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2.
JMIR Public Health Surveill ; 7(4): e27433, 2021 04 28.
Article in English | MEDLINE | ID: covidwho-2141323

ABSTRACT

BACKGROUND: Sentinel surveillance of influenza-like illness (ILI) in Egypt started in 2000 at 8 sentinel sites geographically distributed all over the country. In response to the COVID-19 pandemic, SARS-CoV-2 was added to the panel of viral testing by polymerase chain reaction for the first 2 patients with ILI seen at one of the sentinel sites. We report the first SARS-CoV-2 and influenza A(H1N1) virus co-infection with mild symptoms detected through routine ILI surveillance in Egypt. OBJECTIVE: This report aims to describe how the case was identified and the demographic and clinical characteristics and outcomes of the patient. METHODS: The case was identified by Central Public Health Laboratory staff, who contacted the ILI sentinel surveillance officer at the Ministry of Health. The case patient was contacted through a telephone call. Detailed information about the patient's clinical picture, course of disease, and outcome was obtained. The contacts of the patient were investigated for acute respiratory symptoms, disease confirmation, and outcomes. RESULTS: Among 510 specimens collected from patients with ILI symptoms from October 2019 to August 2020, 61 (12.0%) were COVID-19-positive and 29 (5.7%) tested positive for influenza, including 15 (51.7%) A(H1N1), 11 (38.0%) A(H3N2), and 3 (10.3%) influenza B specimens. A 21-year-old woman was confirmed to have SARS-CoV-2 and influenza A(H1N1) virus coinfection. She had a high fever of 40.2 °C and mild respiratory symptoms that resolved within 2 days with symptomatic treatment. All five of her family contacts had mild respiratory symptoms 2-3 days after exposure to the confirmed case, and their symptoms resolved without treatment or investigation. CONCLUSIONS: This case highlights the possible occurrence of SARS-CoV-2/influenza A(H1N1) coinfection in younger and healthy people, who may resolve the infection rapidly. We emphasize the usefulness of the surveillance system for detection of viral causative agents of ILI and recommend broadening of the testing panel, especially if it can guide case management.


Subject(s)
COVID-19/diagnosis , Coinfection , Influenza A Virus, H1N1 Subtype/isolation & purification , Influenza, Human/diagnosis , SARS-CoV-2/isolation & purification , Sentinel Surveillance , COVID-19/epidemiology , Egypt/epidemiology , Female , Humans , Influenza, Human/epidemiology , Young Adult
3.
Virol J ; 19(1): 188, 2022 11 16.
Article in English | MEDLINE | ID: covidwho-2117139

ABSTRACT

INTRODUCTION: We investigated the performance of the cobas® 6800 system and cobas SARS-CoV-2 & Influenza A/B, a fully automated molecular testing system for influenza viruses and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This enabled an assay in a batch of 96 samples in approximately 3 h. METHODS: An assay was performed using the cobas SARS-CoV-2 & Influenza A/B on the cobas 6800 system for samples collected in four facilities between November 2019 and March 2020 in our previous study. The results were compared with those obtained using the reference methods. RESULTS: Of the 127 samples analyzed, the cobas SARS-CoV-2 & Influenza A/B detected influenza A virus in 75 samples, of which 73 were positive using the reference methods. No false negative results were observed. The overall positive and negative percent agreement for influenza A virus detection were 100.0% and 96.3%, respectively. There were no positive results for the influenza B virus or SARS-CoV-2. CONCLUSION: The cobas 6800 system and cobas SARS-CoV-2 & Influenza A/B showed high accuracy for influenza A virus detection and can be useful for clinical laboratories, especially those that routinely assay many samples.


Subject(s)
COVID-19 , Influenza, Human , Orthomyxoviridae , Humans , Influenza, Human/diagnosis , SARS-CoV-2/genetics , Molecular Diagnostic Techniques
4.
Obstet Gynecol ; 140(5): 874-877, 2022 11 01.
Article in English | MEDLINE | ID: covidwho-2107619

ABSTRACT

Influenza testing and case-confirmation rates in pregnant populations have not been reported during the coronavirus disease 2019 (COVID-19) pandemic. Using electronic medical record data from a cohort of nearly 20,000 pregnancies in the United States, this retrospective cohort study examines the frequency of acute respiratory or febrile illness encounters, influenza testing, and influenza positivity during the 2020-2021 influenza season, which occurred during the COVID-19 pandemic, compared with the 2019-2020 influenza season, which largely did not. The ratios of influenza tests to acute respiratory or febrile illness visits were similar in the 2019-2020 and 2020-2021 influenza seasons (approximately 1:8 and 1:9, respectively) but were low and varied by study site. Although influenza testing in pregnant patients continued in the 2020-2021 season, when severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) circulation was widespread in the United States, no cases of influenza were identified in our study cohort.


