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1.
Genome Med ; 14(1): 18, 2022 02 21.
Article in English | MEDLINE | ID: covidwho-1688773

ABSTRACT

BACKGROUND: Measuring host gene expression is a promising diagnostic strategy to discriminate bacterial and viral infections. Multiple signatures of varying size, complexity, and target populations have been described. However, there is little information to indicate how the performance of various published signatures compare to one another. METHODS: This systematic comparison of host gene expression signatures evaluated the performance of 28 signatures, validating them in 4589 subjects from 51 publicly available datasets. Thirteen COVID-specific datasets with 1416 subjects were included in a separate analysis. Individual signature performance was evaluated using the area under the receiving operating characteristic curve (AUC) value. Overall signature performance was evaluated using median AUCs and accuracies. RESULTS: Signature performance varied widely, with median AUCs ranging from 0.55 to 0.96 for bacterial classification and 0.69-0.97 for viral classification. Signature size varied (1-398 genes), with smaller signatures generally performing more poorly (P < 0.04). Viral infection was easier to diagnose than bacterial infection (84% vs. 79% overall accuracy, respectively; P < .001). Host gene expression classifiers performed more poorly in some pediatric populations (3 months-1 year and 2-11 years) compared to the adult population for both bacterial infection (73% and 70% vs. 82%, respectively; P < .001) and viral infection (80% and 79% vs. 88%, respectively; P < .001). We did not observe classification differences based on illness severity as defined by ICU admission for bacterial or viral infections. The median AUC across all signatures for COVID-19 classification was 0.80 compared to 0.83 for viral classification in the same datasets. CONCLUSIONS: In this systematic comparison of 28 host gene expression signatures, we observed differences based on a signature's size and characteristics of the validation population, including age and infection type. However, populations used for signature discovery did not impact performance, underscoring the redundancy among many of these signatures. Furthermore, differential performance in specific populations may only be observable through this type of large-scale validation.


Subject(s)
Bacterial Infections/diagnosis , Datasets as Topic/statistics & numerical data , Host-Pathogen Interactions/genetics , Transcriptome , Virus Diseases/diagnosis , Adult , Bacterial Infections/epidemiology , Bacterial Infections/genetics , Biomarkers/analysis , COVID-19/diagnosis , COVID-19/genetics , Child , Cohort Studies , Diagnosis, Differential , Gene Expression Profiling/statistics & numerical data , Genetic Association Studies/statistics & numerical data , Humans , Publications/statistics & numerical data , SARS-CoV-2/pathogenicity , Validation Studies as Topic , Virus Diseases/epidemiology , Virus Diseases/genetics
2.
BMC Pediatr ; 22(1): 166, 2022 03 31.
Article in English | MEDLINE | ID: covidwho-2038686

ABSTRACT

BACKGROUND: Respiratory virus infection is common in early childhood, and children may be symptomatic or symptom-free. Little is known regarding the association between symptomatic/asymptomatic infection and particular clinical factors such as breastfeeding as well as the consequences of such infection. METHOD: We followed an unselected cohort of term neonates to two years of age (220 infants at recruitment, 159 who remained in the study to 24 months), taking oral swabs at birth and oropharyngeal swabs at intervals subsequently (at 1.5, 6, 9, 12, 18 and 24 months and in a subset at 3 and 4.5 months) while recording extensive metadata including the presence of respiratory symptoms and breastfeeding status. After 2 years medical notes from the general practitioner were inspected to ascertain whether doctor-diagnosed wheeze had occurred by this timepoint. Multiplex PCR was used to detect a range of respiratory viruses: influenza (A&B), parainfluenza (1-4), bocavirus, human metapneumovirus, rhinovirus, coronavirus (OC43, 229E, NL63, HKU1), adenovirus, respiratory syncytial virus (RSV), and polyomavirus (KI, WU). Logistic regression and generalised estimating equations were used to identify associations between clinical factors and virus detection. RESULTS: Overall respiratory viral incidence increased with age. Rhinovirus was the virus most frequently detected. The detection of a respiratory virus was positively associated with respiratory symptoms, male sex, season, childcare and living with another child. We did not observe breastfeeding (whether assessed as the number of completed months of breastfeeding or current feed status) to be associated with the detection of a respiratory virus. There was no association between early viral infection and doctor-diagnosed wheeze by age 2 years. CONCLUSION: Asymptomatic and symptomatic viral infection is common in the first 2 years of life with rhinovirus infection being the most common. Whilst there was no association between early respiratory viral infection and doctor-diagnosed wheeze, we have not ruled out an association of early viral infections with later asthma, and long-term follow-up of the cohort continues.


