A reverse transcription loop-mediated isothermal amplification for broad coverage detection of Asian and African Zika virus lineages

Teoh, Boon‐Teong; Chin, Kim-Ling; Samsudin, Nur-Izyan; Loong, Shih Keng; Sam, Sing‐Sin; Tan, Kian Lam; Khor, Chee‐Sieng; Abd-Jamil, Juraina; Zainal, Nurhafiza; Wilder‐Smith, Annelies; Zandi, Keivan; AbuBakar, Sazaly

doi:10.1186/s12879-020-05585-4

Cited by 4 publications

(4 citation statements)

References 63 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Furthermore, when using the AB7500 fast instrument, the estimated cost per reaction was £2.40 for the RT-LAMP and £4.80 for the RT-qPCR assay, whereas the reaction time was at least four times shorter for the RT-LAMP assay. With the current interest in the use of LAMP technology for rapid detection of emerging human viruses such as SARS-CoV-2 [39] or Zika virus [40], the upscaling of RT-LAMP for high throughput screening in diagnostic laboratories could make this technology a good alternative to RT-qPCR, especially during a shortage of RT-qPCR diagnostic reagents, as noted during the COVID-19 pandemic, but, crucially, when a cheap but fast assay is preferable.…”

Section: Discussionmentioning

confidence: 99%

Development of a Novel Loop Mediated Isothermal Amplification Assay (LAMP) for the Rapid Detection of Epizootic Haemorrhagic Disease Virus

Rajko-Nenow

Howson

Clark

et al. 2021

Viruses

View full text Add to dashboard Cite

Epizootic haemorragic disease (EHD) is an important disease of white-tailed deer and can cause a bluetongue-like illness in cattle. A definitive diagnosis of EHD relies on molecular assays such as real-time RT-qPCR or conventional PCR. Reverse transcription loop-mediated isothermal amplification (RT-LAMP) is a cost-effective, specific, and sensitive technique that provides an alternative to RT-qPCR. We designed two sets of specific primers targeting segment-9 of the EHD virus genome to enable the detection of western and eastern topotypes, and evaluated their performance in singleplex and multiplex formats using cell culture isolates (n = 43), field specimens (n = 20), and a proficiency panel (n = 10). The limit of detection of the eastern and western RT-LAMP assays was estimated as ~24.36 CT and as ~29.37 CT in relation to real-time RT-qPCR, respectively, indicating a greater sensitivity of the western topotype singleplex RT-LAMP. The sensitivity of the western topotype RT-LAMP assay, relative to the RT-qPCR assay, was 72.2%, indicating that it could be theoretically used to detect viraemic cervines and bovines. For the first time, an RT-LAMP assay was developed for the rapid detection of the EHD virus that could be used as either a field test or high throughput screening tool in established laboratories to control the spread of EHD.

show abstract

Section: Discussionmentioning

confidence: 99%

Development of a Novel Loop Mediated Isothermal Amplification Assay (LAMP) for the Rapid Detection of Epizootic Haemorrhagic Disease Virus

Rajko-Nenow

Howson

Clark

et al. 2021

Viruses

View full text Add to dashboard Cite

show abstract

“…The characteristics of primers and probe including the GC content, melting temperature, formation of hairpin and dimers were analysed by using web IDT OligoAnalyser Tool (https:// sg.idtdna.com/calc/analyzer). In this study, the last 5 nucleotides at 3' end of primers and 5' end of probe were considered to be the critical regions for priming (Teoh et al, 2020;Chin et al, 2022). The nucleotide mismatches of primers and probe with 730 global CHIKV sequences were analysed in silico.…”

Section: Design Of Chikv-specific Primers and Probementioning

confidence: 99%

A TaqMan minor groove binder probe-based quantitative reverse transcription polymerase chain reaction for detection and quantification of chikungunya virus

Y.Z.

