Articles related to Diagnosis of Covid-19.

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Detection of SARS-CoV-2 and the L452R spike mutation using reverse transcription loopmediated isothermal amplification plus bioluminescent assay in real-time (RT-LAMPBART)

Takahiro Iijima1 , Shinnosuke Ando2 , Dai Kanamori1 , Kazumichi Kuroda3 , Tsutomu Nomura4 , Laurence Tisi5 , Paul E. Kilgore6 , Neil Percy7 , Hikaru Kohase2 , Satoshi Hayakawa8 , Mitsuko SekiID1,8*, Tomonori Hoshino

Abstract

The new coronavirus infection (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can be fatal, and several variants of SARS-CoV-2 with mutations of the receptor-binding domain (RBD) have increased avidity for human cell receptors. A single missense mutation of U to G at nucleotide position 1355 (U1355G) in the spike (S) gene changes leucine to arginine (L452R) in the spike protein. This mutation has been observed in the India and California strains (B.1.617 and B.1.427/B.1.429, respectively). Control of COVID-19 requires rapid and reliable detection of SARS-CoV-2. Therefore, we established a reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay plus a bioluminescent assay in real-time (BART) to detect SARS-CoV-2 and the L452R spike mutation. The specificity and sensitivity of the RT-LAMP-BART assay was evaluated using synthetic RNAs including target sequences and RNA-spiked clinical nasopharyngeal and saliva specimens as well as reference strains representing five viral and four bacterial pathogens. The novel RT-LAMP-BART assay to detect SARS-CoV-2 was highly specific compared to the conventional real-time RT-PCR. Within 25 min, the RTLAMP-BART assay detected 80 copies of the target gene in a sample, whereas the conventional real-time RT-PCR method detected 5 copies per reaction within 130 min. Using RNAspiked specimens, the sensitivity of the RT-LAMP-BART assay was slightly attenuated compared to purified RNA as a template. The results were identical to those of the conventional real-time RT-PCR method. Furthermore, using a peptide nucleic acid (PNA) probe, the RT-LAMP-BART method correctly identified the L452R spike mutation. This is the first report describes RT-LAMP-BART as a simple, inexpensive, rapid, and useful assay for detection of SARS-CoV-2, its variants of concern, and for screening of COVID-19.

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AI-driven quantification of ground glass opacities in lungs of COVID-19 patients using 3D computed tomography imaging

Monjoy SahaID1 *, Sagar B. Amin2 , Ashish Sharma1 , T. K. Satish Kumar3 , Rajiv K. Kalia3,4,5,6

Abstract

Objectives Ground-glass opacity (GGO)—a hazy, gray appearing density on computed tomography (CT) of lungs—is one of the hallmark features of SARS-CoV-2 in COVID-19 patients. This AI-driven study is focused on segmentation, morphology, and distribution patterns of GGOs. Method We use an AI-driven unsupervised machine learning approach called PointNet++ to detect and quantify GGOs in CT scans of COVID-19 patients and to assess the severity of the disease. We have conducted our study on the “MosMedData”, which contains CT lung scans of 1110 patients with or without COVID-19 infections. We quantify the morphologies of GGOs using Minkowski tensors and compute the abnormality score of individual regions of segmented lung and GGOs. Results PointNet++ detects GGOs with the highest evaluation accuracy (98%), average class accuracy (95%), and intersection over union (92%) using only a fraction of 3D data. On average, the shapes of GGOs in the COVID-19 datasets deviate from sphericity by 15% and anisotropies in GGOs are dominated by dipole and hexapole components. These anisotropies may help to quantitatively delineate GGOs of COVID-19 from other lung diseases. Conclusion The PointNet++ and the Minkowski tensor based morphological approach together with abnormality analysis will provide radiologists and clinicians with a valuable set of tools when interpreting CT lung scans of COVID-19 patients. Implementation would be particularly useful in countries severely devastated by COVID-19 such as India, where the number of cases has outstripped available resources creating delays or even breakdowns in patient care. This AI-driven approach synthesizes both the unique GGO distribution pattern and severity of the disease to allow for more efficient diagnosis, triaging and conservation of limited resources.

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Meta-analysis of the robustness of COVID-19 diagnostic kit performance during the early pandemic

Chandrakumar Shanmugam ,1 Michael Behring,2 Vishwas Luthra ,3 Sixto M Leal,4 Sooryanarayana Varambally,4 George J Netto,4 Upender Manne

ABSTRACT

Background: Accurate detection of SARS-CoV-2 is necessary to mitigate the COVID-19 pandemic. However, the test reagents and assay platforms are varied and may not be sufficiently robust to diagnose COVID-19.

