Lechiile Kwana, Moyo Sikhulile, Woo Kinshella Mai-Lei, Choga Wonderful T, Tawe Leabaneng, Strysko Jonathan, Bagatiseng Gofaone, Kayda Iryna, Seru Kedumetse, Zuze Boitumelo J L, Motshosi Patience, Mosepele Mosepele, Gobe Irene, Gaseitsiwe Simani, Mokomane Margaret, Goldfarb David M
School of Allied Health Sciences, University of Botswana, Gaborone, Botswana.
Botswana Harvard Health Partnership, Gaborone, Botswana.
Microbiol Spectr. 2025 Jul;13(7):e0202324. doi: 10.1128/spectrum.02023-24. Epub 2025 May 22.
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.
During 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.
2019年冠状病毒病大流行凸显了诊断周期中样本采集环节的重要性和挑战。尽管联合鼻咽拭子和口咽拭子（NOS）历来是采样的金标准，但盐水漱口（SG）采样方法已在多个司法管辖区进行评估并用于呼吸道病原体检测。事实证明，该方法患者接受度高、采集简单，与拭子相比，通过分子方法检测严重急性呼吸综合征冠状病毒2（SARS-CoV-2）时灵敏度高。我们开展了一项前瞻性横断面研究，在博茨瓦纳评估SG采集方法与NOS采集方法用于SARS-CoV-2分子检测和下一代测序（NGS）的效果。采集配对的SG和NOS样本，并在分子检测前进行核酸提取。SG的总体灵敏度为81.3%（95%CI：68.8%-96.0%），而NOS的总体灵敏度为96.9%（95%CI：84.3%-99.4%）。平均交叉阈值<35的配对样本也进行了NGS。SG样本的基因组中位数覆盖率为94.7%（四分位间距[IQR]87.0%-99.2%），NOS样本的基因组中位数覆盖率为99.6%（IQR 90.0%-99.6%）。生物信息学分析显示，15对成功匹配的样本属于BA.1和BA.2分支，表明为奥密克戎变异株。核苷酸水平的进一步分析显示，NOS和SG之间的平均相似度为99.998%±0.00465%。该方法有可能克服基于拭子采样进行SARS-CoV-2检测所带来的挑战，并且可能是检测其他病毒病原体的一种替代方法。
在2019年冠状病毒病（COVID-19）大流行期间，一个主要挑战是严重急性呼吸综合征冠状病毒2（SARS-CoV-2）检测的采样不足。儿科患者在样本采集方面带来了额外挑战，他们以及其他人也有因拭子采集而出现罕见并发症的风险。盐水漱口（SG）采样方法已在多个司法管辖区进行评估并作为拭子采集的替代方法引入。我们的研究证实了盐水漱口法用于SARS-CoV-2分子检测的可接受性能，并且还确定SG样本不会对SARS-CoV-2的基因组测序造成障碍。SG方法可能是SARS-CoV-2检测和下一代测序的可靠替代方法，有助于在资源有限的环境中开展COVID-19监测工作。
