RT-LAMP Multicenter Study for SARS-CoV-2 Genome Molecular Detection in Brazilian Swab and Saliva Samples
Vanessa Duarte da Costa,
Alanna Calheiros Santos,
Lucas Lima da Silva,
Wilian Jean Wiggers,
Claudia Alexandra Pontes Ivantes,
Danielle Malta Lima,
Jeová Keny Baima Colares,
Deusilene Souza Vieira Dallacqua,
Ana Rita Coimbra Motta-Castro,
Alberto Martín Rivera Dávila,
Sheila Araujo Teles,
Megmar Aparecida dos Santos Carneiro,
Karlla Antonieta Amorim Caetano,
Fernando Antonio Costa Anunciação,
Vanessa Salete de Paula,
Livia Melo Villar,
on behalf of The Brazilian COVID-19 Research Group
Affiliations
Vanessa Duarte da Costa
Brazilian Reference Laboratory of Viral Hepatitis, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro 21040-360, Brazil
Alanna Calheiros Santos
Brazilian Reference Laboratory of Viral Hepatitis, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro 21040-360, Brazil
Lucas Lima da Silva
Brazilian Reference Laboratory of Viral Hepatitis, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro 21040-360, Brazil
Wilian Jean Wiggers
Service of Gastroenterology, Hepatology and Liver Transplantation, Hospital Nossa Senhora das Graças, Curitiba 80810-040, Brazil
Claudia Alexandra Pontes Ivantes
Service of Gastroenterology, Hepatology and Liver Transplantation, Hospital Nossa Senhora das Graças, Curitiba 80810-040, Brazil
Danielle Malta Lima
Graduate Program in Medical Sciences, University of Fortaleza, Fortaleza 60811-905, Brazil
Jeová Keny Baima Colares
Graduate Program in Medical Sciences, University of Fortaleza, Fortaleza 60811-905, Brazil
Deusilene Souza Vieira Dallacqua
Molecular Virology Laboratory, Oswaldo Cruz Foundation, FIOCRUZ, Porto Velho 76812-245, Brazil
Ana Rita Coimbra Motta-Castro
Federal Faculty, University of Mato Grosso do Sul, Campo Grande 79070-900, Brazil
Alberto Martín Rivera Dávila
Computational and Systems Biology Laboratory, Graduate Program in Biodiversity and Health, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro 21040-360, Brazil
Sheila Araujo Teles
Federal Faculty, University of Goiás, Goiânia 74690-900, Brazil
Megmar Aparecida dos Santos Carneiro
Federal Faculty, University of Goiás, Goiânia 74690-900, Brazil
Karlla Antonieta Amorim Caetano
Federal Faculty, University of Goiás, Goiânia 74690-900, Brazil
Fernando Antonio Costa Anunciação
Hospital Getúlio Vargas, Teresina 64001-020, Brazil
Vanessa Salete de Paula
Molecular Virology Laboratory, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro 21040-360, Brazil
Livia Melo Villar
Brazilian Reference Laboratory of Viral Hepatitis, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro 21040-360, Brazil
on behalf of The Brazilian COVID-19 Research Group
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.
