Performance of saliva and mid-turbinate swabs for detection of the beta variant in South Africa

Chu, Chun Yat; Marais, Gert; Opperman, C J; Doolabh, Deelan; Iranzadeh, Arash; Marais, C.; Cox, Helen; Williamson, Carolyn; Hardie, Diana; Brink, Adrian

doi:10.1016/s1473-3099(21)00405-9

Cited by 14 publications

(13 citation statements)

References 4 publications

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“…Therefore, the use of complementary tools, for example, RT‐PCR screening, for the detection of VOC is important to monitor their transmission and circulation, as similarly described in Vogels et al 1 This method allowed not only assessment of the presence/absence of VOC in approximately 85% of the positive samples but also monitored the emergence and dominance of Gamma between March and July 2021, which is consistent with studies using sequencing data 10 . A recent study showed that saliva is also highly sensitive for detecting Beta variants 11 …”

Section: Discussionsupporting

confidence: 70%

See 1 more Smart Citation

Use of saliva and RT‐PCR screening for SARS‐CoV‐2 variants of concern: Surveillance and monitoring

Zerbinati

Palmieri

Schwab

et al. 2022

Journal of Medical Virology

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Genomic surveillance has been applied since the beginning of the COVID-19 pandemic to track the spread of the virus, leading to the characterization of multiple SARS-CoV-2 variants, including variants of concern (VOC). Although sequencing is the standard method, a rapid molecular test for screening and surveillance of VOC is considered for detection. Furthermore, using alternative saliva as specimen collection facilitates the implementation of a less invasive, self-collected sample.In this study, we applied a combinatory strategy of saliva collection and reverse transcription polymerase chain reaction (RT-PCR) for SARS-CoV-2 VOC detection.Saliva samples from patients attending a tertiary hospital with suspected COVID-19 were collected and SARS-CoV-2 RNA was detected using SARS-CoV-2 RT-qPCR reagent kit (PerkinElmer). Positive saliva samples were screened for SARS-CoV-2 VOC with previously described RT-PCR for Alpha, Beta, and Gamma variants. Saliva samples were positive in 171 (53%) of 324 tested. A total of 108 (74%) from positive samples were also positive for VOC by RT-PCR screening. Those samples were found between January and August 2021. This approach allowed us to successfully use an alternative and complementary tool to genomic surveillance to monitor the circulation of SARS-CoV-2 VOC in the studied population.

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Section: Discussionsupporting

confidence: 70%

“…10 A recent study showed that saliva is also highly sensitive for detecting Beta variants. 11 Saliva sampling has been increasingly used as an alternative to the standard nasopharyngeal swab for the detection of SARS-CoV-2.…”

Section: Resultsmentioning

confidence: 99%

Use of saliva and RT‐PCR screening for SARS‐CoV‐2 variants of concern: Surveillance and monitoring

Zerbinati

Palmieri

Schwab

et al. 2022

Journal of Medical Virology

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“…Although nasopharyngeal swabs (NPS) are the standard for the detection of SARS-CoV-2 by most researchers, collection requires the use of trained professionals, can cause discomfort to the patients, and may pose greater risks to health care workers during sample collection ( 1 – 4 ). Midturbinate swabs (MTS) are sometimes used as an alternative to NPS to reduce patient discomfort and occupational exposures to health care workers ( 4 – 6 ). NPS is inserted into the nostril with a distance approximating that from the patient’s nostril to the ear, and anterior nasal swabs are inserted to a depth of one to one and a half centimeters, a MTS represents a less invasive alternative to the NPS and is inserted to a depth of about two centimeters ( 1 ).…”

Section: Introductionmentioning

confidence: 99%

Comparison of Saliva and Midturbinate Swabs for Detection of SARS-CoV-2

et al. 2022

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The findings of this manuscript are increasingly important with new variants that appear to have shorter incubation periods emerging, which may be more prone to detection in saliva before detection in nasal swabs. Therefore, there is an urgent need to provide the science to support the use of a detection method that is highly sensitive and widely acceptable to the public to improve screening rates and early detection.

