Alternative SARS-CoV-2 detection protocol from self-collected saliva for mass diagnosis and epidemiological studies in low-incoming regions

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Rolim de Oliveira, Luana Prado ; Cabral, Aline Diniz ; dos Santos Carmo, Andreia Moreira ; Duran, Adriana Feliciano ; Fermino, Diego Marin ; Luciano Veiga, Glaucia Raquel ; Aguiar Alves, Beatriz da Costa ; Santana, Carla Moreira ; Garcia, Felipe Baena ; Santos, Edmar Silva ; Jordao, Felipe Trovalim ; Siqueira, Andressa Moreira ; de Campos, Ivana Barros ; Colpas, Daniela Rodrigues ; Almeida, Fernanda Nascimento ; Affonso Fonseca, Fernando Luiz ; Speranca, Marcia Aparecida

• Document type: Journal article
• Source: Journal of Virological Methods; v. 300, p. 8-pg., 2022-02-01.

Abstract

Until mass vaccination befalls, control of the new betacoronavirus-associated severe acute respiratory syndrome pandemic (SARS-CoV-2) is based on decreasing virus circulation by social distancing and blocking transmission foci after diagnosis. Globally adopted SARS-CoV-2 diagnostic criteria embrace viral RNA detection by quantitative reverse-transcription polymerase chain reaction (qRT-PCR) on nasopharynx secretions, which requires healthcare facilities and specialized personnel for sample collection. To develop an alternative protocol, hydrophilic cotton as the material and saliva as the source for biological sample collection in qRT-PCR/RTendpoint-PCR SARS-CoV-2 diagnostic methods prepared with local consumables were evaluated using 99 archived nasopharynx samples previously diagnosed as positive for SARS-CoV-2 and 111 prospective saliva samples pared with nasopharynx samples from patients attending the local reference ABC Medical School diagnostic laboratory. The kappa agreement coefficient between the SARS-CoV-2 qRT-PCR and RT-endpoint-PCR was k = 0.97 (95 % CI 0.92 1.00) and k = 0.90 (95 % CI 0.81 0.99), respectively, on SARS-CoV-2-positive archived samples, with the initial qRT-PCR CT under 25. The agreement coefficient of the SARS-CoV-2 alternative saliva diagnostic protocol, when used to test the paired nasopharynx samples, was k = 0.79 (95 % CI 0.56-1,00). These data support that the SARS-CoV-2 diagnostic assay based on self-collected saliva on cotton represents an alternative protocol for mass diagnosis and epidemiological studies in low-income regions. (AU)

• FAPESP's process: 19/11384-0 - Investigation of alphaviruses in hematophagous insects
• Grantee: Luana Prado Rolim de Oliveira
• Support Opportunities: Scholarships in Brazil - Master