Subject(s)
Coronavirus , Respiratory Tract Infections , Virus Diseases , Child , Child, Preschool , Cohort Studies , Humans , Infant , Infant, Newborn , Life Style , Male , Respiratory Tract Infections/diagnosis , Respiratory Tract Infections/epidemiology , Virus Diseases/diagnosis
3.
Forensic Sci Int ; 339: 111419, 2022 Oct.
Article in English | MEDLINE | ID: covidwho-2015271

ABSTRACT

Respiratory viruses can cause fatal systemic infections; therefore, post-mortem diagnosis is essential in forensic autopsy cases. However, little is known regarding the distribution of respiratory viruses in the body. In this study, we investigated the anatomical distribution of respiratory viruses in 48 forensic autopsy cases suspected of viral infections at our institute. Fast Track Diagnostics (FTD) Respiratory Pathogens 21 was used as a screening test for 20 respiratory viruses in nasopharyngeal swabs. In cases with positive results for virus detection by the screening test, the detected viruses were quantified in body fluid and organ specimens by virus-specific real-time reverse transcription polymerase chain reaction (RT-PCR) and digital PCR. Viruses were detected in 33 cases, with the viral distribution and load differing among the cases. Since various respiratory viruses were detected from the nasopharyngeal swab and its viral load was higher than those of other body fluid specimens, the nasopharyngeal swab was suggested as a useful specimen for the post-mortem detection of respiratory viruses. Viruses were detected in almost all specimens including the serum in six cases. Considering the viral distribution in the body, pathological findings, and ante-mortem symptoms, these cases were presumed to be systemically infected, having died in the acute infection phase. In conclusion, the anatomical distribution of respiratory viruses can help indicate ante-mortem systemic conditions and the cause of death.


Subject(s)
Respiratory Tract Infections , Virus Diseases , Viruses , Autopsy , Humans , Real-Time Polymerase Chain Reaction , Respiratory Tract Infections/diagnosis , Virus Diseases/diagnosis , Viruses/genetics
4.
Appl Microbiol Biotechnol ; 106(18): 5863-5877, 2022 Sep.
Article in English | MEDLINE | ID: covidwho-2007131

ABSTRACT

This mini review focuses on the diagnosis and treatment of virus diseases using Crisper-Cas technology. The present paper describes various strategies involved in diagnosing diseases using Crispr-Cas-based assays. Additionally, CRISPR-Cas systems offer great potential as new therapeutic tools for treating viral infections including HIV, Influenza, and SARS-CoV-2. There are several major challenges to be overcome before this technology can be applied routinely in clinical settings, such as finding a suitable delivery tool, toxicity, and immunogenicity, as well as off-target effects. This review also discusses ways to deal with the challenges associated with Crisper-Cas technology. KEY POINTS: • Crisper technology is being applied to diagnose infectious and non-infectious diseases. • A new generation of CRISPR-Cas-based assays has been developed which detect pathogens within minutes, providing rapid diagnosis of diseases. • Crispr-Cas tools can be used to combat viral infections, specifically HIV, influenza, and SARS-CoV-2.


Subject(s)
COVID-19 , HIV Infections , Influenza, Human , Virus Diseases , Antiviral Agents/therapeutic use , COVID-19/diagnosis , COVID-19/drug therapy , COVID-19 Testing , CRISPR-Cas Systems , HIV Infections/diagnosis , HIV Infections/drug therapy , Humans , Influenza, Human/diagnosis , Influenza, Human/drug therapy , SARS-CoV-2/genetics , Virus Diseases/diagnosis , Virus Diseases/drug therapy
5.
J Clin Virol ; 156: 105274, 2022 11.
Article in English | MEDLINE | ID: covidwho-2004205

ABSTRACT

BACKGROUND: Acute viral respiratory infections are a major health burden in children worldwide. In recent years, rapid and sensitive multiplex nucleic acid amplification tests (NAATs) have replaced conventional methods for routine virus detection in the clinical laboratory. OBJECTIVE/STUDY DESIGN: We compared BioFire® FilmArray® Respiratory Panel (FilmArray V1.7), Luminex NxTag® Respiratory Pathogen Panel (NxTag RPP) and Applied Biosystems TaqMan Array Card (TAC) for the detection of eight viruses in pediatric respiratory specimens. Results from the three platforms were analyzed with a single-plex real-time RT-PCR (rRT-PCR) assay for each virus. RESULTS: Of the 170/210 single-plex virus-positive samples, FilmArray detected a virus in 166 (97.6%), TAC in 163 (95.8%) and NxTag RPP in 160 (94.1%) samples. The Positive Percent Agreement (PPA) of FilmArray, NxTag RPP and TAC was highest for influenza B (100%, 100% and 95.2% respectively) and lowest for seasonal coronaviruses on both FilmArray (90.2%) and NxTag RPP (81.8%), and for parainfluenza viruses 1- 4 on TAC (84%). The Negative Percent Agreement (NPA) was lowest for rhinovirus/enterovirus (92.9%, 96.7% and 97.3%) on FilmArray, NxTag RPP and TAC respectively. NPA for all three platforms was highest (100%) for both parainfluenza viruses 1- 4 and influenza A and B, and 100% for human metapneumovirus with TAC as well. CONCLUSION: All three multiplex platforms displayed high overall agreement (>90%) and high NPA (>90%), while PPA was pathogen dependent and varied among platforms; high PPA (>90%) was observed for FilmArray for all eight viruses, TAC for six viruses and NxTag RPP for 4 viruses.


