Saline gargle collection method is comparable to nasopharyngeal/oropharyngeal swabbing for the molecular detection and sequencing of SARS-CoV-2 in Botswana
ABSTRACT The coronavirus disease 2019 pandemic has highlighted the importance and challenges of the sample collection component of the diagnostic cycle. Although combined nasopharyngeal and oropharyngeal swabs (NOS) have historically been the gold standard of sampling, the saline gargle (SG) samplin...
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| Language: | English |
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American Society for Microbiology
2025-07-01
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| Series: | Microbiology Spectrum |
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| Online Access: | https://journals.asm.org/doi/10.1128/spectrum.02023-24 |
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| author | Kwana Lechiile Sikhulile Moyo Mai-Lei Woo Kinshella Wonderful T. Choga Leabaneng Tawe Jonathan Strysko Gofaone Bagatiseng Iryna Kayda Kedumetse Seru Boitumelo J. L. Zuze Patience Motshosi Mosepele Mosepele Irene Gobe Simani Gaseitsiwe Margaret Mokomane David M. Goldfarb |
| author_facet | Kwana Lechiile Sikhulile Moyo Mai-Lei Woo Kinshella Wonderful T. Choga Leabaneng Tawe Jonathan Strysko Gofaone Bagatiseng Iryna Kayda Kedumetse Seru Boitumelo J. L. Zuze Patience Motshosi Mosepele Mosepele Irene Gobe Simani Gaseitsiwe Margaret Mokomane David M. Goldfarb |
| author_sort | Kwana Lechiile |
| collection | DOAJ |
| description | ABSTRACT The coronavirus disease 2019 pandemic has highlighted the importance and challenges of the sample collection component of the diagnostic cycle. Although combined nasopharyngeal and oropharyngeal swabs (NOS) have historically been the gold standard of sampling, the saline gargle (SG) sampling method has been evaluated and implemented in multiple jurisdictions for respiratory pathogen detection. It has proven to be user-acceptable to patients, simple to collect, and highly sensitive to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detection by molecular methods when compared to swabs. We performed a prospective cross-sectional study to evaluate the SG collection method against the NOS collection method for molecular detection and next-generation sequencing (NGS) of SARS-CoV-2 in Botswana. Paired SG and NOS samples were collected and underwent nucleic acid extraction prior to molecular detection. The SG had an overall sensitivity of 81.3% (95% CI: 68.8%%–96.0%), while the NOS had an overall sensitivity of 96.9% (95% CI: 84.3–99.4). Paired samples with a mean crossing threshold value of <35 also underwent NGS. SG specimens had a median genome coverage of 94.7% (interquartile range [IQR] 87.0%–99.2%) and NOS specimens had a median genome coverage of 99.6% (IQR 90.0%–99.6%). Bioinformatics analysis showed the 15 successfully matched pairs belong to clades BA.1 and BA.2 indicative of the Omicron variant. Further analysis at the nucleotide level showed a mean similarity of 99.998% ± 0.00465% between NOS and SG. This method has the potential to overcome the challenges that come with swab-based sampling for SARS-CoV-2 testing and may be an alternative in testing for other viral pathogens.IMPORTANCEDuring the coronavirus disease 2019 (COVID-19) pandemic, a major challenge has been inadequate sampling for detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Pediatric patients posed additional challenges with sample collection, and they and others are also at risk of rare complications from swab collection. Saline gargle (SG) sampling method has been evaluated and introduced as an alternative to swab collection in several jurisdictions. Our study affirms the acceptable performance of the saline gargle method for the molecular detection of SARS-CoV-2 and also establishes that SG samples do not pose an obstacle for genomic sequencing of SARS-CoV-2. The SG method may be a reliable alternative for SARS-CoV-2 detection and next-generation sequencing, facilitating COVID-19 surveillance efforts in resource-constraint settings. |
| format | Article |
| id | doaj-art-e3303e80826249089772e1c4ffef8c3e |
| institution | Kabale University |
| issn | 2165-0497 |
| language | English |
| publishDate | 2025-07-01 |
| publisher | American Society for Microbiology |
| record_format | Article |
| series | Microbiology Spectrum |
