ABSTRACT
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.
Subject(s)
COVID-19 , Severe Acute Respiratory SyndromeABSTRACT
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.
Subject(s)
COVID-19ABSTRACT
The SARS-CoV-2 Omicron (B.1.1.529) variant first emerged as the BA.1 sub-lineage, with extensive escape from neutralizing immunity elicited by previous infection with other variants, vaccines, or combinations of both. Two new sub-lineages, BA.4 and BA.5, are now emerging in South Africa with changes relative to BA.1, including L452R and F486V mutations in the spike receptor binding domain. We isolated live BA.4 and BA.5 viruses and tested them against neutralizing immunity elicited to BA.1 infection in participants who were Omicron/BA.1 infected but unvaccinated (n=24) and participants vaccinated with Pfizer BNT162b2 or Johnson and Johnson Ad26.CoV.2S with breakthrough Omicron/BA.1 infection (n=15). In unvaccinated individuals, FRNT50, the inverse of the dilution for 50% neutralization, declined from 275 for BA.1 to 36 for BA.4 and 37 for BA.5, a 7.6 and 7.5-fold drop, respectively. In vaccinated BA.1 breakthroughs, FRNT50 declined from 507 for BA.1 to 158 for BA.4 (3.2-fold) and 198 for BA.5 (2.6-fold). Absolute BA.4 and BA.5 neutralization levels were about 5-fold higher in this group versus unvaccinated BA.1 infected participants. The observed escape of BA.4 and BA.5 from BA.1 elicited immunity is more moderate than of BA.1 against previous immunity. However, the low absolute neutralization levels for BA.4 and BA.5, particularly in the unvaccinated group, are unlikely to protect well against symptomatic infection. This may indicate that, based on neutralization escape, BA.4 and BA.5 have potential to result in a new infection wave.
ABSTRACT
Omicron (B.1.1.529) shows extensive escape from vaccine immunity, although vaccination reduces severe disease and death. Boosting with vaccines incorporating variant spike sequences could possibly broaden immunity. One approach to choose the variant may be to measure immunity elicited by vaccination combined with variant infection. Here we investigated Omicron neutralization in people infected with the Beta (B.1.351) variant and subsequently vaccinated with Pfizer BNT162b2. We observed that Beta infection alone elicited poor Omicron cross-neutralization, similar to what we previously found with BNT162b2 vaccination alone or in combination with ancestral or Delta virus infection. In contrast, Beta infection combined with BNT162b2 vaccination elicited neutralization with substantially lower Omicron escape.