Comparison of qualitative and quantitative analyses of COVID-19 clinical samples

Dang, Yan; Liu, Ning; Tan, Chianru; Feng, Yingmei; Yuan, Xingxing; Fan, Dongdong; Peng, Yanke; Jin, Ronghua; Guo, Yong; Lou, Jinli

doi:10.1016/j.cca.2020.08.033

Cited by 36 publications

(36 citation statements)

References 12 publications

(14 reference statements)

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“…175 The transcriptome of single human primary fibroblasts by drop-seq procedure during the first hours of HSV-1 lytic infection gave a deep insight into biological processes involving the early stages of HSV-1 infection. 176 scseq-RNA is a useful tool for virus-host analysis.…”

Section: Chinese Researchers Have Introduced a Pcr-based Crispr-cas13amentioning

confidence: 99%

Droplet digital PCR of viral ‎DNA/RNA, current progress, challenges, and future perspectives

Kojabad

Farzanehpour

Galeh

et al. 2021

Journal of Medical Virology

114

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High‐throughput droplet‐based digital PCR (ddPCR) is a refinement of the conventional polymerase chain reaction (PCR)‎ methods. In ddPCR, DNA/RNA is encapsulated stochastically inside the microdroplets as reaction chambers. A small percentage of the reaction chamber contains one or fewer copies of the DNA or RNA. After PCR amplification, concentrations are determined based on the proportion of nonfluorescent partitions through the Poisson distribution. Some of the main features of ddPCR include high sensitivity and specificity, absolute quantification without a standard curve, high reproducibility, good tolerance to PCR inhibitor, and high efficacy compared to conventional molecular methods. These advantages make ddPCR a valuable addition to the virologist's toolbox. The following review outlines the recent technological advances in ddPCR methods and their applications in viral identification.

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Section: Chinese Researchers Have Introduced a Pcr-based Crispr-cas13amentioning

confidence: 99%

Droplet digital PCR of viral ‎DNA/RNA, current progress, challenges, and future perspectives

Kojabad

Farzanehpour

Galeh

et al. 2021

Journal of Medical Virology

114

View full text Add to dashboard Cite

show abstract

“…Therefore, future research should address the association of ultra-low SARS-CoV-2 loads with infectivity, specific immunity and, particularly, the induction of neutralising antibodies. Based on the above arguments, semiquantitative results relative to viral load (high, middle and low viral load, borderline within the grey zone) instead of only qualitative RT-qPCR test results (positive × negative) would better assist clinicians in risk-stratifying patients and their contacts and choosing more appropriate quarantine conditions [ 9 ] and, eventually, more appropriate therapies [ 21 , 32 ].…”

Section: Resultsmentioning

confidence: 99%

Excellent option for mass testing during the SARS-CoV-2 pandemic: painless self-collection and direct RT-qPCR

Kriegová

Fillerová

Raška

et al. 2021

Virol J

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The early identification of asymptomatic yet infectious cases is vital to curb the 2019 coronavirus (COVID-19) pandemic and to control the disease in the post-pandemic era. In this paper, we propose a fast, inexpensive and high-throughput approach using painless nasal-swab self-collection followed by direct RT-qPCR for the sensitive PCR detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This approach was validated in a large prospective cohort study of 1038 subjects, analysed simultaneously using (1) nasopharyngeal swabs obtained with the assistance of healthcare personnel and analysed by classic two-step RT-qPCR on RNA isolates and (2) nasal swabs obtained by self-collection and analysed with direct RT-qPCR. Of these subjects, 28.6% tested positive for SARS-CoV-2 using nasopharyngeal swab sampling. Our direct RT-qPCR approach for self-collected nasal swabs performed well with results similar to those of the two-step RT-qPCR on RNA isolates, achieving 0.99 positive and 0.98 negative predictive values (cycle threshold [Ct] < 37). Our research also reports on grey-zone viraemia, including samples with near-cut-off Ct values (Ct ≥ 37). In all investigated subjects (n = 20) with grey-zone viraemia, the ultra-small viral load disappeared within hours or days with no symptoms. Overall, this study underscores the importance of painless nasal-swab self-collection and direct RT-qPCR for mass testing during the SARS-CoV-2 pandemic and in the post-pandemic era.

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“…Moreover, dPCR showed higher sensitivity than RT‐qPCR in the testing of clinical samples. Some samples from patients with confirmed COVID‐19 were classified as positive by dPCR but found inconclusive or negative by RT‐qPCR 16,18–22 . For example, Suo et al 16 .…”

Section: Applications Of Digital Pcr In Covid‐19 Pandemicmentioning

confidence: 99%

Applications of digital PCR in COVID‐19 pandemic

Tan

Fan

Wang

et al. 2021

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The coronavirus disease 2019 (COVID‐19) pandemic has led to a public health crisis and global panic. This infectious disease is caused by a novel coronavirus named severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2). Digital polymerase chain reaction (dPCR), which is an emerging nucleic acid amplification technology that allows absolute quantification of nucleic acids, plays an important role in the detection of SARS‐CoV‐2. In this review, we introduce the principle and advantages of dPCR, and review the applications of dPCR in the COVID‐19 pandemic, including detection of low copy number viruses, measurement of the viral load, preparation of reference materials, monitoring of virus concentration in the environment, detection of viral mutations, and evaluation of anti‐SARS‐CoV‐2 drugs. We also discuss the challenges of dPCR in clinical practice.

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Comparison of qualitative and quantitative analyses of COVID-19 clinical samples

Cited by 36 publications

References 12 publications

Droplet digital PCR of viral ‎DNA/RNA, current progress, challenges, and future perspectives

Droplet digital PCR of viral ‎DNA/RNA, current progress, challenges, and future perspectives

Excellent option for mass testing during the SARS-CoV-2 pandemic: painless self-collection and direct RT-qPCR

Applications of digital PCR in COVID‐19 pandemic

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