An Update on Molecular Diagnostics for COVID-19

Recent findings and applications of biomedical engineering for COVID-19 diagnosis: a critical review

COVID-19 is one of the most severe global health crises that humanity has ever faced. Researchers have restlessly focused on developing solutions for monitoring and tracing the viral culprit, SARS-CoV-2, as vital steps to break the chain of infection. Even though biomedical engineering (BME) is considered a rising field of medical sciences, it has demonstrated its pivotal role in nurturing the maturation of COVID-19 diagnostic technologies. Within a very short period of time, BME research applied to COVID-19 diagnosis has advanced with ever-increasing knowledge and inventions, especially in adapting available virus detection technologies into clinical practice and exploiting the power of interdisciplinary research to design novel diagnostic tools or improve the detection efficiency. To assist the development of BME in COVID-19 diagnosis, this review highlights the most recent diagnostic approaches and evaluates the potential of each research direction in the context of the pandemic.

Performance and usefulness of a novel automated immunoassay HISCL SARS-CoV-2 Antigen assay kit for the diagnosis of COVID-19

Here, we aimed to evaluate the clinical performance of a novel automated immunoassay HISCL SARS-CoV-2 Antigen assay kit designed to detect the nucleocapsid (N) protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This kit comprises automated chemiluminescence detection systems. Western blot analysis confirmed that anti-SARS-CoV antibodies detected SARS-CoV-2N proteins. The best cut-off index was determined, and clinical performance was tested using 115 nasopharyngeal swab samples obtained from 46 patients with coronavirus disease 2019 (COVID-19) and 69 individuals who tested negative for COVID-19 through reverse transcription quantitative polymerase chain reaction (RT-qPCR). The HISCL Antigen assay kit showed a sensitivity of 95.4% and 16.6% in samples with copy numbers > 100 and < 99, respectively. The kit did not cross-react with human coronaviruses causing seasonal common cold and influenza, and none of the 69 individuals without COVID-19 were diagnosed with positive results. Importantly, 81.8% of the samples with low virus load (< 50 copy numbers) were diagnosed as negative. Thus, using HISCL antigen assay kits may reduce overdiagnosis compared with RT-qPCR tests. The rapid and high-throughput HISCL SARS-CoV-2 Antigen assay kit developed here proved suitable for screening infectious COVID-19 and may help control the pandemic.

Point-of-need detection of pathogen-specific nucleic acid targets using magnetic particle spectroscopy

The ongoing COVID-19 pandemic stresses the need for widely available diagnostic tests for the presence of SARS-CoV-2 in individuals. Due to the limited availability of vaccines, diagnostic assays which are cheap, easy-to-use at the point-of-need, reliable and fast, are currently the only way to control the pandemic situation.

Here we present a diagnostic assay for the detection of pathogen-specific nucleic acids based on changes of the magnetic response of magnetic nanoparticles: The target-mediated hybridization of modified nanoparticles leads to an increase in the hydrodynamic radius. This resulting change in the magnetic behaviour in an ac magnetic field can be measured via magnetic particle spectroscopy (MPS), providing a viable tool for the accurate detection of target nucleic acids.

In this work we show that single stranded DNA can be detected in a concentration-dependent manner by these means. In addition to detecting synthetic DNA with an arbitrary sequence in a concentration down to 500 pM, we show that RNA and SARS-CoV-2-specific DNA as well as saliva as a sample medium can be used for an accurate assay. These proof-of-principle experiments show the potential of MPS based assays for the reliable and fast diagnostics of pathogens like SARS-CoV-2 in a point-of-need fashion without the need of complex sample preparation.

The relationship between COVID-19 and HLA in kidney transplant recipients, an evaluation of predictive and prognostic factors

INTRODUCTION

The purpose of this study was to determine the predictive and prognostic factors for COVID-19 infection and its relationship with human leukocyte antigen (HLA) in kidney transplant recipients.

MATERIAL AND METHOD

Three hundred fifty kidney transplant recipients were included in the study. Recipients were divided into two groups: COVID-19(+) (n = 100) and control (n = 250). The relationships between HLA frequencies, COVID-19 infection, and prognostic factors (age, donor type, immunosuppression protocol, etc.) were then evaluated. Logistic regression analysis, heatmap, and decision tree methods were used to determine predictive and prognostic factors. The study was performed retrospectively.

