Should RT-PCR be considered a gold standard in the diagnosis of COVID-19?

Evaluation and Clinical Validation of Guanidine-Based Inactivation Transport Medium for Preservation of SARS-CoV-2

WHO declared the outbreak of COVID-19, caused by SARS-CoV-2, a pandemic in March 2020. More than 223 million cases and approximately 4.6 million deaths have been confirmed. Early diagnosis and immediate treatment became a priority during this pandemic. However, COVID-19 diagnostic testing resources are limited, especially early in the pandemic. Apart from being limited, the COVID-19 diagnostic tests using reverse transcription polymerase chain reaction (RT-PCR) have encountered storage, transportation, and safety issues. These problems are mainly experienced by developing poor countries, countries in the equatorial region, and archipelagic countries. VITPAD® is a guanidine-based inactivation transport medium (ITM) formulated to maintain the RNA quality of SARS-CoV-2 during transportation without cold chains. This study, conducted from September 2020 to March 2021, performed clinical validation of VITPAD® by comparing its performance with a globally commercially available ITM from the NEST brand. Its stability at room temperature, safety, and resistance at high temperatures was also tested using RT-PCR analysis. VITPAD® can reduce the infectious nature of the specimen, preserve the SARS-CoV-2 for 18 days at an ambient temperature, and resist high temperatures (40°C for 3 hours). A guanidine-based transport medium, such as VITPAD®, is compatible and recommended for RT-PCR-based molecular diagnosis of COVID-19.

Rapid self-test of unprocessed viruses of SARS-CoV-2 and its variants in saliva by portable wireless graphene biosensor

We have developed a DNA aptamer-conjugated graphene field-effect transistor (GFET) biosensor platform to detect receptor-binding domain (RBD), nucleocapsid (N), and spike (S) proteins, as well as viral particles of original Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) coronavirus and its variants in saliva samples. The GFET biosensor is a label-free, rapid (≤20 min), ultrasensitive handheld wireless readout device. The limit of detection (LoD) and the limit of quantitation (LoQ) of the sensor are 1.28 and 3.89 plaque-forming units (PFU)/mL for S protein and 1.45 and 4.39 PFU/mL for N protein, respectively. Cognate spike proteins of major variants of concern (N501Y, D614G, Y453F, Omicron-B1.1.529) showed sensor response ≥40 mV from the control (aptamer alone) for fM to nM concentration range. The sensor response was significantly lower for viral particles and cognate proteins of Middle East Respiratory Syndrome (MERS) compared to SARS-CoV-2, indicating the specificity of the diagnostic platform for SARS-CoV-2 vs. MERS viral proteins. During the early phase of the pandemic, the GFET sensor response agreed with RT-PCR data for oral human samples, as determined by the negative percent agreement (NPA) and positive percent agreement (PPA). During the recent Delta/Omicron wave, the GFET sensor also reliably distinguished positive and negative clinical saliva samples. Although the sensitivity is lower during the later pandemic phase, the GFET-defined positivity rate is in statistically close alignment with the epidemiological population-scale data. Thus, the aptamer-based GFET biosensor has a high level of precision in clinically and epidemiologically significant SARS-CoV-2 variant detection. This universal pathogen-sensing platform is amenable for a broad range of public health applications and real-time environmental monitoring.

Eight pruning deep learning models for low storage and high-speed COVID-19 computed tomography lung segmentation and heatmap-based lesion localization: A multicenter study using COVLIAS 2.0

BACKGROUND

COVLIAS 1.0: an automated lung segmentation was designed for COVID-19 diagnosis. It has issues related to storage space and speed. This study shows that COVLIAS 2.0 uses pruned AI (PAI) networks for improving both storage and speed, wiliest high performance on lung segmentation and lesion localization.

METHOD

ology: The proposed study uses multicenter ∼9,000 CT slices from two different nations, namely, CroMed from Croatia (80 patients, experimental data), and NovMed from Italy (72 patients, validation data). We hypothesize that by using pruning and evolutionary optimization algorithms, the size of the AI models can be reduced significantly, ensuring optimal performance. Eight different pruning techniques (i) differential evolution (DE), (ii) genetic algorithm (GA), (iii) particle swarm optimization algorithm (PSO), and (iv) whale optimization algorithm (WO) in two deep learning frameworks (i) Fully connected network (FCN) and (ii) SegNet were designed. COVLIAS 2.0 was validated using "Unseen NovMed" and benchmarked against MedSeg. Statistical tests for stability and reliability were also conducted.

RESULTS

Pruning algorithms (i) FCN-DE, (ii) FCN-GA, (iii) FCN-PSO, and (iv) FCN-WO showed improvement in storage by 92.4%, 95.3%, 98.7%, and 99.8% respectively when compared against solo FCN, and (v) SegNet-DE, (vi) SegNet-GA, (vii) SegNet-PSO, and (viii) SegNet-WO showed improvement by 97.1%, 97.9%, 98.8%, and 99.2% respectively when compared against solo SegNet. AUC > 0.94 (p < 0.0001) on CroMed and > 0.86 (p < 0.0001) on NovMed data set for all eight EA model. PAI <0.25 s per image. DenseNet-121-based Grad-CAM heatmaps showed validation on glass ground opacity lesions.

CONCLUSIONS

Eight PAI networks that were successfully validated are five times faster, storage efficient, and could be used in clinical settings.

COVID-19 Diagnosis: A Comprehensive Review of the RT-qPCR Method for Detection of SARS-CoV-2

The world is grappling with the coronavirus disease 2019 (COVID-19) pandemic, the causative agent of which is severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). COVID-19 symptoms are similar to the common cold, including fever, sore throat, cough, muscle and chest pain, brain fog, dyspnoea, anosmia, ageusia, and headache. The manifestation of the disease can vary from being asymptomatic to severe life-threatening conditions warranting hospitalization and ventilation support. Furthermore, the emergence of mutecated variants of concern (VOCs) is paramount to the devastating effect of the pandemic. This highly contagious virus and its emergent variants challenge the available advanced viral diagnostic methods for high-accuracy testing with faster result yields. This review is to shed light on the natural history, pathology, molecular biology, and efficient diagnostic methods of COVID-19, detecting SARS-CoV-2 in collected samples. We reviewed the gold standard RT-qPCR method for COVID-19 diagnosis to confer a better understanding and application to combat the COVID-19 pandemic. This comprehensive review may further develop awareness about the management of the COVID-19 pandemic.

Prevalence of the Clinical Symptoms and PCR Test Results on Patients With COVID-19 in South of Tehran

Background:

The first human case of COVID-19 was reported on 19 February 2020 in Iran, since then the number of infected cases has dramatically increased to about 1.800 million and about 62 000 deaths, also elderly people have accounted for the largest frequency of mortality.

Objective:

This study aims to evaluate the prevalence of Covid-19 RT-PCR positive among Iranian patients and to evaluate the most important clinical symptoms of identified patients based on age, gender, and their background diseases to be used as an aid for early diagnosis.

Methods:

During 9 months, swab samples of 11 034 patients’ nasopharynx and oropharynx secretions were obtained and were referred to the laboratory for Covid-19 RT-PCR test. In addition, the history of signs and symptoms from patients was recorded.

Results:

In total, 11 034 Covid-19 RT-PCR tests that performed, 3358 samples had positive results (30.4%). Headache was the most commonly reported, which was found in 42.5% of our cases. Fever was the second most common symptom among the patients studied, with a prevalence rate of 36.2%.

Conclusion:

In this study, almost 30% of symptomatic patients had positive Covid-19 RT-PCR test results. Headache was the most common symptom; also diarrhea and nausea were the least common symptoms among patients under this study.