Subject(s)
Molecular Diagnostic Techniques , Respiratory Tract Infections , Virus Diseases , Child , Coronavirus , Humans , Influenza, Human , Molecular Diagnostic Techniques/methods , Multiplex Polymerase Chain Reaction/methods , Paramyxoviridae Infections , Respiratory Tract Infections/diagnosis , Respiratory Tract Infections/virology , Virus Diseases/diagnosis
6.
J Clin Virol ; 153: 105221, 2022 08.
Article in English | MEDLINE | ID: covidwho-1907271

ABSTRACT

OBJECTIVES: Viral respiratory infections are common in children, and usually associated with non-specific symptoms. Respiratory panel-based testing was implemented during the COVID-19 pandemic, for the rapid differentiation between SARS-CoV-2 and other viral infections, in children attending the emergency department (ED) of the teaching hospital of Lille, northern France, between February 2021 and January 2022. METHODS: Samples were collected using nasopharyngeal swabs. Syndromic respiratory testing was performed with two rapid multiplex molecular assays: the BioFire® Respiratory Panel 2.1 - plus (RP2.1 plus) or the QIAstat-Dx Respiratory SARS-CoV-2 Panel. SARS-CoV-2 variant was screened using mutation-specific PCR-based assays and genome sequencing. RESULTS: A total of 3517 children were included in the study. SARS-CoV-2 was detected in samples from 265 children (7.5%). SARS-CoV-2 infected patients were younger than those without SARS-CoV-2 infection (median age: 6 versus 12 months, p < 0.0001). The majority of infections (61.5%) were associated with the Omicron variant. The median weekly SARS-CoV-2 positivity rate ranged from 1.76% during the Alpha variant wave to 24.5% with the emergence of the Omicron variant. Most children (70.2%) were treated as outpatients, and seventeen patients were admitted to the intensive care unit. Other respiratory viruses were more frequently detected in SARS-CoV-2 negative children than in positive ones (82.1% versus 37.4%, p < 0.0001). Human rhinovirus/enterovirus and respiratory syncytial virus were the most prevalent in both groups. CONCLUSIONS: We observed a low prevalence of SARS-CoV-2 infection in children attending pediatric ED, despite the significant increase due to Delta and Omicron variants, and an important circulation of other respiratory viruses. Severe disease was overall rare in children.


Subject(s)
COVID-19 , Respiratory Tract Infections , Virus Diseases , COVID-19/diagnosis , COVID-19/epidemiology , Emergency Service, Hospital , France , Humans , Infant , Pandemics , Respiratory Tract Infections/diagnosis , Respiratory Tract Infections/virology , SARS-CoV-2 , Virus Diseases/diagnosis
7.
Biosensors (Basel) ; 12(5)2022 Apr 28.
Article in English | MEDLINE | ID: covidwho-1875479

ABSTRACT

Infectious diseases remain a pervasive threat to global and public health, especially in many countries and rural urban areas. The main causes of such severe diseases are the lack of appropriate analytical methods and subsequent treatment strategies due to limited access to centralized and equipped medical centers for detection. Rapid and accurate diagnosis in biomedicine and healthcare is essential for the effective treatment of pathogenic viruses as well as early detection. Plasma-engineered polymers are used worldwide for viral infections in conjunction with molecular detection of biomarkers. Plasma-engineered polymers for biomarker-based viral detection are generally inexpensive and offer great potential. For biomarker-based virus detection, plasma-based polymers appear to be potential biological probes and have been used directly with physiological components to perform highly multiplexed analyses simultaneously. The simultaneous measurement of multiple clinical parameters from the same sample volume is possible using highly multiplexed analysis to detect human viral infections, thereby reducing the time and cost required to collect each data point. This article reviews recent studies on the efficacy of plasma-engineered polymers as a detection method against human pandemic viruses. In this review study, we examine polymer biomarkers, plasma-engineered polymers, highly multiplexed analyses for viral infections, and recent applications of polymer-based biomarkers for virus detection. Finally, we provide an outlook on recent advances in the field of plasma-engineered polymers for biomarker-based virus detection and highly multiplexed analysis.


