ABSTRACT
Background: The aim of this study was to evaluate three commercially available methods (Allplex SARS-CoV-2 Assay, Allplex SARS-CoV-2/FluA/FluB/RSV Assay and Novaplex SARS-CoV-2 Variants I Assay) for screening of the SARS-CoV-2 VOC 202012/01 B.1.1.7 variant. Methods A total of 160 nasopharyngeal samples (150 positive and 10 negative for SARS-CoV-2) were tested with all three molecular assays. Next-generation sequencing (NGS) was used as the reference method to determine analytical performance. Results Total (100%) agreement was found for SARS-CoV-2 detection with all three assays. For B.1.1.7 screening, the sensitivity of the Allplex SARS-CoV-2 Assay, the Allplex SARS-CoV-2/FluA/FluB/RSV Assay and the Novaplex SARS-CoV-2 Variants I Assay (Seegene Inc.) were 94.5%, 98.7% and 100 %, respectively, while the specificities of the assays were 98.6%, 81.7% and 100%, respectively. Conclusions Although the best results for identifying the B.1.1.7 variant in this study were achieved with the Novaplex Variants I Assay, the three approaches evaluated can be considered cost-effective primary screening tools to rapidly monitor the VOC 202012/01 B.1.1.7 variant.
ABSTRACT
Importance: The actual demand on SARS-CoV-2 diagnosis is a current challenge for clinical laboratories. Sample pooling may help to ameliorate workload in clinical laboratories. Objective: to evaluate the efficacy of sample pooling compared to the individual analysis for the diagnosis of CoVID-19, by using different commercial platforms for nucleic acid extraction and amplification. Design and settings: observational, prospective, multicentre study across 9 Spanish clinical microbiology laboratories including SARS-CoV-2 RNA testing performed in April 2020, during the first three days after acceptance to participate. Participants and Methods: 3519 naso-oro-pharyngeal samples received at the participating laboratories were processed individually and in pools (351 pools) according to the existing methodology in each of the centres. Results: We found that 253 pools (2519 samples) were negative, and 99 pools (990 samples) were positive; with 241 positive samples (6.85%), our pooling strategy would have saved 2167 PCR tests. For 29 pools (made out of 290 samples) we found discordant results when compared to their correspondent individual samples: in 24/29 pools (30 samples), minor discordances were found; for five pools (5 samples), we found major discordances. Sensitivity, specificity, positive and negative predictive values for pooling were 97.93%, 100%, 100% and 99.85% respectively; accuracy was 99.86% and kappa concordant coefficient was 0.988. As a result of the sample dilution effect of pooling, a loss of 2-3 Cts was observed for E, N or RdRP genes. Conclusion: we show a high efficiency of pooling strategies for SARS-CoV-2 RNA testing, across different RNA extraction and amplification platforms, with excellent performance in terms of sensitivity, specificity, and positive and negative predictive values. We believe that our results may help clinical laboratories to respond to the actual demand and clinical need on SARS-CoV-2 testing, especially for the screening of low prevalence populations.