Evaluation of 5′-untranslated region amplification and sequencing for enterovirus serotypes identification diagnosis
10.3760/cma.j.issn.1003-9279.2018.05.008
- VernacularTitle: 肠道病毒5′-非翻译区测序分型的应用评估
- Author:
Shihuan TANG
1
;
Zhenghua XIE
;
Duoduo LIU
;
Ying YUAN
;
Manjun CHEN
;
Xiaodi FAN
;
Xixia DING
;
Nan YU
Author Information
1. Department of Clinical Laboratory, Zhujiang Hospital Affiliated to Southern Medical University, Key Laboratory of Pathogenic Microorganisms of Emerging Infection Diseases, Guangzhou 510282, China
- Publication Type:Journal Article
- Keywords:
Enterovirus;
5′-untranslated region;
Reverse transcription-polymerase chain reaction;
Sequencing;
Serotyping
- From:
Chinese Journal of Experimental and Clinical Virology
2018;32(5):488-491
- CountryChina
- Language:Chinese
-
Abstract:
Objective:To evaluate an assay permitting amplification of target 5′-untranslated region (5′-UTR) sequences directly from clinical specimens and distinction among serotypes of enterovirus (EV).
Methods:A 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.
Results:A 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.
Conclusions:The 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.