| spelling | doaj-art-e3303e80826249089772e1c4ffef8c3e2025-08-20T03:28:26ZengAmerican Society for MicrobiologyMicrobiology Spectrum2165-04972025-07-0113710.1128/spectrum.02023-24Saline gargle collection method is comparable to nasopharyngeal/oropharyngeal swabbing for the molecular detection and sequencing of SARS-CoV-2 in BotswanaKwana Lechiile0Sikhulile Moyo1Mai-Lei Woo Kinshella2Wonderful T. Choga3Leabaneng Tawe4Jonathan Strysko5Gofaone Bagatiseng6Iryna Kayda7Kedumetse Seru8Boitumelo J. L. Zuze9Patience Motshosi10Mosepele Mosepele11Irene Gobe12Simani Gaseitsiwe13Margaret Mokomane14David M. Goldfarb15School of Allied Health Sciences, University of Botswana, Gaborone, BotswanaSchool of Allied Health Sciences, University of Botswana, Gaborone, BotswanaUniversity of British Columbia, Vancouver, CanadaBotswana Harvard Health Partnership, Gaborone, BotswanaBotswana-UPenn Partnership, Gaborone, BotswanaBotswana-UPenn Partnership, Gaborone, BotswanaBotswana Harvard Health Partnership, Gaborone, BotswanaUniversity of British Columbia, Vancouver, CanadaBotswana Harvard Health Partnership, Gaborone, BotswanaBotswana Harvard Health Partnership, Gaborone, BotswanaBotswana Harvard Health Partnership, Gaborone, BotswanaBotswana Harvard Health Partnership, Gaborone, BotswanaSchool of Allied Health Sciences, University of Botswana, Gaborone, BotswanaSchool of Allied Health Sciences, University of Botswana, Gaborone, BotswanaSchool of Allied Health Sciences, University of Botswana, Gaborone, BotswanaBotswana-UPenn Partnership, Gaborone, BotswanaABSTRACT The coronavirus disease 2019 pandemic has highlighted the importance and challenges of the sample collection component of the diagnostic cycle. Although combined nasopharyngeal and oropharyngeal swabs (NOS) have historically been the gold standard of sampling, the saline gargle (SG) sampling method has been evaluated and implemented in multiple jurisdictions for respiratory pathogen detection. It has proven to be user-acceptable to patients, simple to collect, and highly sensitive to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detection by molecular methods when compared to swabs. We performed a prospective cross-sectional study to evaluate the SG collection method against the NOS collection method for molecular detection and next-generation sequencing (NGS) of SARS-CoV-2 in Botswana. Paired SG and NOS samples were collected and underwent nucleic acid extraction prior to molecular detection. The SG had an overall sensitivity of 81.3% (95% CI: 68.8%%–96.0%), while the NOS had an overall sensitivity of 96.9% (95% CI: 84.3–99.4). Paired samples with a mean crossing threshold value of <35 also underwent NGS. SG specimens had a median genome coverage of 94.7% (interquartile range [IQR] 87.0%–99.2%) and NOS specimens had a median genome coverage of 99.6% (IQR 90.0%–99.6%). Bioinformatics analysis showed the 15 successfully matched pairs belong to clades BA.1 and BA.2 indicative of the Omicron variant. Further analysis at the nucleotide level showed a mean similarity of 99.998% ± 0.00465% between NOS and SG. This method has the potential to overcome the challenges that come with swab-based sampling for SARS-CoV-2 testing and may be an alternative in testing for other viral pathogens.IMPORTANCEDuring the coronavirus disease 2019 (COVID-19) pandemic, a major challenge has been inadequate sampling for detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Pediatric patients posed additional challenges with sample collection, and they and others are also at risk of rare complications from swab collection. Saline gargle (SG) sampling method has been evaluated and introduced as an alternative to swab collection in several jurisdictions. Our study affirms the acceptable performance of the saline gargle method for the molecular detection of SARS-CoV-2 and also establishes that SG samples do not pose an obstacle for genomic sequencing of SARS-CoV-2. The SG method may be a reliable alternative for SARS-CoV-2 detection and next-generation sequencing, facilitating COVID-19 surveillance efforts in resource-constraint settings.https://journals.asm.org/doi/10.1128/spectrum.02023-24diagnosticsSARS-CoV-2gargle |
| spellingShingle | Kwana Lechiile Sikhulile Moyo Mai-Lei Woo Kinshella Wonderful T. Choga Leabaneng Tawe Jonathan Strysko Gofaone Bagatiseng Iryna Kayda Kedumetse Seru Boitumelo J. L. Zuze Patience Motshosi Mosepele Mosepele Irene Gobe Simani Gaseitsiwe Margaret Mokomane David M. Goldfarb Saline gargle collection method is comparable to nasopharyngeal/oropharyngeal swabbing for the molecular detection and sequencing of SARS-CoV-2 in Botswana Microbiology Spectrum diagnostics SARS-CoV-2 gargle |
| title | Saline gargle collection method is comparable to nasopharyngeal/oropharyngeal swabbing for the molecular detection and sequencing of SARS-CoV-2 in Botswana |
| title_full | Saline gargle collection method is comparable to nasopharyngeal/oropharyngeal swabbing for the molecular detection and sequencing of SARS-CoV-2 in Botswana |
| title_fullStr | Saline gargle collection method is comparable to nasopharyngeal/oropharyngeal swabbing for the molecular detection and sequencing of SARS-CoV-2 in Botswana |
| title_full_unstemmed | Saline gargle collection method is comparable to nasopharyngeal/oropharyngeal swabbing for the molecular detection and sequencing of SARS-CoV-2 in Botswana |
| title_short | Saline gargle collection method is comparable to nasopharyngeal/oropharyngeal swabbing for the molecular detection and sequencing of SARS-CoV-2 in Botswana |
| title_sort | saline gargle collection method is comparable to nasopharyngeal oropharyngeal swabbing for the molecular detection and sequencing of sars cov 2 in botswana |
| topic | diagnostics SARS-CoV-2 gargle |
| url | https://journals.asm.org/doi/10.1128/spectrum.02023-24 |
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