Methods: We reviewed 85 studies (21 530 patients), published from five regions of the world, to highlight issues involved in the diagnosis of COVID-19 in the early phase of the pandemic. All relevant articles, published up to 31 May 2020, in PubMed, BioRiXv, MedRiXv and Google Scholar, were included. We evaluated the qualitative (9749 patients) and quantitative (10 355 patients) performance of RT-PCR and serologic diagnostic tests for real-world samples, and assessed the concordance (5538 patients) between test performance in meta-analyses. Synthesis of results was done using random effects modelling and bias was evaluated according to QUADAS-2 guidelines.

Results: The RT-PCR tests exhibited heterogeneity in the primers and reagents used. Of 1957 positive RTPCR COVID-19 participants, 1585 had positive serum antibody (IgM±IgG) tests (sensitivity 0.81, 95%CI 0.66 to 0.90). While 3509 of 3581 participants RTPCR negative for COVID-19 were found negative by serology testing (specificity 0.98, 95%CI 0.94 to 0.99). The chemiluminescent immunoassay exhibited the highest sensitivity, followed by ELISA and lateral flow immunoassays. Serology tests had higher sensitivity and specificity for laboratory approval than for real-world reporting data.

Discussion: The robustness of the assays/platforms is influenced by variability in sampling and reagents. Serological testing complements and may minimise false negative RT-PCR results. Lack of standardised assay protocols in the early phase of pandemic might have contributed to the spread of COVID-19.

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External quality assessment of COVID-19 real time reverse transcription PCR laboratories in India

Authors: Harmanmeet Kaur1, Labanya MukhopadhyayID1, Nivedita GuptaID1 *, Neeraj Aggarwal1 , Lucky Sangal2 , Varsha Potdar3 , Francis Yesuraj Inbanathan2 , Jitendra Narayan1 , Swati Gupta1 , Salaj RanaID1 , Neetu Vijay1 , Harpreet Singh4 , Jasmine Kaur4 , Vinit Kumar4 , Nirmal Kaundal5 , Priya Abraham3 , Vasanthapuram Ravi6

Abstract: Sudden emergence and rapid spread of COVID-19 created an inevitable need for expansion of the COVID-19 laboratory testing network across the world. The strategy to test-track-treat was advocated for quick detection and containment of the disease. Being the second most populous country in the world, India was challenged to make COVID-19 testing available and accessible in all parts of the country. The molecular laboratory testing network was augmented expeditiously, and number of laboratories was increased from one in January 2020 to 2951 till mid-September, 2021. This rapid expansion warranted the need to have inbuilt systems of quality control/ quality assurance. In addition to the ongoing inter-laboratory quality control (ILQC), India implemented an External Quality Assurance Program (EQAP) with assistance from World Health Organization (WHO) and Royal College of Pathologists, Australasia. Out of the 953 open system rRTPCR laboratories in both public and private sector who participated in the first round of EQAP, 891(93.4%) laboratories obtained a passing score of > = 80%. The satisfactory performance of Indian COVID-19 testing laboratories has boosted the confidence of the public and policy makers in the quality of testing. ILQC and EQAP need to continue to ensure adherence of the testing laboratories to the desired quality standards.

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Neuroimaging manifestations in children with SARS-CoV-2 infection: a multinational, multicentre collaborative study

Authors: Camilla E Lindan, MD,a Kshitij Mankad, FRCR,b Dipak Ram, FRCPCH,c Larry K Kociolek, MD,d V Michelle Silvera, MD,e Nathalie Boddaert, Prof, MD,f Stavros Michael Stivaros, Prof, PhD,g,h,i,* Susan Palasis, MD,j,*,*

Background

The CNS manifestations of COVID-19 in children have primarily been described in case reports, which limit the ability to appreciate the full spectrum of the disease in paediatric patients. We aimed to identify enough cases that could be evaluated in aggregate to better understand the neuroimaging manifestations of COVID-19 in the paediatric population.

Methods

An international call for cases of children with encephalopathy related to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and abnormal neuroimaging findings was made. Clinical history and associated plasma and cerebrospinal fluid data were requested. These data were reviewed by a central neuroradiology panel, a child neurologist, and a paediatric infectious diseases expert. The children were categorised on the basis of their time of probable exposure to SARS-CoV-2. In addition, cases were excluded when a direct link to SARS-CoV-2 infection could not be established or an established alternate diagnostic cause could be hypothesised. The accepted referral centre imaging data, from ten countries, were remotely reviewed by a central panel of five paediatric neuroradiologists and a consensus opinion obtained on the imaging findings.

