Evaluation of colorimetric RT-LAMP for screening of SARS-CoV-2 in untreated wastewater

被引：12

作者：

Akter, Jesmin ^{[1
,2
,3
]}

Smith, Wendy J. M. ^{[3
]}

Gebrewold, Metasebia ^{[3
]}

Kim, Ilho ^{[1
,2
]}

Simpson, Stuart L. ^{[4
]}

Bivins, Aaron ^{[5
]}

Ahmed, Warish ^{[3
,6
]}

机构：

[1] Univ Sci & Technol, Dept Civil & Environm Engn, Daejeon, South Korea

[2] Korea Inst Civil Engn & Bldg Technol KICT, Dept Environm Res, Goyang, South Korea

[3] CSIRO Environm, Ecosci Precinct, 41 Boggo Rd, Dutton Pk, Qld 4102, Australia

[4] CSIRO Environm, Lucas Heights, NSW 2234, Australia

[5] Louisiana State Univ, Dept Civil & Environm Engn, Baton Rouge, LA 70803 USA

[6] Ecosci Precinct, 41 Boggo Rd, Dutton Pk, Qld 4102, Australia

来源：

SCIENCE OF THE TOTAL ENVIRONMENT | 2024年 / 907卷

基金：

新加坡国家研究基金会;

关键词：

RT-LAMP; RT-qPCR; SARS-CoV-2; Surveillance; Wastewater; COVID-19; MEDIATED ISOTHERMAL AMPLIFICATION; POLYMERASE-CHAIN-REACTION; QUANTITATIVE DETECTION; RAPID DETECTION; COVID-19; SAMPLES; ASSAY; CHIP; PCR;

D O I：

10.1016/j.scitotenv.2023.167964

中图分类号：

X [环境科学、安全科学];

学科分类号：

08 ; 0830 ;

摘要：

This study compared reverse transcription-loop-mediated isothermal amplification (RT-LAMP) and three reverse transcription-quantitative polymerase chain reaction (RT-qPCR) assays targeting the N and E genes of the SARSCoV-2 genome for detecting RNA in untreated wastewater samples. RT-qPCR assays exhibited consistent amplification down to 2 x 102 GC/reaction, with greater analytical sensitivity at 2 x 101 GC/reaction by US CDC N1 and US CDC N2 assays. In contrast, RT-LAMP exhibited lower sensitivity, detecting SARS-CoV-2 only at or above 2 x 103 GC/reaction. For SARS-CoV-2 seeded wastewater samples, the US CDC N1 assay exhibited greater analytical sensitivity than the US CDC N2, E_Sarbeco, and RT-LAMP assays. Out of 30 wastewater samples, RTqPCR detected endogenous SARS-CoV-2 RNA in 29 samples, while RT-LAMP identified 27 positive samples, with 20 displaying consistent amplifications in all three RT-LAMP technical replicates. Agreement analysis revealed a strong concordance between RT-LAMP and the US CDC N1 and E_Sarbeco RT-qPCR assays (kappa = 0.474) but lower agreement with the US CDC N2 RT-qPCR assay (kappa = 0.359). Quantification of SARS-CoV-2 RNA in positive samples revealed a strong correlation between the US CDC N1 and E_Sarbeco assays, while the US CDC N1 and US CDC N2 assays exhibited weak correlation. Logistic regression analysis indicated that RT-LAMP results correlated with RNA quantified by the US CDC N1 and E_Sarbeco assays, with 95 % limits of detection of 3.99 and 3.47 log10 GC/15 mL, respectively. In conclusion, despite lower sensitivity compared to RT-qPCR assays, RTLAMP may offer advantages for wastewater surveillance, such as rapid results (estimated as twice as fast), and simplicity, making it a valuable tool in the shifting landscape of COVID-19 wastewater surveillance. Furthermore, LAMP positive wastewater samples might be prioritized for SARS-CoV-2 sequencing due to reduced analytical sensitivity. These findings support the use of RT-LAMP as a specific and efficient method for screening wastewater samples for SARS-CoV-2, particularly in resource-limited settings.

引用

页数：9

共 61 条

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