Optimizing RT-semi-nested PCR Conditions with Newly Developed Primers for the Specific Detection of Human Enterovirus D68 and its Identification from Clinical Specimens

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  • 臨床検体からエンテロウイルスD68 型を特異的に検出・同定するためのプライマー開発と RT-Seminested PCR 条件の決定
  • リンショウケンタイ カラ エンテロウイルス D68ガタ オ トクイテキ ニ ケンシュツ ・ ドウテイ スル タメ ノ プライマー カイハツ ト RT-Seminested PCR ジョウケン ノ ケッテイ

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Abstract

<p>Human enterovirus D68 (EV-D68) is a member of the Enterovirus genus (EVs) within the Picornaviridae family, and generally associated with respiratory tract infection. Meanwhile, previous reports suggest that EV-D68 was also associated with acute flaccid paralysis in the clinical cases in USA and Japan. Two conventional PCR assays have been commonly used for genetic analysis of EVs. One is the RTsemi-nested PCR assay (VP4-VP2-PCR) that amplifies the VP4-VP2 region for detection of EVs with high sensitivity and the other is the CODEHOP RT-semi-nested PCR assay (CODEHOP PCR) that amplifies the VP1 region for typing. These assays are useful for detection and identification of EVs in many clinical cases. However, we experienced some cases in which we could not identify EV-D68 with CODEHOP PCR from clinical specimens in spite of the results that EV-D68 sequences were detected by VP4-VP2-PCR. In addition, these assays would have trouble in detecting target sequences in those cases where the specimens under examination have been acquired from patients infected with multiple types of EVs. Therefore, we tried to develop a novel RT-semi-nested PCR assay that has high sensitivity and specificity for EV-D68. We designed original primers to be used for the amplification of the VP1 region of EV-D68 and optimized the RT-semi-nested PCR conditions. Sensitivity and specificity were examined with previously accumulated clinical specimens. As a result, we could confirm that our developed PCR assay had higher sensitivity than VP4-VP2-PCR and the assay had no cross reactivity with 23 kinds of enterovirus types, HRV-A, HRV-B, and HRV-C. We could identify EV-D68 with the assay in 2 specimens that were typed as another one by CODEHOP PCR. Furthermore, 1st-PCR of the assay had a higher detection capability from the clinical specimens, and we could obtain sequence data of the VP1 region sufficient to construct a phylogenetic tree. The results of the phylogenetic analysis revealed that lineage 1, 2 and 3 were detected in Saitama City. In conclusion, the PCR assay we developed in this study was useful in the diagnosis of EV-D68 from various kinds of clinical specimens.</p>

Journal

  • Kansenshogaku Zasshi

    Kansenshogaku Zasshi 91 (3), 376-386, 2017-05-20

    The Japanese Association for Infectious Diseases

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