RESULTS

Advanced age and deceased transplantation emerged as predictive of SARS-CoV-2 infection, while the presence of HLA-A*11, the HLA match ratio, and high-dose tacrolimus were identified as prognostic factors in kidney transplant recipients. HLA-A10, HLA-B*13, HLA-B22, and HLA-B*55 were shown to be associated with SARS-CoV-2 infection at univariate analysis, and HLA-B*57, HLA-DRB1*11, and HLA-DRB1*13 at logistic regression analysis.

CONCLUSION

HLA-A10, HLA-B*13, HLA-B*55, HLA-B*57, HLA-DRB1*11, and HLA-DRB1*13 were identified for the first time in the literature associated with SARS-CoV-2 infection in kidney transplant recipients.

A Novel Rapid Test to Detect Anti-SARS-CoV-2 N Protein IgG Based on Shear Horizontal Surface Acoustic Wave (SH-SAW)

Since the Coronavirus disease 2019 (COVID-19) pandemic outbreak, many methods have been used to detect antigens or antibodies to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), including viral culture, nucleic acid test, and immunoassay. The shear-horizontal surface acoustic wave (SH-SAW) biosensor is a novel pathogen detection platform with the advantages of high sensitivity and short detection time. The objective of this study is to develop a SH-SAW biosensor to detect the anti-SARS-CoV-2 nucleocapsid antibody. The rabbit sera collected from rabbits on different days after SARS-CoV-2 N protein injection were evaluated by SH-SAW biosensor and enzyme-linked immunosorbent assay (ELISA). The results showed that the SH-SAW biosensor achieved a high correlation coefficient (R = 0.9997) with different concentrations (34.375–1100 ng/mL) of the “spike-in” anti-N protein antibodies. Compared to ELISA, the SH-SAW biosensor has better sensitivity and can detect anti-N protein IgG signals earlier than ELISA on day 6 (p < 0.05). Overall, in this study, we demonstrated that the SH-SAW biosensor is a promising platform for rapid in vitro diagnostic (IVD) testing, especially for antigen or antibody testing.

Physiopathology and prospectives for therapeutic treatment of pulmonary fibrotic state in COVID-19 patients

The COVID-19 global pandemic has caused about 4,30 Mln deaths. Recently the first vaccines have been licensed, representing the most powerful weapon available to stop the pandemic. The COVID-19 viral infection in the most severe cases can cause severe lung lesions with the presence of fibrotic tissue. Even among cured individuals, the presence of pulmonary fibrotic tissue may be the major cause of long-term complications of COVID-19 requiring antifibrotic therapeutic treatment even in the post-COVID-19 infection phase to accelerate the healing process and fully recover lung function. This article reviews the fibrogenic mechanism of SARS-CoV-2-induced viral damage and the antifibrotic treatments indicated to treat sequelae post COVID-19 infection.

Covid 19 Pandemic-Training of Healthcare Workers in Obtaining a Nasopharyngeal Swab: Our Experience

To describe the training of healthcare workers (HCW) in nasopharyngeal swabbing during the COVID 19 pandemic. Study design: Retrospective study. Setting: Tertiary care teaching hospital. Subjects and methods: One hundred and seventy eight health care workers were trained from May 2020 to January 2021. Three modules were designed to train the health care workers in the technique of obtaining a nasopharyngeal swab specimen.Training consisted of an instructional video on how to perform nasopharyngeal swabs and live demonstration followed by hands-on supervised training. The trainees included 30 doctors, 101 nurses, 31 respiratory therapists, 3 physiotherapists, 9 interns and 4 lab technicians. There were 39 male and 139 female trainees. After attending all 3 modules of training, they were confident and efficient in taking a non-traumatic nasopharyngeal swab. Good knowledge and adequate training is key to a good nasopharyngeal sampling for SARS CoV-2 testing.

