Original Article
Evaluation of 5′-untranslated region amplification and sequencing for enterovirus serotypes identification diagnosis
Shihuan Tang, Zhenghua Xie, Duoduo Liu, Ying Yuan, Manjun Chen, Xiaodi Fan, Xixia Ding, Nan Yu
Published 2018-10-30
Cite as Chinese J Exp Clin Virol, 2018, 32(5): 488-491. DOI: 10.3760/cma.j.issn.1003-9279.2018.05.008
Abstract
ObjectiveTo evaluate an assay permitting amplification of target 5′-untranslated region (5′-UTR) sequences directly from clinical specimens and distinction among serotypes of enterovirus (EV).
MethodsA total of 518 rectal swabs and 148 nasal swabs tested positive by pan-enterovirus real-time PCR were collected. 5′-UTR and the viral protein 1 (VP1) gene fragments were amplified and sequenced separately for serotyping. The inconsistent samples by 5′-UTR and VP1 serotyping were further determined by using the serotype-specific RT-PCR.
ResultsA total of 553 (83.0%) samples were detected by 5′-UTR serotyping and 318 (47.7%) were detected by VP1 serotyping in all 666 positive specimens, and there was significant difference in the detection rates between two methods in rectal and nasal swabs (P<0.001). For the rectal swabs, the mainly detected serotypes were CoxA6 (217), CoxA16 (88), EVA71 (40), CoxA10 (28) and CoxA4 (27) by 5′-UTR serotyping. Compared with the VP1 serotyping, the sensitivity and specificity of 5′-UTR serotyping were 57.1%-100% and 67.4%-98.1% respectively, with varied consistence with serotypes (kappa value 0.214-0.283). For the nasal swabs, the most frequently detected serotype was EVD68, with the sensitivity of 100%, the specificity of 91.1%, and the poor consistence (kappa value 0.217). CoxA6, CoxA16, EVA71, CoxA10 and EVD68 were further confirmed by serotype-specific RT-PCR. Using VP1 serotyping combined with serotype-specific RT-PCR as a reference method , the effect of performance of 5′-UTR serotyping on diagnosis was increased.
ConclusionsThe performances of 5′-UTR serotyping in enterovirus vary with serotypes. The application of 5′-UTR serotyping should be considered comprehensively according to the purpose of the study.
Key words:
Enterovirus; 5′-untranslated region; Reverse transcription-polymerase chain reaction; Sequencing; Serotyping
Contributor Information
Shihuan Tang
Department of Clinical Laboratory, Zhujiang Hospital Affiliated to Southern Medical University, Key Laboratory of Pathogenic Microorganisms of Emerging Infection Diseases, Guangzhou 510282, China
Zhenghua Xie
Duoduo Liu
Ying Yuan
Manjun Chen
Xiaodi Fan
Xixia Ding
Nan Yu