jul 30 [cited 2013 Aug 11].
WPR GISRS. Epidemiological and virological characteristics of influenza in the Western Pacific Region of the World Health Organization, 2006-2010. PLoS One [Internet]. 2012 Jan [cited 2012 Nov 6];7(5):e37568.
WHO. Influenza Update N °308. 2018;(February):1–3.
WHO. Influenza Update N ° 306. 2017;(Dêcmber):1–3.
Region WP, People L, Caledonia N, Nam V, Region WP. Bi-weekly Influenza Situation Update Virological Surveillance Summary Bi-weekly Influenza Situation Update Countries in the temperate zone of the Northern Hemisphere. 2016;1004(June):1–7.
WHO. The use of PCR in the surveillance and diagnosis of influenza. Who. 2011;(June):1–10.
Who T, Centre C, Atlanta CDC, States U. CDC protocol of realtime RTPCR for influenza A ( H1N1 ) Characterization of Swine Influenza ( version 2009 ) General Comments. 2009;1(April).
WHO. Global influenza surveillance and response system. 2013.
Mukherjee S. Impact of Microarray Technology in Influenza Virus Research and Diagnostics. J Proteomics Bioinform [Internet]. 2013;01(S6).
Van den Hoecke S, Verhelst J, Vuylsteke M, Saelens X. Analysis of the genetic diversity of influenza A viruses using next-generation DNA sequencing. BMC Genomics. 2015;16(1):1–23.
Kawai Y, Kimura Y, Lezhava A, Kanamori H, Usui K, Hanami T, et al. One-step detection of the 2009 pandemic influenza a(H1N1) virus by the RT-smartamp assay and its clinical validation. PLoS One. 2012;7(1).
Tenorio-Abreu A, Eiros JM, Rodríguez E, Bermejo JF, Domínguez-Gil M, Vega T, et al. Influenza surveillance by molecular methods. Expert Rev antiinfective Ther [Internet]. 2010;8(5):517–27.
