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Deep Throat Saliva as Alternative Specimen for Detection of SARS-CoV-2 Using RT-PCR

Author: Suhana Hashim

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Abstract

Suhana Hashim¹, Amanda Khalida Che Kamarul Wzaman², Syahida Omar³, Siti Nabilallhuda Azmi,  Noor Hafizan Mat Salleh⁵  

Objectives. Naso/oropharyngeal (NPS/OPS) swabs are widely accepted as the main specimens for detection of  SARS-CoV-2, however due to its limitation, easier and safer sampling methods are proposed, including  deep throat saliva (DTS). The aim of this study is to evaluate the result performance of DTS specimen and its correlation with NPS/OPS specimen using reverse‐transcription polymerase chain reaction (RT‐ PCR) and to review the possible factors that can affect the result. 

Methods. A cross-sectional study was conducted in the first week of April 2021, with a total of 65 patient matched paired specimens were received and analysed. A set of NPS/OPS and DTS from the same  patient were collected simultaneously at the selected Klinik Kesihatan from each district. A briefing on  proper DTS collection and other related procedures were demonstrated to the Klinik Kesihatan prior to  the study. All specimens were tested for SARS‐CoV‐2 by RT-PCR. 

Results. The overall agreement between NPS/OPS and DTS RT-PCR was 95.4%. Sensitivity of the DTS specimen  was 81.8% with specificity of 98%. The estimated PPV and NPV were 90% and 96.4% respectively.  All the discrepancy results involving cycle threshold (CT) value of more than 30 with no logistic issue  identified. Nine (9) DTS specimens were detected for SARS-CoV-2 with almost equal distribution  among male and female, median age of 33 and mostly are close contacts of confirmed case and  asymptomatic.  

Conclusion. DTS specimen is a valid alternative to NPS/OPS for RT PCR SARS-CoV-2. Nonetheless further study  will be needed by involving larger sample size and more positive specimens with a wide range of CT  value.  

Keyword: DTS, NPS/OPS, RT-PCR, SARS-CoV-2

 

  1. Dr Suhana Hashim, Clinical Microbiologist, Kota Bharu Public Health Laboratory, Lot 522 KM 10 Jalan Kuala Krai, 16010 Kota Bharu Kelantan Malaysia.  
  2. Medical Officer, Kota Bharu Public Health Laboratory.  
  3. Science Officer, Kota Bharu Public Health Laboratory.  
  4. Medical Officer, Kota Bharu Public Health Laboratory.  
  5. Public Health Specialist, Director of Kota Bharu Public Health Laboratory.  

 

Correspondence toDr Suhana Hashim, Clinical Microbiologist, Kota Bharu Public Health Laboratory, Lot 522 KM 10 Jalan Kuala Krai,  16010 Kota Bharu Kelantan, Malaysia  Email: [email protected] 

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