False-Negative RT-PCR Findings and Double Mutant Variant as Factors of an Overwhelming Second Wave of COVID-19 in India: an Emerging Global Health Disaster

Background: Even though Real-Time Polymerase Chain Reaction (RT-PCR) is a gold standard for confirming COVID-19, it continues to be plagued by a lack of RT-PCR kits and the potential of false-negative results. Hence, during the second wave of COVID-19 in India, Computed Tomography (CT) scan is an emerging diagnostic tool in evaluating the severity of illness in COVID-19 pneumonia. The present study endeavored to assess chest CT features of COVID-19 pneumonia in Indian population. Methods: This was a single-center, retrospective, observational study conducted in 300 consecutive adults RT-PCR confirmed COVID-19 patients from 1, Jan 2021 to 31, March 2021 at a private radio diagnostic center. Data regarding baseline demographics, clinical and laboratory characteristics, extent, pattern, and type of abnormal CT findings were noted. Results: The study population (204 males and 108 females) had mean age of 43.18 ± 8.27 years. Our study's most common clinical presentation was cough (48.1%) and fever (47.1%), respectively. Lung parenchymal abnormalities were found in 294 (94.2%) patients. Abnormal CT findings revealed the involvement of bilateral (45.6%) and multilobar (42.9%) with a predominant peripheral (92.3%) and posterior (80.8%) distribution. According to the type of opacity, Ground Glass Opacity (GGO) was the dominant abnormality found in 270 (91.8%) patients, in which pure GGO (36.7%), GGO with crazy paving pattern (39.8%), and GGO mixed with consolidation (52.0 %) were noted. Peri-lesional or intralesional segmental or subsegmental pulmonary vessel enlargement was found in 192 (65.3 %) patients. Conclusion: During the second wave of COVID-19, a chest CT scan is a modality of choice in diagnosing COVID-19 pneumonia and related lung parenchymal changes.

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Second wave of COVID-19 pandemic is depressing: is there any hope?

International Journal of Community Medicine and Public Health ◽

10.18203/2394-6040.ijcmph20213828 ◽

2021 ◽

Vol 8 (10) ◽

pp. 5156

Author(s):

Gaurav Govil ◽

Lavindra Tomar ◽

Pawan Dhawan

Keyword(s):

Mental Health ◽

Double Mutant ◽

Mutant Variant ◽

The Impact ◽

Second Wave ◽

High Infectivity

We read the article detailing the impact on the mental health amongst the residents of Assam during COVID-19 lockdown with a lot of anguish and concern. The rise of second wave of COVID-19 pandemic is more unforgiving due to the high infectivity of the double mutant variant. The deadly cost of ignorance has compounded the misery aggravating the mental imbalance.Hope seems elusive during the evolving crisis with highly constrained healthcare infrastructure, resources and high fatality.

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Scoring System for the Diagnosis of COVID-19

The Open Public Health Journal ◽

10.2174/1874944502013010413 ◽

2020 ◽

Vol 13 (1) ◽

pp. 413-414 ◽

Cited By ~ 1

Author(s):

Mohamed Farouk Allam

Keyword(s):

Scoring System ◽

Clinical Symptoms ◽

False Negative ◽

Nasopharyngeal Swab ◽

Rt Pcr ◽

Pcr Assay ◽

Negative Results ◽

False Negative Results ◽

Symptoms And Signs

Due to the international spread of COVID-19, the difficulty of collecting nasopharyngeal swab specimen from all suspected patients, the costs of RT-PCR and CT, and the false negative results of RT-PCR assay in 41% of COVID-19 patients, a scoring system is needed to classify the suspected patients in order to determine the need for follow-up, home isolation, quarantine or the conduction of further investigations. A scoring system is proposed as a diagnostic tool for suspected patients. It includes Epidemiological Evidence of Exposure, Clinical Symptoms and Signs, and Investigations (if available). This scoring system is simple, could be calculated in a few minutes, and incorporates the main possible data/findings of any patient.

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Viral Dynamics and Real-Time RT-PCR Ct Values Correlation with Disease Severity in COVID-19

Diagnostics ◽

10.3390/diagnostics11061091 ◽

2021 ◽

Vol 11 (6) ◽

pp. 1091

Author(s):

Ali A. Rabaan ◽

Raghavendra Tirupathi ◽

Anupam A Sule ◽

Jehad Aldali ◽

Abbas Al Mutair ◽

...

