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

Costa, Vanessa Duarte da; Santos, Alanna Calheiros; Silva, Lucas Lima da; Wiggers, Wilian Jean; Ivantes, Claudia Alexandra Pontes; Lima, Danielle Malta; Colares, Jeová Keny Baima; Dallacqua, Deusilene Souza Vieira; Motta-Castro, Ana Rita Coimbra; Dávila, Alberto M. R.; Teles, Sheila Araújo; Carneiro, Megmar Aparecida dos Santos; Caetano, Karlla Antonieta Amorim; Anunciação, Fernando Antonio Costa; Paula, Vanessa Salete de; Villar, Lívia Melo

doi:10.3390/diagnostics13020210

Cited by 5 publications

(2 citation statements)

References 43 publications

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“…The use of this type of sample represents an advantage by reducing invasiveness (32,33). In addition, pilot studies could be implemented in difficult-to-access geographical areas for the identification of vulnerable groups (20).…”

Section: Discussionmentioning

confidence: 99%

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Reverse transcription loop‑mediated isothermal amplification has a high performance in the detection of SARS‑CoV‑2 in saliva samples and nasal swabs from asymptomatic and symptomatic individuals

Reyes‑Morales,

Segundo‑Ibañez,

Flores‑de Los Ángeles

et al. 2023

Exp Ther Med

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The detection of coronavirus disease 2019 cases represents a significant challenge at the epidemiological level. Limitations exist in effectively detecting asymptomatic cases, achieving good follow-up in hospitals without the infrastructure for reverse transcription-quantitative PCR (RT-qPCR) or in difficult-to-access areas and developing methods with the need for less invasive sampling procedures. Therefore, the present study evaluated the performance of the direct reverse transcription loop-mediated isothermal amplification (RT-LAMP) test for detecting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the saliva and nasal samples of asymptomatic individuals belonging to the university population. In addition, this test was also assessed for effectiveness in symptomatic individuals referred from a hospital with poor infrastructure in molecular biology and located outside the urban area. The RT-LAMP assay was compared with the results obtained from the RT-qPCR nasopharyngeal swab test, where the diagnosis was confirmed by lateral flow immunoassay test for rapid antigen detection. A total of 128 samples were analyzed, of which 43% were symptomatic positive individuals, 25% were asymptomatic positive individuals and 32% were SARS-CoV2-negative control individuals. Among positive individuals, no differences were found between the Cq values determined by RT-qPCR. A sensitivity of 96.5% and a specificity of 97.6% was reported for the detection of SARS-CoV-2 in symptomatic individuals by salivary and nasal RT-LAMP, as well as a sensitivity of 100% and a specificity of 97.6% for the detection of SARS-CoV-2 in asymptomatic individuals. These findings indicated that performance of the direct RT-LAMP test using saliva and nasal samples has high sensitivity and specificity, which in turn suggest that it is a viable and reliable alternative for use in epidemiological monitoring.

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Section: Discussionmentioning

confidence: 99%

“…For the diagnosis of SARS-CoV-2 by RT-LAMP, a sensitivity of >80% has been reported based on saliva, nasal or nasopharyngeal samples with or without the previous step of viral RNA extraction (19,20), which holds an advantage over other tests. In Mexico, there are few diagnostic studies regarding the detection of SARS-CoV-2 with RT-LAMP.…”

Section: Introductionmentioning

confidence: 99%

Reverse transcription loop‑mediated isothermal amplification has a high performance in the detection of SARS‑CoV‑2 in saliva samples and nasal swabs from asymptomatic and symptomatic individuals

Reyes‑Morales,

Segundo‑Ibañez,

Flores‑de Los Ángeles

et al. 2023

Exp Ther Med

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Rapid detection of bat coronaviruses from fecal samples using loop-mediated isothermal amplification assay in the field

Tsengel,

Wu,

Chen

2024

Journal of Virological Methods

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In silico thermodynamic evaluation of the effectiveness of RT-LAMP primers to SARS-CoV-2 variants detection

Miranda,

Alves,

do Monte-Neto

et al. 2023

Preprint

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Viral mutations are the primary cause of mismatches in primer-target hybridisation, affecting the sensibility of molecular techniques, potentially leading to detection dropouts. Despite its importance, little is known about the quantitative effect of mismatches in primer-target hybridisation. We use up-to-date and highly detailed thermodynamic model parameters of DNA mismatches to evaluate the sensibility to variants of SARS-CoV-2 RT-LAMP primers. We aligned 18 RT-LAMP primer sets, which were underwent clinical validation, to the genomes of Wuhan strain (ws), 7 variants and 4 subvariants, and calculated hybridisation temperatures allowing up to three consecutive mismatches. We calculate the coverage when the mismatched melting temperature falls by more than 5C in comparison to the matched alignments. If no mismatches are considered, the average coverage found would be 94% for ws, falling the lowest value for Omicron: 84%. However, considering mismatches the coverage is much higher: 97% (ws) to 88% (Omicron). Stabilizing mismatches (higher melting temperatures), account for roughly 1/3 of this increase. The number of primer dropouts increases for new each variant, however the effect is much less severe if mismatches are considered. We suggest using melting temperature calculations to continuously assess the trend of primer dropouts.

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

Cited by 5 publications

References 43 publications

Reverse transcription loop‑mediated isothermal amplification has a high performance in the detection of SARS‑CoV‑2 in saliva samples and nasal swabs from asymptomatic and symptomatic individuals

Reverse transcription loop‑mediated isothermal amplification has a high performance in the detection of SARS‑CoV‑2 in saliva samples and nasal swabs from asymptomatic and symptomatic individuals

Rapid detection of bat coronaviruses from fecal samples using loop-mediated isothermal amplification assay in the field

In silico thermodynamic evaluation of the effectiveness of RT-LAMP primers to SARS-CoV-2 variants detection

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