Comparison between Saliva and Nasopharyngeal Swabs for the Rapid Detection of Respiratory Viruses Using the Roche Cobas® Liat® Polymerase Chain Reaction System in Rural Guatemala

• Published in: The American journal of tropical medicine and hygiene Vol. 113; no. 2; pp. 334 - 337
• Main Authors: Paiz-Reyes, Claudia, Arias, Kareen, del Cid-Villatoro, Julio, Vásquez, Daniel, Gomez, Melissa, Rojop, Neudy, Mejia, Wanda, Lamb, Molly M., Chu, May, Calvimontes Barrientos, Diva M., Asturias, Edwin J., Olson, Daniel
• Format: Journal Article
• Language: English
• Published: United States Institute of Tropical Medicine 06.08.2025
• Subjects: Adolescent; Adult; Aged; COVID-19 - diagnosis; COVID-19 - epidemiology; COVID-19 - virology; Female; Guatemala - epidemiology; Humans; Influenza; Influenza A virus - genetics; Influenza A virus - isolation & purification; Influenza B virus - genetics; Influenza B virus - isolation & purification; Influenza, Human - diagnosis; Influenza, Human - virology; Male; Middle Aged; Nasopharynx - virology; Polymerase chain reaction; Respiratory syncytial virus; Respiratory Syncytial Virus Infections - diagnosis; Respiratory Syncytial Virus Infections - virology; Respiratory Syncytial Virus, Human - genetics; Respiratory Syncytial Virus, Human - isolation & purification; Rural Population; Saliva - virology; SARS-CoV-2 - genetics; SARS-CoV-2 - isolation & purification; Sensitivity and Specificity; Severe acute respiratory syndrome coronavirus 2; Young Adult; Guatemala
• ISSN: 0002-9637; 1476-1645; 1476-1645
• DOI: 10.4269/ajtmh.24-0184

We evaluated the performance of saliva compared with nasopharyngeal (NP) swabs for the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), influenza A/B, and respiratory syncytial virus (RSV) using the Roche cobas ® Liat ® point-of-care platform (Roche, Basel, Switzerland). Within an existing adult cohort in Guatemala, consenting participants with influenza-like illness (ILI) provided paired saliva and NP swabs, which were tested for SARS-CoV-2, influenza A/B, and RSV on the Liat platform. Among 138 ILI episodes from 123 enrolled subjects, 35/124 (28.2%), 5/135 (3.7%), 6/135 (4.4%), and 7/135 (5.2%) samples were reverse transcription polymerase chain reaction-positive for SARS-CoV-2, influenza A, influenza B, and RSV, respectively. For SARS-CoV-2, saliva/NP agreement was 90.3% (Cohen’s kappa = 0.731); 12 (9.7%) of the samples were discordant (three saliva-positive only, nine NP-positive only); and the median cycle threshold (Ct) for saliva was higher than that for NP (26.53 versus 23.54; P = 0.005). In our setting, saliva had a lower viral load correlate (Ct) but maintained a good correlation with NP swabs for the detection of SARS-CoV-2 on the Liat platform.