PA-390 Evaluation of the Saline Gargle collection method for the molecular detection and sequencing of SARS-CoV-2 in Botswana
Bibliographic record
Abstract
Background Inadequate sampling poses challenges in the COVID-19 diagnostic cycle. Nasopharyngeal swabs are gold-standard but often associated with patient discomfort, require trained healthcare workers (HCW), and are resource intensive. The saline gargle (SG) method has proven to be acceptable for respiratory pathogen detection. We performed a prospective cross-sectional study to evaluate the SG method against the nasopharyngeal and oropharyngeal (NO/OP) method in the molecular detection and next generation sequencing (NGS) of SARS-CoV-2 in Botswana. Methods Eligible participants aged ≥5 years, who were close contacts of a positive case, and/or presented with clinical symptoms of COVID-19, were recruited December 2021- January 2022, and July-September 2022. NP/OP samples were HCW-collected followed by SG collection where participants swished and gargled 5ml sterile 0.9% saline for 20 seconds. Samples collected December 2021-January 2022 underwent nucleic acid extraction and RT-PCR while samples collected July-September 2022 were tested with GeneXpert SARS-CoV-2 Assay. McNemar exact test was used to analyze comparability of testing with significance set as P<0.05. Post-recruitment, random sampling of 10 lab-confirmed SARS-Cov-2 positive stored sample pairs underwent NGS. Results Of 127 pairs, 25 matched samples tested positive for SARS-CoV-2 on both sampling methods. Additionally, SG had 6 false negatives and one sample which was positive but negative with NP/OP. Statistical analysis revealed some evidence of a difference in the detection of SARS-CoV-2 between SG and NP/OP samples (p=0.031). SG showed an overall sensitivity of 81.25% (95%CI 68.8%-96.0%). NGS was successful in 16 samples, 10 SG and 6 NP/OP. The 5 matched successful pairs revealed similar genomic strains (73–100% relatedness). All samples had mutations of high affinity to ACE2 receptor in the Spike gene suggesting circulation of Omicron variant. Conclusion The SG method is a reliable and logistically easier alternative for SAR-CoV-2 detection and NGS to contribute toward efforts of COVID-19 surveillance in Botswana.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.004 | 0.004 |
| Meta-epidemiology (narrow) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.000 | 0.001 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.001 | 0.001 |
| Scholarly communication | 0.001 | 0.000 |
| Open science | 0.001 | 0.001 |
| Research integrity | 0.001 | 0.000 |
| Insufficient payload (model declined to judge) | 0.002 | 0.001 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".