Keyword(s):

Viral Load ◽

Real Time ◽

Disease Severity ◽

False Negative ◽

Influential Factors ◽

Confirmatory Test ◽

Acid Extraction ◽

Rt Pcr ◽

Viral Kinetics ◽

Ct Value

Real-time RT-PCR is considered the gold standard confirmatory test for coronavirus disease 2019 (COVID-19). However, many scientists disagree, and it is essential to understand that several factors and variables can cause a false-negative test. In this context, cycle threshold (Ct) values are being utilized to diagnose or predict SARS-CoV-2 infection. This practice has a significant clinical utility as Ct values can be correlated with the viral load. In addition, Ct values have a strong correlation with multiple haematological and biochemical markers. However, it is essential to consider that Ct values might be affected by pre-analytic, analytic, and post-analytical variables such as collection technique, specimen type, sampling time, viral kinetics, transport and storage conditions, nucleic acid extraction, viral RNA load, primer designing, real-time PCR efficiency, and Ct value determination method. Therefore, understanding the interpretation of Ct values and other influential factors could play a crucial role in interpreting viral load and disease severity. In several clinical studies consisting of small or large sample sizes, several discrepancies exist regarding a significant positive correlation between the Ct value and disease severity in COVID-19. In this context, a revised review of the literature has been conducted to fill the knowledge gaps regarding the correlations between Ct values and severity/fatality rates of patients with COVID-19. Various databases such as PubMed, Science Direct, Medline, Scopus, and Google Scholar were searched up to April 2021 by using keywords including “RT-PCR or viral load”, “SARS-CoV-2 and RT-PCR”, “Ct value and viral load”, “Ct value or COVID-19”. Research articles were extracted and selected independently by the authors and included in the present review based on their relevance to the study. The current narrative review explores the correlation of Ct values with mortality, disease progression, severity, and infectivity. We also discuss the factors that can affect these values, such as collection technique, type of swab, sampling method, etc.

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Evaluation of SARS-CoV-2 antigen-based rapid diagnostic kits in Pakistan: formulation of COVID-19 national testing strategy

Virology Journal ◽

10.1186/s12985-021-01505-3 ◽

2021 ◽

Vol 18 (1) ◽

Author(s):

Umar Saeed ◽

Sara Rizwan Uppal ◽

Zahra Zahid Piracha ◽

Azhar Rasheed ◽

Zubair Aftab ◽

...

Keyword(s):

Gold Standard ◽

Injection Drug Users ◽

Drug Users ◽

Diagnostic Testing ◽

False Negative ◽

Cross Sectional Study ◽

Nasopharyngeal Swab ◽

Rt Pcr ◽

Cross Sectional ◽

Negative Results

AbstractRapid diagnosis of SARS-CoV-2 during pandemic enables timely treatment and prevention of COVID-19. Evaluating the accuracy and reliability of rapid diagnostic testing kits is crucial for surveillance and diagnosis of SARS-CoV-2 infections in general population, injection drug users, multi-transfused populations, healthcare workers, prisoners, barbers and other high risk populations. The aim of this study was to evaluate performance and effectiveness of nasopharyngeal swab (NSP) and saliva based rapid antigen detection testing kits in comparison with USFDA approved triple target gold standard real-time polymerase chain reaction. A cross-sectional study was conducted on 33,000 COVID-19 suspected patients. From RT-PCR positive patients, nasopharyngeal swab (NSP) and saliva samples were obtained for evaluation of rapid COVID-19 testing kits (RDT). 100/33,000 (0.3%) of specimens were RT-PCR positive for SARS-CoV-2. Among RT-PCR positive, 62% were males, 34% were females, and 4% were children. The NSP-RDT (Lepu Medical China) analysis revealed 53% reactivity among males, 58% reactivity among females, and 25% reactivity among children. However saliva based RDT (Lepu Medical China) analysis showed 21% reactivity among males and 23% among females, and no reactivity in children. False negative results were significantly more pronounced in saliva based RDT as compared to NSP-RDT. The sensitivity of these NSP-RDT and saliva based RDT were 52% and 21% respectively. The RDTs evaluated in this study showed limited sensitivities in comparison to gold standard RT-PCR, indicating that there is a dire need in Pakistan for development of suitable testing to improve accurate COVID-19 diagnosis in line with national demands.

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Superiority of MALDI-TOF Mass Spectrometry over Real-Time PCR for SARS-CoV-2 RNA Detection

Viruses ◽

10.3390/v13050730 ◽

2021 ◽

Vol 13 (5) ◽

pp. 730

Author(s):

Magda Rybicka ◽

Ewa Miłosz ◽

Krzysztof Piotr Bielawski

Keyword(s):

