Different Respiratory Samples for COVID-19 Detection by Standard and Direct Quantitative RT-PCR: A Literature Review

Enhanced Multi-Model Deep Learning for Rapid and Precise Diagnosis of Pulmonary Diseases Using Chest X-Ray Imaging

Background: The global burden of respiratory diseases such as influenza, tuberculosis, and viral pneumonia necessitates rapid, accurate diagnostic tools to improve healthcare responses. Current methods, including RT-PCR and chest radiography, face limitations in accuracy, speed, accessibility, and cost-effectiveness, especially in resource-constrained settings, often delaying treatment and increasing transmission. Methods: This study introduces an Enhanced Multi-Model Deep Learning (EMDL) approach to address these challenges. EMDL integrates an ensemble of five pre-trained deep learning models (VGG-16, VGG-19, ResNet, AlexNet, and GoogleNet) with advanced image preprocessing (histogram equalization and contrast enhancement) and a novel multi-stage feature selection and optimization pipeline (PCA, SelectKBest, Binary Particle Swarm Optimization (BPSO), and Binary Grey Wolf Optimization (BGWO)). Results: Evaluated on two independent chest X-ray datasets, EMDL achieved high accuracy in the multiclass classification of influenza, pneumonia, and tuberculosis. The combined image enhancement and feature optimization strategies significantly improved diagnostic precision and model robustness. Conclusions: The EMDL framework provides a scalable and efficient solution for accurate and accessible pulmonary disease diagnosis, potentially improving treatment efficacy and patient outcomes, particularly in resource-limited settings.

From Tradition to Innovation: Diverse Molecular Techniques in the Fight Against Infectious Diseases

Infectious diseases impose a significant burden on global health systems due to high morbidity and mortality rates. According to the World Health Organization, millions die from infectious diseases annually, often due to delays in accurate diagnosis. Traditional diagnostic methods in clinical microbiology, primarily culture-based techniques, are time-consuming and may fail with hard-to-culture pathogens. Molecular biology advancements, notably the polymerase chain reaction (PCR), have revolutionized infectious disease diagnostics by allowing rapid and sensitive detection of pathogens' genetic material. PCR has become the gold standard for many infections, particularly highlighted during the COVID-19 pandemic. Following PCR, next-generation sequencing (NGS) has emerged, enabling comprehensive genomic analysis of pathogens, thus facilitating the detection of new strains and antibiotic resistance tracking. Innovative approaches like CRISPR technology are also enhancing diagnostic precision by identifying specific DNA/RNA sequences. However, the implementation of these methods faces challenges, particularly in low- and middle-income countries due to infrastructural and financial constraints. This review will explore the role of molecular diagnostic methods in infectious disease diagnosis, comparing their advantages and limitations, with a focus on PCR and NGS technologies and their future potential.

Flexible upscaling of laboratory PCR testing capacity at the Robert Koch Institute during the SARS-CoV-2 pandemic

BACKGROUND

Over the course of the COVID-19 pandemic, laboratories worldwide have been facing an unprecedented increase in demand for PCR testing because of the high importance of diagnostics for prevention and control of virus spread. Moreover, testing demand has been varying considerably over time, depending on the epidemiological situation, rendering efficient resource allocation difficult. Here, we present a scalable workflow which we implemented in our laboratory to increase PCR testing capacity while maintaining high flexibility regarding the number of samples to be processed.

METHODS

We compared the performance of five automated extraction instruments, using dilutions of SARS-CoV-2 cell culture supernatant as well as clinical samples. To increase PCR throughput, we combined the two duplex PCR reactions of our previously published SARS-CoV-2 PCR assay into one quadruplex reaction and compared their limit of detection as well as their performance on the detection of low viral loads in clinical samples. Furthermore, we developed a sample pooling protocol with either two or four samples per pool, combined with a specifically adapted SARS-CoV-2 quadruplex PCR assay, and compared the diagnostic sensitivity of pooled testing and individual testing.