COVLIAS 2.0-cXAI: Cloud-Based Explainable Deep Learning System for COVID-19 Lesion Localization in Computed Tomography Scans

Background: The previous COVID-19 lung diagnosis system lacks both scientific validation and the role of explainable artificial intelligence (AI) for understanding lesion localization. This study presents a cloud-based explainable AI, the “COVLIAS 2.0-cXAI” system using four kinds of class activation maps (CAM) models. Methodology: Our cohort consisted of ~6000 CT slices from two sources (Croatia, 80 COVID-19 patients and Italy, 15 control patients). COVLIAS 2.0-cXAI design consisted of three stages: (i) automated lung segmentation using hybrid deep learning ResNet-UNet model by automatic adjustment of Hounsfield units, hyperparameter optimization, and parallel and distributed training, (ii) classification using three kinds of DenseNet (DN) models (DN-121, DN-169, DN-201), and (iii) validation using four kinds of CAM visualization techniques: gradient-weighted class activation mapping (Grad-CAM), Grad-CAM++, score-weighted CAM (Score-CAM), and FasterScore-CAM. The COVLIAS 2.0-cXAI was validated by three trained senior radiologists for its stability and reliability. The Friedman test was also performed on the scores of the three radiologists. Results: The ResNet-UNet segmentation model resulted in dice similarity of 0.96, Jaccard index of 0.93, a correlation coefficient of 0.99, with a figure-of-merit of 95.99%, while the classifier accuracies for the three DN nets (DN-121, DN-169, and DN-201) were 98%, 98%, and 99% with a loss of ~0.003, ~0.0025, and ~0.002 using 50 epochs, respectively. The mean AUC for all three DN models was 0.99 (p < 0.0001). The COVLIAS 2.0-cXAI showed 80% scans for mean alignment index (MAI) between heatmaps and gold standard, a score of four out of five, establishing the system for clinical settings. Conclusions: The COVLIAS 2.0-cXAI successfully showed a cloud-based explainable AI system for lesion localization in lung CT scans.

An all-in-one point-of-care testing device for multiplexed detection of respiratory infections

The impact of the COVID-19 pandemic has reinforced the need for rapid, cost-effective, and reliable point-of-care testing (POCT) devices for massive population screening. The co-circulation of SARS-CoV-2 with several seasonal respiratory viruses highlights the need for multiplexed biosensing approaches. Herein, we present a fast and robust all-in-one POCT device for parallel viral antigen and serological analysis. The biosensing approach consists of a functionalized polycarbonate disc-shaped surface with microfluidic structures, where specific bioreagents are immobilized in microarray format, and a portable optoelectronic analyzer. The biosensor quantifies the concentration of viral antigens and specific immunoglobulins G and M for SARS-CoV-2, influenza A/B, adenovirus, and respiratory syncytial virus, using 30 μL of a sample. The semi-automated analysis of 6 samples is performed in 30 min. Validation studies performed with 135 serum samples and 147 nasopharyngeal specimens reveal high diagnostic sensitivity (98–100%) and specificity (84–98%), achieving an excellent agreement (κ = 0.937) with commercial immunoassays, which complies with the World Health Organization criteria for POC COVID-19 diagnostic tests. The versatility of the POCT device paves the way for the detection of other pathogens and analytes in the incoming post-pandemic world, integrating specific bioreagents against different variants of concerns and interests.

Building a predictive model to identify clinical indicators for COVID-19 using machine learning method

Although some studies tried to identify risk factors for COVID-19, the evidence comparing COVID-19 and community-acquired pneumonia (CAP) is inconclusive, and CAP is the most common pneumonia with similar symptoms as COVID-19. We conducted a case-control study with 35 routine-collected clinical indicators and demographic factors to identify predictors for COVID-19 with CAP as controls. We randomly split the dataset into a training set (70%) and testing set (30%). We built Explainable Boosting Machine to select the important factors and built a decision tree on selected variables to interpret their relationships. The top five individual predictors of COVID-19 are albumin, total bilirubin, monocyte count, alanine aminotransferase, and percentage of monocyte with the importance scores ranging from 0.078 to 0.567. The top systematic predictors for COVID-19 are liver function, monocyte increasing, plasma protein, granulocyte, and renal function (importance scores ranging 0.009-0.096). We identified five combinations of important indicators to screen COVID-19 patients from CAP patients with differentiating abilities ranging 83.3-100%. An online predictive tool for our model was published. Certain clinical indicators collected routinely from most hospitals could help screen and distinguish COVID-19 from CAP. While further verification is needed, our findings and predictive tool could help screen suspected COVID-19 cases.

Combining rapid antigen testing and syndromic surveillance improves community-based COVID-19 detection in a low-income country

Diagnostics for COVID-19 detection are limited in many settings. Syndromic surveillance is often the only means to identify cases but lacks specificity. Rapid antigen testing is inexpensive and easy-to-deploy but can lack sensitivity. We examine how combining these approaches can improve surveillance for guiding interventions in low-income communities in Dhaka, Bangladesh. Rapid-antigen-testing with PCR validation was performed on 1172 symptomatically-identified individuals in their homes. Statistical models were fitted to predict PCR-status using rapid-antigen-test results, syndromic data, and their combination. Under contrasting epidemiological scenarios, the models' predictive and classification performance was evaluated. Models combining rapid-antigen-testing and syndromic data yielded equal-to-better performance to rapid-antigen-test-only models across all scenarios with their best performance in the epidemic growth scenario. These results show that drawing on complementary strengths across rapid diagnostics, improves COVID-19 detection, and reduces false-positive and -negative diagnoses to match local requirements; improvements achievable without additional expense, or changes for patients or practitioners.

Comparison between Suspected and Confirmed COVID-19 Respiratory Patients: What Is beyond the PCR Test

COVID-19 modified the healthcare system. Nasal-pharyngeal swab (NPS), with real-time reverse transcriptase-polymerase (PCR), is the gold standard for the diagnosis; however, there are difficulties related to the procedure that may postpone it. The study aims to evaluate whether other elements than the PCR-NPS are reliable and confirm the diagnosis of COVID-19. This is a cross-sectional study on data from the Lung Unit of Pavia (confirmed) and at the Emergency Unit of Palermo (suspected). COVID-19 was confirmed by positive NPS, suspected tested negative. We compared clinical, laboratory and radiological variables and performed Logistic regression to estimate which variables increased the risk of COVID-19. The derived ROC-AUCcurve, assessed the accuracy of the model to distinguish between COVID-19 suspected and confirmed. We selected 50 confirmed and 103 suspected cases. High Reactive C-Protein (OR: 1.02; CI95%: 0.11–1.02), suggestive CT-images (OR: 11.43; CI95%: 3.01–43.3), dyspnea (OR: 10.48; CI95%: 2.08–52.7) and respiratory failure (OR: 5.84; CI95%: 1.73–19.75) increased the risk of COVID-19, whereas pleural effusion decreased the risk (OR: 0.15; CI95%: 0.04–0.63). ROC confirmed the discriminative role of these variables between suspected and confirmed COVID-19 (AUC 0.91). Clinical, laboratory and imaging features predict the diagnosis of COVID-19, independently from the NPS result.

Supervised and weakly supervised deep learning models for COVID-19 CT diagnosis: A systematic review

Artificial intelligence (AI) and computer vision (CV) methods become reliable to extract features from radiological images, aiding COVID-19 diagnosis ahead of the pathogenic tests and saving critical time for disease management and control. Thus, this review article focuses on cascading numerous deep learning-based COVID-19 computerized tomography (CT) imaging diagnosis research, providing a baseline for future research. Compared to previous review articles on the topic, this study pigeon-holes the collected literature very differently (i.e., its multi-level arrangement). For this purpose, 71 relevant studies were found using a variety of trustworthy databases and search engines, including Google Scholar, IEEE Xplore, Web of Science, PubMed, Science Direct, and Scopus. We classify the selected literature in multi-level machine learning groups, such as supervised and weakly supervised learning. Our review article reveals that weak supervision has been adopted extensively for COVID-19 CT diagnosis compared to supervised learning. Weakly supervised (conventional transfer learning) techniques can be utilized effectively for real-time clinical practices by reusing the sophisticated features rather than over-parameterizing the standard models. Few-shot and self-supervised learning are the recent trends to address data scarcity and model efficacy. The deep learning (artificial intelligence) based models are mainly utilized for disease management and control. Therefore, it is more appropriate for readers to comprehend the related perceptive of deep learning approaches for the in-progress COVID-19 CT diagnosis research.