Subject(s)
COVID-19 , Influenza, Human , Humans , Pregnancy , Female , United States/epidemiology , Influenza, Human/diagnosis , Influenza, Human/epidemiology , Pandemics , Seasons , SARS-CoV-2 , COVID-19/epidemiology , Retrospective Studies
5.
EBioMedicine ; 85: 104295, 2022 Nov.
Article in English | MEDLINE | ID: covidwho-2104816

ABSTRACT

BACKGROUND: A comparison of pneumonias due to SARS-CoV-2 and influenza, in terms of clinical course and predictors of outcomes, might inform prognosis and resource management. We aimed to compare clinical course and outcome predictors in SARS-CoV-2 and influenza pneumonia using multi-state modelling and supervised machine learning on clinical data among hospitalised patients. METHODS: This multicenter retrospective cohort study of patients hospitalised with SARS-CoV-2 (March-December 2020) or influenza (Jan 2015-March 2020) pneumonia had the composite of hospital mortality and hospice discharge as the primary outcome. Multi-state models compared differences in oxygenation/ventilatory utilisation between pneumonias longitudinally throughout hospitalisation. Differences in predictors of outcome were modelled using supervised machine learning classifiers. FINDINGS: Among 2,529 hospitalisations with SARS-CoV-2 and 2,256 with influenza pneumonia, the primary outcome occurred in 21% and 9%, respectively. Multi-state models differentiated oxygen requirement progression between viruses, with SARS-CoV-2 manifesting rapidly-escalating early hypoxemia. Highly contributory classifier variables for the primary outcome differed substantially between viruses. INTERPRETATION: SARS-CoV-2 and influenza pneumonia differ in presentation, hospital course, and outcome predictors. These pathogen-specific differential responses in viral pneumonias suggest distinct management approaches should be investigated. FUNDING: This project was supported by NIH/NCATS UL1 TR002345, NIH/NCATS KL2 TR002346 (PGL), the Doris Duke Charitable Foundation grant 2015215 (PGL), NIH/NHLBI R35 HL140026 (CSC), and a Big Ideas Award from the BJC HealthCare and Washington University School of Medicine Healthcare Innovation Lab and NIH/NIGMS R35 GM142992 (PS).


Subject(s)
COVID-19 , Influenza, Human , Pneumonia, Viral , Humans , SARS-CoV-2 , Influenza, Human/diagnosis , Influenza, Human/epidemiology , Retrospective Studies , Hospitals
6.
Semin Respir Crit Care Med ; 42(6): 771-787, 2021 12.
Article in English | MEDLINE | ID: covidwho-2084534

ABSTRACT

Influenza infection causes severe illness in 3 to 5 million people annually, with up to an estimated 650,000 deaths per annum. As such, it represents an ongoing burden to health care systems and human health. Severe acute respiratory infection can occur, resulting in respiratory failure requiring intensive care support. Herein we discuss diagnostic approaches, including development of CLIA-waived point of care tests that allow rapid diagnosis and treatment of influenza. Bacterial and fungal coinfections in severe influenza pneumonia are associated with worse outcomes, and we summarize the approach and treatment options for diagnosis and treatment of bacterial and Aspergillus coinfection. We discuss the available drug options for the treatment of severe influenza, and treatments which are no longer supported by the evidence base. Finally, we describe the supportive management and ventilatory approach to patients with respiratory failure as a result of severe influenza in the intensive care unit.