Subject(s)
Communicable Diseases , Virus Diseases , Viruses , Biomarkers , Communicable Diseases/diagnosis , Humans , Polymers , Virus Diseases/diagnosis
8.
JAMA Netw Open ; 5(4): e227299, 2022 04 01.
Article in English | MEDLINE | ID: covidwho-1787611

ABSTRACT

Importance: Bacterial and viral causes of acute respiratory illness (ARI) are difficult to clinically distinguish, resulting in the inappropriate use of antibacterial therapy. The use of a host gene expression-based test that is able to discriminate bacterial from viral infection in less than 1 hour may improve care and antimicrobial stewardship. Objective: To validate the host response bacterial/viral (HR-B/V) test and assess its ability to accurately differentiate bacterial from viral infection among patients with ARI. Design, Setting, and Participants: This prospective multicenter diagnostic study enrolled 755 children and adults with febrile ARI of 7 or fewer days' duration from 10 US emergency departments. Participants were enrolled from October 3, 2014, to September 1, 2019, followed by additional enrollment of patients with COVID-19 from March 20 to December 3, 2020. Clinical adjudication of enrolled participants identified 616 individuals as having bacterial or viral infection. The primary analysis cohort included 334 participants with high-confidence reference adjudications (based on adjudicator concordance and the presence of an identified pathogen confirmed by microbiological testing). A secondary analysis of the entire cohort of 616 participants included cases with low-confidence reference adjudications (based on adjudicator discordance or the absence of an identified pathogen in microbiological testing). Thirty-three participants with COVID-19 were included post hoc. Interventions: The HR-B/V test quantified the expression of 45 host messenger RNAs in approximately 45 minutes to derive a probability of bacterial infection. Main Outcomes and Measures: Performance characteristics for the HR-B/V test compared with clinical adjudication were reported as either bacterial or viral infection or categorized into 4 likelihood groups (viral very likely [probability score <0.19], viral likely [probability score of 0.19-0.40], bacterial likely [probability score of 0.41-0.73], and bacterial very likely [probability score >0.73]) and compared with procalcitonin measurement. Results: Among 755 enrolled participants, the median age was 26 years (IQR, 16-52 years); 360 participants (47.7%) were female, and 395 (52.3%) were male. A total of 13 participants (1.7%) were American Indian, 13 (1.7%) were Asian, 368 (48.7%) were Black, 131 (17.4%) were Hispanic, 3 (0.4%) were Native Hawaiian or Pacific Islander, 297 (39.3%) were White, and 60 (7.9%) were of unspecified race and/or ethnicity. In the primary analysis involving 334 participants, the HR-B/V test had sensitivity of 89.8% (95% CI, 77.8%-96.2%), specificity of 82.1% (95% CI, 77.4%-86.6%), and a negative predictive value (NPV) of 97.9% (95% CI, 95.3%-99.1%) for bacterial infection. In comparison, the sensitivity of procalcitonin measurement was 28.6% (95% CI, 16.2%-40.9%; P < .001), the specificity was 87.0% (95% CI, 82.7%-90.7%; P = .006), and the NPV was 87.6% (95% CI, 85.5%-89.5%; P < .001). When stratified into likelihood groups, the HR-B/V test had an NPV of 98.9% (95% CI, 96.1%-100%) for bacterial infection in the viral very likely group and a positive predictive value of 63.4% (95% CI, 47.2%-77.9%) for bacterial infection in the bacterial very likely group. The HR-B/V test correctly identified 30 of 33 participants (90.9%) with acute COVID-19 as having a viral infection. Conclusions and Relevance: In this study, the HR-B/V test accurately discriminated bacterial from viral infection among patients with febrile ARI and was superior to procalcitonin measurement. The findings suggest that an accurate point-of-need host response test with high NPV may offer an opportunity to improve antibiotic stewardship and patient outcomes.


Subject(s)
Bacterial Infections , COVID-19 , Virus Diseases , Adult , Bacteria , Bacterial Infections/drug therapy , COVID-19/diagnosis , Child , Female , Fever/diagnosis , Gene Expression , Humans , Male , Procalcitonin , Virus Diseases/diagnosis
9.
Cell Signal ; 94: 110325, 2022 06.
Article in English | MEDLINE | ID: covidwho-1767965

ABSTRACT

Efforts to discover antiviral drugs and diagnostic platforms have intensified to an unprecedented level since the outbreak of COVID-19. Nano-sized endosomal vesicles called exosomes have gained considerable attention from researchers due to their role in intracellular communication to regulate the biological activity of target cells through cargo proteins, nucleic acids, and lipids. According to recent studies, exosomes play a vital role in viral diseases including covid-19, with their interaction with the host immune system opening the door to effective antiviral treatments. Utilizing the intrinsic nature of exosomes, it is imperative to elucidate how exosomes exert their effect on the immune system or boost viral infectivity. Exosome biogenesis machinery is hijacked by viruses to initiate replication, spread infection, and evade the immune response. Exosomes, however, also participate in protective mechanisms by triggering the innate immune system. Besides that, exosomes released from the cells can carry a robust amount of information about the diseased state, serving as a potential biomarker for detecting viral diseases. This review describes how exosomes increase virus infectivity, act as immunomodulators, and function as a potential drug delivery carrier and diagnostic biomarker for diseases caused by HIV, Hepatitis, Ebola, and Epstein-Barr viruses. Furthermore, the review analyzes various applications of exosomes within the context of COVID-19, including its management.


