Diagnostic Sensitivity of Saliva and Other Respiratory Tract Samples of SARS-CoV-2 Variants in Patients with COVID-19

Panchali, Merlin Jayalal Lawrence; Kim, Choon-Mee; Lee, Yu‐Mi; Seo, Jun-Won; Kim, Da Young; Yun, Na Ra; Kim, Dong-Min

doi:10.1128/spectrum.03076-22

Cited by 4 publications

(1 citation statement)

References 29 publications

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“…This study was conducted before the emergence of the Omicron variant. Omicron and similar emerging variants should have a higher detection rate through SalivaDirect than through NPS due to having different tropism and a higher detection rate in saliva ( 22 , 23 ). Studies must address these concerns to help us better prepare for future outbreaks and reemergence of respiratory diseases such as COVID-19.…”

Section: Discussionmentioning

confidence: 99%

SalivaDirect: an alternative to a conventional RNA extraction protocol for molecular detection of SARS-CoV-2 in a clinical setting

Uddin,

Hossain,

Ami

et al. 2024

Microbiol Spectr

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Severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) continues to spread and evolve, giving rise to new surges in cases and deaths. Although nasopharyngeal swab (NPS) samples are the gold standard for diagnosing SARS-CoV2, NPS sampling is invasive and requires skilled staff, specialized transport medium, and nucleic acid extraction. The SalivaDirect method uses saliva samples and a simplified, flexible approach to overcome these drawbacks. In our study conducted at the COVID-19 Screening Unit of the Dhaka Hospital of icddr,b (International Centre for Diarrheal Disease Research, Bangladesh), the diagnostic performance of SalivaDirect and NPS was compared using paired samples. SARS-CoV2 was detected by performing RT-qPCR using RNA extracted from saliva samples with the SalivaDirect method and from the NPS with extracted RNA. A total of 200 participants were enrolled from February to March 2021, among whom 78 (39.0%) tested positive for SAR-CoV2 from at least one sample. Among the 78 participants testing positive, 65 (83.3%) tested positive in both specimens, eight (10.3%) tested positive only in NPS, and five (6.4%) tested positive only in saliva. SalivaDirect had a sensitivity of 89.0% and specificity of 96.1%, with NPS as the reference test. The sensitivity of NPS and SalivaDirect was 93.6% and 89.7% respectively, with a composite reference standard (where patients are defined as positive if tested positive in either method) as the reference. Our findings demonstrated that the SalivaDirect method can be used as an alternative to NPS in our clinical setting and also supports the use of SalivaDirect in other settings. IMPORTANCE Affordable and accessible tests for COVID-19 allow for timely disease treatment and pandemic management. SalivaDirect is a faster and easier method to implement than NPS sampling. Patients can self-collect saliva samples at home or in other non-clinical settings without the help of a healthcare professional. Sample processing in SalivaDirect is less complex and more adaptable than in conventional nucleic acid extraction methods. We found that SalivaDirect has good diagnostic performance and is ideal for large-scale testing in settings where supplies may be limited or trained healthcare professionals are unavailable.

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Section: Discussionmentioning

confidence: 99%

SalivaDirect: an alternative to a conventional RNA extraction protocol for molecular detection of SARS-CoV-2 in a clinical setting

Uddin,

Hossain,

Ami

et al. 2024

Microbiol Spectr

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SARS-CoV-2 Variants May Affect Saliva RT-PCR Assay Sensitivity