Treatment decision for cancer patients with fever during the coronavirus disease 2019 (COVID-19) pandemic

Background

Cancer patients have been disproportionally affected by the coronavirus disease 2019 (COVID-19) pandemic, with high rates of severe outcomes and mortality. Fever is the most common symptom in COVID-19 patients. During the COVID-19 pandemic, physicians may have difficulty in determining the cause of fever (COVID-19, another infection, or cancer fever) in cancer patients. Furthermore, there are no specific guidelines for managing cancer patients with fever during the COVID-19 pandemic. Thus, this study evaluated the clinical characteristics and outcomes of cancer patients with fever during the COVID-19 pandemic.

Methods

This study retrospectively reviewed the medical records of 328 cancer patients with COVID-19 symptoms (fever) admitted to five hospitals in Daegu, Korea from January to October 2020. We obtained data on demographics, clinical manifestations, laboratory test results, chest computed tomography images, cancer history, cancer treatment, and outcomes of all enrolled patients from electronic medical records.

Results

The most common COVID-19-like symptoms were fever (n=256, 78%). Among 256 patients with fever, only three (1.2%) were diagnosed with COVID-19. Most patients (253, 98.8%) with fever were not diagnosed with COVID-19. The most common solid malignancies were lung cancer (65, 19.8%) and hepatobiliary cancer (61, 18.6%). Twenty patients with fever experienced a delay in receiving cancer treatment. Eighteen patients discontinued active cancer treatment because of fever. Major events during the treatment delay period included death (2.7%), cancer progression (1.5%), and major organ dysfunction (2.7%).

Conclusion

Considering that only 0.9% of patients tested for COVID-19 were positive, screening for COVID-19 in cancer patients with fever should be based on the physician’s clinical decision, and patients might not be routinely tested.

Antibodies Targeting Two Epitopes in SARS-CoV-2 Neutralize Pseudoviruses with the Spike Proteins from Different Variants

The COVID-19 pandemic was caused by SARS-CoV-2 infection. To prevent the spread of SARS-CoV-2, an effective vaccine is required. Two linear peptides from potential B-cell epitopes in the spike protein of SARS-CoV-2 (a.a. 440–460; a.a. 494–506) were synthesized and used to immunize rabbits. High-titer antibodies of IgG were produced, purified, and verified by Western blot analysis. Antibodies against these two epitopes could effectively neutralize SARS-CoV-2 pseudoviral particles with the spike proteins from not only the original strain (basal; wild-type), but also a strain with a single point mutation (D614G), and two other emerging variants (the Alpha and Beta variants) prevalent around the world, but not from SARS-CoV. In conclusion, antibodies against these two epitopes are protective. This information is important for the development of vaccines against SARS-CoV-2.

The Role of Indoor Plants in air Purification and Human Health in the Context of COVID-19 Pandemic: A Proposal for a Novel Line of Inquiry

The last two decades have seen the discovery of novel retroviruses that have resulted in severe negative consequences for human health. In late 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged with a high transmission rate and severe effects on human health, with 5% infected persons requiring hospitalisation and 3.81 million deaths to date globally. Aerosol particles containing virions are considered the main source of SARS CoV-2 transmission in this pandemic, with increased infection rates in confined spaces. Consequently, public and private institutions had to institute mitigation measures including the use of facial masks and social distancing to limit the spread of the virus. Moreover, the role of air purification and bio-decontamination is understood as being essential to mitigate viral spread. Various techniques can be applied to bio-decontaminate the air such as the use of filtration and radiation; however, these methods are expensive and not feasible for home use. Another method of air purification is where indoor plants can purify the air by the removal of air pollutants and habituated airborne microbes. The use of indoor plants could prove to be a cost-efficient way of indoor air-purification that could be adapted for a variety of environments with no need for special requirements and can also add an aesthetic value that can have an indirect impact on human health. In this review, we discuss the emergence of the COVID-19 pandemic and the currently used air purification methods, and we propose the use of indoor plants as a new possible eco-friendly tool for indoor air purification and for reducing the spread of COVID-19 in confined places.