Enhanced Detection of Viral RNA Species Using FokI-Assisted Digestion of DNA Duplexes and DNA/RNA Hybrids

The accurate detection of nucleic acids from certain biological pathogens is critical for the diagnosis of human diseases. However, amplified detection of RNA molecules from a complex sample by direct detection of RNA/DNA hybrids remains a challenge. Here, we show that type IIS endonuclease FokI is able to digest DNA duplexes and DNA/RNA hybrids when assisted by a dumbbell-like fluorescent sensing oligonucleotide. As proof of concept, we designed a battery of sensing oligonucleotides against specific regions of the SARS-CoV-2 genome and interrogated the role of FokI relaxation as a potential nicking enzyme for fluorescence signal amplification. FokI-assisted digestion of SARS-CoV-2 probes increases the detection signal of ssDNA and RNA molecules and decreases the limit of detection more than 3.5-fold as compared to conventional molecular beacon approaches. This cleavage reaction is highly specific to its target molecules, and no detection of other highly related B-coronaviruses was observed in the presence of complex RNA mixtures. In addition, the FokI-assisted reaction has a high multiplexing potential, as the combined detection of different viral RNAs, including different SARS-CoV-2 variants, was achieved in the presence of multiple combinations of fluorophores and sensing oligonucleotides. When combined with isothermal rolling circle amplification technologies, FokI-assisted digestion reduced the detection time of SARS-CoV-2 in COVID-19-positive human samples with adequate sensitivity and specificity compared to conventional reverse transcription polymerase chain reaction approaches, highlighting the potential of FokI-assisted signal amplification as a valuable sensing mechanism for the detection of human pathogens.

Performance of Three Tests for SARS-CoV-2 on a University Campus Estimated Jointly with Bayesian Latent Class Modeling

Accurate tests for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been critical in efforts to control its spread. The accuracy of tests for SARS-CoV-2 has been assessed numerous times, usually in reference to a gold standard diagnosis. One major disadvantage of that approach is the possibility of error due to inaccuracy of the gold standard, which is especially problematic for evaluating testing in a real-world surveillance context. We used an alternative approach known as Bayesian latent class modeling (BLCM), which circumvents the need to designate a gold standard by simultaneously estimating the accuracy of multiple tests. We applied this technique to a collection of 1,716 tests of three types applied to 853 individuals on a university campus during a 1-week period in October 2020. We found that reverse transcriptase PCR (RT-PCR) testing of saliva samples performed at a campus facility had higher sensitivity (median, 92.3%; 95% credible interval [CrI], 73.2 to 99.6%) than RT-PCR testing of nasal samples performed at a commercial facility (median, 85.9%; 95% CrI, 54.7 to 99.4%). The reverse was true for specificity, although the specificity of saliva testing was still very high (median, 99.3%; 95% CrI, 98.3 to 99.9%). An antigen test was less sensitive and specific than both of the RT-PCR tests, although the sample sizes with this test were small and the statistical uncertainty was high. These results suggest that RT-PCR testing of saliva samples at a campus facility can be an effective basis for surveillance screening to prevent SARS-CoV-2 transmission in a university setting. IMPORTANCE Testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been vitally important during the COVID-19 pandemic. There are a variety of methods for testing for this virus, and it is important to understand their accuracy in choosing which one might be best suited for a given application. To estimate the accuracy of three different testing methods, we used a data set collected at a university that involved testing the same samples with multiple tests. Unlike most other estimates of test accuracy, we did not assume that one test was perfect but instead allowed for some degree of inaccuracy in all testing methods. We found that molecular tests performed on saliva samples at a university facility were similarly accurate as molecular tests performed on nasal samples at a commercial facility. An antigen test appeared somewhat less accurate than the molecular tests, but there was high uncertainty about that.

The role of Monocyte Distribution Width (MDW) in the prognosis and monitoring of COVID-19 patients

The new parameter derived from the standard deviation of the monocyte distribution width (MDW) has shown a good diagnostic efficacy in COVID-19 patients. In this study, we propose MDW as a prognostic and monitoring parameter in patients with severe forms of COVID-19. Sixty SARS-CoV-2-positive patients admitted to the San Donato Hospital in Arezzo were enrolled. A blood sample taken to measure the complete blood count was used for the determination of MDW using a UniCel DxH 900 instrument (Beckman Coulter). For each patient, a mean of 6 ± 2 measurements of MDW were taken. The difference between the last and first MDW results was reported as the ΔMDW variable. The ΔMDW and age were significantly correlated to the outcome. In non-survivors patients, the difference in the mean of the MDW between the first and other points was not significant, while in survivors, the first point was higher than the other points (p <0.005), with the exception of the mean of the second point (p-value= NS). The ΔMDW area under the curve (AUC) was 0.84, and with a cut-off lower than 0.00 the sensitivity and specificity were 88% and 81%, respectively. The most important result of this study is the ΔMDW calculated on the basis of the difference between the first and third measurement, after approximately the 5-7^th day of hospitalisation. A ΔMDW less than one was indicative of an unfavourable prognosis. The data reported suggest that MDW could be used to support monitoring and surveillance, alongside other tests such as procalcitonin, in critically ill patients in the ICU.

SARS-CoV-2 Gene Expression as a Prognosis Predictor for COVID-19

Introduction: Real time quantitative PCR is the gold standard for detection of SARS-CoV-2 which is specific, sensitive, and simple quantitative. The target of RT-qPCR is to assess the expression level of the SARS-CoV-2 gene through cycle threshold values (CT-value). The purpose of this study was to analyze the association of the level of SARS-CoV-2 gene expression and the severity of COVID-19 in patients hospitalized. Method: This research is an analytic observational study with cross sectional method. While the research sample was taken using a consecutive sampling technique from the Medical Records of Sumedang Hospital and Cideres Hospital, West Java, Indonesia from December 2020 to March 2021. Patient parameters include analysis of age, sex, comorbidity, and disease severity. The severity of the patient is classified based on complaints and oxygen saturation. The expression level of the SARS-CoV-2 N gene and E gene were assessed by calculating the relative quantification by comparing the expression of the E and N gene with the expression of the internal control gene by Livak formula (2-ΔΔCT Formula). Result: The Spearman correlation test showed that there was a relationship between the expression of SARS-CoV-2 genes E and N genes with the severity of COVID-19 patients (with r=0.374 and p<0.0001) and (with r=0.452 and p<0.0001). Conclusions:  There is an correlation between the level of expression of genes E and gene N with the severity of patients.  

RNA reference materials with defined viral RNA loads of SARS-CoV-2-A useful tool towards a better PCR assay harmonization

SARS-CoV-2, the cause of COVID-19, requires reliable diagnostic methods to track the circulation of this virus. Following the development of RT-qPCR methods to meet this diagnostic need in January 2020, it became clear from interlaboratory studies that the reported Ct values obtained for the different laboratories showed high variability. Despite this the Ct values were explored as a quantitative cut off to aid clinical decisions based on viral load. Consequently, there was a need to introduce standards to support estimation of SARS-CoV-2 viral load in diagnostic specimens. In a collaborative study, INSTAND established two reference materials (RMs) containing heat-inactivated SARS-CoV-2 with SARS-CoV-2 RNA loads of ~107 copies/mL (RM 1) and ~106 copies/mL (RM 2), respectively. Quantification was performed by RT-qPCR using synthetic SARS-CoV-2 RNA standards and digital PCR. Between November 2020 and February 2021, German laboratories were invited to use the two RMs to anchor their Ct values measured in routine diagnostic specimens, with the Ct values of the two RMs. A total of 305 laboratories in Germany were supplied with RM 1 and RM 2. The laboratories were requested to report their measured Ct values together with details on the PCR method they used to INSTAND. This resultant 1,109 data sets were differentiated by test system and targeted gene region. Our findings demonstrate that an indispensable prerequisite for linking Ct values to SARS-CoV-2 viral loads is that they are treated as being unique to an individual laboratory. For this reason, clinical guidance based on viral loads should not cite Ct values. The RMs described were a suitable tool to determine the specific laboratory Ct for a given viral load. Furthermore, as Ct values can also vary between runs when using the same instrument, such RMs could be used as run controls to ensure reproducibility of the quantitative measurements.

