COVIDSeq as Laboratory Developed Test (LDT) for Diagnosis of SARSCoV- 2 Variants of Concern (VOC)

Carpenter, Rob E.; Tamrakar, Vaibhav K; Almas, Sadia; Brown, Emily; Sharma, Rahul

doi:10.26502/acbr.50170309

Cited by 9 publications

(3 citation statements)

References 34 publications

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“…Therefore, the modified protocol could 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 [ 8 ]. High accuracy and reproducibility of this approach have been demonstrated in validating the COVIDSeq™ RUO assay for clinical application according to Clinical Laboratory Improvement Amendments (CLIA) and College of American Pathologists (CAP) guidelines [ 6 ].…”

Section: Discussionmentioning

confidence: 99%

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

Carpenter

Tamrakar

Almas³

et al. 2023

Practical Laboratory Medicine

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Section: Discussionmentioning

confidence: 99%

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

Carpenter

Tamrakar

Almas³

et al. 2023

Practical Laboratory Medicine

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“…First, SARS-CoV-2, the responsible agent for the COVID-19 pandemic with global deaths of 6.5 million and climbing [56]. The importance of including a probed target for SARS-CoV-2 in any respiratory case or laboratory test cannot be understated, and we leave this discussion to scholars who have written much on this topic [57][58][59]. We do, however, consider in more depth the additional two microorganisms exclusively identified by mNGS that were characterized in this group: CAV and HRV-C-both targeting bronchial and alveolar epithelial cells and explicit for excessive uncontrolled lung inflammation if not cleared.…”

Section: (Which Was Not Certified By Peer Review)mentioning

confidence: 99%

Deciphering microbiota of acute upper respiratory infections: a comparative analysis of PCR and mNGS methods for lower respiratory trafficking potential

Almas¹,

Carpenter

Singh

et al. 2023

Preprint

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Although it is clinically important for acute respiratory tract (co)infections to have rapid and accurate diagnosis, it is critical that respiratory medicine understand the advantages of current laboratory methods. In this study, we tested nasopharyngeal samples (n=29) with a commercially available PCR assay and compared the results with hybridization capture-based mNGS workflow. Detection criteria for positive PCR samples was Ct<35 and for mNGS samples >40% target coverage, median depth of 1X and RPKM>10. A high degree of concordance (98.33% PPA and 100% NPA) was recorded. However, mNGS yielded positive 29 additional microorganisms (23 bacteria, 4 viruses, and 2 fungi) beyond PCR. We then characterize the microorganisms of each method into three phenotypic categories using the IDbyDNA Explify Platform for consideration of infectivity and trafficking potential to the lower respiratory region. The findings are significant for providing a comprehensive yet clinically relevant microbiology profile of acute upper respiratory infection, especially important in immunocompetent respiratory cases or where traditional syndromic approaches fail to identify pathogenicity. Accordingly, this technology can be used to supplement current syndromic-based tests and data can quickly and effectively be phenotypically characterized for trafficking potential, clinical (co)infection, and comorbid consideration with promise to reduce morbidity and mortality.

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“…Next-generation sequencing (NGS) technology has revolutionized our approach to managing outbreaks, such as the COVID-19 pandemic, and accumulating evidence supports its clinical applications for infectious diseases [1,2]. Over the past decade, molecular diagnostic techniques have experienced significant advancements, becoming increasingly integral to clinical microbiology laboratories.…”

Section: Introductionmentioning

confidence: 99%

Advancing Clinical Microbiology: Applications and Future of Next-Generation Sequencing

Carpenter

2024

SAR J Pathol Microbiol

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Next-generation sequencing (NGS) has reformed infectious disease management, including COVID-19. While real-time polymerase chain reaction (PCR) is widely used for rapid pathogen detection, it requires predefined targets. NGS offers an unbiased approach, detecting multiple pathogens simultaneously without prior knowledge. Despite its potential, NGS implementation in clinical settings faces challenges like high costs and technical complexity. NGS platforms like Illumina, Ion Torrent, and Nanopore provide high-throughput sequencing, identifying pathogens and resistance markers. Applications include whole genome sequencing (WGS), metagenomic NGS (mNGS), and targeted NGS (tNGS). Integrating NGS with conventional methods could improve diagnostics, but current evidence is mixed for supporting its widespread clinical use.

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COVIDSeq as Laboratory Developed Test (LDT) for Diagnosis of SARSCoV- 2 Variants of Concern (VOC)

Cited by 9 publications

References 34 publications

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

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

Deciphering microbiota of acute upper respiratory infections: a comparative analysis of PCR and mNGS methods for lower respiratory trafficking potential

Advancing Clinical Microbiology: Applications and Future of Next-Generation Sequencing

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