Subject(s)
Coinfection , Influenza, Human , Respiratory Insufficiency , Critical Care , Humans , Influenza, Human/complications , Influenza, Human/diagnosis , Influenza, Human/drug therapy , Intensive Care Units , Respiratory Insufficiency/etiology , Respiratory Insufficiency/therapy
7.
Rev Med Chil ; 150(3): 316-323, 2022 Mar.
Article in Spanish | MEDLINE | ID: covidwho-2055642

ABSTRACT

BACKGROUND: In a decade, we faced two pandemic viruses, influenza A H1N1pdm09 and SARS CoV-2, whose most serious manifestation is pneumonia. AIM: To compare the clinical, epidemiological and management aspects of pneumonias caused by each pandemic virus in adults requiring hospitalization. MATERIAL AND METHODS: Comparative, observational study carried out at a regional Chilean hospital, including 75 patients with influenza A H1N1pdm09 prospectively studied in 2009 and 142 patients with SARS-CoV-2 studied in 2020. RESULTS: Patients with SARS-CoV-2 pneumonia were older (56 and 39.7 years respectively, p < 0.01) and had significantly more comorbidities. Cough, fever and myalgias were more frequent in influenza. Dyspnea was more frequent in COVID-19. Patients with COVID-19 had more extensive lung involvement and a longer hospitalization (13.6 and 8.6 days respectively, p = 0.01). There was no difference on ICU admission requirements and mortality attributable to pneumonia. Patients with influenza had greater APACHE scores and a higher frequency of a PaO2/FiO2 ratio ≤ 200. During COVID-19pandemic chest sean replaced x-ray examination. Also high-flow nasal cannulas and awake prone position ventilation were added as treatments. CONCLUSIONS: COVID-19 patients were older, had fewer classic flu symptoms but more dyspnea and longer hospitalization periods than patients with influenza.


Subject(s)
COVID-19 , Influenza, Human , Pneumonia, Viral , Adult , COVID-19/epidemiology , Dyspnea , Hospitalization , Humans , Influenza, Human/diagnosis , Influenza, Human/epidemiology , Pandemics , Pneumonia, Viral/diagnosis , Pneumonia, Viral/epidemiology , Pneumonia, Viral/therapy , SARS-CoV-2
8.
Clin Infect Dis ; 75(Supplement_2): S205-S215, 2022 Oct 03.
Article in English | MEDLINE | ID: covidwho-2051346

ABSTRACT

BACKGROUND: Concurrent detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and another respiratory virus in individuals can document contemporaneous circulation. We used an ongoing, community-based study of school-aged children and their households to evaluate SARS-CoV-2 codetections with other respiratory viruses in a non-medically attended population over a 2-year period. METHODS: Household enrollment was predicated on an acute respiratory illness in a child residing in that household who was also a kindergarten through 12th-grade student in the participating school district. Demographic, symptom, and household composition data and self-collected nasal specimens were obtained on the recruitment day, and 7 and 14 days later, from the index child and all other household members. All specimens were tested for SARS-CoV-2 and influenza A/B by reverse-transcription polymerase chain reaction. Day 0 specimens from the index children were simultaneously tested for 16 pathogens using a commercial respiratory pathogen panel (RPP). To assess viral codetections involving SARS-CoV-2, all household specimens were tested via RPP if the index child's day 0 specimen tested positive to any of the 16 pathogen targets in RPP and any household member tested positive for SARS-CoV-2. RESULTS: Of 2109 participants (497 index children in 497 households with 1612 additional household members), 2 (0.1%) were positive for both SARS-CoV-2 and influenza A; an additional 11 (0.5%) were positive for SARS-CoV-2 and another RPP-covered respiratory virus. Codetections predominantly affected school-aged children (12 of 13 total) and were noted in 11 of 497 households. CONCLUSIONS: SARS-CoV-2 codetections with other respiratory viruses were uncommon and predominated in school-aged children.


Subject(s)
COVID-19 , Influenza, Human , Viruses , COVID-19/diagnosis , COVID-19/epidemiology , Child , Humans , Influenza, Human/diagnosis , Influenza, Human/epidemiology , SARS-CoV-2 , Wisconsin/epidemiology
9.
Clin Infect Dis ; 75(Supplement_2): S271-S284, 2022 Oct 03.
Article in English | MEDLINE | ID: covidwho-2051343