Nanobioengineering: A promising approach for early detection of COVID-19

Unique pneumonia due to an unknown source emerged in December 2019 in the city of Wuhan, China. Consequently, the World Health Organization (WHO) declared this condition as a new coronavirus disease-19 also known as COVID-19 on February 11, 2020, which on March 13, 2020 was declared as a pandemic. The virus that causes COVID-19 was found to have a similar genome (80% similarity) with the previously known acute respiratory syndrome also known as SARS-CoV. The novel virus was later named Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). SARS-CoV-2 falls in the family of Coronaviridae which is further divided into Nidovirales and another subfamily called Orthocoronavirinae. The four generations of the coronaviruses belongs to the Orthocoronavirinae family that consists of alpha, beta, gamma and delta coronavirus which are denoted as α-CoV, β-CoV, γ-CoV, δ-CoV respectively. The α-CoV and β-CoVs are mainly known to infect mammals whereas γ-CoV and δ-CoV are generally found in birds. The β-CoVs also comprise of SARS-CoV and also include another virus that was found in the Middle East called the Middle East respiratory syndrome virus (MERS-CoV) and the cause of current pandemic SARS-CoV-2. These viruses initially cause the development of pneumonia in the patients and further development of a severe case of acute respiratory distress syndrome (ARDS) and other related symptoms that can be fatal leading to death.

Transmission Dynamics and Short-Term Forecasts of COVID-19: Nepal 2020/2021

Nepal was hard hit by a second wave of COVID-19 from April-May 2021. We investigated the transmission dynamics of COVID-19 at the national and provincial levels by using data on laboratory-confirmed RT-PCR positive cases from the official national situation reports. We performed 8 week-to-week sequential forecasts of 10-days and 20-days at national level using three dynamic phenomenological growth models from 5 March 2021-22 May 2021. We also estimated effective and instantaneous reproduction numbers at national and provincial levels using established methods and evaluated the mobility trends using Google's mobility data. Our forecast estimates indicated a declining trend of COVID-19 cases in Nepal as of June 2021. Sub-epidemic and Richards models provided reasonable short-term projections of COVID-19 cases based on standard performance metrics. There was a linear pattern in the trajectory of COVID-19 incidence during the first wave (deceleration of growth parameter (p) = 0.41-0.43, reproduction number (Rt) at 1.1 (95% CI: 1.1, 1.2)), and a sub-exponential growth pattern in the second wave (p = 0.61 (95% CI: 0.58, 0.64)) and Rt at 1.3 (95% CI: 1.3, 1.3)). Across provinces, Rt ranged from 1.2 to 1.5 during the early growth phase of the second wave. The instantaneous Rt fluctuated around 1.0 since January 2021 indicating well sustained transmission. The peak in mobility across different areas coincided with an increasing incidence trend of COVID-19. In conclusion, we found that the sub-epidemic and Richards models yielded reasonable short-terms projections of the COVID-19 trajectory in Nepal, which are useful for healthcare utilization planning.

Can a radioimmunoassay kit be developed for accurate detection of the S protein of severe acute respiratory syndrome coronavirus 2?

The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) at the end of 2019 spread worldwide within only a few months. The screening and timely isolation of infected individuals have been regarded as an effective means of epidemic prevention and control. Therefore, effective screening of infected individuals plays a vital role in epidemic prevention and control. At present, reverse transcription-polymerase chain reaction (RT–PCR) is the main method for the in vitro detection of SARS-CoV-2. However, RT–PCR requires certified laboratories, expensive equipment, and trained technicians. Therefore, it is necessary to develop simpler and more convenient methods. Some studies have shown that the PepKAA peptide has a high affinity for the S protein of SARS-CoV-2. The tyrosine in PepKAA is labeled with ¹²⁵I and used to design a radioimmunoassay kit for the detection of the S protein of SARS-CoV-2, which is of great significance for the early diagnosis of COVID-19.

Diagnostic value of chest computed tomography imaging for COVID-19 based on reverse transcription-polymerase chain reaction: a meta-analysis

Background

The computed tomography (CT) diagnostic value of COVID-19 is controversial. We summarized the value of chest CT in the diagnosis of COVID-19 through a meta-analysis based on the reference standard.

Methods

All Chinese and English studies related to the diagnostic value of CT for COVID-19 across multiple publication platforms, was searched for and collected. Studies quality evaluation and plotting the risk of bias were estimated. A heterogeneity test and meta-analysis, including plotting sensitivity (Sen), specificity (Spe) forest plots, pooled positive likelihood ratio (+LR), negative likelihood ratio (-LR), dignostic odds ratio (DOR) values and 95% confidence interval (CI), were estimated. If there was a threshold effect, summary receiver operating characteristic curves (SROC) was further plotted. Pooled area under the receiver operating characteristic curve (AUROC) and 95% CI were also calculated.

Results

Twenty diagnostic studies that represented a total of 9004 patients were included from 20 pieces of literatures after assessing all the aggregated studies. The reason for heterogeneity was caused by the threshold effect, so the AUROC = 0.91 (95% CI: 0.89–0.94) for chest CT of COVID-19. Pooled sensitivity, specificity, +LR, -LR from 20 studies were 0.91 (95% CI: 0.88–0.94), 0.71 (95% CI: 0.59–0.80), 3.1(95% CI: 2.2–4.4), 0.12 (95% CI: 0.09–0.17), separately. The I² was 85.6% (P = 0.001) by Q-test.

Conclusions

The results of this study showed that CT diagnosis of COVID-19 was close to the reference standard. The diagnostic value of chest CT may be further enhanced if there is a unified COVID-19 diagnostic standard. However, please pay attention to rational use of CT.

Graphic Abstract

Clinical evaluation of periodontal pathogen levels by real-time polymerase chain reaction in peri-implantitis patients

OBJECTIVE

The mechanisms underlying the onset and progression of peri-implantitis are similar to those of periodontitis, and the causative bacteria are believed to similar. Previous studies support an association between peri-implantitis and periodontal pathogen. Thus, we investigated the bacterial flora of peri-implantitis patients in comparison to those of healthy implant and periodontitis patients.

MATERIALS AND METHODS

In total, 70 patients visiting Tokyo Dental College Chiba Hospital were divided into four groups: healthy, periodontitis, healthy implant, and peri-implantitis. For each group, the following five periodontal pathogens were detected using real-time polymerase chain reaction: Porphyromonas gingivalis, Aggregatibacter actinomycetemcomitans, Tannerella forsythia, Treponema denticola, and Prevotella intermedia.

RESULTS

The average copy number of total bacteria was significantly higher in the periodontitis group than in the other groups. P. gingivalis was detected in the periodontitis and peri-implantitis groups at levels as high as 18.92% and 12.29%, respectively, and P. intermedia was found in the peri-implantitis group at a rate of 2.06%. Nevertheless, periodontal pathogens were generally detected at lower levels in the peri-implantitis group than in the periodontitis group.

CONCLUSION

We found lower bacterial counts in the peri-implantitis group relative to the periodontitis group. Our results suggest that the peri-implant tissue is less resistant to bacteria, so even a small number of bacteria can be a risk factor for peri-implantitis and the causative agent of peri-implantitis can be bacteria other than periodontal pathogen.