Subject(s)
COVID-19 , Exosomes , Virus Diseases , Antiviral Agents/metabolism , Antiviral Agents/pharmacology , Antiviral Agents/therapeutic use , Biomarkers/metabolism , COVID-19/diagnosis , Endosomes/metabolism , Exosomes/metabolism , Humans , Virus Diseases/diagnosis , Virus Diseases/metabolism
10.
Ital J Pediatr ; 48(1): 43, 2022 Mar 15.
Article in English | MEDLINE | ID: covidwho-1745433

ABSTRACT

BACKGROUND: Investigations on haematological alterations in paediatric COVID-19 have been focused mostly on lymphocytes and clotting profiles. Neutropenia has been occasionally reported and its course and impact on the disease have not been elucidated. The aim of this study was to describe the epidemiology, course, and impact of neutropenia in children with COVID-19 hospitalised in a tertiary care referral paediatric ward. METHODS: A single-centre retrospective study was conducted. Hospitalised children between 1 month and 18 years with confirmed COVID-19 and neutropenia were included and compared to non neutropenic patients. Complete blood picture with differential blood count, serum biochemistry, clotting profiles were performed; clinical data, length of hospitalisation, and prescription of drugs were collected. RESULTS: Twelve out of 95 patients (12.63%) with documented SARS-CoV-2 infection were neutropenic and met the inclusion criteria. The mean age was 161 days (range 38-490 days). The mean duration of symptoms in neutropenic children was 3.82 days, while the mean length of hospitalisation was 7.67 days. These findings were not significantly different in the two study groups. All patients had mild clinical manifestations and were discharged without sequelae. CONCLUSIONS: We provided the first comprehensive study on neutropenia in mild paediatric COVID-19 infection. Our findings show that the main features of this haematological disorder in COVID-19 are analogous to the well-known transient benign neutropenia associated with other common viral infections. In our setting, neutropenia does not emerge as a potential negative prognostic factor in paediatric COVID-19.


Subject(s)
COVID-19 , Neutropenia , Virus Diseases , COVID-19/epidemiology , Child , Humans , Neutropenia/complications , Neutropenia/epidemiology , Retrospective Studies , SARS-CoV-2 , Virus Diseases/diagnosis
11.
Cells ; 11(6)2022 03 15.
Article in English | MEDLINE | ID: covidwho-1742343

ABSTRACT

Viruses are one of the most important concerns for human health, and overcoming viral infections is a worldwide challenge. However, researchers have been trying to manipulate viral genomes to overcome various disorders, including cancer, for vaccine development purposes. CRISPR (clustered regularly interspaced short palindromic repeats) is becoming one of the most functional and widely used tools for RNA and DNA manipulation in multiple organisms. This approach has provided an unprecedented opportunity for creating simple, inexpensive, specific, targeted, accurate, and practical manipulations of viruses, such as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), human immunodeficiency virus-1 (HIV-1), and vaccinia virus. Furthermore, this method can be used to make an effective and precise diagnosis of viral infections. Nevertheless, a valid and scientifically designed CRISPR system is critical to make more effective and accurate changes in viruses. In this review, we have focused on the best and the most effective ways to design sgRNA, gene knock-in(s), and gene knock-out(s) for virus-targeted manipulation. Furthermore, we have emphasized the application of CRISPR technology in virus diagnosis and in finding significant genes involved in virus-host interactions.


Subject(s)
COVID-19 , Virus Diseases , Viruses , COVID-19/diagnosis , CRISPR-Cas Systems/genetics , Clustered Regularly Interspaced Short Palindromic Repeats/genetics , DNA Viruses , Host Microbial Interactions , Humans , SARS-CoV-2/genetics , Virus Diseases/diagnosis , Virus Diseases/genetics , Viruses/genetics
12.
Semin Respir Crit Care Med ; 43(1): 60-74, 2022 02.
Article in English | MEDLINE | ID: covidwho-1688937

ABSTRACT

Severe viral infections may result in severe illnesses capable of causing acute respiratory failure that could progress rapidly to acute respiratory distress syndrome (ARDS), related to worse outcomes, especially in individuals with a higher risk of infection, including the elderly and those with comorbidities such as asthma, diabetes mellitus and chronic respiratory or cardiovascular disease. In addition, in cases of severe viral pneumonia, co-infection with bacteria such as Streptococcus pneumoniae and Staphylococcus aureus is related to worse outcomes. Respiratory viruses like influenza, rhinovirus, parainfluenza, adenovirus, metapneumovirus, respiratory syncytial virus, and coronavirus have increasingly been detected. This trend has become more prevalent, especially in critically ill patients, due to the availability and implementation of molecular assays in clinical practice. Respiratory viruses have been diagnosed as a frequent cause of severe pneumonia, including cases of community-acquired pneumonia, hospital-acquired pneumonia, and ventilator-associated pneumonia. In this review, we will discuss the epidemiology, diagnosis, clinical characteristics, management, and prognosis of patients with severe infections due to respiratory viruses, with a focus on influenza viruses, non-influenza viruses, and coronaviruses.