Findings

38 children with neurological disease related to SARS-CoV-2 infection were identified from France (n=13), the UK (n=8), the USA (n=5), Brazil (n=4), Argentina (n=4), India (n=2), Peru (n=1), and Saudi Arabia (n=1). Recurring patterns of disease were identified, with neuroimaging abnormalities ranging from mild to severe. The most common imaging patterns were postinfectious immune-mediated acute disseminated encephalomyelitis-like changes of the brain (16 patients), myelitis (eight patients), and neural enhancement (13 patients). Cranial nerve enhancement could occur in the absence of corresponding neurological symptoms. Splenial lesions (seven patients) and myositis (four patients) were predominantly observed in children with multisystem inflammatory syndrome. Cerebrovascular complications in children were less common than in adults. Significant pre-existing conditions were absent and most children had favourable outcomes. However, fatal atypical CNS co-infections developed in four previously healthy children infected with SARS-CoV-2.

Interpretation

Acute-phase and delayed-phase SARS-CoV-2-related CNS abnormalities are seen in children. Recurring patterns of disease and atypical neuroimaging manifestations can be found and should be recognised being as potentially due to SARS-CoV-2 infection as an underlying aetiological factor. Studies of paediatric specific cohorts are needed to better understand the effects of SARS-CoV-2 infection on the CNS at presentation and on long-term follow-up in children.

Funding

American Society of Pediatric Neuroradiology, University of Manchester (Manchester, UK).

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A novel G-quadruplex aptamer-based spike trimeric antigen test for the detection of SARS-CoV-2

Authors: Ankit Gupta,1,# Anjali Anand,1,# Neha Jain,2 Sandeep Goswami,3 Anbalagan Ananthraj,4 Sharanabasava Patil,4 Rahul Singh,5 Amit Kumar,2 Tripti Shrivastava,3 Shinjini Bhatnagar,4 Guruprasad R. Medigeshi,4 Tarun Kumar Sharma,1,∗ and DBT India Consortium for COVID-19 ResearchΦ

Abstract:

Recent SARS-CoV-2 outbreak has been declared as a global health emergency. It takes years to vaccinate the whole population to protect them from this deadly virus, hence the management of SARS-CoV-2 largely depends on the widespread availability of an accurate diagnostic test. Towards addressing the unmet need of a reliable diagnostic test in the current work by utilizing the power of Systematic Evolution of Ligands by EXponential enrichment, a 44-mer G-quadruplex forming DNA aptamer against spike trimer antigen of SARS-CoV-2 was identified. The lead aptamer candidate (S14) was characterized thoroughly for its binding, selectivity, affinity, structure and batch-to-batch variability by utilizing various-biochemical, biophysical, and in silico techniques. S14 has demonstrated a low nanomolar Kd, confirming its tight binding to a spike antigen of SARS-CoV-2. S14 can detect as low as 2 nM of antigen. The clinical evaluation of S14 aptamer on nasopharyngeal swab specimens (n = 232) has displayed a highly discriminatory response between SARS-CoV-2 infected individuals from the non-infected one with a sensitivity and specificity of ∼91 % and 98 %, respectively. Importantly, S14 aptamer-based test has evinced comparable performance with that of RT-PCR-based assay. Altogether, this study established the utility of aptamer technology for the detection of SARS-CoV-2.

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A proposal for testing kit of corona viruses using 3D photonic structure

Authors: Sangram Kishore Mohanty, Subhankar Das, [...], and G. Palai

Abstract

Design of corona virus testing kit is proposed in this paper using silicon based 3D photonic structure through zirconium quantum dot solution at the signal of 412 nm. The principle of measurement depends on the computation of reflectance, absorbance and transmittance of virus based quantum dot solution. In this paper, the reflectance is studied through the analysis of photonic band gap and absorbance is made through its numerical treatment. Further, the numerical investigation shows that the transmitted energy through photonic structure would determine the type of corona virus. For example; if the transmitted energy lies within the visible spectrum the sample would be normal corona virus. However, the sample could be IBV (SARS COV-2) if the transmitted energy would be Infrared.