Recent advances in detection technologies for COVID-19

Corona Virus Disease 2019 (COVID-19) is a highly infectious respiratory illness that was caused by the SARS-CoV-2. It spread around the world in just a few months and became a worldwide pandemic. Quick and accurate diagnosis of infected patients is very important for controlling transmission. In addition to the commonly used Real-time reverse-transcription polymerase chain reaction (RT-PCR) detection techniques, other diagnostic techniques are also emerging endlessly. This article reviews the current diagnostic methods for COVID-19 and discusses their advantages and disadvantages. It provides an important reference for the diagnosis of COVID-19.

Severe acute respiratory syndrome-coronavirus 2 in domesticated animals and its potential of transmission: A meta-analysis

BACKGROUND AND AIM

The coronavirus diseases-2019 (COVID-19) pandemic has caused a global lockdown, which has limited the mobility of the public, and thus, more time is spent with their pets. Unfortunately, many social media have blamed pet animals as a reservoir of severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2), the etiologic agent of COVID-19, triggering a panic abandonment of pets. However, no article has summarized the information regarding the role of pets as SARS-CoV-2 reservoirs. This study aimed to evaluate the role of pets as a reservoir of SARS-CoV-2 on the basis of research papers (i.e., animal model, surveillance, and case report) published in 2020.

MATERIALS AND METHODS

The review was conducted using articles from the PubMed database in 2020, using the keywords "COVID-19 in domesticated animals," which were screened and analyzed. Only the data from research articles were mimicked and transformed to conduct a meta-analysis. The meta-analysis was conducted regarding the effects of inhabitation and viral shedding in pets. In this study, we used 95% confidence intervals.

RESULTS

A total of 132 papers in PubMed were related to the keywords, whereas only 12 papers were appropriate to answer the dynamics of the role of pets as the reservoir for SARS-CoV-2. Seven studies indicated the potential of cat-cat (4/7), human-cat (2/7), and human-dog (1/7) SARS-CoV-2 transmission. No study proved the presence of cat-human transmission. Another study showed that comingling did not affect SARS-CoV-2 viral shedding among a cat and dog. Furthermore, the viral shedding of cats and dogs caused asymptomatic manifestations and generated neutralizing antibodies within a short period of time.

CONCLUSION

SARS-CoV-2 transmission is present in domesticated animals, especially in pet cats and dogs, and transmission occurs between animals of the same species (cat-cat). The reverse zoonosis (zooanthroponosis) was found from human to cat/dog (comingled) with asymptomatic clinical signs due to the representation of neutralizing antibodies.

A Seroprevalence Study of Anti-SARS-CoV-2 Antibodies in Patients with Inflammatory Bowel Disease during the Second Wave of the COVID-19 Pandemic in Italy

Background and Objectives: Studies have shown a lower prevalence of anti-SARS-CoV-2 antibodies in patients with inflammatory bowel disease (IBD), including amongst those receiving biological therapy. Aims were to determine the seroprevalence of anti-SARS-CoV-2 antibodies in IBD patients and to assess any association between seropositivity and IBD characteristics. Materials and Methods: Serum from adult IBD patients was prospectively collected between December 2020 and January 2021 and analyzed for anti-SARS-CoV-2 antibodies. Information about IBD characteristics and SARS-CoV-2 exposure risk factors was collected and analyzed. Serum from non-IBD healthcare workers formed the control group. Results: 311 IBD patients on biologics and 75 on mesalazine were enrolled. Ulcerative colitis (UC) extension (p < 0.001), Crohn's disease (CD) phenotype (p = 0.009) and use of concomitant corticosteroids (p < 0.001) were significantly different between the two IBD groups. Overall seroprevalence among IBD patients was 10.4%. The control group showed a prevalence of 13.0%, not significantly different to that of IBD patients (p = 0.145). Only a close contact with SARS-CoV-2 positive individuals and the use of non-FFP2 masks were independently associated with a higher likelihood of seropositivity amongst IBD patients. Conclusion: In IBD patients, the prevalence of anti-SARS-CoV-2 antibodies is not determined by their ongoing treatment. Disease-related characteristics are not associated with a greater risk of antibody seropositivity.

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

RT-PCR is considered to be the standard gold diagnostic test for detecting COVID-19 causing SARS-CoV-2. Recent reports and recent pieces of evidence from scientific literature, however, tell a different story. There have been speculations of SARS-CoV-2 escaping the RT-PCR because of the series of mutations it has gone through. It is possible that host-dependent RNA editing and high person-to-person transmission have equipped the virus with mutations enabling it to spread faster and even evade the RT-PCR. Added to this is burnout among healthcare workers and technicians handling the RT-PCR machines and sampling. All of these factors may be working in unison to result in the deluge of false-negative cases India is facing during the second COVID-19 wave. The mutant strains are spreading to other parts, posing challenges to the whole world. These circumstances warrant supplementary diagnostic tests such as serological and radiological findings to deal with cases of high clinical suspicion. Even one misdiagnosed COVID-19 patient poses a risk to hundreds of others in the vicinity. Healthcare workers' burnout also has to be dealt with. Erroneous staff should be re-trained.

Early Laboratory Diagnosis of COVID-19 by Antigen Detection in Blood Samples of the SARS-CoV-2 Nucleocapsid Protein

The purpose of this study was to characterize the diagnostic performance of a newly developed enzyme-linked immunosorbent assay (ELISA) for detection of SARS-CoV-2 nucleocapsid protein (NP) in blood. Blood samples were collected during hospitalization of 165 inpatients with PCR-confirmed SARS-CoV-2 infection and from 505 outpatients predominantly with relevant symptoms of COVID-19 simultaneously with PCR testing. For the 143 inpatients who had their first blood sample collected within 2 weeks after PCR-confirmed infection, the diagnostic sensitivity of the ELISA was 91.6%. The mean NP concentration of the 131 ELISA-positive blood samples was 1,734 pg/ml (range, 10 to 3,840 pg/ml). An exponential decline in NP concentration was observed for 368 blood samples collected over the first 4 weeks after PCR-confirmed SARS-CoV-2 infection, and all blood samples taken later had an NP concentration below the 10-pg/ml diagnostic cutoff. The diagnostic sensitivity of the ELISA was 81.4% for the 43 blood samples collected from outpatients with a simultaneous positive PCR test, and the mean NP concentration of the 35 ELISA-positive samples was 157 pg/ml (range, 10 to 1,377 pg/ml). For the 462 outpatients with a simultaneous negative PCR test, the diagnostic specificity of the ELISA was 99.8%. In conclusion, the SARS-CoV-2 NP ELISA is a suitable laboratory diagnostic test for COVID-19, particularly for hospitals, where blood samples are readily available and screening of serum or plasma by ELISA can facilitate prevention of nosocomial infections and reduce the requirement for laborious swab sampling and subsequent PCR analysis to confirmatory tests only.

Chest Radiograph Scoring Alone or Combined with Other Risk Scores for Predicting Outcomes in COVID-19

Background

Radiographic severity may help predict patient deterioration and outcomes from COVID-19 pneumonia.

Purpose

To assess the reliability and reproducibility of three chest radiograph reporting systems (radiographic assessment of lung edema [RALE], Brixia, and percentage opacification) in patients with proven SARS-CoV-2 infection and examine the ability of these scores to predict adverse outcomes both alone and in conjunction with two clinical scoring systems, National Early Warning Score 2 (NEWS2) and International Severe Acute Respiratory and Emerging Infection Consortium: Coronavirus Clinical Characterization Consortium (ISARIC-4C) mortality.

Materials and Methods

This retrospective cohort study used routinely collected clinical data of patients with polymerase chain reaction–positive SARS-CoV-2 infection admitted to a single center from February 2020 through July 2020. Initial chest radiographs were scored for RALE, Brixia, and percentage opacification by one of three radiologists. Intra- and interreader agreement were assessed with intraclass correlation coefficients. The rate of admission to the intensive care unit (ICU) or death up to 60 days after scored chest radiograph was estimated. NEWS2 and ISARIC-4C mortality at hospital admission were calculated. Daily risk for admission to ICU or death was modeled with Cox proportional hazards models that incorporated the chest radiograph scores adjusted for NEWS2 or ISARIC-4C mortality.