2D materials as a diagnostic platform for the detection and sensing of the SARS-CoV-2 virus: a bird's-eye view

Worldwide infections and fatalities caused by the SARS-CoV-2 virus and its variants responsible for COVID-19 have significantly impeded the economic growth of many nations. People in many nations have lost their livelihoods, it has severely impacted international relations and, most importantly, health infrastructures across the world have been tormented. This pandemic has already left footprints on human psychology, traits, and priorities and is certainly going to lead towards a new world order in the future. As always, science and technology have come to the rescue of the human race. The prevention of infection by instant and repeated cleaning of surfaces that are most likely to be touched in daily life and sanitization drives using medically prescribed sanitizers and UV irradiation of textiles are the first steps to breaking the chain of transmission. However, the real challenge is to develop and uplift medical infrastructure, such as diagnostic tools capable of prompt diagnosis and instant and economic medical treatment that is available to the masses. Two-dimensional (2D) materials, such as graphene, are atomic sheets that have been in the news for quite some time due to their unprecedented electronic mobilities, high thermal conductivity, appreciable thermal stability, excellent anchoring capabilities, optical transparency, mechanical flexibility, and a unique capability to integrate with arbitrary surfaces. These attributes of 2D materials make them lucrative for use as an active material platform for authentic and prompt (within minutes) disease diagnosis via electrical or optical diagnostic tools or via electrochemical diagnosis. We present the opportunities provided by 2D materials as a platform for SARS-CoV-2 diagnosis.

Mass spectrometry analytical responses to the SARS-CoV2 coronavirus in review

This article reviews the many and varied mass spectrometry based responses to the SARS-CoV2 coronavirus amidst a continuing global healthcare crisis. Although RT-PCR is the most prevalent molecular based surveillance approach, improvements in the detection sensitivities with mass spectrometry coupled to the rapid nature of analysis, the high molecular precision of measurements, opportunities for high sample throughput, and the potential for in-field testing, offer advantages for characterising the virus and studying the molecular pathways by which it infects host cells. The detection of biomarkers by MALDI-TOF mass spectrometry, studies of viral peptides using proteotyping strategies, targeted LC-MS analyses to identify abundant peptides in clinical specimens, the analysis of viral protein glycoforms, proteomics approaches to understand impacts of infection on host cells, and examinations of point-of-care breath analysis have all been explored. This review organises and illustrates these applications with reference to the many studies that have appeared in the literature since the outbreak. In this respect, those studies in which mass spectrometry has a major role are the focus, and only those which have peer-reviewed have been cited.

Evidence of the presence of SARS-CoV-2 virus in atmospheric air and surfaces of a dedicated COVID hospital

The present study was conducted from July 1, 2020 to September 25, 2020 in a dedicated coronavirus disease 2019 (COVID‐19) hospital in Delhi, India to provide evidence for the presence of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) virus in atmospheric air and surfaces of the hospital wards. Swabs from hospital surfaces (patient's bed, ward floor, and nursing stations area) and suspended particulate matter in ambient air were collected by a portable air sampler from the medicine ward, intensive care unit, and emergency ward admitting COVID‐19 patients. By performing reverse‐transcriptase polymerase chain reaction (RT‐PCR) for E‐gene and RdRp gene, SARS‐CoV‐2 virus was detected from hospital surfaces and particulate matters from the ambient air of various wards collected at 1 and 3‐m distance from active COVID‐19 patients. The presence of the virus in the air beyond a 1‐m distance from the patients and surfaces of the hospital indicates that the SARS‐CoV‐2 virus has the potential to be transmitted by airborne and surface routes from COVID‐19 patients to health‐care workers working in COVID‐19 dedicated hospital. This warrants that precautions against airborne and surface transmission of COVID‐19 in the community should be taken when markets, industries, educational institutions, and so on, reopen for normal activities.

COVID-19 Diagnostic Strategies. Part I: Nucleic Acid-Based Technologies

The novel Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has caused respiratory infection, resulting in more than two million deaths globally and hospitalizing thousands of people by March 2021. A considerable percentage of the SARS-CoV-2 positive patients are asymptomatic or pre-symptomatic carriers, facilitating the viral spread in the community by their social activities. Hence, it is critical to have access to commercialized diagnostic tests to detect the infection in the earliest stages, monitor the disease, and follow up the patients. Various technologies have been proposed to develop more promising assays and move toward the mass production of fast, reliable, cost-effective, and portable PoC diagnostic tests for COVID-19 detection. Not only COVID-19 but also many other pathogens will be able to spread and attach to human bodies in the future. These technologies enable the fast identification of high-risk individuals during future hazards to support the public in such outbreaks. This paper provides a comprehensive review of current technologies, the progress in the development of molecular diagnostic tests, and the potential strategies to facilitate innovative developments in unprecedented pandemics.

