Detection and discrimination of multiple strains of Zika virus by reverse transcription-loop-mediated isothermal amplification
Abstract Background Monitoring both invasion of Zika virus disease into free countries and circulation in endemic countries is essential to avoid a global pandemic. However, the difficulty lies in detecting Zika virus due to the large variety of mutations in its genomic sequence. To develop a rapid...
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| Format: | Article |
| Language: | English |
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BMC
2020-10-01
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| Series: | Tropical Medicine and Health |
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| Online Access: | http://link.springer.com/article/10.1186/s41182-020-00274-z |
| _version_ | 1818408120948359168 |
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| author | Hiroka Aonuma Itoe Iizuka-Shiota Tokio Hoshina Shigeru Tajima Fumihiro Kato Seiji Hori Masayuki Saijo Hirotaka Kanuka |
| author_facet | Hiroka Aonuma Itoe Iizuka-Shiota Tokio Hoshina Shigeru Tajima Fumihiro Kato Seiji Hori Masayuki Saijo Hirotaka Kanuka |
| author_sort | Hiroka Aonuma |
| collection | DOAJ |
| description | Abstract Background Monitoring both invasion of Zika virus disease into free countries and circulation in endemic countries is essential to avoid a global pandemic. However, the difficulty lies in detecting Zika virus due to the large variety of mutations in its genomic sequence. To develop a rapid and simple method with high accuracy, reverse transcription-loop-mediated isothermal amplification (RT-LAMP) was adopted for the detection of Zika virus strains derived from several countries. Results Common primers for RT-LAMP were designed based on the genomic sequences of two standard Zika strains: African lineage, MR-766, and Asian lineage, PRVABC59. RT-LAMP reactions using a screened primer set, targeting the NS3 region, detected both Zika virus strains. The minimum detectable quantity was 3 × 10−2 ng of virus RNA. Measurable lag of reaction times among strains was observed. The RT-LAMP method amplified the target virus sequence from the urine and serum of a patient with a travel history in the Caribbean Islands and also provided a prediction about which lineage of Zika virus strain was present. Conclusions The RT-LAMP method using a well-optimized primer set demonstrated high specificity and sensitivity for the detection of Zika virus strains with a variety in genomic RNA sequences. In combination with the simplicity of LAMP reaction in isothermal conditions, the optimized primer set established in this study may facilitate rapid and accurate diagnosis of Zika fever patients with virus strain information. |
| first_indexed | 2024-12-14T09:38:41Z |
| format | Article |
| id | doaj.art-2a7a11b653ba4aeca46fe08099bece5a |
| institution | Directory Open Access Journal |
| issn | 1349-4147 |
| language | English |
| last_indexed | 2024-12-14T09:38:41Z |
| publishDate | 2020-10-01 |
| publisher | BMC |
| record_format | Article |
| series | Tropical Medicine and Health |
| spelling | doaj.art-2a7a11b653ba4aeca46fe08099bece5a2022-12-21T23:07:51ZengBMCTropical Medicine and Health1349-41472020-10-0148111010.1186/s41182-020-00274-zDetection and discrimination of multiple strains of Zika virus by reverse transcription-loop-mediated isothermal amplificationHiroka Aonuma0Itoe Iizuka-Shiota1Tokio Hoshina2Shigeru Tajima3Fumihiro Kato4Seiji Hori5Masayuki Saijo6Hirotaka Kanuka7Department of Tropical Medicine, The Jikei University School of MedicineDepartment of Tropical Medicine, The Jikei University School of MedicineDepartment of Tropical Medicine, The Jikei University School of MedicineDepartment of Virology 1, National Institute of Infectious DiseasesDepartment of Virology 1, National Institute of Infectious DiseasesDepartment of Infectious Diseases and Infection Control, The Jikei University School of MedicineDepartment of Virology 1, National Institute of Infectious DiseasesDepartment of Tropical Medicine, The Jikei University School of MedicineAbstract Background Monitoring both invasion of Zika virus disease into free countries and circulation in endemic countries is essential to avoid a global pandemic. However, the difficulty lies in detecting Zika virus due to the large variety of mutations in its genomic sequence. To develop a rapid and simple method with high accuracy, reverse transcription-loop-mediated isothermal amplification (RT-LAMP) was adopted for the detection of Zika virus strains derived from several countries. Results Common primers for RT-LAMP were designed based on the genomic sequences of two standard Zika strains: African lineage, MR-766, and Asian lineage, PRVABC59. RT-LAMP reactions using a screened primer set, targeting the NS3 region, detected both Zika virus strains. The minimum detectable quantity was 3 × 10−2 ng of virus RNA. Measurable lag of reaction times among strains was observed. The RT-LAMP method amplified the target virus sequence from the urine and serum of a patient with a travel history in the Caribbean Islands and also provided a prediction about which lineage of Zika virus strain was present. Conclusions The RT-LAMP method using a well-optimized primer set demonstrated high specificity and sensitivity for the detection of Zika virus strains with a variety in genomic RNA sequences. In combination with the simplicity of LAMP reaction in isothermal conditions, the optimized primer set established in this study may facilitate rapid and accurate diagnosis of Zika fever patients with virus strain information.http://link.springer.com/article/10.1186/s41182-020-00274-zZika feverZika virusRNALoop-mediated isothermal amplificationPatient |
| spellingShingle | Hiroka Aonuma Itoe Iizuka-Shiota Tokio Hoshina Shigeru Tajima Fumihiro Kato Seiji Hori Masayuki Saijo Hirotaka Kanuka Detection and discrimination of multiple strains of Zika virus by reverse transcription-loop-mediated isothermal amplification Tropical Medicine and Health Zika fever Zika virus RNA Loop-mediated isothermal amplification Patient |
| title | Detection and discrimination of multiple strains of Zika virus by reverse transcription-loop-mediated isothermal amplification |
| title_full | Detection and discrimination of multiple strains of Zika virus by reverse transcription-loop-mediated isothermal amplification |
| title_fullStr | Detection and discrimination of multiple strains of Zika virus by reverse transcription-loop-mediated isothermal amplification |
| title_full_unstemmed | Detection and discrimination of multiple strains of Zika virus by reverse transcription-loop-mediated isothermal amplification |
| title_short | Detection and discrimination of multiple strains of Zika virus by reverse transcription-loop-mediated isothermal amplification |
| title_sort | detection and discrimination of multiple strains of zika virus by reverse transcription loop mediated isothermal amplification |
| topic | Zika fever Zika virus RNA Loop-mediated isothermal amplification Patient |
| url | http://link.springer.com/article/10.1186/s41182-020-00274-z |
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