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Serological evidence of human infection with SARS-CoV-2: a systematic review and meta-analysis

Authors: Xinhua Chen, BSc,a,* Zhiyuan Chen, BSc,a,* Andrew S Azman, PhD,d,e,f,* Xiaowei Deng, MSc,a Ruijia Sun, BSc,a Zeyao Zhao, BSc,a Nan Zheng, BSc,a Xinghui Chen, BSc,a Wanying Lu, BSc,a Tingyu Zhuang, BSc,a Juan Yang, PhD,a Cecile Viboud, PhD,g Marco Ajelli, PhD,h Daniel T Leung, MD,i,† and Hongjie Yu, Prof, PhDa,b,c,†*

BackgroundA rapidly increasing number of serological surveys for antibodies to SARS-CoV-2 have been reported worldwide. We aimed to synthesise, combine, and assess this large corpus of data.MethodsIn this systematic review and meta-analysis, we searched PubMed, Embase, Web of Science, and five preprint servers for articles published in English between Dec 1, 2019, and Dec 22, 2020. Studies evaluating SARS-CoV-2 seroprevalence in humans after the first identified case in the area were included. Studies that only reported serological responses among patients with COVID-19, those using known infection status samples, or any animal experiments were all excluded. All data used for analysis were extracted from included papers. Study quality was assessed using a standardised scale. We estimated age-specific, sex-specific, and race-specific seroprevalence by WHO regions and subpopulations with different levels of exposures, and the ratio of serology-identified infections to virologically confirmed cases. This study is registered with PROSPERO, CRD42020198253.Findings16 506 studies were identified in the initial search, 2523 were assessed for eligibility after removal of duplicates and inappropriate titles and abstracts, and 404 serological studies (representing tests in 5 168 360 individuals) were included in the meta-analysis. In the 82 studies of higher quality, close contacts (18·0%, 95% CI 15·7–20·3) and high-risk health-care workers (17·1%, 9·9–24·4) had higher seroprevalence than did low-risk health-care workers (4·2%, 1·5–6·9) and the general population (8·0%, 6·8–9·2). The heterogeneity between included studies was high, with an overall I2 of 99·9% (p<0·0001). Seroprevalence varied greatly across WHO regions, with the lowest seroprevalence of general populations in the Western Pacific region (1·7%, 95% CI 0·0–5·0). The pooled infection-to-case ratio was similar between the region of the Americas (6·9, 95% CI 2·7–17·3) and the European region (8·4, 6·5–10·7), but higher in India (56·5, 28·5–112·0), the only country in the South-East Asia region with data.InterpretationAntibody-mediated herd immunity is far from being reached in most settings. Estimates of the ratio of serologically detected infections per virologically confirmed cases across WHO regions can help provide insights into the true proportion of the population infected from routine confirmation data.FundingNational Science Fund for Distinguished Young Scholars, Key Emergency Project of Shanghai Science and Technology Committee, Program of Shanghai Academic/Technology Research Leader, National Science and Technology Major project of China, the US National Institutes of Health.
94.pdf

Fano Resonance-Based Blood Plasma Monitoring and Sensing using Plasmonic Nanomatryoshka

Authors: Pankaj Pathania and Manmohan Singh Shishodia

Abstract

The fast label-free detection of specific antibodies and their concentration in blood plasma is useful for many applications, e.g., in Covid-19 patients. The change in biophysical properties like the refractive index of blood plasma due to the production of antibodies during infection may be very helpful in estimating the level and intensity of infection and subsequent treatment based on blood plasma therapy. In this article, Fano resonance-based refractive index sensor using plasmonic nanomatryoshka is proposed for blood plasma sensing. The interaction between hybridized modes (bright and dark modes) in optimized nanomatryoshka leads to Fano resonance, which by virtue of steeper dispersion can confine the light more efficiently compared with Lorentzian resonance. We propose the excitation of Fano resonances in sub 100-nm size nanomatryoshka based on newly emerging plasmonic materials ZrN and HfN, and one of the most widely used conventional plasmonic material, Au. Fano resonance-based plasmonic sensors leads to sensitivity = 188.5 nm/RIU, 242.5 nm/RIU, and 244.9 nm/RIU for Au, ZrN, and HfN, respectively. The corresponding figure of merit (nm/RIU) is ~ 3.5 103, 3.1 103, and 2.8 103 for Au, ZrN, and HfN, respectively. Present theoretical analysis shows that refractive index sensors with high sensitivity and figure of merit are feasible using Fano modes of plasmonic nanomatryoshka.

