Real-time PCR Ct value in SARS-CoV-2 detection: RdRp or N gene?

Abbasi, Hamidreza; Tabaraei, Alijan; Hosseini, Seyed Mehran; Khosravi, Ayyoob; Nikoo, Hadi Razavi

doi:10.1007/s15010-021-01674-x

Cited by 17 publications

(14 citation statements)

References 12 publications

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“…Relative to the original strain, Omicron has 37 mutations in the S protein, of which 15 are in the receptor-binding domain, which is the target of many neutralizing antibodies [3,4,23]. Of note is that previous studies show that the N-gene primer and probe set has a higher specificity compared to that of the RdRp gene, making it one of the best and most accurate targets for SARS-CoV-2 detection [24]. This is in accordance to our findings which suggest that the E gene, followed by N and nsp14, based on the Ct value appearance, present more favourable targets for amplification, in comparison to the RdRp.…”

Section: Discussionmentioning

confidence: 99%

Does pre-existing immunity determine the course of SARS-CoV-2 infection in health-care workers? Single-center experience

Laura¹,

Dalmatin-Dragišić

Martinović

et al. 2022

Infection

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Objectives To assess the severity of symptoms, duration of infection and viral loads of health-care workers (HCWs) who tested positive for Coronavirus disease 2019 (COVID-19) during Omicron's prevalence, in regard to vaccination and previous infection. Methods During 2 weeks of highest rate of COVID-19 cases in Bosnia and Herzegovina, the positive nasopharyngeal swabs were analysed in 141 HCWs by reverse transcription quantitative PCR, targeting four different genes: RdRp, E, N and nsp14. Uniformed questionnaire was used to collect relevant sociodemographic and epidemiological data from HCWs divided into four groups: unvaccinated/not previously infected (group 1); unvaccinated/previously infected (group 2); vaccinated/not previously infected (group 3); and vaccinated/previously infected (group 4). ResultsWe observed that occurrence of fever and smell or taste loss were more frequent in group 1 (86.4% and 25%) and group 3 (76.9% and 19.2%), in comparison to group 2 (64.4% and 6.7%) and group 4 (69.2% and 3.8%), (p = 0.023 and p = 0.003). Although statistically not significant, group 2 (61.9%), group 3 (65.4%), and group 4 (70.8%) experienced negativization within 7 days of positive RT-qPCR test, whereas 51.2% of HCWs from group 1 tested negative later on. There is no significant difference between all four groups regarding Ct values of analysed genes. Conclusion During Omicron's prevalence, the vaccination had less substantial effect on symptomatic disease among HCWs, while fever and loss of smell or taste were considerably less likely to occur upon reinfection. Since viral loads and negativization periods do not seem to significantly vary, irrespective of pre-existing immunity, systemic vaccination and mask-wearing should still be considered among HCWs.

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Section: Discussionmentioning

confidence: 99%

Does pre-existing immunity determine the course of SARS-CoV-2 infection in health-care workers? Single-center experience

Laura¹,

Dalmatin-Dragišić

Martinović

et al. 2022

Infection

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“…Ct value analysis of SARS‐CoV‐2 RT‐PCR detection in the clinical samples showed that the N‐gene is one of the favorable targets for amplification. 20 Thus, N gene was selected as MIRA target. The MIRA reactions were performed to enrich the target site in the SARS‐CoV‐2 N gene with products from AMP‐Future Biotech Co. Ltd. 21 The principle for the MIRA primer design is the same as that of recombinase polymerase amplification, recommending 30−35nt length.…”

Section: Methodsmentioning

confidence: 99%

“…Ct value analysis of SARS-CoV-2 RT-PCR detection in the clinical samples showed that the N-gene is one of the favorable targets for amplification. 20 Thus, N gene was selected as MIRA target. The MIRA reactions were performed to enrich the target site in the SARS-CoV-2 N gene with products from AMP-Future Biotech Co.…”

Section: Multienzyme Isothermal Rapid Amplification (Mira)mentioning

confidence: 99%

Highly sensitive and rapid detection of SARS‐CoV‐2 via a portable CRISPR‐Cas13a‐based lateral flow assay

