Surveillance testing using salivary RT-PCR for SARS-CoV-2 in managed quarantine facilities in Australia: A laboratory validation and implementation study.
Adam Jenney, Doris Chibo, Mitch Batty, Julian Druce, Robert Melvin, Andrew Stewardson, Amanda Dennison, Sally Symes, Paul Kinsella, Thomas Tran, Charlene Mackenzie, Douglas Johnson, Irani Thevarajan, Christian McGrath, Amelia Matlock, Jacqueline Prestedge, Megan Gooey, Janine Roney, Joanne Bobbitt, Sarah Yallop, Mike Catton, Deborah A Williamson
Author Information
Adam Jenney: Microbiology Unit, Alfred Hospital, Melbourne, Victoria, Australia.
Doris Chibo: Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia.
Mitch Batty: Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia.
Julian Druce: Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia.
Robert Melvin: Hotel Support Services, Alfred Hospital, Melbourne, Victoria, Australia.
Andrew Stewardson: Department of Infectious Diseases, Alfred Hospital, Melbourne, Victoria, Australia.
Amanda Dennison: Microbiology Unit, Alfred Hospital, Melbourne, Victoria, Australia.
Sally Symes: Pathology, Engagement and Testing, Victorian Department of Health, Melbourne, Victoria, Australia.
Paul Kinsella: Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia.
Thomas Tran: Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia.
Charlene Mackenzie: Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia.
Douglas Johnson: Department of Infectious Diseases, Royal Melbourne Hospital, Melbourne, Victoria, Australia.
Irani Thevarajan: Department of Infectious Diseases, Royal Melbourne Hospital, Melbourne, Victoria, Australia.
Christian McGrath: Department of Infectious Diseases, Northern Health, Melbourne, Victoria, Australia.
Amelia Matlock: Pathology, Engagement and Testing, Victorian Department of Health, Melbourne, Victoria, Australia.
Jacqueline Prestedge: Department of Infectious Diseases, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia.
Megan Gooey: Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia.
Janine Roney: Clinical Research Unit, Department of Infectious Diseases, Alfred Hospital, Melbourne, Victoria, Australia.
Joanne Bobbitt: Pathology, Engagement and Testing, Victorian Department of Health, Melbourne, Victoria, Australia.
Sarah Yallop: Pathology, Engagement and Testing, Victorian Department of Health, Melbourne, Victoria, Australia.
Mike Catton: Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia.
Deborah A Williamson: Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia.
Background: Regular repeat surveillance testing is a strategy to identify asymptomatic individuals with SARS-CoV-2 infections in high-risk work settings to prevent onward community transmission. Saliva sampling is less invasive compared to nasal/oropharyngeal sampling, thus making it suitable for regular testing. In this multi-centre evaluation, we aimed to validate RT-PCR using salivary swab testing of SARS-CoV-2 for large-scale surveillance testing and assess implementation amongst staff working in the hotel quarantine system in Victoria, Australia. Methods: A multi-centre laboratory evaluation study was conducted to systematically validate the and clinical performance of salivary swab RT-PCR for implementation of SARS-CoV-2 surveillance testing. Analytical sensitivity for multiple RT-PCR platforms was assessed using a dilution series of known SARS-CoV-2 viral loads, and assay specificity was examined using a panel of viral pathogens other than SARS-CoV-2. In addition, we tested capacity for large-scale saliva testing using a four-sample pooling approach, where positive pools were subsequently decoupled and retested. Regular, frequent self-collected saliva swab RT-PCR testing was implemented for staff across fourteen quarantine hotels. Samples were tested at three diagnostic laboratories validated in this study, and results were provided back to staff in real-time. Findings: The agreement of self-collected saliva swabs for RT-PCR was 84.5% (95% CI 68.6 to 93.8) compared to RT-PCR using nasal/oropharyngeal swab samples collected by a healthcare practitioner, when saliva samples were collected within seven days of symptom onset. Between 7th December 2020 and 17th December 2021, almost 500,000 RT-PCR tests were performed on saliva swabs self-collected by 102 staff working in quarantine hotels in Melbourne. Of these, 20 positive saliva swabs were produced by 13 staff (0.004%). The majority of staff that tested positive occurred during periods of community transmission of the SARS-CoV-2 Delta variant. Interpretation: Salivary RT-PCR had an acceptable level of agreement compared to standard nasal/oropharyngeal swab RT-PCR within early symptom onset. The scalability, tolerability and ease of self-collection highlights utility for frequent or repeated testing in high-risk settings, such as quarantine or healthcare environments where regular monitoring of staff is critical for public health, and protection of vulnerable populations. Funding: This work was funded by the Victorian Department of Health.
