High—throughput and automated screening for COVID-19

Jonguitud‐Borrego, Nestor; Malcı, Koray; Anand, Mihir; Baluku, Erikan; Webb, Calum; Liu, Liang; Barba-Ostria, Carlos; Guamán, Linda P.; Liu, Hui; Rios‐Solis, Leonardo

doi:10.3389/fmedt.2022.969203

Cited by 8 publications

(4 citation statements)

References 50 publications

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“…59 The COVID-19 pandemic has also increased the implementation and popularity of automated high-throughput reverse transcriptasepolymerase chain reaction (RT-qPCR) for COVID-19 testing, which may benefit the development of molecular testing and precision cancer treatment. 60 Moreover, due to the effectiveness of ensuring biosafety and limiting infection, COVID-19 testing has become a landmark in patient care, with its relatively rapid turnaround and reliability.…”

Section: Reduc Ti On S In the Volume Of C Y Topathology S Pecimen S W...mentioning

confidence: 99%

The COVID‐19 pandemic has impeded cytopathology practices and hindered cancer screening and management

Huang

Chen

2023

Cytopathology

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The COVID‐19 pandemic has had a global impact on the environment and economy and has affected hospital administration and patient behaviour. Since human‐to‐human coronavirus transmission occurs via droplets and physical contact, health care professionals are particularly vulnerable to contracting COVID‐19. Many cytopathology laboratories updated their workflow, established new standard biosafety protocols, and built digital pathology or telescope platforms to mitigate these risks and deal with the shortage of health care personnel. The COVID‐19 pandemic also disrupted medical education—all indoor training events, including conferences, multidisciplinary tumour boards, seminars, and microscope inspections were postponed. As a result, many laboratories now use new web‐based applications and platforms to maintain educational programs and multidisciplinary tumour boards. To comply with government directives, health care facilities postponed non‐emergency surgeries, reduced the number of routine medical examinations, restricted visitor numbers, and scaled back cancer screening activities, resulting in a sharp decline in cytopathology diagnoses, cancer screening specimens, and molecular testing for cancer. Subsequent misses or delays in the diagnosis and treatment of cancer were not uncommon. This review aims to provide comprehensive summaries of the consequences of the COVID‐19 pandemic for cytopathology, particularly in terms of cancer diagnosis, workload, human resources, and molecular testing.

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Section: Reduc Ti On S In the Volume Of C Y Topathology S Pecimen S W...mentioning

confidence: 99%

The COVID‐19 pandemic has impeded cytopathology practices and hindered cancer screening and management

Huang

Chen

2023

Cytopathology

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“…However, their long production cycles and high costs make them less ideal for POC diagnostics 27 – 31 . Recent developments in sample-to-answer systems for COVID-19 diagnosis include rapid testing, high-throughput methods, and automated detection 32 – 34 . However, these systems have not become commonplace due to their cost, size, or design deficiencies.…”

Section: Introductionmentioning

confidence: 99%

An integrated microfluidic platform for nucleic acid testing

Sun,

Vopařilová,

Liu

et al. 2024

Microsyst Nanoeng

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This study presents a rapid and versatile low-cost sample-to-answer system for SARS-CoV-2 diagnostics. The system integrates the extraction and purification of nucleic acids, followed by amplification via either reverse transcription-quantitative polymerase chain reaction (RT–qPCR) or reverse transcription loop-mediated isothermal amplification (RT–LAMP). By meeting diverse diagnostic and reagent needs, the platform yields testing results that closely align with those of commercial RT-LAMP and RT‒qPCR systems. Notable advantages of our system include its speed and cost-effectiveness. The assay is completed within 28 min, including sample loading (5 min), ribonucleic acid (RNA) extraction (3 min), and RT-LAMP (20 min). The cost of each assay is ≈ $9.5, and this pricing is competitive against that of Food and Drug Administration (FDA)-approved commercial alternatives. Although some RNA loss during on-chip extraction is observed, the platform maintains a potential limit of detection lower than 297 copies. Portability makes the system particularly useful in environments where centralized laboratories are either unavailable or inconveniently located. Another key feature is the platform’s versatility, allowing users to choose between RT‒qPCR or RT‒LAMP tests based on specific requirements.

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“…But some of the mutations acquired during the evolution of the viral genome may lead to failure in RT-PCR amplification, for instance the 69-70 del in the S gene [ 9 , 10 ] as well as mutations occurring in the N gene [ 11 , 12 ]. Globally, this technique is considered the gold standard for the diagnosis of COVID-19 due to its sensitivity; therefore, many industries had developed commercial kits to reduce the typical run time and improve the methodology protocol [ 13 , 14 , 15 ]. The importance of a solid and proven stability of genomic regions is pivotal to design targets for a diagnostic kit, therefore in this study we compared 48 samples identified during the daily diagnostic workflow presenting a PCR peculiar result.…”

Section: Introductionmentioning

confidence: 99%

Genomic and Temporal Analysis of Deletions Correlated to qRT-PCR Dropout in N Gene in Alpha, Delta and Omicron Variants

Gatti,

Brandolini,

Mancini

et al. 2023

Viruses

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Since the first SARS-CoV-2 outbreak, mutations such as single nucleotide polymorphisms (SNPs) and insertion/deletions (INDELs) have changed and characterized the viral genome sequence, structure and protein folding leading to the onset of new variants. The presence of those alterations challenges not only the clinical field but also the diagnostic demand due to failures in gene detection or incompleteness of polymerase chain reaction (PCR) results. In particular, the analysis of understudied genes such as N and the investigation through whole-genome next generation sequencing (WG-NGS) of regions more prone to mutate can help in the identification of new or reacquired mutations, with the aim of designing robust and long-lasting primers. In 48 samples of SARS-CoV-2 (including Alpha, Delta and Omicron variants), a lack of N gene amplification was observed in the genomes analyzed through WG-NGS. Three gene regions were detected hosting the highest number of SNPs and INDELs. In several cases, the latter can interfere deeply with both the sensitivity of diagnostic methodologies and the final protein folding. The monitoring over time of the viral evolution and the reacquisition among different variants of the same mutations or different alterations within the same genomic positions can be relevant to avoid unnecessary consumption of resources.

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High—throughput and automated screening for COVID-19

Cited by 8 publications

References 50 publications

The COVID‐19 pandemic has impeded cytopathology practices and hindered cancer screening and management

The COVID‐19 pandemic has impeded cytopathology practices and hindered cancer screening and management

An integrated microfluidic platform for nucleic acid testing

Genomic and Temporal Analysis of Deletions Correlated to qRT-PCR Dropout in N Gene in Alpha, Delta and Omicron Variants

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