Background: The ongoing pandemic of SARS-COV-2 has already infected more than eight million people worldwide. The majority of COVID-19 patients either are asymptomatic or have mild symptoms. Yet, about 15% of the cases experience severe complications and require intensive care. Factors determining disease severity are not yet fully characterized. Aim: Here, we investigated the within-host virus diversity in COVID-19 patients with different clinical manifestations. Methods: We compared SARS-COV-2 genetic diversity in 19 mild and 27 severe cases. Viral RNA was extracted from nasopharyngeal samples and sequenced using the Illumina MiSeq platform. This was followed by deep-sequencing analyses of SARS-CoV-2 genomes at both consensus and sub-consensus sequence levels. Results: Consensus sequences of all viruses were very similar, showing more than 99.8% sequence identity regardless of the disease severity. However, the sub-consensus analysis revealed significant differences in within-host diversity between mild and severe cases. Patients with severe symptoms exhibited a significantly (p-value 0.001) higher number of variants in coding and non-coding regions compared to mild cases. Analysis also revealed higher prevalence of some variants among severe cases. Most importantly, severe cases exhibited significantly higher within-host diversity (mean = 13) compared to mild cases (mean = 6). Further, higher within-host diversity was observed in patients above the age of 60 compared to the younger age group. Conclusion: These observations provided evidence that within-host diversity might play a role in the development of severe disease outcomes in COVID-19 patients; however, further investigations are required to elucidate this association.
Background The current standard for COVID-19 diagnosis, RT-qPCR, has important drawbacks for its use as a tool for epidemiological control, including the need of laboratory-processing, high cost, and long turnaround from sampling to results release. Antigen-based rapid diagnostic tests (Ag-RDT) provide a promising alternative for this purpose.
Methods We assessed the analytical and clinical performance of the Ag-RDT Panbio COVID-19 Ag Test (Abbott), using RT-qPCR as a reference test. The clinical performance was assessed using nasopharyngeal swabs, collected in routine practice for case confirmation and contact tracing, and nasal mid-turbinate swabs, collected in preventive screenings of asymptomatic individuals. Fresh samples were analysed by RT-q-PCR, stored at -80 °C, and analysed using the Ag-RDT according to the manufacturer instructions.
Findings The Ag-RDT had a limit of detection of 6·5×105 copies/reaction. The clinical performance was assessed on 1,406 frozen swabs with a PCR result available: 951 (67·7%) positive and 455 (32·4%) negative. The Ag-RDT identified the presence of SARS-CoV-2 in 872 of 951 PCR-positive samples (91·7%; 95% CI 89·8-93·4 and ruled out its presence in 450 of 455 PCR-negative samples (specificity 98·9%; 95% CI 97·5– 99·6). Sensitivity increased in samples with lower Ct values (Ct <25, 98·2%; Ct<30, 94·9%) and was higher among symptomatic cases (92·6%) and their contacts (94·2%) than among asymptomatic individuals (79·5%). In the setting of asymptomatic screening, sensitivity also increased with lower Ct values (Ct <25, 100%; Ct<30, 98·6%). Assuming a pre-test probability of 5%, the negative and positive predictive values were 99·6% (99·5 – 99·6) and 81·5% (65·0 – 93·2), respectively.
Interpretation The Panbio COVID-19 Ag-RDT has high sensitivity for detecting the presence of SARS-CoV-2 in nasal or nasopharyngeal swabs of both, symptomatic and asymptomatic individuals. The diagnostic performance of the test is particularly good in samples with viral loads associated with high risk of viral transmission (Ct <25), which show high positive and negative predictive values even when assuming a prevalence as low as 5%.
Background The current standard for COVID-19 diagnosis, RT-qPCR, has important drawbacks for its use as a tool for epidemiological control, including the need of laboratory-processing, high cost, and long turnaround from sampling to results release. Antigen-based rapid diagnostic tests (Ag-RDT) provide a promising alternative for this purpose.
Methods We assessed the analytical and clinical performance of the Ag-RDT Panbio COVID-19 Ag Test (Abbott), using RT-qPCR as a reference test. The clinical performance was assessed using nasopharyngeal swabs, collected in routine practice for case confirmation and contact tracing, and nasal mid-turbinate swabs, collected in preventive screenings of asymptomatic individuals. Fresh samples were analysed by RT-q-PCR, stored at -80 °C, and analysed using the Ag-RDT according to the manufacturer instructions.
Findings The Ag-RDT had a limit of detection of 6·5×105 copies/reaction. The clinical performance was assessed on 1,406 frozen swabs with a PCR result available: 951 (67·7%) positive and 455 (32·4%) negative. The Ag-RDT identified the presence of SARS-CoV-2 in 872 of 951 PCR-positive samples (91·7%; 95% CI 89·8-93·4 and ruled out its presence in 450 of 455 PCR-negative samples (specificity 98·9%; 95% CI 97·5– 99·6). Sensitivity increased in samples with lower Ct values (Ct <25, 98·2%; Ct<30, 94·9%) and was higher among symptomatic cases (92·6%) and their contacts (94·2%) than among asymptomatic individuals (79·5%). In the setting of asymptomatic screening, sensitivity also increased with lower Ct values (Ct <25, 100%; Ct<30, 98·6%). Assuming a pre-test probability of 5%, the negative and positive predictive values were 99·6% (99·5 – 99·6) and 81·5% (65·0 – 93·2), respectively.
Interpretation The Panbio COVID-19 Ag-RDT has high sensitivity for detecting the presence of SARS-CoV-2 in nasal or nasopharyngeal swabs of both, symptomatic and asymptomatic individuals. The diagnostic performance of the test is particularly good in samples with viral loads associated with high risk of viral transmission (Ct <25), which show high positive and negative predictive values even when assuming a prevalence as low as 5%.