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“…Studies comparing paired specimen types in the same person at the same timepoint have found that cycle threshold (Ct, a proxy for viral load) values can differ significantly between specimen types. [14][15][16][17] In some cases, viral loads in one specimen type are low or even absent while viral loads in another type may be high. 16 Viral variant plays a role too; one study 15 suggested that healthcare-worker-acquired mid-turbinate (MT) swabs had significantly better performance than self-collected oral swabs for Beta and Delta variants but not Omicron.…”

Section: Introductionmentioning

confidence: 99%

Extreme differences in SARS-CoV-2 viral loads among respiratory specimen types during presumed pre-infectious and infectious periods

Winnett

Akana

Shelby

et al. 2022

Preprint

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Background. Screening testing, often via self-collected specimens, remains a key strategy to detect infections early and prevent SARS-CoV-2 transmission, and to enable earlier initiation of treatment. However, which specimen type best detects the earliest days of infection remains controversial. Further, the analytical sensitivity of diagnostic tests must also be considered, as viral loads below a test's limit of detection (LOD) are likely to yield false-negative results. Comparisons of quantitative, longitudinal SARS-CoV-2 viral-load timecourses in multiple specimen types can determine the best specimen type and test analytical sensitivity for earliest detection of infection. Methods. We conducted a COVID-19 household transmission study between November 2021 and February 2022 that enrolled 228 participants and analyzed 6,825 samples using RT-qPCR to quantify viral-load timecourses in three specimen types (saliva [SA], anterior-nares swab [ANS], and oropharyngeal swab [OPS]). From this study population, 14 participants enrolled before or at the incidence of infection with the Omicron variant. We compared the viral loads in specimens collected from each person at the same timepoint, and the longitudinal viral load timecourses from each participant. Using these viral loads, we inferred the clinical sensitivity of each specimen type to detect infected, pre-infectious and infectious individuals (based on presumably infectious viral load levels) using assays with a range of analytical sensitivities. We also inferred the clinical sensitivity of computationally contrived specimen types representing combinations of single specimen types. Results. We found extreme differences (up to 109 copies/mL) in viral loads between paired specimen types in the same person at the same timepoint, and that longitudinal viral load timecourses across specimen types did not correlate. Because of this lack of correlation, infectious viral loads were often observed in different specimen types asynchronously throughout the course of the infection. In the first 4 days of infection, no single specimen type was inferred to achieve >95% detection of infected or infectious individuals, even with the highest analytical sensitivity assays. In nearly all participants (11/14), a rise in ANS viral loads was delayed (as many as 7 days) relative to SA and OPS. We also observed that ANS and OPS had the most complementary viral load timecourses, resulting in optimal inferred performance with a computationally contrived combined anterior nares-oropharyngeal (AN-OP) swab specimen type. The combination AN-OP swab had superior inferred clinical sensitivity the first 8 days of infection with both high- and low-analytical-sensitivity assays. This AN-OP swab was also inferred to significantly improve detection of pre-infectious and infectious individuals over any single specimen type. Conclusion. Our work demonstrates that the viral load in one specimen type cannot reliably predict the viral load in another specimen type. Combination specimen types may offer a more robust approach for earliest detection of new variants and respiratory viruses when viral kinetics are still unknown.

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Performance of saliva and mid-turbinate swabs for detection of the beta variant in South Africa

Cited by 14 publications

References 4 publications

Use of saliva and RT‐PCR screening for SARS‐CoV‐2 variants of concern: Surveillance and monitoring

Use of saliva and RT‐PCR screening for SARS‐CoV‐2 variants of concern: Surveillance and monitoring

Comparison of Saliva and Midturbinate Swabs for Detection of SARS-CoV-2

Extreme differences in SARS-CoV-2 viral loads among respiratory specimen types during presumed pre-infectious and infectious periods

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