False-negative rate of SARS-CoV-2 RT-PCR tests and its relationship to test timing and illness severity: A case series

Takahashi, Hidenori; Ichinose, Naoki; Okada, Yoshinori

doi:10.1016/j.idcr.2022.e01496

Cited by 14 publications

(8 citation statements)

References 17 publications

(26 reference statements)

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“…Figure 7 shows that while the noise has very limited effects on the number of tests required by each GT scheme, it does have the expected effect of increasing the FNR of both individual and group tests. For individual testing, the noise function we fit appears to correspond to an FNR of just under 0.05, which is comparable to the empirically determined values reported in [33] and [35]. The FNR values of both GT schemes are also consistently slightly higher than those of individual testing.…”

Section: Algorithms and Resultssupporting

confidence: 84%

Semi-Quantitative Group Testing for Efficient and Accurate qPCR Screening of Pathogens with a Wide Range of Loads

Nambiar

Pan

Rana

et al. 2023

Preprint

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Pathogenic infections pose a significant threat to global health, affecting millions of people every year and presenting substantial challenges to healthcare systems worldwide. Efficient and timely testing plays a critical role in disease control and transmission prevention. Group testing is a well-established method for reducing the number of tests needed to screen large populations when the disease prevalence is low. However, it does not fully utilize the quantitative information provided by qPCR methods, nor is it able to accommodate a wide range of pathogen loads. To address these issues, we introduce a novel adaptive semi-quantitative group testing (SQGT) scheme to efficiently screen populations via two-stage qPCR testing. The SQGT method quantizes cycle threshold (Ct) values into multiple bins, leveraging the information from the first stage of screening to improve the detection sensitivity. Dynamic Ct threshold adjustments mitigate dilution effects and enhance test accuracy. Comparisons with traditional binary outcome GT methods show that SQGT reduces the number of tests by 24% while maintaining a negligible false negative rate.

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Section: Algorithms and Resultssupporting

confidence: 84%

Semi-Quantitative Group Testing for Efficient and Accurate qPCR Screening of Pathogens with a Wide Range of Loads

Nambiar

Pan

Rana

et al. 2023

Preprint

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“…The presence of anti-NC-positivity in individuals vaccinated with BNT162b2 in HCW Group B1 who had no COVID-19 history might indicate asymptomatic infections or low viral loads. Takahashi et al [ 26 ] indicated that stage of infection can lead to false-negative PCR results due to low viral load levels.…”

Section: Discussionmentioning

confidence: 99%

COVID-19 Antibody Levels among Various Vaccination Groups, One-Year Antibody Follow-Up in Two University Hospitals from Western and Central Turkey

Soylu,

Sağıroğlu,

Özarslan

et al. 2024

Vaccines

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Various clinical outcomes, reinfections, vaccination programs, and antibody responses resulted from the COVID-19 pandemic. This study investigated the time-dependent changes in SARS-CoV-2 antibody responses in infected and/or vaccinated and unvaccinated individuals and to provide insights into spike and nucleocapsid antibodies, which fluctuate during infectious and non-infectious states. This cohort study was carried out at the Ege University Faculty of Medicine hospital in İzmir (western Turkey) and the Erciyes University Faculty of Medicine hospital in Kayseri (central Turkey) between December 2021 and January 2023, which coincided with the second half of COVID-19 pandemic. The study included 100 COVID-19 PCR-positive patients and 190 healthcare workers (HCWs). Antibody levels were followed up via quantitative anti-SARS-CoV-2 spike and qualitative anti-nucleocapsid immunoassays (Elecsys™). Antibody levels declined after infection but persisted for at least 6–8 months. Individuals who had received only CoronaVac had higher anti-nucleocapsid antibody levels in the early months than those who received mixed vaccination. However, anti-spike antibodies persisted longer and at higher levels in individuals who had received mixed vaccinations. This suggests that combining two different vaccine platforms may provide a synergistic effect, resulting in more durable and broad-spectrum immunity against SARS-CoV-2. The study provides information about the vaccination and antibody status of healthcare workers in the second half of the pandemic and provides valuable insights into the dynamics of antibody responses to COVID-19 infection and vaccination.

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“…Due to cost and time factors, serological assays that are positively associated with true antibody concentration (IgM/IgG) can be an important approach to identify asymptomatic patients by conducting epidemiological surveys. Additionally, these assays can also be used for COVID patients with negative rRT-PCR results in the later stages of infection [3,4]. Serological assays, such as lateral flow assays (LFAs) and enzyme-linked immunosorbent assays (ELISAs), are valuable tools for epidemiological surveys, helping to understand the spread of the disease, the impact of containment measures, monitoring herd immunity, predicting risk, and prioritizing groups for vaccination [5][6][7].…”

Section: Introductionmentioning

confidence: 99%

VLP-ELISA for the Detection of IgG Antibodies against Spike, Envelope, and Membrane Antigens of SARS-CoV-2 in Indian Population

et al. 2023

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Background: Serological methods to conduct epidemiological survey are often directed only against the spike protein. To overcome this limitation, we have designed PRAK-03202, a virus-like particle (VLP), by inserting three antigens (Spike, envelope and membrane) of SARS-CoV-2 into a highly characterized S. cerevisiae-based D-Crypt™ platform. Methods: Dot blot analysis was performed to confirm the presence of S, E, and M proteins in PRAK-03202. The number of particles in PRAK-03202 was measured using nanoparticle tracking analysis (NTA). The sensitivity of VLP-ELISA was evaluated in 100 COVID positive. PRAK-03202 was produced at a 5 L scale using fed-batch fermentation. Results: Dot blot confirmed the presence of S, E, and M proteins in PRAK-03202. The number of particles in PRAK-03202 was 1.21 × 109 mL−1. In samples collected >14 days after symptom onset, the sensitivity, specificity, and accuracy of VLP-ELISA were 96%. We did not observe any significant differences in sensitivity, specificity, and accuracy when post-COVID-19 samples were used as negative controls compared to pre-COVID-samples. At a scale of 5 L, the total yield of PRAK-03202 was 100–120 mg/L. Conclusion: In conclusion, we have successfully developed an in-house VLP-ELISA to detect IgG antibodies against three antigens of SARS-CoV-2 as a simple and affordable alternative test.

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False-negative rate of SARS-CoV-2 RT-PCR tests and its relationship to test timing and illness severity: A case series

Cited by 14 publications

References 17 publications

Semi-Quantitative Group Testing for Efficient and Accurate qPCR Screening of Pathogens with a Wide Range of Loads

Semi-Quantitative Group Testing for Efficient and Accurate qPCR Screening of Pathogens with a Wide Range of Loads

COVID-19 Antibody Levels among Various Vaccination Groups, One-Year Antibody Follow-Up in Two University Hospitals from Western and Central Turkey

VLP-ELISA for the Detection of IgG Antibodies against Spike, Envelope, and Membrane Antigens of SARS-CoV-2 in Indian Population

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