Mass Spectrometry ◽

Gold Standard ◽

Viral Genome ◽

False Negative ◽

Rt Pcr ◽

Rna Detection ◽

Maldi Tof ◽

Negative Results ◽

False Negative Results ◽

Pcr Test

At present, the RT-PCR test remains the gold standard for early diagnosis of SARS-CoV-2. Nevertheless, there is growing evidence demonstrating that this technique may generate false-negative results. Here, we aimed to compare the new mass spectrometry-based assay MassARRAY® SARS-CoV-2 Panel with the RT-PCR diagnostic test approved for clinical use. The study group consisted of 168 suspected patients with symptoms of a respiratory infection. After simultaneous analysis by RT-PCR and mass spectrometry methods, we obtained discordant results for 17 samples (10.12%). Within fifteen samples officially reported as presumptive positive, 13 were positive according to the MS-based assay. Moreover, four samples reported by the officially approved RT-PCR as negative were positive in at least one MS assay. We have successfully demonstrated superior sensitivity of the MS-based assay in SARS-CoV-2 detection, showing that MALDI-TOF MS seems to be ideal for the detection as well as discrimination of mutations within the viral genome.

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Performance of Unobserved Self-Collected Nasal Swabs for Detection of SARS-CoV-2 by RT-PCR Utilizing a Remote Specimen Collection Strategy

Open Forum Infectious Diseases ◽

10.1093/ofid/ofab039 ◽

2021 ◽

Author(s):

Ron M Kagan ◽

Amy A Rogers ◽

Gwynngelle A Borillo ◽

Nigel J Clarke ◽

Elizabeth M Marlowe

Keyword(s):

Return To Work ◽

Screening Program ◽

False Negative ◽

N Gene ◽

Rt Pcr ◽

Pooled Testing ◽

Specimen Collection ◽

Asymptomatic Patients ◽

Nasal Swabs ◽

The Impact

Abstract Background The use of a remote specimen collection strategy employing a kit designed for unobserved self-collection for SARS-CoV-2 RT-PCR can decrease the use of PPE and exposure risk. To assess the impact of unobserved specimen self-collection on test performance, we examined results from a SARS-CoV-2 qualitative RT-PCR test for self-collected specimens from participants in a return-to-work screening program and assessed the impact of a pooled testing strategy in this cohort. Methods Self-collected anterior nasal swabs from employee return to work programs were tested using the Quest Diagnostics SARS-CoV-2 RT-PCR EUA. The Ct values for the N1 and N3 N-gene targets and a human RNase P (RP) gene control target were tabulated. For comparison, we utilized Ct values from a cohort of HCP-collected specimens from patients with and without COVID-19 symptoms. Results Among 47,923 participants, 1.8% were positive. RP failed to amplify for 13/115,435 (0.011%) specimens. The median (IQR) Cts were 32.7 (25.0-35.7) for N1 and 31.3 (23.8-34.2) for N3. Median Ct values in the self-collected cohort were significantly higher than those of symptomatic, but not asymptomatic patients. Based on Ct values, pooled testing with 4 specimens would have yielded inconclusive results in 67/1,268 (5.2%) specimens but only a single false-negative result. Conclusions Unobserved self-collection of nasal swabs provides adequate sampling for SARS-CoV-2 RT-PCR testing. These findings alleviate concerns of increased false negatives in this context. Specimen pooling could be used for this population as the likelihood of false negative results is very low due when using a sensitive, dual-target methodology.

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Incorporating false negative tests in epidemiological models for SARS-CoV-2 transmission and reconciling with seroprevalence estimates

Scientific Reports ◽

10.1038/s41598-021-89127-1 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Rupam Bhattacharyya ◽

Ritoban Kundu ◽

Ritwik Bhaduri ◽

Debashree Ray ◽

Lauren J. Beesley ◽

...

Keyword(s):

False Negative ◽

Population Based ◽

Training Data ◽

Epidemiological Models ◽

Rt Pcr ◽

Antibody Prevalence ◽

Igg Antibody ◽

False Negatives ◽

Seir Model ◽

Study Population

AbstractSusceptible-Exposed-Infected-Removed (SEIR)-type epidemiologic models, modeling unascertained infections latently, can predict unreported cases and deaths assuming perfect testing. We apply a method we developed to account for the high false negative rates of diagnostic RT-PCR tests for detecting an active SARS-CoV-2 infection in a classic SEIR model. The number of unascertained cases and false negatives being unobservable in a real study, population-based serosurveys can help validate model projections. Applying our method to training data from Delhi, India, during March 15–June 30, 2020, we estimate the underreporting factor for cases at 34–53 (deaths: 8–13) on July 10, 2020, largely consistent with the findings of the first round of serosurveys for Delhi (done during June 27–July 10, 2020) with an estimated 22.86% IgG antibody prevalence, yielding estimated underreporting factors of 30–42 for cases. Together, these imply approximately 96–98% cases in Delhi remained unreported (July 10, 2020). Updated calculations using training data during March 15-December 31, 2020 yield estimated underreporting factor for cases at 13–22 (deaths: 3–7) on January 23, 2021, which are again consistent with the latest (fifth) round of serosurveys for Delhi (done during January 15–23, 2021) with an estimated 56.13% IgG antibody prevalence, yielding an estimated range for the underreporting factor for cases at 17–21. Together, these updated estimates imply approximately 92–96% cases in Delhi remained unreported (January 23, 2021). Such model-based estimates, updated with latest data, provide a viable alternative to repeated resource-intensive serosurveys for tracking unreported cases and deaths and gauging the true extent of the pandemic.