Subject(s)
Respiratory Tract Infections , Virus Diseases , Aged , Coronavirus , Humans , Patient Acuity , Prognosis , Respiratory Tract Infections/diagnosis , Respiratory Tract Infections/epidemiology , Respiratory Tract Infections/therapy , Respiratory Tract Infections/virology , Virus Diseases/diagnosis , Virus Diseases/epidemiology , Virus Diseases/therapy
13.
Pediatr Infect Dis J ; 41(4): e146-e148, 2022 04 01.
Article in English | MEDLINE | ID: covidwho-1706949

ABSTRACT

Respiratory viruses were detected by multiplex-polymerase chain reaction from oropharyngeal swabs in 114/168 (67.9%) children with acute respiratory infection presenting to 5 pediatric practices in Germany between November 2020 and April 2021. In contrast to rhino- (48.8%), adeno- (14.3%) and endemic coronaviruses (14.9%), SARS-CoV-2 and influenza virus were detected only once; respiratory syncytial virus was not detected. This demonstrates differing impacts of pandemic infection control measures on the spread of respiratory viruses.


Subject(s)
Primary Health Care , Respiratory Tract Infections/epidemiology , Respiratory Tract Infections/etiology , Virus Diseases/epidemiology , Virus Diseases/etiology , Adolescent , COVID-19/epidemiology , COVID-19/virology , Child , Child, Preschool , Disease Susceptibility , Female , Humans , Incidence , Infant , Infant, Newborn , Influenza, Human/epidemiology , Influenza, Human/virology , Male , Pandemics , Respiratory Syncytial Virus Infections/epidemiology , Respiratory Syncytial Virus Infections/virology , Respiratory Tract Infections/diagnosis , Respiratory Tract Infections/therapy , SARS-CoV-2 , Virus Diseases/diagnosis , Virus Diseases/therapy
14.
Adv Exp Med Biol ; 1352: 173-193, 2021.
Article in English | MEDLINE | ID: covidwho-1669703

ABSTRACT

INTRODUCTION: In recent years, viral infections and associated diseases have become a big challenge for humanity due to high morbidity rates globally. However, timely, accurate, and rapid detection of viral infection may lead to the control of morbidity as well as provide enough time for vaccine preparation and early antiviral therapy. Existing virus detection methods based on immunological and molecular diagnosis found drawbacks, such as its time-consuming and costly one. Recently, the introduction of nanomaterials having multiple unique properties with a series of smart and innovative nano-based technologies have been under investigation for rapid viral detection. This chapter aims to critically review recent literature to illustrate the encompassing applications of nano-engineered materials and further highlighting the role of their active surface in improving the virus detection with high sensitivity and detection range, and in a short time. METHODS: The authors review the research findings related to emerging nanotechnology-based virus detection systems and their applicability for diagnostics of infectious viruses. RESULTS: Recent advances in nanotechnology allow for the development of robust, rapid, and sensitive detection of infectious virus to overcome deficiencies of conventional detection technologies. Nanoparticles have several distinctive physical and chemical characteristics such as unique optical, electronic, and magnetic properties compared to their bulk form enabling them the detection of biological agents like viruses. Further, high surface area to volume ratios of nanoparticles also provides a platform for multi-functionalization with various organic or biological ligands for the selective binding and detection of biological targets like viruses. For instance, colloidal gold nanoparticle-based lateral-flow (AuNP-LF) provides rapid diagnosis and on-site diagnosis of SARS-CoV-2 virus via the IgM detection using the indirect immune-chromatography method. CONCLUSION: The distinct properties of nanomaterials such as plasmon resonance absorption, conductivity, redox behavior, etc. along with surface functionalization might be used in the development of the nano-sensing system with high accuracy and rapid detection of infectious viral diagnosis at the point of care application.


Subject(s)
COVID-19 , Metal Nanoparticles , Virus Diseases , Gold , Humans , Nanotechnology , SARS-CoV-2 , Virus Diseases/diagnosis
15.
J Nanobiotechnology ; 20(1): 41, 2022 Jan 21.
Article in English | MEDLINE | ID: covidwho-1643157

ABSTRACT

Early detection of viral pathogens by DNA-sensors in clinical samples, contaminated foods, soil or water can dramatically improve clinical outcomes and reduce the socioeconomic impact of diseases such as COVID-19. Clustered regularly interspaced short palindromic repeat (CRISPR) and its associated protein Cas12a (previously known as CRISPR-Cpf1) technology is an innovative new-generation genomic engineering tool, also known as 'genetic scissors', that has demonstrated the accuracy and has recently been effectively applied as appropriate (E-CRISPR) DNA-sensor to detect the nucleic acid of interest. The CRISPR-Cas12a from Prevotella and Francisella 1 are guided by a short CRISPR RNA (gRNA). The unique simultaneous cis- and trans- DNA cleavage after target sequence recognition at the PAM site, sticky-end (5-7 bp) employment, and ssDNA/dsDNA hybrid cleavage strategies to manipulate the attractive nature of CRISPR-Cas12a are reviewed. DNA-sensors based on the CRISPR-Cas12a technology for rapid, robust, sensitive, inexpensive, and selective detection of virus DNA without additional sample purification, amplification, fluorescent-agent- and/or quencher-labeling are relevant and becoming increasingly important in industrial and medical applications. In addition, CRISPR-Cas12a system shows great potential in the field of E-CRISPR-based bioassay research technologies. Therefore, we are highlighting insights in this research direction.