Results

Admission chest radiographs of 50 patients (mean age, 74 years ± 16 [standard deviation]; 28 men) were scored by all three radiologists, with good interreader reliability for all scores, as follows: intraclass correlation coefficients were 0.87 for RALE (95% CI: 0.80, 0.92), 0.86 for Brixia (95% CI: 0.76, 0.92), and 0.72 for percentage opacification (95% CI: 0.48, 0.85). Of 751 patients with a chest radiograph, those with greater than 75% opacification had a median time to ICU admission or death of just 1–2 days. Among 628 patients for whom data were available (median age, 76 years [interquartile range, 61–84 years]; 344 men), opacification of 51%–75% increased risk for ICU admission or death by twofold (hazard ratio, 2.2; 95% CI: 1.6, 2.8), and opacification greater than 75% increased ICU risk by fourfold (hazard ratio, 4.0; 95% CI: 3.4, 4.7) compared with opacification of 0%–25%, when adjusted for NEWS2 score.

Conclusion

Brixia, radiographic assessment of lung edema, and percentage opacification scores all reliably helped predict adverse outcomes in SARS-CoV-2 infection.

© RSNA, 2021

Online supplemental material is available for this article.

See also the editorial by Little in this issue.

Evolution of Supramolecular Systems Towards Next-Generation Biosensors

Supramolecular materials, which rely on dynamic non-covalent interactions, present a promising approach to advance the capabilities of currently available biosensors. The weak interactions between supramolecular monomers allow for adaptivity and responsiveness of supramolecular or self-assembling systems to external stimuli. In many cases, these characteristics improve the performance of recognition units, reporters, or signal transducers of biosensors. The facile methods for preparing supramolecular materials also allow for straightforward ways to combine them with other functional materials and create multicomponent sensors. To date, biosensors with supramolecular components are capable of not only detecting target analytes based on known ligand affinity or specific host-guest interactions, but can also be used for more complex structural detection such as chiral sensing. In this Review, we discuss the advancements in the area of biosensors, with a particular highlight on the designs of supramolecular materials employed in analytical applications over the years. We will first describe how different types of supramolecular components are currently used as recognition or reporter units for biosensors. The working mechanisms of detection and signal transduction by supramolecular systems will be presented, as well as the important hierarchical characteristics from the monomers to assemblies that contribute to selectivity and sensitivity. We will then examine how supramolecular materials are currently integrated in different types of biosensing platforms. Emerging trends and perspectives will be outlined, specifically for exploring new design and platforms that may bring supramolecular sensors a step closer towards practical use for multiplexed or differential sensing, higher throughput operations, real-time monitoring, reporting of biological function, as well as for environmental studies.

Screening Antibodies Raised against the Spike Glycoprotein of SARS-CoV-2 to Support the Development of Rapid Antigen Assays

Severe acute respiratory coronavirus-2 (SARS-CoV-2) is a novel viral pathogen and therefore a challenge to accurately diagnose infection. Asymptomatic cases are common and so it is difficult to accurately identify infected cases to support surveillance and case detection. Diagnostic test developers are working to meet the global demand for accurate and rapid diagnostic tests to support disease management. However, the focus of many of these has been on molecular diagnostic tests, and more recently serologic tests, for use in primarily high-income countries. Low- and middle-income countries typically have very limited access to molecular diagnostic testing due to fewer resources. Serologic testing is an inappropriate surrogate as the early stages of infection are not detected and misdiagnosis will promote continued transmission. Detection of infection via direct antigen testing may allow for earlier diagnosis provided such a method is sensitive. Leading SARS-CoV-2 biomarkers include spike protein, nucleocapsid protein, envelope protein, and membrane protein. This research focuses on antibodies to SARS-CoV-2 spike protein due to the number of monoclonal antibodies that have been developed for therapeutic research but also have potential diagnostic value. In this study, we assessed the performance of antibodies to the spike glycoprotein, acquired from both commercial and private groups in multiplexed liquid immunoassays, with concurrent testing via a half-strip lateral flow assays (LFA) to indicate antibodies with potential in LFA development. These processes allow for the selection of pairs of high-affinity antispike antibodies that are suitable for liquid immunoassays and LFA, some of which with sensitivity into the low picogram range with the liquid immunoassay formats with no cross-reactivity to other coronavirus S antigens. Discrepancies in optimal ranking were observed with the top pairs used in the liquid and LFA formats. These findings can support the development of SARS-CoV-2 LFAs and diagnostic tools.

Screening Antibodies Raised against the Spike Glycoprotein of SARS-CoV-2 to Support the Development of Rapid Antigen Assays

Severe acute respiratory coronavirus-2 (SARS-CoV-2) is a novel viral pathogen and therefore a challenge to accurately diagnose infection. Asymptomatic cases are common and so it is difficult to accurately identify infected cases to support surveillance and case detection. Diagnostic test developers are working to meet the global demand for accurate and rapid diagnostic tests to support disease management. However, the focus of many of these has been on molecular diagnostic tests, and more recently serologic tests, for use in primarily high-income countries. Low- and middle-income countries typically have very limited access to molecular diagnostic testing due to fewer resources. Serologic testing is an inappropriate surrogate as the early stages of infection are not detected and misdiagnosis will promote continued transmission. Detection of infection via direct antigen testing may allow for earlier diagnosis provided such a method is sensitive. Leading SARS-CoV-2 biomarkers include spike protein, nucleocapsid protein, envelope protein, and membrane protein. This research focuses on antibodies to SARS-CoV-2 spike protein due to the number of monoclonal antibodies that have been developed for therapeutic research but also have potential diagnostic value. In this study, we assessed the performance of antibodies to the spike glycoprotein, acquired from both commercial and private groups in multiplexed liquid immunoassays, with concurrent testing via a half-strip lateral flow assays (LFA) to indicate antibodies with potential in LFA development. These processes allow for the selection of pairs of high-affinity antispike antibodies that are suitable for liquid immunoassays and LFA, some of which with sensitivity into the low picogram range with the liquid immunoassay formats with no cross-reactivity to other coronavirus S antigens. Discrepancies in optimal ranking were observed with the top pairs used in the liquid and LFA formats. These findings can support the development of SARS-CoV-2 LFAs and diagnostic tools.

The Performance of SARS-CoV-2 Serology Testing in the Diagnosis of COVID-19

BACKGROUND & OBJECTIVE

COVID-19 reverse transcription-polymerase chain reaction (RT-PCR) has been a reference test for diagnosing a disease since the very beginning of the pandemic. COVID-19 serology tests have also been developed and used to estimate the prevalence of individuals who have already been infected. We aimed to evaluate the performance of serology tests for the diagnosis of patients who had been referred to medical centers with acute symptoms.

METHODS

In this cross-sectional study, 80 individuals suspected of COVID-19 who had been referred to Imam Khomeini Hospital Complex, Tehran, Iran, were examined. Upper respiratory tract specimens for RT-PCR and blood samples for COVID-19 IgM and IgG antibody level tests were collected and the results were compared.

RESULTS

The overall proportion in agreement, the agreement between positive results, and the agreement between negative results when comparing RT-PCR and IgM serology test were 40% (kappa = -0.006, P = 0.9), 32%, and 66.6%, respectively, and when comparing RT-PCR and IgG serology test were 46% (kappa = -0.006, P = 0.94), 43.5%, and 55.5%, respectively.

CONCLUSION

The absence of a gold standard method for the diagnosis of COVID-19 makes it very challenging to determine the true sensitivity and specificity of different methods. The study results revealed no agreement between the two methods; so the RT-PCR test for upper respiratory tract specimen cannot be replaced with COVID-19 serology test for the diagnosis of patients with acute symptoms.

