CRISPR-Cas12a-Based Detection for the Major SARS-CoV-2 Variants of Concern

We described CRISPR-Cas12-based multiplex allele-specific assay for rapid SARS-CoV-2 variant genotyping. The new system has the potential to be quickly developed, continuously updated, and easily implemented for screening of SARS-CoV-2 variants in resource-limited settings. This approach can be adapted for emerging mutations and implemented in laboratories already conducting SARS-CoV-2 nucleic acid amplification tests using existing resources and extracted nucleic acid.

HIV-2 infections: a lesson in diagnostic test selection in Egypt

The first HIV-2 infection in an Egyptian national is documented in this report. Infection with HIV-2 was recognized only after a HIV-1 specific assay yielded negative results in an individual previously identified as being HIV-seropositive by a HIV-1/HIV-2 assay. This emphasizes the importance of using assays capable of detecting both HIV-1 and HIV-2 for testing blood supplies and diagnosis of HIV infections in regions where the prevalence of HIV-2 infections is extremely low.

Kinetics and seroprevalence of SARS-CoV-2 antibodies: a comparison of 3 different assays

Comparing seroprevalence and antibody kinetics in three different commercially available assays for SARS-CoV-2. Serostatus of COVID-19 patients was analyzed 5 months and 10 months after their infection, using three different assays: Diasorin LIAISON, Euroimmun, Abbott Diagnostics ARCHITECT. Seropositivity at baseline differed significantly depending on the assay (Diasorin 81%, Euroimmun 83%, Abbott 59%). At follow-up antibody levels detected in the Diasorin assay were stable, while there was a significant loss in seropositivity in the Euroimmun and Abbott assays. There are significant differences in SARS-CoV-2 antibody kinetics based on the specific assay used.

Kinetics and seroprevalence of SARS-CoV-2 antibodies – a comparison of 3 different assays

Purpose: Comparing seroprevalence and antibody kinetics in three different commercially available assays for SARS-CoV-2. Methods: Serostatus of COVID-19 patients was analyzed 5 months and 10 months after their infection, using three different assays: Diasorin LIAISON®, Euroimmun®, Abbott Diagnostics® ARCHITECT. Results: Seropositivity at baseline differed significantly depending on the assay (Diasorin 81%, Euroimmun 83%, Abbott 59%). At follow-up antibody levels detected in the Diasorin assay were stable, while there was a significant loss in seropositivity in the Euroimmun and Abbott assays. Conclusion: There are significant differences in SARS-CoV-2 antibody kinetics based on the specific assay used.Trial registration number, date of registration DRKS00022549, 29.07.2020 “retrospectively registered”

Kinetics and seroprevalence of SARS-CoV-2 antibodies – a comparison of 3 different assays

PurposeComparing seroprevalence and antibody kinetics in three different commercially available assays for SARS-CoV-2.MethodsSerostatus of COVID-19 patients was analyzed 5 months and 10 months after their infection, using three different assays: Diasorin LIAISON®, Euroimmun®, Abbott Diagnostics® ARCHITECT.ResultsSeropositivity at baseline differed significantly depending on the assay (Diasorin 81%, Euroimmun 83%, Abbott 59%). At follow-up antibody levels detected in the Diasorin assay were stable, while there was a significant loss in seropositivity in the Euroimmun and Abbott assays.ConclusionThere are significant differences in SARS-CoV-2 antibody kinetics based on the specific assay used.Trial registration number, date of registrationDRKS00022549, 29.07.2020 “retrospectively registered”

A Novel Multiplex PCR Based Detection Assay Using Saliva or Nasopharyngeal Samples for SARS-Cov-2, Influenza A and B – Clinical Validation and Utility for Mass Surveillance

BackgroundThe COVID-19 pandemic has resulted in a significant diversion of human and material resources to COVID-19 diagnostics, to the extent that testing of viral pathogens normally contributing to seasonal respiratory tract infections have been markedly neglected. The global health burden due to influenza viruses and co-infection in COVID-19 patients remains undocumented but clearly pose serious public health consequences. To address these clinical and technical challenges, we have optimized and validated a highly sensitive RT-PCR based multiplex assay for the detection of SARS-CoV-2, Influenza A and B viruses in a single test.MethodsThis study evaluated clinical specimens (n=1411) that included 1019 saliva and 392 nasopharyngeal swab (NPS) samples collected in either healthcare or community setting. Samples were tested using two assays: FDA-EUA approved SARS-CoV-2 assay that targets N and ORF1ab gene, and the PKamp RT-PCR based assay that targets SARS-CoV-2, Influenza viruses A and B. The limit of detection (LoD) studies was conducted as per the FDA guidelines using SARS-CoV-2 and Influenza A and B reference control materials.ResultsOf the 1019 saliva samples, 17.0% (174/1019) tested positive for SARS-CoV-2 using either assay. The detection rate for SARS-CoV-2 was higher with our multiplex assay compared to SARS-specific assay [91.9% (160/174) vs. 87.9% (153/174)], respectively. Of the 392 NPS samples, 10.4% (41/392) tested positive for SARS-CoV-2 using either assay. The detection rate for SARS-CoV-2 was higher with our multiplex assay compared to SARS-specific assay [97.5% (40/41) vs. 92.1% (39/41)], respectively. The Ct values for SARS-CoV-2 were comparable between the two assays, whereas the Ct values of the housekeeping gene was significantly lower with multiplex assay compared to SARS-specific assay. The LoD was established as 60 copies/ml for SARS-CoV-2 and 180 copies/ml for Influenza A and B viruses for both saliva and NPS samples.ConclusionThis study presents clinical validation of a multiplex PCR assay for testing SARS-CoV-2, Influenza A and B viruses, using NPS and saliva samples, and demonstrates the feasibility of implementing the assay without disrupting the existing laboratory workflow. This novel assay uses the same instruments, sample types, supplies, and laboratory personnel as needed for the testing of SARS-CoV-2 virus.