RESULTS

All tested automated extraction instruments yielded comparable results regarding the subsequent sensitivity of SARS-CoV-2 detection by PCR. While the limit of detection of the quadruplex SARS-CoV-2 PCR assay (E-Gene assay: 28.7 genome equivalents (ge)/reaction, orf1ab assay: 32.0 ge/reaction) was slightly higher than that of our previously published duplex PCR assays (E-Gene assay: 9.8 ge/reaction, orf1ab assay: 6.6 ge/reaction), the rate of correctly identified positive patient samples was comparable for both assays. Sample pooling with optimized downstream quadruplex PCR showed no loss in diagnostic sensitivity compared to individual testing.

CONCLUSION

Specific adaptation of PCR assays can help overcome the potential loss of sensitivity due to higher levels of PCR multiplexing or sample dilution in pooled testing. Combining these adapted PCR assays with different sample processing strategies provides a simple and highly adjustable workflow for resource-efficient SARS-CoV-2 diagnostics. The presented principles can easily be adopted in a variety of laboratory settings as well as be adapted to pathogens other than SARS-CoV-2, making it feasible for any laboratory that conducts PCR diagnostics.

Do COVID-19 CT features vary between patients from within and outside mainland China? Findings from a meta-analysis

BACKGROUND

Chest computerized tomography (CT) plays an important role in detecting patients with suspected coronavirus disease 2019 (COVID-19), however, there are no systematic summaries on whether the chest CT findings of patients within mainland China are applicable to those found in patients outside.

METHODS

Relevant studies were retrieved comprehensively by searching PubMed, Embase, and Cochrane Library databases before 15 April 2022. Quality assessment of diagnostic accuracy studies (QUADAS) was used to evaluate the quality of the included studies, which were divided into two groups according to whether they were in mainland China or outside. Data on diagnostic performance, unilateral or bilateral lung involvement, and typical chest CT imaging appearances were extracted, and then, meta-analyses were performed with R software to compare the CT features of COVID-19 pneumonia between patients from within and outside mainland China.

RESULTS

Of the 8,258 studies screened, 19 studies with 3,400 patients in mainland China and 14 studies with 554 outside mainland China were included. Overall, the risk of quality assessment and publication bias was low. The diagnostic value of chest CT is similar between patients from within and outside mainland China (93, 91%). The pooled incidence of unilateral lung involvement (15, 7%), the crazy-paving sign (31, 21%), mixed ground-glass opacities (GGO) and consolidations (51, 35%), air bronchogram (44, 25%), vascular engorgement (59, 33%), bronchial wall thickening (19, 12%), and septal thickening (39, 26%) in patients from mainland China were significantly higher than those from outside; however, the incidence rates of bilateral lung involvement (75, 84%), GGO (78, 87%), consolidations (45, 58%), nodules (12, 17%), and pleural effusion (9, 15%) were significantly lower.

CONCLUSION

Considering that the chest CT features of patients in mainland China may not reflect those of the patients abroad, radiologists and clinicians should be familiar with various CT presentations suggestive of COVID-19 in different regions.

Visual Detection of COVID-19 from Materials Aspect

Abstract

In the recent COVID-19 pandemic, World Health Organization emphasized that early detection is an effective strategy to reduce the spread of SARS-CoV-2 viruses. Several diagnostic methods, such as reverse transcription-polymerase chain reaction (RT-PCR) and lateral flow immunoassay (LFIA), have been applied based on the mechanism of specific recognition and binding of the probes to viruses or viral antigens. Although the remarkable progress, these methods still suffer from inadequate cellular materials or errors in the detection and sampling procedure of nasopharyngeal/oropharyngeal swab collection. Therefore, developing accurate, ultrafast, and visualized detection calls for more advanced materials and technology urgently to fight against the epidemic. In this review, we first summarize the current methodologies for SARS-CoV-2 diagnosis. Then, recent representative examples are introduced based on various output signals (e.g., colorimetric, fluorometric, electronic, acoustic). Finally, we discuss the limitations of the methods and provide our perspectives on priorities for future test development.

Graphical Abstract