ABSTRACT

BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and influenza viruses continue to co-circulate, representing 2 major public health threats from respiratory infections with similar clinical presentations. SARS-CoV-2 and influenza vaccines can also now be co-administered. However, data on antibody responses to SARS-CoV-2 and influenza coinfection and vaccine co-administration remain limited. METHODS: We developed a 41-plex antibody immunity assay that can simultaneously characterize antibody landscapes to SARS-CoV-2/influenza/common human coronaviruses. We analyzed sera from 840 individuals (11-93 years), including sera from reverse transcription-polymerase chain reaction (RT-PCR)-confirmed SARS-CoV-2-positive (n = 218) and -negative (n = 120) cases, paired sera from SARS-CoV-2 vaccination (n = 29) and infection (n = 11), and paired sera from influenza vaccination (n = 56) and RT-PCR-confirmed influenza infection (n = 158) cases. Last, we analyzed sera collected from 377 individuals who exhibited acute respiratory illness (ARI) in 2020. RESULTS: This 41-plex assay has high sensitivity and specificity in detecting SARS-CoV-2 infections. It differentiated SARS-CoV-2 vaccination (antibody responses only to spike protein) from infection (antibody responses to both spike and nucleoprotein). No cross-reactive antibodies were induced to SARS-CoV-2 from influenza vaccination and infection, and vice versa, suggesting no interaction between SARS-CoV-2 and influenza antibody responses. However, cross-reactive antibodies were detected between spike proteins of SARS-CoV-2 and common human coronaviruses that were removed by serum adsorption. Among 377 individuals who exhibited ARI in 2020, 129 were influenza positive; none had serological evidence of SARS-CoV-2/influenza coinfections. CONCLUSIONS: Multiplex detection of antibody landscapes can provide in-depth analysis of the antibody protective immunity to SARS-CoV-2 in the context of other respiratory viruses, including influenza.


Subject(s)
COVID-19 , Coinfection , Influenza Vaccines , Influenza, Human , Antibodies, Viral , COVID-19/diagnosis , COVID-19 Vaccines , Humans , Influenza, Human/diagnosis , Influenza, Human/prevention & control , Nucleoproteins , SARS-CoV-2 , Spike Glycoprotein, Coronavirus , Vaccination
10.
BMJ Open ; 12(9): e061727, 2022 09 22.
Article in English | MEDLINE | ID: covidwho-2038309

ABSTRACT

OBJECTIVES: As clinical presentation and complications of both viruses overlap, it was hypothesised that influenza vaccination was associated with lower general practitioner (GP)-diagnosed COVID-19 rates and lower all-cause mortality rates. STUDY DESIGN: From a primary care population-based cohort in the Netherlands, GP-diagnosed COVID-19 (between 10 March and 22 November 2020) and all-cause mortality events (between 30 December 2019 and 22 November 2020) were recorded. 223 580 persons were included, representing the influenza vaccination 2019 target group (all aged ≥60 years, and those <60 years with a medical indication). Proportional hazards regression analyses evaluated associations between influenza vaccination in 2019 and two outcomes: GP-diagnosed COVID-19 and all-cause mortality. Covariables were sex, age, comorbidities and number of acute respiratory infection primary care consultations in 2019. RESULTS: A slightly positive association (HR 1.15; 95% CI 1.08 to 1.22) was found between influenza vaccination in 2019 and GP-diagnosed COVID-19, after adjusting for covariables. A slightly protective effect for all-cause mortality rates (HR 0.90; 95% CI 0.83 to 0.97) was found for influenza vaccination, after adjusting for covariables. A subgroup analysis among GP-diagnosed COVID-19 cases showed no significant association between influenza vaccination in 2019 and all-cause mortality. CONCLUSIONS: Our hypothesis of a possibly negative association between influenza vaccination in 2019 and GP-diagnosed COVID-19 was not confirmed as we found a slightly positive association. A slightly protective effect on all-cause mortality was found after influenza vaccination, possibly by a wider, overall protective effect on health. Future research designs should include test-confirmed COVID-19 cases and controls, adjustments for behavioural, socioeconomic and ethnic factors and validated cause-specific mortality cases.


