Usability of saliva as a reliable and non-invasive sample for SARS-CoV-2 detection in Durban, South Africa (preprint)

Background Saliva has been proposed as a potential more convenient, cost-effective, and easier sample for diagnosing SARS-CoV-2 infections, but there is limited knowledge of the impact of saliva volumes and stages of infection on its sensitivity and specificity.Methods In this study, we evaluated the performance of SARS-CoV-2 testing in 171 saliva samples across different volumes (50, 100, 300 and 500ul of saliva) and at different stages of disease (at screening, day 7, 14 and 28 post SARS-CoV-2 diagnosis) from 52 mostly mild symptomatic patients. Imperfect nasopharyngeal swab samples were used as a reference.Results Overall, 52 of the 171 samples were positive, with sensitivity of 73.2% and specificity of 81.0%. The sensitivity of saliva samples ranged from 70.6% for 50µl to 83.3% for 300µl of saliva collected. The specificity values ranged between 78.8% for 500µl and 86.4% for 100µl saliva. The overall percentage of positive results in nasopharyngeal swabs and saliva specimens remained comparable throughout the study visits. We observed no significant difference in cycle number values between saliva and nasopharyngeal swab specimens, irrespective of saliva volume tested.Conclusions The saliva collection offers a promising approach for population-based testing. Implementing robust saliva-based testing strategies could contribute significantly to controlling and managing the COVID-19 pandemic.

Field evaluations of four SARS-CoV-2 rapid antigen tests during SARS-CoV-2 Delta variant wave in South Africa (preprint)

Background: Rapid antigen tests detecting SARS-CoV-2 are being increasingly used across the globe and were shown to be a useful tool in managing the COVID-19 pandemic. The purpose of this prospective study was to characterise the performance of four SARS-CoV-2 rapid antigen tests in a South African setting. Methods: Rapid antigen test evaluations were performed through drive-through testing centres in Durban, South Africa from July-December 2021. Two evaluation studies were performed: nasal Panbio COVID-19 Ag Rapid Test Device (Abbott) was evaluated in parallel with the nasopharyngeal Espline SARS-CoV-2 Ag test (Fujirebio, nasopharyngeal); followed by the evaluation of nasal RightSign COVID-19 Antigen Rapid test Cassette (Hangzhou Biotest Biotech) in parallel with the nasopharyngeal STANDARD Q COVID-19 Ag test (SD Biosensor). The Abbott RealTime SARS-CoV-2 assay was used as a reference test. Results: Evaluation of Panbio and Espline Ag tests was performed on 494 samples (31% positivity) while the evaluation of Standard Q and RightTest Ag tests was performed on 539 samples (13.17 % positivity). The overall sensitivity for all four tests ranged between 60-72% with excellent specificity values (>98%). Sensitivity increased to >80% in all tests in samples with Ct value <20. All four tests performed best in samples from patients presenting within the first week of symptom onset. Conclusions: All four evaluated tests detected a majority of the cases within the first week of symptom onset with high viral load and could be a valuable diagnostic tool for controlling the spread of SARS-CoV-2.

High Resolution analysis of Transmission Dynamics of Sars-Cov-2 in Two Major Hospital Outbreaks in South Africa Leveraging Intrahost Diversity (preprint)

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes acute, highly transmissible respiratory infection in both humans and wide range of animal species. Its rapid spread globally and devasting effects have resulted into a major public health emergency prompting the need for methodological interventions to understand and control its spread. In particular, The ability to effectively retrace its transmission pathways in outbreaks remains a major challenge. This is further exacerbated by our limited understanding of its underlying evolutionary mechanism. Using NGS whole-genome data, we determined whether inter- and intra-host diversity coupled with bottleneck analysis can retrace the pathway of viral transmission in two epidemiologically well characterised nosocomial outbreaks in healthcare settings supported by phylogenetic analysis. Additionally, we assessed the mutational landscape, selection pressure and diversity of the identified variants. Our findings showed evidence of intrahost variant transmission and evolution of SARS-CoV-2 after infection These observations were consistent with the results from the bottleneck analysis suggesting that certain intrahost variants in this study could have been transmitted to recipients. In both outbreaks, we observed iSNVs and SNVs shared by putative source-recipients pairs. Majority of the observed iSNVs were positioned in the S and ORF1ab region. AG, CT and TC nucleotide changes were enriched across SARS-COV-2 genome. Moreover, SARS-COV-2 genome had limited diversity in some loci while being highly conserved in others. Overall, Our findings show that the synergistic effect of combining withinhost diversity and bottleneck estimations greatly enhances resolution of transmission events in Sars-Cov-2 outbreaks. They also provide insight into the genome diversity suggesting purifying selection may be involved in the transmission. Together these results will help in developing strategies to elucidate transmission events and curtail the spread of Sars-Cov-2