Keywords: Plasmonics, Sensor, Fano resonance, Mie-theory, Transition metal nitrides

100.pdf

New insights into application of nanoparticles in the diagnosis and screening of novel coronavirus (SARS-CoV-2)

Author: Abhimanyu Tharayil, R. Rajakumari, [...], and Sabu Thomas

Abstract

Novel coronavirus disease 2019 (COVID-19) is by far the worst pandemic disease in the current millennium. The first human-to-human transmission was observed in December 2019 in China and is caused by the highly contagious severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which has infected millions of people within months across the globe. SARS-CoV-2 is a spike protein enveloped virus with particle-like characteristics and a diameter of 60–140 nm. Real-time PCR, reverse transcriptase PCR, isothermal PCR, immunological-based detection technique and nano-based diagnostic system have been explained for the identification and differentiation of different types of virus including SARS-COV-2. Synthetic nanoparticles can closely mimic the virus and interact strongly with its virulent proteins due to their morphological similarities. Some of the antiviral nanomaterials are also discussed, for example zinc oxide nanoparticle is an antiviral agent with a tetrapod morphology that mimics the cell surface by interacting with the viral capsid. It suppressed the viral proteins upon UV radiation due to reaction caused by photocatalysis. Hence, nanoparticle-based strategies for tackling viruses have immense potential. The second part of the review points to the latest in vitro and in vivo procedures for screening viral particles and the usage of nanoparticles in diagnostic and therapeutics. This would be beneficial for early detection and assists for the safe and effective therapeutic management of COVID-19.

Keywords: COVID-19, Biosensor, Nanotechnology, In vitro assay, COVID-19 testing


134.pdf

Febrile neutropenia due to COVID-19 in an immunocompetent patient

Authors: Yumkham Monica Devi,1 Amit Sehrawat,2 Prasan Kumar Panda, 3 and Uttam Kumar Nath2

Abstract:

While lymphopenia has been a common finding in COVID-19 infection, particularly in severe cases, febrile neutropenia has been very rarely reported in immunocompetent patients with COVID-19. Herein, we report the case of a 76-year-old hypertensive and diabetic man who was hospitalised with severe COVID-19 infection and developed delayed-onset severe neutropenia with neutropenic fever, which responded to treatment with antibiotics and granulocyte colony-stimulating factor. This case highlights the importance of identifying a rare complication (febrile neutropenia on the fifth week) of COVID-19 infection in hospitalised patients by intensive monitoring and aggressive management for favourable outcomes.

Keywords: COVID-19, haematology (drugs and medicines), infectious diseases, adult intensive care

92.pdf

The perspectives of biomarker-based electrochemical immunosensors, artificial intelligence and the Internet of Medical Things toward COVID-19 diagnosis and management

Authors: A.K. Yadav, D. Verma, [...], and P.R. Solanki

AbstractThe World Health Organization (WHO) has declared the COVID-19 an international health emergency due to the severity of infection progression, which became more severe due to its continuous spread globally and the unavailability of appropriate therapy and diagnostics systems. Thus, there is a need for efficient devices to detect SARS-CoV-2 infection at an early stage. Nowadays, the reverse transcription polymerase chain reaction (RT-PCR) technique is being applied for detecting this virus around the globe; however, factors such as stringent expertise, long diagnostic times, invasive and painful screening, and high costs have restricted the use of RT-PCR methods for rapid diagnostics. Therefore, the development of cost-effective, portable, sensitive, prompt and selective sensing systems to detect SARS-CoV-2 in biofluids at fM/pM/nM concentrations would be a breakthrough in diagnostics. Immunosensors that show increased specificity and sensitivity are considerably fast and do not imply costly reagents or instruments, reducing the cost for COVID-19 detection. The current developments in immunosensors perhaps signify the most significant opportunity for a rapid assay to detect COVID-19, without the need of highly skilled professionals and specialized tools to interpret results. Artificial intelligence (AI) and the Internet of Medical Things (IoMT) can also be equipped with this immunosensing approach to investigate useful networking through database management, sharing, and analytics to prevent and manage COVID-19. Herein, we represent the collective concepts of biomarker-based immunosensors along with AI and IoMT as smart sensing strategies with bioinformatics approach to monitor non-invasive early stage SARS-CoV-2 development, with fast point-of-care (POC) diagnostics as the crucial goal. This approach should be implemented quickly and verified practicality for clinical samples before being set in the present times for mass-diagnostic research.Keywords: Diagnostics, Electrochemical biosensors, Pandemic, Point-of-care, SARS-CoV-2