Subject(s)
CRISPR-Cas Systems/physiology , DNA, Viral/isolation & purification , Nucleic Acid Amplification Techniques , Animals , Biosensing Techniques/methods , Biosensing Techniques/trends , COVID-19/virology , DNA, Viral/analysis , Environmental Pollutants/analysis , Environmental Pollutants/isolation & purification , Food Contamination/analysis , Humans , Molecular Typing/methods , Molecular Typing/trends , Nucleic Acid Amplification Techniques/methods , Nucleic Acid Amplification Techniques/trends , SARS-CoV-2/genetics , Virology/methods , Virology/trends , Virus Diseases/classification , Virus Diseases/diagnosis , Virus Diseases/virology
16.
Br J Gen Pract ; 72(716): e217-e224, 2022 03.
Article in English | MEDLINE | ID: covidwho-1608429

ABSTRACT

BACKGROUND: There is little evidence about the relationship between aetiology, illness severity, and clinical course of respiratory tract infections (RTIs) in primary care. Understanding these associations would aid in the development of effective management strategies for these infections. AIM: To investigate whether clinical presentation and illness course differ between RTIs where a viral pathogen was detected and those where a potential bacterial pathogen was found. DESIGN AND SETTING: Post hoc analysis of data from a pragmatic randomised trial on the effects of oseltamivir in patients with flu-like illness in primary care (n = 3266) in 15 European countries. METHOD: Patient characteristics and their signs and symptoms of disease were registered at baseline. Nasopharyngeal (adults) or nasal and pharyngeal (children) swabs were taken for polymerase chain reaction analysis. Patients were followed up until 28 days after inclusion. Regression models and Kaplan-Meier curves were used to analyse the relationship between aetiology, clinical presentation at baseline, and course of disease including complications. RESULTS: Except for a less prominent congested nose (odds ratio [OR] 0.55, 95% confidence interval [CI] = 0.35 to 0.86) and acute cough (OR 0.42, 95% CI = 0.27 to 0.65) in patients with flu-like illness in whom a possible bacterial pathogen was isolated, there were no clear clinical differences in presentations between those with a possible bacterial aetiology compared with those with a viral aetiology. Also, course of disease and complications were not related to aetiology. CONCLUSION: Given current available microbiological tests and antimicrobial treatments, and outside pandemics such as COVID-19, microbiological testing in primary care patients with flu-like illness seems to have limited value. A wait-and-see policy in most of these patients with flu-like illness seems the best option.


Subject(s)
COVID-19 , Respiratory Tract Infections , Virus Diseases , Adult , Child , Humans , Pandemics , Respiratory Tract Infections/diagnosis , Respiratory Tract Infections/drug therapy , Respiratory Tract Infections/microbiology , SARS-CoV-2 , Virus Diseases/complications , Virus Diseases/diagnosis , Virus Diseases/epidemiology
17.
J Nanobiotechnology ; 19(1): 348, 2021 Oct 30.
Article in English | MEDLINE | ID: covidwho-1555350

ABSTRACT

Viral infections are the most common among diseases that globally require around 60 percent of medical care. However, in the heat of the pandemic, there was a lack of medical equipment and inpatient facilities to provide all patients with viral infections. The detection of viral infections is possible in three general ways such as (i) direct virus detection, which is performed immediately 1-3 days after the infection, (ii) determination of antibodies against some virus proteins mainly observed during/after virus incubation period, (iii) detection of virus-induced disease when specific tissue changes in the organism. This review surveys some global pandemics from 1889 to 2020, virus types, which induced these pandemics, and symptoms of some viral diseases. Non-analytical methods such as radiology and microscopy also are overviewed. This review overlooks molecular analysis methods such as nucleic acid amplification, antibody-antigen complex determination, CRISPR-Cas system-based viral genome determination methods. Methods widely used in the certificated diagnostic laboratory for SARS-CoV-2, Influenza A, B, C, HIV, and other viruses during a viral pandemic are outlined. A comprehensive overview of molecular analytical methods has shown that the assay's sensitivity, accuracy, and suitability for virus detection depends on the choice of the number of regions in the viral open reading frame (ORF) genome sequence and the validity of the selected analytical method.