Chwa,

Shin,

Lee

et al. 2024

The Journal of Applied Laboratory Medicine

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Background Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) variants demonstrate predilection for different regions of the respiratory tract. While saliva-based reverse transcription-polymerase chain reaction (RT-PCR) testing is a convenient, cost-effective alternative to nasopharyngeal swabs (NPS), few studies to date have investigated whether saliva sensitivity differs across variants of concern. Methods SARS-CoV-2 RT-PCR was performed on paired NPS and saliva specimens collected from individuals with acute coronavirus disease 2019 (COVID-19) symptoms or exposure to a COVID-19 household contact. Viral genome sequencing of NPS specimens and Los Angeles County surveillance data were used to determine the variant of infection. Saliva sensitivity was calculated using NPS-positive RT-PCR as the reference standard. Factors contributing to the likelihood of saliva SARS-CoV-2 RT-PCR positivity were evaluated with univariate and multivariable analyses. Results Between June 2020 and December 2022, 548 saliva samples paired with SARS-CoV-2 positive NPS samples were tested by RT-PCR. Overall, saliva sensitivity for SARS-CoV-2 detection was 61.7% (95% CI, 57.6%–65.7%). Sensitivity was highest with Delta infection (79.6%) compared to pre-Delta (58.5%) and Omicron (61.5%) (P = 0.003 and 0.01, respectively). Saliva sensitivity was higher in symptomatic individuals across all variants compared to asymptomatic cases [pre-Delta 80.6% vs 48.3% (P < 0.001), Delta 100% vs 72.5% (P = 0.03), Omicron 78.7% vs 51.2% (P < 0.001)]. Infection with Delta, symptoms, and high NPS viral load were independently associated with 2.99-, 3.45-, and 4.0-fold higher odds of SARS-CoV-2 detection by saliva-based RT-PCR (P = 0.004, <0.001, and <0.001), respectively. Conclusions As new variants emerge, evaluating saliva-based testing approaches may be crucial to ensure effective virus detection.

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Correlation of patient symptoms with SARS-CoV-2 Omicron variant viral loads in nasopharyngeal and saliva samples and their influence on the performance of rapid antigen testing

Shiraishi,

Chong,

Goto

et al. 2024

Microbiol Spectr

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Evaluating SARS-CoV-2 viral loads in nasopharyngeal (NP) and saliva samples, factors affecting viral loads, and the performance of rapid antigen testing (RAT) have not been comprehensively conducted during SARS-CoV-2 Omicron epidemic. This prospective study included outpatients enrolled during Omicron variant period in Japan. Paired NP swab and saliva samples were collected to measure viral loads by reverse transcription-quantitative polymerase chain reaction (RT-qPCR). The correlation between viral loads and clinical symptoms was examined. The performance of an immunochromatography-based RAT kit was also assessed. A total of 153 patients tested within 3 days of symptom onset were included. The mean viral load was 5.60 log 10 copies/test and 3.65 log 10 copies/test in NP and saliva samples, respectively, resulting in a significant difference ( P < 0.0001). Fever over 37°C (axillary temperature) and total number of symptoms other than fever were identified as independent factors positively correlated with the viral loads in both NP and saliva samples. RAT sensitivity using NP and saliva samples was 92% and 68%, respectively, using positive RT-qPCR results as the reference. The sensitivity of RAT using NP and saliva samples was significantly higher in patients with fever ≥37°C and/or at least one symptom than in those with fever <37°C and/or no symptoms (97% vs 83% in NP swabs; 80% vs 50% in saliva). Distinct symptoms, including fever ≥37°C, may reflect high Omicron variant viral loads. Rapid antigen testing, not only using nasopharyngeal swabs but also using saliva, would be useful for COVID-19 diagnosis as point-of-care testing, particularly for symptomatic patients. IMPORTANCE We examined nasopharyngeal and salivary viral loads using samples collected from outpatients with SARS-CoV-2 infection during the Omicron epidemic in Japan and explored the outpatient factors correlated with viral loads. In addition, we evaluated the performance of an authorized rapid antigen testing (RAT) kit using nasopharyngeal and saliva samples with RT-PCR testing as the reference. Intriguingly, a correlation between fever and other symptoms and SARS-CoV-2 viral loads in nasopharyngeal and saliva samples was observed based on one COVID-19 outpatient visit. RAT sensitivity was influenced by viral loads. Nevertheless, nasopharyngeal RAT is considered useful for SARS-CoV-2 point-of-care diagnosis. In patients with distinct symptoms, including high-grade fever, salivary RAT could be a practical diagnostic tool because of the higher estimated viral loads. After the Omicron epidemic, outpatients with mild COVID-19 have become the main focus of diagnosis and treatment. Our study provides valuable information regarding the point-of-care diagnosis of these patients.

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Diagnostic Sensitivity of Saliva and Other Respiratory Tract Samples of SARS-CoV-2 Variants in Patients with COVID-19

Cited by 4 publications

References 29 publications

SalivaDirect: an alternative to a conventional RNA extraction protocol for molecular detection of SARS-CoV-2 in a clinical setting

SalivaDirect: an alternative to a conventional RNA extraction protocol for molecular detection of SARS-CoV-2 in a clinical setting

SARS-CoV-2 Variants May Affect Saliva RT-PCR Assay Sensitivity

Correlation of patient symptoms with SARS-CoV-2 Omicron variant viral loads in nasopharyngeal and saliva samples and their influence on the performance of rapid antigen testing

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