Does the E gene provide additional information in SARS-CoV-2 PCR?

Zóka, András; Bekő, Gabriella

doi:10.1016/j.jiac.2021.08.017

Cited by 5 publications

(3 citation statements)

References 7 publications

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“…Although the ORF1ab gene is highly specific, it is considered to be less sensitive than other targets [26]. By contrast, among the possible RT-PCR targets, the E gene is the least specific, as it shows substantial sequence homology to other seasonal coronaviruses [27]. Therefore, we believe that in low-incidence settings (especially outside the winter season when circulation of other coronaviruses is uncommon), the detection of the E gene alone is suggestive of SARS-CoV-2 infection.…”

Section: Discussionmentioning

confidence: 99%

Comparative Diagnostic Accuracy of the STANDARD M10 Assay for the Molecular Diagnosis of SARS-CoV-2 in the Point-of-Care and Critical Care Settings

Domnich

Orsi

Trombetta

et al. 2022

JCM

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Accurate and rapid molecular diagnosis of COVID-19 is a crucial step to tackle the ongoing pandemic. The primary objective of this study was to estimate the real-world performance of the novel RT-PCR STANDARD M10 SARS-CoV-2 assay in a large number of nasopharyngeal (NP) specimens eluted in universal transport medium. The secondary objective was to evaluate the compatibility of this kit in testing NP samples eluted in an inactivated transport medium (essential for point-of-care testing) and lower respiratory tract (LRT) specimens, which are commonly collected in critical care. A total of 591 samples were analyzed. Compared with the standard extraction-based RT-PCR Allplex 2019-nCoV (time-to-result of 270 min), the sensitivities of the STANDARD M10 were 100% (95% CI: 98.1–100%), 95.5% (95% CI: 91.7–97.6%), and 99.5% (95% CI: 97.2–99.9%) for ≥1 gene, the ORF1ab gene, and the E gene, respectively, while the specificity was 100% (95% CI: 98.7–100%). The diagnostic accuracy was 100% in testing both NP samples eluted in an inactivated transport medium and LRT specimens. STANDARD M10 reliably detects SARS-CoV-2 in 60 min, may be used as a POC tool, and is suitable for testing LRT specimens in the critical care setting.

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Section: Discussionmentioning

confidence: 99%

Comparative Diagnostic Accuracy of the STANDARD M10 Assay for the Molecular Diagnosis of SARS-CoV-2 in the Point-of-Care and Critical Care Settings

Domnich

Orsi

Trombetta

et al. 2022

JCM

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“…4) The Maccura kit targets three different genes ( ORF1ab , N , and E ), whereas the Sansure kit only targets two genes ( ORF1ab and N ). Compared to the ORF1ab and N genes, the E gene is less specific because it has 93.5% sequence homology with other coronaviruses (Sarbecovirus SARS-CoV) [ 31 ]. It has also been shown that E gene mutations could affect the detection efficiency of the kits [ 32 ].…”

Section: Discussionmentioning

confidence: 99%

Comparison of the performance of two real-time fluorescent quantitative PCR kits for the detection of SARS-CoV-2 nucleic acid: a study based on large real clinical samples

Wang

et al. 2022

Virol J

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Background The global pandemic of coronavirus disease 2019 (COVID-19) has led to the development of multiple detection kits by national manufacturers for severe acute respiratory syndrome coronavirus 2 viral nucleic acid testing. The purpose of this study is to evaluate the performance of different kits (i.e., Maccura kit and Sansure kit) in real clinical work using clinical samples, which will help with the optimization of the test kits. Method During the past three months (March–May 2022), 1399 pharyngeal swabs from suspected COVID-19 patients have been initially screened using the Maccura kit in Jilin, China, and the test results were verified using the Sansure kit. The cycle threshold (Ct) values generated by the two kits were compared at different viral load levels. Correlation and consistency of the Ct values were investigated using Spearman correlation, Deming regression, and Bland–Altman plots. The cut-off Ct values of the Maccura kit were recalculated by referencing the result of the Sansure kit as a standard. Furthermore, another 163 pharyngeal swabs from suspected COVID-19 patients were collected to verify the new cut-off values. Results As a result of the Maccura kit testing, 1192 positive cases and 207 suspected COVID-19 cases were verified. After re-examination by the Sansure kit, 1118 positive cases were confirmed. The difference between the Ct values provided by the two kits was statistically significant, except for the N gene at high viral load. The Ct values obtained from the two kits presented a linear positive correlation. The Maccura kit used new cut-off Ct values of 35.00 (ORF1ab gene) and 35.07 (N gene). Based on that, the validation pass rate for the new cut-off Ct values was 91.41%. Conclusion Since the Maccura kit is found to have false positives in actual clinical work, recalculation of the cut-off values can reduce this occurrence. In order to improve the accuracy of the testing, laboratories should use two kits for COVID-19 testing, and the adjusting and optimizing of the kits for their situation are needed.