Subject(s)
Clinical Laboratory Techniques , Virus Diseases/diagnosis , Viruses/isolation & purification , Biosensing Techniques , COVID-19/diagnosis , COVID-19/epidemiology , Humans , Nucleic Acid Amplification Techniques , Pandemics , SARS-CoV-2/genetics , SARS-CoV-2/immunology , SARS-CoV-2/isolation & purification , Viral Proteins/genetics , Viral Proteins/immunology , Virus Diseases/epidemiology , Viruses/classification , Viruses/genetics , Viruses/immunology
18.
Viruses ; 13(12)2021 11 29.
Article in English | MEDLINE | ID: covidwho-1542801

ABSTRACT

Nestled within the Rocky Mountain National Forest, 114 scientists and students gathered at Colorado State University's Mountain Campus for this year's 21st annual Rocky Mountain National Virology Association meeting. This 3-day retreat consisted of 31 talks and 30 poster presentations discussing advances in research pertaining to viral and prion diseases. The keynote address provided a timely discussion on zoonotic coronaviruses, lessons learned, and the path forward towards predicting, preparing, and preventing future viral disease outbreaks. Other invited speakers discussed advances in SARS-CoV-2 surveillance, molecular interactions involved in flavivirus genome assembly, evaluation of ethnomedicines for their efficacy against infectious diseases, multi-omic analyses to define risk factors associated with long COVID, the role that interferon lambda plays in control of viral pathogenesis, cell-fusion-dependent pathogenesis of varicella zoster virus, and advances in the development of a vaccine platform against prion diseases. On behalf of the Rocky Mountain Virology Association, this report summarizes select presentations.


Subject(s)
Virology , Animals , Host-Pathogen Interactions , Humans , Pandemics/prevention & control , Prion Diseases/diagnosis , Prion Diseases/prevention & control , Prions/immunology , Prions/isolation & purification , Prions/pathogenicity , Vaccines , Virology/organization & administration , Virus Diseases/diagnosis , Virus Diseases/epidemiology , Virus Diseases/prevention & control , Virus Diseases/virology , Viruses/classification , Viruses/immunology , Viruses/isolation & purification , Viruses/pathogenicity
19.
Biomark Med ; 16(1): 41-50, 2022 01.
Article in English | MEDLINE | ID: covidwho-1523645

ABSTRACT

Viral diseases remain a significant global health threat, and therefore prioritization of limited healthcare resources is required to effectively manage dangerous viral disease outbreaks. In a pandemic of a newly emerged virus that is yet to be well understood, a noninvasive host-derived prognostic biomarker is invaluable for risk prediction. Red blood cell distribution width (RDW), an index of red blood cell size disorder (anisocytosis), is a potential predictive biomarker for severity of many diseases. In view of the need to prioritize resources during response to outbreaks, this review highlights the prospects and challenges of RDW as a prognostic biomarker for viral infections, with a focus on hepatitis and COVID-19, and provides an outlook to improve the prognostic performance of RDW for risk prediction in viral diseases.


Subject(s)
Erythrocyte Indices , Virus Diseases/diagnosis , Animals , Biomarkers/analysis , Biomarkers/blood , COVID-19/blood , COVID-19/diagnosis , Erythrocytes/cytology , Hepatitis/blood , Hepatitis/diagnosis , Humans , Prognosis , Virus Diseases/blood
20.
Viruses ; 13(11)2021 10 25.
Article in English | MEDLINE | ID: covidwho-1481025

ABSTRACT

Solid organ transplantation is often lifesaving, but does carry an increased risk of infection. Respiratory viral infections are one of the most prevalent infections, and are a cause of significant morbidity and mortality, especially among lung transplant recipients. There is also data to suggest an association with acute rejection and chronic lung allograft dysfunction in lung transplant recipients. Respiratory viral infections can appear at any time post-transplant and are usually acquired in the community. All respiratory viral infections share similar clinical manifestations and are all currently diagnosed using nucleic acid testing. Influenza has good treatment options and prevention strategies, although these are hampered by resistance to neuraminidase inhibitors and lower vaccine immunogenicity in the transplant population. Other respiratory viruses, unfortunately, have limited treatments and preventive methods. This review summarizes the epidemiology, clinical manifestations, therapies and preventive measures for clinically significant RNA and DNA respiratory viruses, with the exception of SARS-CoV-2. This area is fast evolving and hopefully the coming decades will bring us new antivirals, immunologic treatments and vaccines.


Subject(s)
Organ Transplantation , Respiratory Tract Infections , Transplant Recipients , Virus Diseases , Antiviral Agents/therapeutic use , Graft Rejection , Humans , Lung Transplantation , Respiratory Tract Infections/diagnosis , Respiratory Tract Infections/drug therapy , Respiratory Tract Infections/epidemiology , Respiratory Tract Infections/prevention & control , Virus Diseases/diagnosis , Virus Diseases/drug therapy , Virus Diseases/epidemiology , Virus Diseases/prevention & control
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