Efficacy of systematic coronavirus screening by PCR and viral cultures in addition to triage in limiting the spread of SARS-CoV-2 within a hemodialysis unit

BACKGROUND

Patients with end-stage-renal-disease (ESRD) undergoing hemodialysis (HD) represent a vulnerable population for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection, due to their intrinsic fragility and increased exposure to the virus. Therefore, applying effective screening strategies and infection control measures is essential to control the spread of the epidemic within hemodialysis centers.

OBJECTIVE

Description and evaluation of the efficacy of systematic screening by rt-PCR and viral cultures, in addition to triage to limit the spread of the epidemic. Evaluation of the performance of these tests using "post-hoc" SARS-CoV-2 serology as a surrogate marker of infection.

METHODS

One hundred and forty-four patients undergoing hemodialysis in the Nephrology-Hemodialysis center of CHU Brugmann, Brussels, benefited from systematic virological screening using viral cultures in asymptomatic patients, or molecular tests (rt-PCR) for symptomatic ones, in addition to general prevention measures. Post-hoc serology was performed in all patients.

RESULTS

Thirty-eight (26.3%) individuals were infected with SARS-CoV-2. Seventeen infected patients (44.7%) were asymptomatic and thus detected by viral culture. Our strategy allowed us to detect and isolate 97.4% of the infected patients, as proven by post-hoc serology. Only one patient, missed by clinical screening and sequential viral cultures, had a positive serology.

CONCLUSION

The implementation of a control and prevention strategy based on a systematic clinical and virological screening showed its effectiveness in limiting (and shortening) the spread of the SARS-CoV-2 epidemic within our hemodialysis unit.

COVID-19 and pulmonary tuberculosis - A diagnostic dilemma

Coronavirus disease 2019 (COVID-19) is an infectious disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Meanwhile, pulmonary tuberculosis(TB) is one of the most common infective lung diseases in developing nations. The concurrence of pulmonary TB and COVID-19 can lead to poor prognosis, owing to the pre-existing lung damage caused by TB. Case presentation: We describe the imaging findings in 3 cases of COVID-19 pneumonia with co-existing pulmonary TB on HRCT thorax. The concurrence of COVID-19 and pulmonary TB can be a diagnostic dilemma. Correct diagnosis and prompt management is imperative to reduce mortality and morbidity. Hence it is pertinent for imaging departments to identify and report these distinct entities when presenting in conjunction.

Towards Fully Integrated Portable Sensing Devices for COVID-19 and Future Global Hazards: Recent Advances, Challenges, and Prospects

Since the onset of the coronavirus disease 2019 (COVID-19) pandemic, this fatal disease has been the leading cause of the death of more than 3.9 million people around the world. This tragedy taught us that we should be well-prepared to control the spread of such infectious diseases and prevent future hazards. As a consequence, this pandemic has drawn the attention of many researchers to the development of portable platforms with short hands-on and turnaround time suitable for batch production in urgent pandemic situations such as that of COVID-19. Two main groups of diagnostic assays have been reported for the detection of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) including nucleic acid-based and protein-based assays. The main focus of this paper is on the latter, which requires a shorter time duration, less skilled technicians, and faces lower contamination. Furthermore, this paper gives an overview of the complementary metal-oxide-semiconductor (CMOS) biosensors, which are potentially useful for implementing point-of-care (PoC) platforms based on such assays. CMOS technology, as a predominant technology for the fabrication of integrated circuits, is a promising candidate for the development of PoC devices by offering the advantages of reliability, accessibility, scalability, low power consumption, and distinct cost.

Laboratory Readiness and Response for SARS-Cov-2 in Indonesia

The laboratory diagnosis of SARS-CoV-2 infection comprises the informational cornerstone in the effort to contain the infections. Therefore, the ability to leverage laboratories' capacity in diagnostic testing and to increase the number of people being tested are critical. This paper reviews the readiness of Indonesian laboratories during the early months of the pandemic. It discusses the success of cross-sectoral collaboration among previously siloed national and sub-national government institutions, international development agencies, and private sector stakeholders. This collaboration managed to scale-up the COVID-19 referral laboratory network from one Ministry of Health NIHRD laboratory in the capital to 685 laboratories across 34 provinces. However, this rapid growth within 12 months since the first Indonesian case was discovered remained insufficient to cater for the constantly surging testing demands within the world's fourth most populous country. Reflecting on how other countries built their current pandemic preparedness from past emergencies, this paper highlights challenges and opportunities in workforce shortage, logistic distribution, and complex administration that need to be addressed.

Road toward universal COVID-19 testing method - A review

Patients infected with novel coronavirus exhibit a wide range of symptoms from common cold to pneumonia. Furthermore, several cases have been reported as asymptomatic across the globe. Since there are no conclusive clinical manifestations, clinicians have to rely more on laboratory diagnostic methods for confirmation of coronavirus disease. Hematological and biochemical tests are found to be of more prognostic value. Genetic assays by means of rRT-PCR technique is time-consuming but seems to be a more sensitive and specific test among the available testing methods for diagnosis of the coronavirus disease. Radiological imaging of the CT chest of the confirmed positive patients taken during the initial few days doesn't show any significant changes. However, from the second week onward a ground glass lesion pattern is observed. The immunological tests which are being used as a rapid testing method are found to be more false test negative. Hence, based on the effectiveness of various testing methods, it can be concluded that either rRT-PCR or mass antibody testing has to be done, and it has to be compared with CT chest in order to avoid false negatives across the globe which may help in the prevention of community spread of the disease.

Imaging diagnosis of bronchogenic carcinoma (the forgotten disease) during times of COVID-19 pandemic: Current and future perspectives

Patients with bronchogenic carcinoma comprise a high-risk group for coronavirus disease 2019 (COVID-19), pneumonia and related complications. Symptoms of COVID-19 related pulmonary syndrome may be similar to deteriorating symptoms encountered during bronchogenic carcinoma progression. These resemblances add further complexity for imaging assessment of bronchogenic carcinoma. Similarities between clinical and imaging findings can pose a major challenge to clinicians in distinguishing COVID-19 super-infection from evolving bronchogenic carcinoma, as the above-mentioned entities require very different therapeutic approaches. However, the goal of bronchogenic carcinoma management during the pandemic is to minimize the risk of exposing patients to COVID-19, whilst still managing all life-threatening events related to bronchogenic carcinoma. The current pandemic has forced all healthcare stakeholders to prioritize per value resources and reorganize therapeutic strategies for timely management of patients with COVID-19 related pulmonary syndrome. Processing of radiographic and computed tomography images by means of artificial intelligence techniques can facilitate triage of patients. Modified and newer therapeutic strategies for patients with bronchogenic carcinoma have been adopted by oncologists around the world for providing uncompromised care within the accepted standards and new guidelines.

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

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.

Assay System for Simultaneous Detection of SARS-CoV-2 and Other Respiratory Viruses

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) triggers disease with nonspecific symptoms that overlap those of infections caused by other seasonal respiratory viruses (RVs), such as the influenza virus (Flu) or respiratory syncytial virus (RSV). A molecular assay for accurate and rapid detection of RV and SARS-CoV-2 is crucial to manage these infections. Here, we compared the analytical performance and clinical reliability of Allplex™ SARS-CoV-2/FluA/FluB/RSV (SC2FabR; Seegene Inc., Seoul, South Korea) kit with those of four commercially available RV detection kits. Upon testing five target viral strains (SARS-CoV-2, FluA, FluB, RSV A, and RSV B), the analytical performance of SC2FabR was similar to that of the other kits, with no significant difference (p ≥ 0.78) in z-scores. The efficiency of SC2FabR (E-value, 81-104%) enabled reliable SARS-CoV-2 and seasonal RV detection in 888 nasopharyngeal swab specimens processed using a fully automated nucleic acid extraction platform. Bland-Altman analyses revealed an agreement value of 95.4% (SD ± 1.96) for the kits, indicating statistically similar results for all five. In conclusion, SC2FabR is a rapid and accurate diagnostic tool for both SARS-CoV-2 and seasonal RV detection, allowing for high-throughput RV analysis with efficiency comparable to that of commercially available kits. This can be used to help manage respiratory infections in patients during and after the coronavirus disease 2019 pandemic.

