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. 2023 Jan 6;13(2):210.
doi: 10.3390/diagnostics13020210.

RT-LAMP Multicenter Study for SARS-CoV-2 Genome Molecular Detection in Brazilian Swab and Saliva Samples

Vanessa Duarte da Costa  1 , Alanna Calheiros Santos  1 , Lucas Lima da Silva  1 , Wilian Jean Wiggers  2 , Claudia Alexandra Pontes Ivantes  2 , Danielle Malta Lima  3 , Jeová Keny Baima Colares  3 , Deusilene Souza Vieira Dallacqua  4 , Ana Rita Coimbra Motta-Castro  5 , Alberto Martín Rivera Dávila  6 , Sheila Araujo Teles  7 , Megmar Aparecida Dos Santos Carneiro  7 , Karlla Antonieta Amorim Caetano  7 , Fernando Antonio Costa Anunciação  8   9 , Vanessa Salete de Paula  10 , Livia Melo Villar  1 , On Behalf Of The Brazilian Covid-Research Group
Affiliations

RT-LAMP Multicenter Study for SARS-CoV-2 Genome Molecular Detection in Brazilian Swab and Saliva Samples

Vanessa Duarte da Costa et al. Diagnostics (Basel). .

Abstract

Reverse transcription loop-mediated isothermal amplification (RT-LAMP) is a rapid method that can replace RT-qPCR. A simple molecular assay for SARS-CoV-2 RNA detection in gold-standard diagnosis through swabs and alternative specimens such as saliva could be helpful in promoting genomic surveillance. A multicenter study was conducted to evaluate the RT-LAMP assay method as an alternative for the molecular detection of SARS-CoV-2 lineages in swab and saliva samples. A total of 350 swabs from individuals with (n = 276) or without (n = 74) COVID-19 tested by RT-qPCR were collected. Paired saliva was also collected from 90 individuals who had SARS-CoV-2 RNA that was detectable (n = 30) or undetectable (n = 60) via RT-qPCR. For the RT-LAMP methodology, six primers were used for ORF1 gene amplification. As for SARS-CoV-2 genotyping, 39 swabs had the whole genome sequenced by MinION. The sensitivity of RT-LAMP to the swab was 90.2%. For the swab samples with Ct ≤ 30, the sensitivity improved by 96%. Considering saliva with Ct ≤ 30 in RT-qPCR testing, the RT-LAMP sensitivity was 100%. The RT-LAMP specificity was 100% for both the swab and saliva samples. This RT-LAMP assay was capable of detecting all the SARS-CoV-2 lineages circulating in the Brazilian swab samples. The RT-LAMP method has significant potential for use in clinical routines since it was capable of detecting SARS-CoV-2 RNA in swab and saliva samples.

Keywords: COVID-19; LAMP; SARS-CoV-2; diagnosis.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Flowchart demonstrating sensitivity and specificity results for saliva molecular assays.
Figure 2
Figure 2
Genotyping and prevalence of SARS-CoV-2 variants in swab samples.
See this image and copyright information in PMC

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