CRISPR/Cas: a Nobel Prize award-winning precise genome editing technology for gene therapy and crop improvement

Since it was first recognized in bacteria and archaea as a mechanism for innate viral immunity in the early 2010s, clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) has rapidly been developed into a robust, multifunctional genome editing tool with many uses. Following the discovery of the initial CRISPR/Cas-based system, the technology has been advanced to facilitate a multitude of different functions. These include development as a base editor, prime editor, epigenetic editor, and CRISPR interference (CRISPRi) and CRISPR activator (CRISPRa) gene regulators. It can also be used for chromatin and RNA targeting and imaging. Its applications have proved revolutionary across numerous biological fields, especially in biomedical and agricultural improvement. As a diagnostic tool, CRISPR has been developed to aid the detection and screening of both human and plant diseases, and has even been applied during the current coronavirus disease 2019 (COVID-19) pandemic. CRISPR/Cas is also being trialed as a new form of gene therapy for treating various human diseases, including cancers, and has aided drug development. In terms of agricultural breeding, precise targeting of biological pathways via CRISPR/Cas has been key to regulating molecular biosynthesis and allowing modification of proteins, starch, oil, and other functional components for crop improvement. Adding to this, CRISPR/Cas has been shown capable of significantly enhancing both plant tolerance to environmental stresses and overall crop yield via the targeting of various agronomically important gene regulators. Looking to the future, increasing the efficiency and precision of CRISPR/Cas delivery systems and limiting off-target activity are two major challenges for wider application of the technology. This review provides an in-depth overview of current CRISPR development, including the advantages and disadvantages of the technology, recent applications, and future considerations.

Laboratory diagnosis of COVID-19: current status and challenges

The magnitude and pace of global affliction caused by Coronavirus Disease-19 (COVID-19) is unprecedented in the recent past. From starting in a busy seafood market in the Chinese city of Wuhan, the virus has spread across the globe in less than a year, infecting over 76 million people and causing death of close to 1.7 million individuals worldwide. As no specific antiviral treatment is currently available, the major strategy in containing the pandemic is focused on early diagnosis and prompt isolation of the infected individuals. Several diagnostic modalities have emerged within a relatively short period, which can be broadly classified into molecular and immunological assays. While the former category is centered around real-time PCR, which is currently considered the gold standard of diagnosis, the latter aims to detect viral antigens or antibodies specific to the viral antigens and is yet to be recommended as a stand-alone diagnostic tool. This review aims to provide an update on the different diagnostic modalities that are currently being used in diagnostic laboratories across the world as well as the upcoming methods and challenges associated with each of them. In a rapidly evolving diagnostic landscape with several testing platforms going through various phases of development and/or regulatory clearance, it is prudent that the clinical community familiarizes itself with the nuances of different testing modalities currently being employed for this condition.

Updated insight into COVID-19 disease and health management to combat the pandemic

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes COVID-19 disease in humans and is the responsible viral agent for the currently ongoing pandemic. Early cases of COVID-19 were reported from Wuhan, Hubei province of China, the likely birthplace of this outbreak. Currently, over 92 million people in the globe are actively battling this virus, and over 2 million individuals have already succumbed to the disease. The high human-to-human transmission capacity of the virus is among the primary causes for such a rapid global spread of COVID-19. In humans, it causes acute to severe respiratory distress in the form of pneumonia. The presentation of clinical features of the disease ranges from mild in healthy adults to severe among individuals with weakened or immunocompromised immune systems and the elderly. Thus, increasing patient cases of COVID-19 warrants a growing demand for medical attention that is eventually overburdening our health care systems. Rapid detection of COVID-19 in suspected individuals and isolation are among the crucial intervention norms in health management strategies to control the COVID-19 pandemic, in addition to strict observance of public hygienic practices such as reduced public gathering, use of facial masks, and practicing of social distancing. This chapter provides an overview of the epidemiology of COVID-19 and the current classical health management strategies and issues to tackle this pandemic. It particularly highlights the role of standard as well as novel biomolecular diagnostic techniques as a tool for successful implementation of such public safety measures issued by medical policy makers and the governing bodies.