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Pooling of Upper Respiratory Specimens Using a SARS-CoV-2 Real-time RT-PCR Assay Authorized for Emergency Use in Low-Prevalence Populations for High-Throughput Testing

Open Forum Infectious Diseases ◽

10.1093/ofid/ofaa466 ◽

2020 ◽

Vol 7 (11) ◽

Author(s):

Gwynngelle A Borillo ◽

Ron M Kagan ◽

Russell E Baumann ◽

Boris M Fainstein ◽

Lamela Umaru ◽

...

Keyword(s):

Real Time ◽

False Negative ◽

False Negative Rate ◽

Nucleic Acid Amplification ◽

Rt Pcr ◽

Pooled Testing ◽

Negative Results ◽

Single Positive ◽

Upper Respiratory ◽

Respiratory Specimens

Abstract Background Nucleic acid amplification testing is a critical tool for addressing the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic. Specimen pooling can increase throughput and conserve testing resources but requires validation to ensure that reduced sensitivity does not increase the false-negative rate. We evaluated the performance of a real-time reverse transcription polymerase chain reaction (RT-PCR) test authorized by the US Food and Drug Administration (FDA) for emergency use for pooled testing of upper respiratory specimens. Methods Positive specimens were selected from 3 prevalence groups, 1%–3%, >3%–6%, and >6%–10%. Positive percent agreement (PPA) was assessed by pooling single-positive specimens with 3 negative specimens; performance was assessed using Passing-Bablok regression. Additionally, we assessed the distributions of RT-PCR cycle threshold (Ct) values for 3091 positive specimens. Results PPA was 100% for the 101 pooled specimens. There was a linear relationship between Ct values for pooled and single-tested specimens (r = 0.96–0.99; slope ≈ 1). The mean pooled Ct shifts at 40 cycles were 2.38 and 1.90, respectively, for the N1 and N3 targets. The median Cts for 3091 positive specimens were 25.9 (N1) and 24.7 (N3). The percentage of positive specimens with Cts between 40 and the shifted Ct was 1.42% (N1) and 0.0% (N3). Conclusions Pooled and individual testing of specimens positive for SARS-CoV-2 demonstrated 100% agreement, which demonstrates the viability of pooled specimens for SARS-COV-2 testing using a dual-target RT-PCR system. Pooled specimen testing can help increase testing capacity for SARS-CoV-2 with a low risk of false-negative results.

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False Negative Mitigation in Group Testing for COVID-19 Screening

Frontiers in Medicine ◽

10.3389/fmed.2021.661277 ◽

2021 ◽

Vol 8 ◽

Author(s):

Amir Reza Alizad Rahvar ◽

Safar Vafadar ◽

Mehdi Totonchi ◽

Mehdi Sadeghi

Keyword(s):

Viral Load ◽

False Negative ◽

Group Testing ◽

False Negative Rate ◽

Screening Strategy ◽

Web Interface ◽

Rt Pcr ◽

Promising Candidate ◽

Testing Method ◽

High False Negative Rate

After lifting the COVID-19 lockdown restrictions and opening businesses, screening is essential to prevent the spread of the virus. Group testing could be a promising candidate for screening to save time and resources. However, due to the high false-negative rate (FNR) of the RT-PCR diagnostic test, we should be cautious about using group testing because a group's false-negative result identifies all the individuals in a group as uninfected. Repeating the test is the best solution to reduce the FNR, and repeats should be integrated with the group-testing method to increase the sensitivity of the test. The simplest way is to replicate the test twice for each group (the 2Rgt method). In this paper, we present a new method for group testing (the groupMix method), which integrates two repeats in the test. Then we introduce the 2-stage sequential version of both the groupMix and the 2Rgt methods. We compare these methods analytically regarding the sensitivity and the average number of tests. The tradeoff between the sensitivity and the average number of tests should be considered when choosing the best method for the screening strategy. We applied the groupMix method to screening 263 people and identified 2 infected individuals by performing 98 tests. This method achieved a 63% saving in the number of tests compared to individual testing. Our experimental results show that in COVID-19 screening, the viral load can be low, and the group size should not be more than 6; otherwise, the FNR increases significantly. A web interface of the groupMix method is publicly available for laboratories to implement this method.

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