Saliva as an Alternative to Nasopharyngeal Swab for Detection of SARS-CoV-2 using RT-PCR as a Diagnostic Method: A Cross-sectional Study
Introduction: Nasopharyngeal Swab (NPS) sample is considered as gold standard for the detection of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) but is relatively invasive, and is perceived as uncomfortable by the patient while saliva sample collection is easy, non invasive, more...
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| Format: | Article |
| Language: | English |
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JCDR Research and Publications Pvt. Ltd.
2023-07-01
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| Series: | National Journal of Laboratory Medicine |
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| Online Access: | https://www.njlm.net/articles/PDF/2754/60972_CE[Ra1]_F(IS)_PF1(PS_SHU)_reredo_PN(SHU).pdf |
| _version_ | 1797754635938693120 |
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| author | Anju Verma Anagoni Srikar AM Padmalatha Alladi Mohan Mudhigeti Nagaraja Usha Kalawat |
| author_facet | Anju Verma Anagoni Srikar AM Padmalatha Alladi Mohan Mudhigeti Nagaraja Usha Kalawat |
| author_sort | Anju Verma |
| collection | DOAJ |
| description | Introduction: Nasopharyngeal Swab (NPS) sample is considered
as gold standard for the detection of Severe Acute Respiratory
Syndrome Coronavirus 2 (SARS-CoV-2) but is relatively invasive,
and is perceived as uncomfortable by the patient while saliva
sample collection is easy, non invasive, more acceptable and
can be self-collected without requirement of any healthcare
professional or expert.
Aim: To validate the use of saliva as a biological sample for
the diagnosis of SARS-CoV-2 in comparison to NPS for the
detection of SARS-CoV-2 in clinically suspected patients.
Materials and Methods: This was a cross-sectional study
conducted at Department of Clinical Virology, Sri Venkateswara
Institute of Medical Sciences, Andhra Pradesh, India from
28th January 2022 to 16th February 2022. Patients attending
Medicine Outpatient Department (OPD) with signs and symptoms
suggestive of SARS-CoV-2 infection were included in the study.
Self-collected saliva sample and NPS collected by healthcare
personnel from all patients were assigned separate identification
numbers and sent to the laboratory for Reverse Transcription
Polymerase Chain Reaction (RT-PCR). RT-PCR results of the two
tests were compared in terms of percentage agreement and Cycle
Threshold value (CT value). Statistical analysis was done using
Jefferies Amazing Statistical Program 0.16.2 software (JASP).
Results: A total of 352 patients were registered, of which 211
(59.94%) were male and 141 (40.05%) were female. Eight
patients were excluded because of inconclusive results, hence a
total of 344 patients were included in the study. Among the NPS
samples , 88 (25.58%) samples tested positive for SARS-CoV-2
and 256 (74.41%) samples tested negative whereas with saliva
samples, 54 samples (15.40%) tested positive and 290 samples
(84.60%) were negative for SARS-CoV-2. Among NPS positive
samples, only 46 were positive with saliva sample, while among
the NPS negative samples, only 248 were negative and eight
samples were positive for SARS-CoV-2 with saliva samples.
Positive percent agreement, negative percent agreement and
overall agreement of saliva sample with respect to NPS were
52.5%, 96.87% and 85.46%, respectively. Mean and standard
deviation for CT value of E gene, Open Reading Frame (ORF)
gene and Ribonucleic Acid (RNA) dependent RNA polymerase
(RdRp) gene with saliva samples were 26.62±3.7, 27.07±3.9
and 27.05±4.0, respectively and that of NPS were 25.87±4.9,
24.78±5.3 and 24.50±5.2, respectively.
Conclusion: Saliva sample is an easy, convenient, and economic
alternative to NPS but because of its low positive percent
agreement with that of NPS, it should be used only in resourcelimited settings involving a shortage of personal protective
equipment and viral transport media during the pandemic. |
| first_indexed | 2024-03-12T17:35:16Z |
| format | Article |
| id | doaj.art-1affd186ae9d4498af1af2a5f0bcd754 |
| institution | Directory Open Access Journal |
| issn | 2277-8551 2455-6882 |
| language | English |
| last_indexed | 2024-03-12T17:35:16Z |
| publishDate | 2023-07-01 |
| publisher | JCDR Research and Publications Pvt. Ltd. |
| record_format | Article |
| series | National Journal of Laboratory Medicine |
