학술논문
Improved oral detection is a characteristic of Omicron infection and has implications for clinical sampling and tissue tropism.
Document Type
Academic Journal
Author
Marais G; Department of Medical Microbiology, University of Cape Town, Cape Town, South Africa; National Health Laboratory Service, Groote Schuur Hospital, Cape Town, South Africa.; Hsiao NY; Department of Medical Virology, University of Cape Town, Cape Town, South Africa; National Health Laboratory Service, Groote Schuur Hospital, Cape Town, South Africa.; Iranzadeh A; Department of Medical Virology, University of Cape Town, Cape Town, South Africa.; Doolabh D; Department of Medical Virology, University of Cape Town, Cape Town, South Africa.; Joseph R; Department of Medical Virology, University of Cape Town, Cape Town, South Africa.; Enoch A; Green Point Diagnostic Virology Laboratory, National Health Laboratory Service, Cape Town, South Africa.; Chu CY; Department of Medical Microbiology, University of Cape Town, Cape Town, South Africa; National Health Laboratory Service, Groote Schuur Hospital, Cape Town, South Africa.; Williamson C; Department of Medical Virology, University of Cape Town, Cape Town, South Africa.; Brink A; Department of Medical Microbiology, University of Cape Town, Cape Town, South Africa; National Health Laboratory Service, Groote Schuur Hospital, Cape Town, South Africa.; Hardie D; Department of Medical Virology, University of Cape Town, Cape Town, South Africa; National Health Laboratory Service, Groote Schuur Hospital, Cape Town, South Africa. Electronic address: diana.hardie@uct.ac.za.
Source
Publisher: Elsevier Science Country of Publication: Netherlands NLM ID: 9815671 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1873-5967 (Electronic) Linking ISSN: 13866532 NLM ISO Abbreviation: J Clin Virol Subsets: MEDLINE
Subject
Language
English
Abstract
Background: The Omicron variant of concern is characterised by more than 50 distinct mutations, most in the spike protein. The implications of these for disease transmission, tissue tropism and diagnostic testing needs study.
Objectives: We evaluated the performance of RT-PCR on saliva (SA) swabs and antigen testing on mid-turbinate MT samples relative to RT-PCR on MT swabs. Patients (n = 453) presenting for outpatient testing at the Groote Schuur Hospital COVID-19 testing centre in Cape Town South Africa were recruited. Participants were recruited during the Delta (n = 304) and Omicron (n = 149) waves.
Results: In 30 confirmed Delta infections, positive percent agreement (PPA) of RT-PCR on saliva was only 73% compared to a composite standard of either MT or SA RT-PCR positivity, with rapid decay by day 3 after symptom onset. In contrast, in the 70 Omicron infections, SA performed as well as, or better than, MT samples up to day 5, with an overall PPA of SA swabs of 96% and MT of 93%. A change in antigen test performance was noted, with PPA of 93% in Delta, but only 68% for Omicron.
Conclusions: Altered shedding kinetics appear to be present in Omicron-infected patients with more viral RNA detectable in saliva. Saliva swabs are a promising alternative to nasal samples, especially early in infection when sampling of both sites could improve detection. Lower sensitivity of antigen tests in Omicron is a concern and requires further study.
(Copyright © 2022 Elsevier B.V. All rights reserved.)
Objectives: We evaluated the performance of RT-PCR on saliva (SA) swabs and antigen testing on mid-turbinate MT samples relative to RT-PCR on MT swabs. Patients (n = 453) presenting for outpatient testing at the Groote Schuur Hospital COVID-19 testing centre in Cape Town South Africa were recruited. Participants were recruited during the Delta (n = 304) and Omicron (n = 149) waves.
Results: In 30 confirmed Delta infections, positive percent agreement (PPA) of RT-PCR on saliva was only 73% compared to a composite standard of either MT or SA RT-PCR positivity, with rapid decay by day 3 after symptom onset. In contrast, in the 70 Omicron infections, SA performed as well as, or better than, MT samples up to day 5, with an overall PPA of SA swabs of 96% and MT of 93%. A change in antigen test performance was noted, with PPA of 93% in Delta, but only 68% for Omicron.
Conclusions: Altered shedding kinetics appear to be present in Omicron-infected patients with more viral RNA detectable in saliva. Saliva swabs are a promising alternative to nasal samples, especially early in infection when sampling of both sites could improve detection. Lower sensitivity of antigen tests in Omicron is a concern and requires further study.
(Copyright © 2022 Elsevier B.V. All rights reserved.)