2023

Trop Biomed

View full text Add to dashboard Cite

Chikungunya virus (CHIKV) is a mosquito-borne alphavirus with widespread distribution across the globe. Since 2016, CHIKV re-emerged in several countries including Indian subcontinent and Southeast Asia. A proper diagnostic tool for early diagnosis of CHIKV infection is crucial to facilitate patient management and control virus transmission at the earliest stage of outbreak. Therefore, a TaqMan minor groove binder (MGB) probe-based quantitative reverse transcription polymerase chain reaction (qRT-PCR) assay was developed to detect and quantify the CHIKV. The primers and probe were designed based on a conserved genomic region of 730 global CHIKV sequences that is located between nsP1 and nsP2 genes. The nucleotide mismatches of primers and probe with 730 global CHIKV sequences and 13 alphaviruses were then analysed in silico. In this study, the last 5 nucleotides at 3' end of primers and 5' end of probe were considered to be the critical regions for priming. In silico analysis revealed that the critical regions of primers and probe were at least 99.6% matched with the 730 global CHIKV sequences. Besides, the primers and probe showed at least 5/20 (25.0%) and 4/17 (23.5%) nucleotide mismatches with 13 alphaviruses respectively. The amplification efficiency of qRT-PCR assay was 100.59% (95% CI= 93.06, 109.33) with a R 2 score of 0.957. Its limit of detection (LOD) at 95% probability level was 16.6 CHIKV RNA copies (95% CI= 12.9, 28.9). The qRT-PCR assay was specific to CHIKV without cross-reacting with all dengue virus serotypes, Getah virus, Tembusu virus and Zika virus. The diagnostic results of qRT-PCR assay were perfectly agreed (k=1.000, p=0.003) with a commercial trioplex assay, with sensitivity of 100% (95% CI= 61, 100) and specificity of 100% (95% CI= 44, 100). Overall, the developed qRT-PCR assay is ideal for rapid, sensitive and specific detection as well as quantification of CHIKV.

show abstract

“…The performance of the designed qRT-PCR assay was then compared to the reference assay, Genesig Real-Time qRT-PCR ZIKV Detection Kit (Primerdesign Ltd, United Kingdom). The Genesig Real-Time qRT-PCR ZIKV Detection Kit assay was performed as previously described (Teoh et al, 2020).…”

Section: Evaluation Of Qrt-pcr Assay Using Simulated Clinical Specimensmentioning

confidence: 99%

Development of a TaqMan minor groove binding probe-based quantitative reverse transcription polymerase chain reaction for the detection and quantification of Zika virus

et al. 2022

View full text Add to dashboard Cite

Zika virus (ZIKV) infection has emerged as a global health concern following epidemic outbreaks of severe neurological disorders reported in Pacific and Americas since 2016. Therefore, a rapid, sensitive and specific diagnostic test for ZIKV infection is critical for the appropriate patient management and the control of disease spread. A TaqMan minor groove binding (MGB) probe-based quantitative reverse transcription-polymerase chain reaction (qRT-PCR) assay was developed based on the conserved sequence regions of 463 ZIKV NS2B genes. The designed ZIKV qRT-PCR assay was evaluated for its detection limit, strain coverage and cross-reactivity. We further assessed the clinical applicability of qRT-PCR assay for ZIKV RNA detection using a total 18 simulated clinical specimens. The detection limit of the qRT-PCR assay was 11.276 ZIKV RNA copies at the 95% probability level (probit analysis, p< 0.05). Both Asian and African ZIKV strains were detected by the qRT-PCR assay without cross-reacting with DENV-1, DENV-2, DENV-3, DENV-4, CHIKV, JEV, LGTV, GETV and SINV. The qRT-PCR assay demonstrated a perfect agreement (k = 1.000, P < 0.001) with the reference assay; the sensitivity and specificity of the qRT-PCR assay were 100% (95% CI= 79.6-100) and 100% (95% CI= 43.9-100) respectively. The qRT-PCR assay developed in this study is a useful diagnostic tool for the broad coverage detection and quantification of both the Asian and African ZIKV strains.

show abstract

A reverse transcription loop-mediated isothermal amplification for broad coverage detection of Asian and African Zika virus lineages

Cited by 4 publications

References 63 publications

Development of a Novel Loop Mediated Isothermal Amplification Assay (LAMP) for the Rapid Detection of Epizootic Haemorrhagic Disease Virus

Development of a Novel Loop Mediated Isothermal Amplification Assay (LAMP) for the Rapid Detection of Epizootic Haemorrhagic Disease Virus

A TaqMan minor groove binder probe-based quantitative reverse transcription polymerase chain reaction for detection and quantification of chikungunya virus

Development of a TaqMan minor groove binding probe-based quantitative reverse transcription polymerase chain reaction for the detection and quantification of Zika virus

Contact Info

Product

Resources

About