Subject(s)
COVID-19 , General Practitioners , Influenza Vaccines , Influenza, Human , COVID-19/diagnosis , COVID-19/prevention & control , Cohort Studies , Humans , Influenza, Human/diagnosis , Influenza, Human/prevention & control , Vaccination
11.
PLoS One ; 17(9): e0274222, 2022.
Article in English | MEDLINE | ID: covidwho-2021957

ABSTRACT

INTRODUCTION: Using respiratory virus rapid diagnostic tests in the emergency department could allow better and faster clinical management. Point-of-care PCR instruments now provide results in less than 30 minutes. The objective of this study was to assess the impact of the use of a rapid molecular diagnostic test, the cobas® Influenza A/B & RSV Assay, during the clinical management of emergency department patients. METHODS: Patients (adults and children) requiring admission or suffering from an underlying condition at risk of respiratory complications were prospectively recruited in the emergency department of four hospitals in the Brussels region. Physicians' intentions regarding admission, isolation, antibiotic, and antiviral use were collected before and after performing the rapid molecular test. Additionally, a comparison of the analytical performance of this test against antigen rapid tests and viral culture was performed as well as a time-to-result evaluation. RESULTS: Among the 293 patients recruited, 90 had a positive PCR, whereas 44 had a positive antigen test. PCR yielded a sensitivity of 100% for all targets. Antigen tests yielded sensitivities ranging from 66.7% for influenza B to 83.3% for respiratory syncytial virus (RSV). The use of PCR allowed a decrease in the overall need for isolation and treatment by limiting the isolation of negative patients and antibiotic use for positive patients. Meanwhile, antiviral treatments better targeted patients with a positive influenza PCR. CONCLUSION: The use of a rapid influenza and RSV molecular test improves the clinical management of patients admitted to the emergency department by providing a fast and reliable result. Their additional cost compared to antigen tests should be balanced with the benefit of their analytical performance, leading to efficient reductions in the need for isolation and antibiotic use.


Subject(s)
Herpesvirus 1, Cercopithecine , Influenza A virus , Influenza, Human , Respiratory Syncytial Virus Infections , Respiratory Syncytial Virus, Human , Adult , Anti-Bacterial Agents/therapeutic use , Antiviral Agents , Child , Emergency Service, Hospital , Humans , Influenza A virus/genetics , Influenza B virus/genetics , Influenza, Human/diagnosis , Respiratory Syncytial Virus Infections/diagnosis , Respiratory Syncytial Virus, Human/genetics , Sensitivity and Specificity
12.
Medicine (Baltimore) ; 101(34): e30261, 2022 Aug 26.
Article in English | MEDLINE | ID: covidwho-2008667

ABSTRACT

The neutrophil-to-lymphocyte ratio (NLR) is used to predict the prognosis of various diseases, such as coronavirus disease 2019, community-acquired pneumonia, bacteremia, and endocarditis. However, NLR has never been reported to predict patient discharge in geriatric patients with influenza infection. This retrospective case-control study enrolled geriatric patients (≥65 years) with influenza virus infection who visited the emergency department of a medical center between January 01, 2010 and December 31, 2015. Demographic data, vital signs, past histories, influenza subtypes, outcomes, and disposition were analyzed. The optimal NLR cut-off value to predict patient discharge was determined using the Youden index. We also evaluated the accuracy of NLR in predicting patient discharge using logistic regression and receiver operating characteristic analysis. The study included 409 geriatric patients in the emergency department with a mean age of 79.5 years and an approximately equal sex ratio. NLR was significantly lower in the discharged group than in the nondischarged group (5.8 ± 3.7 vs 9.7 ± 8.4). Logistic regression revealed that patients with NLR ≤ 6.5 predicted discharge with an odds ratio of 3.62. The Hosmer-Lemeshow goodness-of-fit test was calculated as 0.36, and the adjusted area under the receiver operating characteristic was 0.75. The negative predictive value of NLR ≤ 6.5, to predict patient discharge, was 91.8%. NLR ≤ 6.5 is a simple and easy-to-obtain laboratory tool to guide the physicians to discharge geriatric patients with influenza infection in the crowded emergency department.