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“…There is a dual critical impact where COVID-19 pandemic worsened TB epidemic globally due to TB-services fragmentation and the additional pressures on health systems, which weakened the National TB programs [12][13][14][15] . RT-PCR (Real time PCR) is a simple, reliable, and rapid test that is widely used for the detection of patients with TB and without TB coinfected with SARS-CoV-2 [16][17][18][19][20][21] . It has a technical limit of detection (LOD) < 10 copies/ reaction and a detection threshold of 3.8 RNA molecules per reaction 22 .…”

Section: Introductionmentioning

confidence: 99%

An Initiative Report on Hospitalized Pulmonary TB Patients Co-Infected by SARS-CoV-2 during the COVID-19 Pandemic from Tertiary Referral Hospitals in Surabaya

Effendy,

Mertaniasih,

Soedarsono

et al. 2023

IJTID

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The enduring effect of SARS-CoV-2 pandemic has been experienced throughout the past and ongoing three years. Incidences of SARS-CoV-2 co-infected tuberculosis patients were reported globally, including in Italy and several European countries and resulted in a more complicated disease with severe clinical features and poorer clinical outcomes. To effectively manage this co-infection, it is important to be informed of the prevalence and characteristics of an acute SARS-CoV-2 co-infection on TB and determining factors of severity. Therefore, early warning signs can be recognized, monitored closely and managed. This retrospective study, carried out on hospitalized TB patients in Dr. Soetomo Hospital and Universitas Airlangga Hospital, Surabaya, Indonesia, used medical records from March 2020 to December 2022. Samples were from inpatients with a molecularly-Gene Xpert MTB/Rif-confirmed tuberculosis, and currently experienced respiratory and fever symptoms that resembles the symptoms of SARS-CoV-2 infection or exacerbation of tuberculosis. They are then screened and examined using a molecular diagnostic test, with real-time RT-PCR for SARS-CoV-2. A total of 54 (0.7%) patients had TB-SARS-CoV-2 co-infection among 7,786 suspected to have TB, of which 35 had Rifampicin Sensitive (TB-RS), while 19 had TB Rifampicin Resistant (TB-RR) co-infected with SARS-CoV-2. The remaining 2,586 suspected TB patients had only MTB, based on the detection methods of X-pert MTB/RIF, but with negative RT-PCR of SARS-CoV-2. The clinical severity and mortality of TB-SARS-CoV2 co-infected patients were significantly associated with the number of co-morbidities (p=0.0156), and serum haemoglobin levels (p=0.0672), in which p value < 0.05 is considered significant.

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Does the E gene provide additional information in SARS-CoV-2 PCR?

Cited by 5 publications

References 7 publications

Comparative Diagnostic Accuracy of the STANDARD M10 Assay for the Molecular Diagnosis of SARS-CoV-2 in the Point-of-Care and Critical Care Settings

Comparative Diagnostic Accuracy of the STANDARD M10 Assay for the Molecular Diagnosis of SARS-CoV-2 in the Point-of-Care and Critical Care Settings

Comparison of the performance of two real-time fluorescent quantitative PCR kits for the detection of SARS-CoV-2 nucleic acid: a study based on large real clinical samples

An Initiative Report on Hospitalized Pulmonary TB Patients Co-Infected by SARS-CoV-2 during the COVID-19 Pandemic from Tertiary Referral Hospitals in Surabaya

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