Potent Molecular Feature-based Neutralizing Monoclonal Antibodies as Promising Therapeutics Against SARS-CoV-2 Infection

The 2019-2020 winter was marked by the emergence of a new coronavirus (SARS-CoV-2) related disease (COVID-19), which started in Wuhan, China. Its high human-to-human transmission ability led to a worldwide spread within few weeks and has caused substantial human loss. Mechanical antiviral control approach, drug repositioning, and use of COVID-19 convalescent plasmas (CPs) were the first line strategies utilized to mitigate the viral spread, yet insufficient. The urgent need to contain this deadly pandemic has led searchers and pharmaceutical companies to develop vaccines. However, not all vaccines manufactured are safe. Besides, an alternative and effective treatment option for such an infectious disease would include pure anti-viral neutralizing monoclonal antibodies (NmAbs), which can block the virus at specific molecular targets from entering cells by inhibiting virus-cell structural complex formation, with more safety and efficiency than the CP. Indeed, there is a lot of molecular evidence about the protector effect and the use of molecular feature-based NmAbs as promising therapeutics to contain COVID-19. Thus, from the scientific publication database screening, we here retrieved antibody-related papers and summarized the repertory of characterized NmAbs against SARS-CoV-2, their molecular neutralization mechanisms, and their immunotherapeutic pros and cons. About 500 anti-SARS-CoV-2 NmAbs, characterized through competitive binding assays and neutralization efficacy, were reported at the writing time (January 2021). All NmAbs bind respectively to SARS-CoV-2 S and exhibit high molecular neutralizing effects against wild-type and/or pseudotyped virus. Overall, we defined six NmAb groups blocking SARS-CoV-2 through different molecular neutralization mechanisms, from which five potential neutralization sites on SARS-CoV-2 S protein are described. Therefore, more efforts are needed to develop NmAbs-based cocktails to mitigate COVID-19.

A retrospective evaluation of the value of COVID-19 screening and testing in patients with cancer: Aiming at a moving target

BACKGROUND

Diagnosis of COVID-19 infection in cancer patients is critical to co-manage their underlying disease and infection appropriately. Our study aimed at evaluating the sensitivity and specificity of screening patients with cancer for COVID-19 infection.

METHODS

All oncology patients receiving care at Department of Oncology at King Abdulaziz Medical City in Riyadh were screened using the acute respiratory infection (ARI) survey. Nasopharyngeal and throat swap for polymerase chain reaction (PCR) testing for severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) was performed on patients who have high ARI score (i.e. ≥ 4), or any patient requiring elective/emergency hospitalization, undergoing a procedure as well as screening asymptomatic patients receiving chemotherapy between April 1st and July 30, 2020. Institutional Review Board approval was obtained. Descriptive and inferential analyses were done and sensitivity, specificity, positive and negative predictive values (PPV and NPV) were calculated considering the COVID-19 PCR as the gold standard.

RESULTS

During the study period, a total of 473 patients were included with a median age was 56 years (14-104), 51% were female, 73% had solid tumors, and 66% received treatment within the last 3 months. These patients underwent 688 PCR tests along with ARI survey screening. Testing was done in the outpatient, inpatient, and emergency department setting in 41%, 40% and 19% of the patients, respectively. Majority of tests were screening of asymptomatic patients and only 23% were tested for suspected infections with ARI ≥ 4. A total of 54 patients (8%) had positive PCR for COVID-19 infection. The prevalence of infection varied from month to month ranging from 1.09% in April up to 19.70% in June and correlated with the average daily and active case load at a national level. The diagnostic yield of the ARI score also correlated with infection burden nationally. The PPV and NPV of the ARI as a screening tool was 18.24% (0-31.8) and 95.6% (86.36-98.86%) with the PPN fluctuating considerably in parallel with the prevalence of COVID-19 result. Similarly, the sensitivity and specificity of the ARI were 55.77% (0-70.59) and 79.4 (69.19-92), respectively.

CONCLUSION

The yield of screening asymptomatic patients with cancer varies based on the community burden of COVID-19 infection. As universal screening can cause delays to patient care, it should be tailored based on the individual patient risks and infection burden in the region.

Prevalence of Anti-SARS-CoV-2 Antibodies in Poznań, Poland, after the First Wave of the COVID-19 Pandemic

In comparison to other European countries, during the first months of the COVID-19 pandemic, Poland reported a relatively low number of confirmed cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections. To estimate the scale of the pandemic in Poland, a serosurvey of antibodies against SARS-CoV-2 was performed after the first wave of COVID-19 in Europe (March–May 2020). Within this study, we collected samples from 28 July to 24 September 2020 and, based on the ELISA results, we found that 1.67% (25/1500, 95% CI 1.13–2.45) of the Poznan (Poland) metropolitan area’s population had antibodies against SARS-CoV-2 after the first wave of COVID-19. However, the presence of anti-SARS-CoV-2 IgG antibodies was confirmed with immunoblotting in 56% (14/25) samples, which finally resulted in a decrease in seroprevalence, i.e., 0.93% (14/1500, 95% CI 0.56–1.56). The positive anti-SARS-CoV-2 IgG results were associated with age, occupation involving constant contact with people, travelling abroad, non-compliance with epidemiological recommendations and direct contact with the novel coronavirus. Our findings confirm the low SARS-CoV-2 incidence in Poland and imply that the population had little herd immunity heading into the second and third wave of the pandemic, and therefore, that herd immunity contributed little to preventing the high numbers of SARS-CoV-2 infections and COVID-19-related deaths in Poland during these subsequent waves.

Analytical Validation and Clinical Application of Rapid Serological Tests for SARS-CoV-2 Suitable for Large-Scale Screening

Recently, large-scale screening for COVID-19 has presented a major challenge, limiting timely countermeasures. Therefore, the application of suitable rapid serological tests could provide useful information, however, little evidence regarding their robustness is currently available. In this work, we evaluated and compared the analytical performance of a rapid lateral-flow test (LFA) and a fast semiquantitative fluorescent immunoassay (FIA) for anti-nucleocapsid (anti-NC) antibodies, with the reverse transcriptase real-time PCR assay as the reference. In 222 patients, LFA showed poor sensitivity (55.9%) within two weeks from PCR, while later testing was more reliable (sensitivity of 85.7% and specificity of 93.1%). Moreover, in a subset of 100 patients, FIA showed high sensitivity (89.1%) and specificity (94.1%) after two weeks from PCR. The coupled application for the screening of 183 patients showed satisfactory concordance (K = 0.858). In conclusion, rapid serological tests were largely not useful for early diagnosis, but they showed good performance in later stages of infection. These could be useful for back-tracing and/or to identify potentially immune subjects.

IgM and IgG Immunoreactivity of SARS-CoV-2 Recombinant M Protein

Diagnostic evaluation of specific antibodies against the SARS-CoV-2 virus is mainly based on spike (S) and nucleocapsid (N) proteins. Despite the critical functions in virus infection and contribution to the pattern of immunodominance in COVID-19, exploitation of the most abundant membrane (M) protein in the SARS-CoV-2 serology tests is minimal. This study investigated the recombinant M protein's immunoreactivity with the sera from COVID-19 convalescents. In silico designed protein was created from the outer N-terminal part (19 aa) and internal C-terminal tail (101-222 aa) of the M protein (YP_009724393.1) and was recombinantly produced and purified. The designed M protein (16,498.74 Da, pI 8.79) revealed both IgM and IgG reactivity with serum samples from COVID-19 convalescents in Western blot. In ELISA, more than 93% (28/30) of COVID-19 sera were positive for IgM detection, and more than 96% (29/30) were positive for specific IgG detection to M protein. Based on the capacity to provoke an immune response and its strong antigenic properties, as shown here, and the fact that it is also involved in the virion entry into host cells, the M protein of the SARS-CoV-2 virus as a good antigen has the potential in diagnostic purposes and vaccine design.