Subject(s)
COVID-19 , Influenza, Human , Aged , Case-Control Studies , Emergency Service, Hospital , Humans , Influenza, Human/diagnosis , Lymphocytes , Neutrophils , Patient Discharge , Prognosis , ROC Curve , Retrospective Studies
13.
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
14.
BMC Public Health ; 22(1): 1541, 2022 08 13.
Article in English | MEDLINE | ID: covidwho-2002147

ABSTRACT

OBJECTIVES: We aimed to characterize the proportion of clients presenting to community pharmacies with influenza-like illness (ILI) and the severity of their illness; the proportion with detectable influenza A, influenza B, and other pathogens (i.e., parainfluenza I, II, and III, adenovirus, respiratory syncytial virus, human metapneumovirus); and to describe their self-medication practices. METHODS: A cross-sectional study was conducted in six pharmacies in Guatemala City. Study personnel collected nasopharyngeal and oropharyngeal swabs from participants who met the ILI case definition and who were self-medicating for the current episode. Participants were tested for influenza A and B and other pathogens using real-time RT-PCR. Participants' ILI-associated self-medication practices were documented using a questionnaire. RESULTS: Of all patients entering the pharmacy during peak hours who responded to a screening survey (n = 18,016) 6% (n = 1029) self-reported ILI symptoms, of which 45% (n = 470/1029) met the study case definition of ILI. Thirty-one percent (148/470) met inclusion criteria, of which 87% (130/148) accepted participation and were enrolled in the study. Among 130 participants, nearly half tested positive for viral infection (n = 55, 42.3%) and belonged to groups at low risk for complications from influenza. The prevalence of influenza A was 29% (n = 35). Thirteen percent of the study population (n = 17) tested positive for a respiratory virus other than influenza. Sixty-four percent of participants (n = 83) reported interest in receiving influenza vaccination if it were to become available in the pharmacy. Medications purchased included symptom-relieving multi-ingredient cold medications (n = 43/100, 43%), nonsteroidal anti-inflammatory drugs (n = 23, 23%), and antibiotics (n = 16, 16%). Antibiotic use was essentially equal among antibiotic users regardless of viral status. The broad-spectrum antibiotics ceftriaxone and azithromycin were the most common antibiotics purchased. CONCLUSIONS: During a typical influenza season, a relatively low proportion of all pharmacy visitors were experiencing influenza symptoms. A high proportion of clients presenting to pharmacies with ILI tested positive for a respiratory virus. Programs that guide appropriate use of antibiotics in this population are needed and become increasingly important during pandemics caused by respiratory viral pathogens.


Subject(s)
Influenza, Human , Pharmacies , Virus Diseases , Anti-Bacterial Agents/therapeutic use , Cross-Sectional Studies , Guatemala/epidemiology , Humans , Influenza, Human/diagnosis , Influenza, Human/drug therapy , Influenza, Human/epidemiology , Seasons
15.
Lab Chip ; 22(18): 3436-3452, 2022 09 13.
Article in English | MEDLINE | ID: covidwho-1991687

ABSTRACT

The pandemic of coronavirus disease 2019 (COVID-19), due to the novel coronavirus (SARS-CoV-2), has created an unprecedented threat to the global health system, especially in resource-limited areas. This challenge shines a spotlight on the urgent need for a point-of-care (POC) quantitative real-time PCR (qPCR) test for sensitive and rapid diagnosis of viral infections. In a POC system, a closed, single-use, microfluidic cartridge is commonly utilized for integration of nucleic acid preparation, PCR amplification and florescence detection. But, most current cartridge systems often involve complicated nucleic acid extraction via active pumping that relies on cumbersome external hardware, causing increases in system complexity and cost. In this work, we demonstrate a gravity-driven cartridge design for an integrated viral RNA/DNA diagnostic test that does not require auxiliary hardware for fluid pumping due to adopted extraction-free amplification. This microfluidic cartridge only contains two reaction chambers for nucleic acid lysis and amplification respectively, enabling a fast qPCR test in less than 30 min. This gravity-driven pumping strategy can help simplify and minimize the microfluidic cartridge, thus enabling high-throughput (up to 12 test cartridges per test) molecular detection via a small cartridge readout system. Thus, this work addresses the scalability limitation of POC molecular testing and can be run in any settings. We verified the analytical sensitivity and specificity of the cartridge testing for respiratory pathogens and sexually transmitted diseases using SARS-CoV-2, influenza A/B RNA samples, and human papillomavirus 16/18 DNA samples. Our cartridge system exhibited a comparable detection performance to the current gold standard qPCR instrument ABI 7500. Moreover, our system showed very high diagnostic accuracy for viral RNA/DNA detection that was well validated by ROC curve analysis. The sample-to-answer molecular testing system reported in this work has the advantages of simplicity, rapidity, and low cost, making it highly promising for prevention and control of infectious diseases in poor-resource areas.