Liu¹,

Chang

Chen³

et al. 2022

Journal of Medical Virology

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To rapidly identify individuals infected with severe acute respiratory syndrome coronavirus‐2 (SARS‐CoV‐2) and control the spread of coronavirus disease (COVID‐19), there is an urgent need for highly sensitive on‐site virus detection methods. A clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR‐associated protein (Cas)‐based molecular diagnostic method was developed for this purpose. Here, a CRISPR system‐mediated lateral flow assay (LFA) for SARS‐CoV‐2 was established based on multienzyme isothermal rapid amplification, CRISPR‐Cas13a nuclease, and LFA. To improve the limit of detection (LoD), the crispr RNA, amplification primer, and probe were screened, in addition to concentrations of various components in the reaction system. The LoD of CRISPR detection was improved to 0.25 copy/μl in both fluorescence‐ and immunochromatography‐based assays. To enhance the quality control of the CRISPR‐based LFA method, glyceraldehyde‐3‐phosphate dehydrogenase was detected as a reference using a triple‐line strip design in a lateral flow strip. In total, 52 COVID‐19‐positive and 101 COVID‐19‐negative clinical samples examined by reverse transcription polymerase chain reaction (RT‐PCR) were tested using the CRISPR immunochromatographic detection technique. Results revealed 100% consistency, indicating the comparable effectiveness of our method to that of RT‐PCR. In conclusion, this approach significantly improves the sensitivity and reliability of CRISPR‐mediated LFA and provides a crucial tool for on‐site detection of SARS‐CoV‐2.

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“…In the symptomatic phase or Viral phase, in which the clinical manifestations of the disease usually start 5 days after exposure, patients may experience symptoms such as fever, dyspnea, sore throat, chest pain, expectoration, cough, and myalgia, but fever, cough, and fatigue are common symptoms of COVID-19 [59]. At the present, there are different confirming diagnostic methods for the detection of SARS-CoV-2 in patients, around the time of symptom onset, in laboratories, as follows: (1) nucleic acid tests like real-time RT-PCR or next-generation sequencing; (2) antibody or antigen detection tests, including enzymelinked immunosorbent assay; (3) chest computed tomography and spectroscopic techniques [60][61][62][63]. Real-time RT-PCR on nasopharyngeal and oropharyngeal swabs is considered the "gold standard" for confirming the diagnosis in clinical cases of COVID-19 [64,65].…”

Section: Inflammatory Responsesmentioning

confidence: 99%

Features of Pathobiology and Clinical Translation of Approved Treatments for Coronavirus Disease 2019

et al. 2021

Self Cite

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Background: The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is currently the most important etiological agent of acute respiratory distress syndrome (ARDS) with millions of infections and deaths in the last two years worldwide. Several reasons and parameters are responsible for the difficult management of coronavirus disease-2019 (COVID-19) patients; the first is virus behavioral factors such as high transmission rate, and the different molecular and cellular mechanisms of pathogenesis remain a matter of controversy, is another factor. Summary: In the present review, we attempted to explain about features of SARS-COV-2, particularly focusing on the various aspects of pathogenesis and treatment strategies. Key Messages: We note evidence for the understanding of the precise molecular and cellular mechanisms of SARS-CoV-2 pathogenesis, which can help design the appropriate drug or vaccine. Additionally, and importantly, we reported the updated issues associated with the history and development of treatment strategies such as, drugs, vaccines, and other medications that have been approved or under consideration in clinics and markets worldwide.

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Real-time PCR Ct value in SARS-CoV-2 detection: RdRp or N gene?

Cited by 17 publications

References 12 publications

Does pre-existing immunity determine the course of SARS-CoV-2 infection in health-care workers? Single-center experience

Does pre-existing immunity determine the course of SARS-CoV-2 infection in health-care workers? Single-center experience

Highly sensitive and rapid detection of SARS‐CoV‐2 via a portable CRISPR‐Cas13a‐based lateral flow assay

Features of Pathobiology and Clinical Translation of Approved Treatments for Coronavirus Disease 2019

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