Dataset Information

Three Novel Real-Time RT-PCR Assays for Detection of COVID-19 Virus.

ABSTRACT:

What is already known on this topic?

A novel human coronavirus, known as SARS-CoV-2 or 2019-nCoV, is the causative agent of the coronavirus disease 2019 (COVID-19). We have released the primers and probes of real-time reverse transcription polymerase chain reaction (rRT-PCR) assays for the laboratory detection of COVID-19 infection.

What is added by this report?

Here we provide detailed technical data and evaluate the performance of three novel rRT-PCR assays targeting the ORF1ab, N, and E genes for detection of COVID-19 infection. The application of rRT-PCR assays among four types of specimens (alveolar lavage, sputum, throat swabs, and stool) from patients with COVID-19 indicated that the mean viral loads detected in sputum were higher than other specimens.

What are the implications for public health practice?

These rRT-PCR assays reported here could be used for laboratory diagnosis of COVID-19 infection with high sensitivity, specificity, and applicability. Sputum rather than throat swabs and stool should be a priority for specimen collection for laboratory detection of COVID-19.

SUBMITTER: Niu P

PROVIDER: S-EPMC8393056 | biostudies-literature | 2020 Jun

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Three Novel Real-Time RT-PCR Assays for Detection of COVID-19 Virus.

Niu Peihua P Lu Roujian R Zhao Li L Wang Huijuan H Huang Baoying B Ye Fei F Wang Wenling W Tan Wenjie W

China CDC weekly 20200601 25

<h4>What is already known on this topic?</h4>A novel human coronavirus, known as SARS-CoV-2 or 2019-nCoV, is the causative agent of the coronavirus disease 2019 (COVID-19). We have released the primers and probes of real-time reverse transcription polymerase chain reaction (rRT-PCR) assays for the laboratory detection of COVID-19 infection.<h4>What is added by this report?</h4>Here we provide detailed technical data and evaluate the performance of three novel rRT-PCR assays targeting the ORF1ab, ...[more]

PMID: 34594677

Similar Datasets

Project description:Epizootic haemorrhagic disease virus (EHDV) is an emerging arboviral pathogen of wild and domestic ruminants worldwide. It is closely related to bluetongue virus (BTV) and is transmitted by adult females of competent Culicoides vector species. The EHDV genome consists of ten linear double-stranded (ds)RNA segments, encoding five non-structural and seven structural proteins. Genome-segment reassortment contributes to a high level of genetic variation in individual virus strains, particularly in the areas where multiple and distinct virus lineages co-circulate. In spite of the relatively close relationship between BTV and EHDV herd-immunity to BTV does not appear to protect against the introduction and infection of animals by EHDV. Although EHDV can cause up to 80% morbidity in affected animals, vaccination with the homologous EHDV serotype is protective. Outer-capsid protein VP2, encoded by Seg-2, is the most variable of the EHDV proteins and determines both the specificity of reactions with neutralizing antibodies and consequently the identity of the eight EHDV serotypes. In contrast, VP6 (the viral helicase), encoded by Seg-9, is highly conserved, representing a virus species/serogroup-specific antigen. We report the development and evaluation of quantitative (q)RT-PCR assays targeting EHDV Seg-9 that can detect all EHDV strains (regardless of geographic origin/topotype/serotype), as well as type-specific assays targeting Seg-2 of the eight EHDV serotypes. The assays were evaluated using orbivirus isolates from the 'Orbivirus reference collection' (ORC) at The Pirbright Institute and were shown to be EHDV pan-reactive or type-specific. They can be used for rapid, sensitive and reliable detection and identification (typing) of EHDV RNA from infected blood, tissue samples, homogenized Culicoides, or tissue culture supernatant. None of the assays detected RNA from closely related but heterologous orbiviruses, or from uninfected host animals or cell cultures. The techniques presented could be used for both surveillance and vaccine matching (serotype identification) as part of control strategies for incursions in wild and domestic animal species.

Project description:BackgroundDengue is one of the leading causes of morbidity in tropical and subtropical regions and infection with any of the four dengue virus serotypes (DENV1-4) result in a wide range of clinical manifestations. Given the geographic expansion of DENV1-4, assays for serotyping are needed to be able to perform surveillance and epidemiological studies. In this study, we describe the design and validation of one-step real-time serotype-specific DENV RT-PCR assays.MethodsThe DENV1, DENV2, DENV3, and DENV4 RT-PCR assays were designed using all available whole genome DENV sequences in the NCBI nucleotide collection. Because of the high mutation rates of RNA viruses, the assays were performed in singleplex format to enable quick modifications to the primer and probe sequences when new genetic variants emerge. The analytical performance of the RT-PCR assays were evaluated using in vitro transcribed RNA and their specificity was determined by testing 24 DENV isolates, external DENV control panels and RNA preparation of non-DENV flaviviruses and non-dengue clinical samples. Additionally, the clinical performance of the serotype-specific DENV RT-PCR were compared to that of the CDC DENV-1-4 RT-PCR using 85 clinical samples collected from patients presenting with acute dengue.ResultsThe RT-PCR assays were found to be specific for their respective serotype and did not cross-react with other flaviviruses or human mRNA. All assays had a linear dynamic range of 10(2) to 10(6) copies/reaction with detection limits between 12 and 44 copies/reaction. When testing sera from 85 confirmed acute dengue cases, the serotype-specific DENV RT-PCR assays had 100 % positive agreement with the FDA-approved CDC DENV-1-4 RT-PCR assay performed in a singleplex format. Additionally 15 samples that tested negative in the CDC DENV-1-4- RT-PCR assay were found positive using the serotype-specific DENV RT-PCR assays.ConclusionsOur results suggest that these RT-PCR assays are useful alternatives to existing methods for serotyping DENV in clinical sera.

Dataset Information

Three Novel Real-Time RT-PCR Assays for Detection of COVID-19 Virus.

What is already known on this topic?

What is added by this report?

What are the implications for public health practice?

Publications

Three Novel Real-Time RT-PCR Assays for Detection of COVID-19 Virus.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets