Confirming Multiplex Q-PCR Use in COVID-19 with Next Generation Sequencing: Strategies for Epidemiological Advantage

Abstract

Rapid classification and tracking of emerging SARS-CoV-2 variants are critical for understanding the transmission dynamics and developing strategies for interrupting the transmission chain. Next-Generation Sequencing (NGS) is an exceptional tool for whole-genome analysis and deciphering new mutations. The technique has been instrumental in identifying the Variants of Concern and tracking this pandemic. However, NGS remains expensive and time-consuming for large-scale monitoring of COVID-19. This study analyzed a total of 78 de-identified samples that screened positive for SARS-CoV-2 from two timeframes, August 2020 and July 2021. All 78 samples were classified into WHO lineages by whole genome sequencing then compared with two commercially available Q-PCR assays for spike protein mutation(s). The data showed good concordance with Q-PCR and NGS analysis for specific SARS-COV-2 lineages and characteristic mutations. Deployment of Q-PCR testing to detect known SARS-COV-2 variants may be extremely beneficial. These assays are quick and cost-effective, thus can be implemented as an alternative to sequencing for screening known mutations of SARS-COV-2 for clinical and epidemiological interest. The findings support the great potential for Q-PCR to be an effective strategy offering several COVID-19 epidemiological advantages.

Advantage of precision metagenomics for urinary tract infection diagnostics

“…The application of mNGS has shown promise in various UTI case studies (Li et al, 2020;Duan et al, 2022). But the adoption of mNGS is slow in the clinical laboratory due to the associated costs, expertise, and bioinformatic workflows required (Sharma et al, 2015;Carpenter et al, 2022). Moreover, extracting clinically relevant information can be challenging for target-agnostic approaches-based on rRNA gene amplification and shotgun sequencing after the depletion of host DNA-that promote a high microbiome yield (Price et al, 2021).…”

Optimization of the Illumina COVIDSeq™protocol for decentralized, cost-effective genomic surveillance

“…This modified protocol can potentially empower small resource-limited laboratories to contribute to local genomic surveillance. We have adopted this modified protocol for sequencing 153 genomes from East Texas, USA, and compared the results with PCR-based variant detection (Carpenter et al, 2022). High accuracy and reproducibility of this approach have been demonstrated in validating the COVIDSeq™ assay for clinical application according to Clinical Laboratory Improvement Amendments and College of American Pathologists guidelines.…”