Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 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.

PubMed Disclaimer

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

References

    1. Zhu N., Zhang D., Wang W., Li X., Yang B., Song J., Zhao X., Huang B., Shi W., Lu R., et al. A Novel Coronavirus from Patients with Pneumonia in China, 2019. N. Engl. J. Med. 2020;382:727–733. doi: 10.1056/NEJMoa2001017. - DOI - PMC - PubMed
    1. Wang C., Horby P.W., Hayden F.G., Gao G.F. A novel coronavirus outbreak of global health concern. Lancet. 2020;395:470–473. doi: 10.1016/S0140-6736(20)30185-9. - DOI - PMC - PubMed
    1. World Health Organization Coronavirus (COVID-19) Dashboard. [(accessed on 16 September 2022)]. Available online: https://covid19.who.int/
    1. Wang Y., Kang H., Liu X., Tong Z. Combination of RT-qPCR testing and clinical features for diagnosis of COVID-19 facilitates management of SARS-CoV-2 outbreak. J. Med. Virol. 2020;92:538–539. doi: 10.1002/jmv.25721. - DOI - PMC - PubMed
    1. Khurshid Z., Asiri F.Y.I., Al Wadaani H. Human Saliva: Non-Invasive Fluid for Detecting Novel Coronavirus (2019-nCoV) Int. J. Environ. Res. Public Health. 2020;17:2225. doi: 10.3390/ijerph17072225. - DOI - PMC - PubMed