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Source: Omicron Diagnostics - Saliva Swabs  Dec 29, 2021  9 months ago
University Of Cape Town Researchers Say That Saliva Swabs May Be More Effective For Omicron Detection Than Nasal Swabs
University Of Cape Town Researchers Say That Saliva Swabs May Be More Effective For Omicron Detection Than Nasal Swabs
Source: Omicron Diagnostics - Saliva Swabs  Dec 29, 2021  9 months ago
Omicron Diagnostics: Researchers from the University of Cape Town-South Africa in a new study have found that saliva swabs are more effective than nasal mid-turbinate swabs for the polymerase chain reaction (PCR)-based detection of omicron variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).


 
The new emerged Omicron variant is characterized by more than 50 distinct mutations, the majority of which are located in the spike protein. The implications of these mutations for disease transmission, tissue tropism and diagnostic testing are still to be determined.

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The study team evaluated the relative performance of saliva and mid-turbinate swabs as RT-PCR samples for the Delta and Omicron variants.
 
It was found that the positive percent agreement (PPA) of saliva swabs and mid-turbinate swabs to a composite standard was 71% (95% CI: 53-84%) and 100% (95% CI: 89-100%), respectively, for the Delta variant. However, for the Omicron variant saliva and mid-turbinate swabs had a 100% (95% CI: 90-100%) and 86% (95% CI: 71-94%) PPA, respectively.
 
The study findings support ex-vivo data of altered tissue tropism from other labs for the Omicron variant. Reassessment of the diagnostic testing standard-of-care may be required as the Omicron variant becomes the dominant variant worldwide.
 
The study findings were published on a preprint server and are currently being peer reviewed. https://www.medrxiv.org/content/10.1101/2021.12.22.21268246v1
 
The newly emerged omicron variant of SARS-CoV-2 has caused a sharp increase in new coronavirus disease 2019 (COVID-19) cases worldwide. The variant has been found to increase the risk of reinfection as well as vaccine breakthrough infections.
 
With a total of around 40 mutations in the spike protein, the variant exhibits significantly increased transmissibility compared to other identified variants of concern (VOCs), including the alpha, beta, gamma, and delta variants.
 
To date, the omicron variant is distinguished from other SARS-CoV-2 variants using the S-gene target failure approach. Because of the presence of a deletion mutation in the spike gene of omicron variant, PCR fails to detect this particular gene. This phenomenon is called S-gene target failure and is used as a marker to detect omicron infections.
 
However, the pattern of viral shedding during omicron infection and its impact on diagnostic sampling methods is still largely unknown.
 
The Omicron Diagnostics study team compared the performance of sal iva swabs and mid-turbinate swabs for PCR-based detection of delta and omicron variants.
 
The team collected saliva swabs and mid-turbinate swabs from 382 symptomatic, non-hospitalized patients who appeared for SARS-CoV-2 testing in a Cape Town hospital between August and December 2021.
 
The study team subsequently tested the samples using reverse transcription PCR (RT-PCR).
 
The detailed categorization of delta and omicron was done based on the whole genome sequencing data, PCR-derived S-gene target failure data, and sampling date.
 
In order to compare between saliva and mid-turbinate samples, a composite standard for SARS-CoV-2 infection was used. The detection of viral RNA in either of the matched samples was considered a positive infection.
 
The study findings obtained from test samples and composite standards were compared to estimate the sensitivity and specificity of saliva and mid-turbinate swabs for the detection of omicron and delta infections (positive percent agreement).
 
It was found that the positive percent agreement of saliva and mid-turbinate swabs to the composite standard was estimated to be 71% and 100% for the delta infection, respectively. In contrast, the saliva and mid-turbinate swabs respectively exhibited 100% and 86% positive percent agreement for the detection of omicron infection.
 
When considering nucleocapsid gene as a target reference, the mean differences in RT-PCR cycle threshold (Ct value) between saliva and mid-turbinate swabs were estimated to be 5.2 and 1.5 for the delta and omicron infections, respectively.
 
It was found that the average duration between symptom onset and the positive test result was 3 days and 2 days for the delta and omicron infections, respectively.
 
The research findings reveal that saliva samples are more useful than mid-turbinate samples for the accurate detection of omicron infection. As observed in the study, the saliva samples contain more viral RNA than nasal samples.
 
One of the reasons for this could be because of altered viral shedding patterns during omicron infection.
 
Furthermore, there is evidence suggesting that the replication rate of omicron variant is significantly higher in the upper respiratory tract than that of the delta variant.
 
However, in the lower respiratory tract, omicron replicates significantly slower than the wildtype SARS-CoV-2 (Wuhan strain).
 
These study observations indicate that certain host tissues preferentially support the growth of the omicron variant (tissue tropism). The altered tissue tropism during omicron infection might be the reason for the altered viral shedding pattern.
 
From the research findings, the study team suggests that currently used diagnostic sampling methods should be reassessed for omicron infections as analyzing nasal or nasopharyngeal samples may lead to a suboptimal diagnosis.  The saliva swabs provide a better and effective alternative.
 
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