Evaluation of Saliva as an Alternative Specimen for SARS-CoV-2 RT-PCR Testing in Mass Screening Settings in Enugu State

Nasopharyngeal swab (NPS) collection for SARS-CoV-2 RT-PCR testing presents practical challenges in mass screening settings due to the need for trained healthcare workers, PPE consumption, and discomfort experienced by subjects. Self-collected saliva samples have emerged as a potentially viable, less invasive alternative. This study evaluated the diagnostic agreement between saliva and NPS specimens for SARS-CoV-2 RT-PCR detection in a mass community screening campaign in Enugu State, Southeast Nigeria. Paired saliva and NPS samples were collected simultaneously from 200 consenting adult volunteers during a community-based screening exercise. Both specimens were processed using the same Roche COBAS SARS-CoV-2 assay. Cycle threshold (Ct) value correlation, percent positive agreement, and Cohen's kappa coefficient were calculated. SARS-CoV-2 positivity was 14.5% by NPS and 12.5% by saliva. Positive percent agreement was 86.2%, with Cohen's kappa of 0.82 indicating strong agreement. Saliva Ct values were on average 2.1 cycles higher than corresponding NPS samples, suggesting marginally lower viral load detection. Saliva sensitivity was 86.2% relative to NPS, with specificity of 98.8%. The study supports the use of self-collected saliva specimens as an acceptable alternative for population-level SARS-CoV-2 surveillance activities in Enugu State, with appropriate Ct value interpretation guidance. Keywords: saliva, SARS-CoV-2, RT-PCR, mass screening, Enugu State.