| spelling | doaj.art-1affd186ae9d4498af1af2a5f0bcd7542023-08-04T11:14:52ZengJCDR Research and Publications Pvt. Ltd.National Journal of Laboratory Medicine2277-85512455-68822023-07-01177343810.7860/NJLM/2023/60972.2754Saliva as an Alternative to Nasopharyngeal Swab for Detection of SARS-CoV-2 using RT-PCR as a Diagnostic Method: A Cross-sectional StudyAnju Verma0Anagoni Srikar1AM Padmalatha2Alladi Mohan3Mudhigeti Nagaraja4Usha Kalawat5Assistant Professor, Department of Clinical Virology, Sri Venkateswara Institute of Medical Sciences, Tirupati, Andhra Pradesh, India.Nonmedical Scientist B, Department of Clinical Virology, Sri Venkateswara Institute of Medical Sciences, Tirupati, Andhra Pradesh, India.Medical Scientist C, Department of Clinical Virology, Sri Venkateswara Institute of Medical Sciences, Tirupati, Andhra Pradesh, India.Senior Professor, Department of Clinical Virology, Sri Venkateswara Institute of Medical Sciences, Tirupati, Andhra Pradesh, India.Nonmedical Scientist C, Department of Clinical Virology, Sri Venkateswara Institute of Medical Sciences, Tirupati, Andhra Pradesh, India.Professor, Department of Clinical Virology, Sri Venkateswara Institute of Medical Sciences, Tirupati, Andhra Pradesh, India.Introduction: Nasopharyngeal Swab (NPS) sample is considered as gold standard for the detection of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) but is relatively invasive, and is perceived as uncomfortable by the patient while saliva sample collection is easy, non invasive, more acceptable and can be self-collected without requirement of any healthcare professional or expert. Aim: To validate the use of saliva as a biological sample for the diagnosis of SARS-CoV-2 in comparison to NPS for the detection of SARS-CoV-2 in clinically suspected patients. Materials and Methods: This was a cross-sectional study conducted at Department of Clinical Virology, Sri Venkateswara Institute of Medical Sciences, Andhra Pradesh, India from 28th January 2022 to 16th February 2022. Patients attending Medicine Outpatient Department (OPD) with signs and symptoms suggestive of SARS-CoV-2 infection were included in the study. Self-collected saliva sample and NPS collected by healthcare personnel from all patients were assigned separate identification numbers and sent to the laboratory for Reverse Transcription Polymerase Chain Reaction (RT-PCR). RT-PCR results of the two tests were compared in terms of percentage agreement and Cycle Threshold value (CT value). Statistical analysis was done using Jefferies Amazing Statistical Program 0.16.2 software (JASP). Results: A total of 352 patients were registered, of which 211 (59.94%) were male and 141 (40.05%) were female. Eight patients were excluded because of inconclusive results, hence a total of 344 patients were included in the study. Among the NPS samples , 88 (25.58%) samples tested positive for SARS-CoV-2 and 256 (74.41%) samples tested negative whereas with saliva samples, 54 samples (15.40%) tested positive and 290 samples (84.60%) were negative for SARS-CoV-2. Among NPS positive samples, only 46 were positive with saliva sample, while among the NPS negative samples, only 248 were negative and eight samples were positive for SARS-CoV-2 with saliva samples. Positive percent agreement, negative percent agreement and overall agreement of saliva sample with respect to NPS were 52.5%, 96.87% and 85.46%, respectively. Mean and standard deviation for CT value of E gene, Open Reading Frame (ORF) gene and Ribonucleic Acid (RNA) dependent RNA polymerase (RdRp) gene with saliva samples were 26.62±3.7, 27.07±3.9 and 27.05±4.0, respectively and that of NPS were 25.87±4.9, 24.78±5.3 and 24.50±5.2, respectively. Conclusion: Saliva sample is an easy, convenient, and economic alternative to NPS but because of its low positive percent agreement with that of NPS, it should be used only in resourcelimited settings involving a shortage of personal protective equipment and viral transport media during the pandemic.https://www.njlm.net/articles/PDF/2754/60972_CE[Ra1]_F(IS)_PF1(PS_SHU)_reredo_PN(SHU).pdfcycle threshold valuereverse transcription polymerase chain reactionsevere acute respiratory syndrome coronavirus 2viral transport medium |
| spellingShingle | Anju Verma Anagoni Srikar AM Padmalatha Alladi Mohan Mudhigeti Nagaraja Usha Kalawat Saliva as an Alternative to Nasopharyngeal Swab for Detection of SARS-CoV-2 using RT-PCR as a Diagnostic Method: A Cross-sectional Study National Journal of Laboratory Medicine cycle threshold value reverse transcription polymerase chain reaction severe acute respiratory syndrome coronavirus 2 viral transport medium |
| title | Saliva as an Alternative to Nasopharyngeal Swab for Detection of SARS-CoV-2 using RT-PCR as a Diagnostic Method: A Cross-sectional Study |
| title_full | Saliva as an Alternative to Nasopharyngeal Swab for Detection of SARS-CoV-2 using RT-PCR as a Diagnostic Method: A Cross-sectional Study |
| title_fullStr | Saliva as an Alternative to Nasopharyngeal Swab for Detection of SARS-CoV-2 using RT-PCR as a Diagnostic Method: A Cross-sectional Study |
| title_full_unstemmed | Saliva as an Alternative to Nasopharyngeal Swab for Detection of SARS-CoV-2 using RT-PCR as a Diagnostic Method: A Cross-sectional Study |
| title_short | Saliva as an Alternative to Nasopharyngeal Swab for Detection of SARS-CoV-2 using RT-PCR as a Diagnostic Method: A Cross-sectional Study |
| title_sort | saliva as an alternative to nasopharyngeal swab for detection of sars cov 2 using rt pcr as a diagnostic method a cross sectional study |
| topic | cycle threshold value reverse transcription polymerase chain reaction severe acute respiratory syndrome coronavirus 2 viral transport medium |
| url | https://www.njlm.net/articles/PDF/2754/60972_CE[Ra1]_F(IS)_PF1(PS_SHU)_reredo_PN(SHU).pdf |
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