Molecular diagnostics in the era of COVID-19

Jayakody, Harindi; Kiddle, Guy; Perera, Semali; Tisi, Laurence; Leese, Hannah S.

doi:10.1039/d1ay00947h

Cited by 10 publications

(8 citation statements)

References 181 publications

(338 reference statements)

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“…Assay sensitivity is an attribute of several factors including sample type, sample collection and RNA extraction method, time of sampling, molecular assay design the number of gene targets, presence of positive/negative/internal extraction controls, among others 5 . The EM kit acquires its sensitivity through several of these factors, including the use of NP swab samples which have been reported to be highly sensitive for SARS-CoV-2 33 .…”

Section: Discussionmentioning

confidence: 99%

“…Thus, diagnosis of SARS-CoV-2 infection has focussed on testing upper respiratory tract specimens including nasopharyngeal (NP) & oropharyngeal (OP) swabs, nasal mid-turbinate specimens, saliva, nasopharyngeal/nasal washes or aspirates and lower respiratory tract specimens 4 . Among the diagnostic platforms available for the testing of COVID-19, reverse transcription polymerase chain reaction (RT-PCR) has been presented as the most sensitive detection method for the diagnosis of SARS-CoV-2 infection 5 . NP swabs are considered the gold standard sample type for SARS-CoV-2 diagnostic testing 6 , despite concerns being raised about the accuracy of NP swab collection when self-collected (due to discomfort) and the potential risk of transmission of SARS-CoV-2 among health care professionals with assisted collection 6 , 7 .…”

Section: Introductionmentioning

confidence: 99%

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Development of a high sensitivity RT-PCR assay for detection of SARS-CoV-2 in individual and pooled nasopharyngeal samples

Jayakody

Rowland

Pereira

et al. 2022

Sci Rep

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The COVID-19 pandemic requires sensitive detection of the SARS-CoV-2 virus from samples to ensure accurate detection of infected patients, an essential component of effective national track and trace programs. Due to the scaling challenges of large sample numbers, sample pooling is an attractive solution to reduce both extraction and amplification reagent costs, if high sensitivity can be maintained. We demonstrate that the Erba Molecular ErbaMDx SARS-CoV-2 RT-PCR Kit (EM kit) delivers high sensitivity, achieving analytical detection of 5 copies/reaction SARS-CoV-2 genomic RNA, and 200 copies/mL SARS-CoV-2 inactivated virus spiked into nasopharyngeal swab (NP) samples and extracted through workflow. Furthermore, the EM Kit demonstrates high sensitivity in both pooled (1 in 5) and non-pooled NP samples when compared to an FDA Emergency Use Authorization approved assay, following published FDA guidelines. These findings demonstrate that the EM Kit is suitable for sample pooling, with minimal impact on assay performance. As the COVID-19 pandemic progresses, high sensitivity assays such as the EM Kit will have an important role in ensuring high throughput and sensitive testing using pooled samples can be maintained, delivering the most cost-effective sample extraction and amplification option for national test and trace programs.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Development of a high sensitivity RT-PCR assay for detection of SARS-CoV-2 in individual and pooled nasopharyngeal samples

Jayakody

Rowland

Pereira

et al. 2022

Sci Rep

Self Cite

View full text Add to dashboard Cite

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“…Isothermal amplification-based methods for SARS-CoV-2 detection are represented by isothermal PCR amplification assays [76][77][78][79]. These methods comprise loop mediated isothermal amplification (RT-LAMP), recombinase polymerase amplification (RPA), nicking endonuclease amplification reaction (RT-NEAR), and transcription mediated amplification (RT-TMA) [80,81]. These methodological approaches provide the advantage of shorter turnaround times in comparison to RT-PCR, of approximately one hour in the majority of cases, and most can be employed at the point-of-care (POC) and within limited resource setting.…”

Section: Isothermal Amplification-based Methodsmentioning

confidence: 99%

Advanced Molecular and Immunological Diagnostic Methods to Detect SARS-CoV-2 Infection

et al. 2022

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COVID-19 emerged in late 2019 in China and quickly spread across the globe, causing over 521 million cases of infection and 6.26 million deaths to date. After 2 years, numerous advances have been made. First of all, the preventive vaccine, which has been implemented in record time, is effective in more than 95% of cases. Additionally, in the diagnostic field, there are numerous molecular and antigenic diagnostic kits that are equipped with high sensitivity and specificity. Real Time-PCR-based assays for the detection of viral RNA are currently considered the gold-standard method for SARS-CoV-2 diagnosis and can be used efficiently on pooled nasopharyngeal, or oropharyngeal samples for widespread screening. Moreover, additional, and more advanced molecular methods such as droplet-digital PCR (ddPCR), clustered regularly interspaced short palindromic repeats (CRISPR) and next-generation sequencing (NGS), are currently under development to detect the SARS-CoV-2 RNA. However, as the number of subjects infected with SARS-CoV-2 continuously increases globally, health care systems are being placed under increased stress. Thus, the clinical laboratory plays an important role, helping to select especially asymptomatic individuals who are actively carrying the live replicating virus, with fast and non-invasive molecular technologies. Recent diagnostic strategies, other than molecular methods, have been adopted to either detect viral antigens, i.e., antigen-based immunoassays, or human anti-SARS-CoV-2 antibodies, i.e., antibody-based immunoassays, in nasal or oropharyngeal swabs, as well as in blood or saliva samples. However, the role of mucosal sIgAs, which are essential in the control of viruses entering the body through mucosal surfaces, remains to be elucidated, and in particular the role of the immune response in counteracting SARS-CoV-2 infection, primarily at the site(s) of virus entry that appears to be promising.

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“…Reverse transcription quantitative PCR (RT-qPCR) has been suggested as the most reliable nucleic acid amplification test for the detection of SARS-CoV-2, and nasopharyngeal (Np) swabs are also considered to be the most suitable specimen for diagnoses [ 4 ]. However, the acquisition of Np swab specimens is an invasive process that poses a potential risk for SARS-CoV-2 transmission among healthcare workers.…”

Section: Introductionmentioning

confidence: 99%

Evaluation of an immunochromatography-based rapid antigen test, Inspecter Kowa® SARS-CoV-2, using saliva specimens for the detection of SARS-CoV-2

Kodana

Orihara

Tezuka

et al. 2023

Journal of Infection and Chemotherapy

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Molecular diagnostics in the era of COVID-19

Abstract: As the COVID-19 pandemic continues to escalate globally and acquires new mutations, accurate diagnostic technologies continue to play a vital role in controlling and understanding the epidemiology of this disease....

Cited by 10 publications

References 181 publications

Development of a high sensitivity RT-PCR assay for detection of SARS-CoV-2 in individual and pooled nasopharyngeal samples

Development of a high sensitivity RT-PCR assay for detection of SARS-CoV-2 in individual and pooled nasopharyngeal samples

Advanced Molecular and Immunological Diagnostic Methods to Detect SARS-CoV-2 Infection

Evaluation of an immunochromatography-based rapid antigen test, Inspecter Kowa® SARS-CoV-2, using saliva specimens for the detection of SARS-CoV-2

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