Subject(s)
COVID-19 , Influenza, Human , COVID-19/diagnosis , COVID-19 Testing , DNA, Viral/genetics , Human papillomavirus 16/genetics , Humans , Influenza, Human/diagnosis , Microfluidics , Nucleic Acid Amplification Techniques , RNA, Viral/analysis , RNA, Viral/genetics , Real-Time Polymerase Chain Reaction , SARS-CoV-2/genetics , Sensitivity and Specificity
16.
Diagn Microbiol Infect Dis ; 104(2): 115764, 2022 Oct.
Article in English | MEDLINE | ID: covidwho-1982919

ABSTRACT

The COVID-19 pandemic highlighted the significance of readily available and easily performed viral testing for surveillance during future infectious pandemics. The objectives of this study were: to assess the performance of the Xpert Xpress Flu and/or RSV test, a multiplex PCR assay for detecting influenza A and B virus and respiratory syncytial virus nucleic acids in respiratory tract specimens, relative to the Quidel Lyra Influenza A+B assay and the Prodesse ProFlu+ assay, and the system's ease of use by minimally trained operators. Overall, the Xpert Xpress Flu/RSV test demonstrated a high positive and negative percent agreement with the comparator assays, and was easy to use and interpret results, based on the operators' feedback. We concluded that the Xpert Xpress Flu/RSV test is sensitive, specific, and easy to use for the diagnosis of influenza and RSV by minimally trained operators and can be a valuable tool in future infectious clusters or pandemics.


Subject(s)
COVID-19 , Influenza A virus , Influenza, Human , Respiratory Syncytial Virus Infections , Respiratory Syncytial Virus, Human , COVID-19/diagnosis , Humans , Influenza A virus/genetics , Influenza B virus/genetics , Influenza, Human/diagnosis , Molecular Diagnostic Techniques/methods , Nasopharynx , Pandemics , Real-Time Polymerase Chain Reaction/methods , Respiratory Syncytial Virus Infections/diagnosis , Respiratory Syncytial Virus, Human/genetics , Sensitivity and Specificity
17.
Angew Chem Int Ed Engl ; 61(40): e202209496, 2022 10 04.
Article in English | MEDLINE | ID: covidwho-1981570

ABSTRACT

Sensitive, rapid and low-cost nucleic acid detection is critical for controlling infectious pathogens. Here, we develop a ready-to-use and multimodal detection based on a rebuilding-free, ultrasensitive and selective strategy named dual hairpin ligation-induced isothermal amplification pro (DHLApro). Taking influenza A, influenza B, MERS-CoV, SARS-CoV-2 as model targets, we demonstrate DHLApro provides ≈zM level ultra-sensitivity, being equaling to 0.45 copy/µL in original sample. By simply changing the recognition module, a set of DHLApro components can be applied to a new target without performance loss. Moreover, DHLApro innovatively allows flexible logic/multiplex assay using one set of primer, for example, the "N pathogens-in-1" OR gate screening and accurate multi-channel multiplex assay. Compared with traditional methods, the cost of this logic/multiplex assay has been largely reduced and the cross-interference between the multiple primer sets is also avoided.


Subject(s)
COVID-19 , Influenza, Human , Nucleic Acids , COVID-19/diagnosis , Genotype , Humans , Influenza, Human/diagnosis , Logic , Nucleic Acid Amplification Techniques/methods , SARS-CoV-2/genetics , Sensitivity and Specificity
18.
Turk J Pediatr ; 64(3): 549-557, 2022.
Article in English | MEDLINE | ID: covidwho-1975713

ABSTRACT

BACKGROUND: Cystic fibrosis (CF) is a degenerative disease distinguished by progressive epithelial secretory gland dysfunction associated with recurrent respiratory tract infections. Despite that bacteria have previously been studied as the main cause of CF airway damage, a strong effect of respiratory viral infections is also now recognized. We aimed to detect the relationship between viral infection and exacerbation in children with cystic fibrosis. METHODS: This is a cross sectional observational study recruiting 60 patients diagnosed as CF following in Cystic Fibrosis Clinic, Children`s Hospital, Cairo University, throughout a period of 7 months. Their age ranged from 6 months to 13 years. Patients had nasal swabs and sputum samples obtained when they developed respiratory exacerbations. Multiplex PCR (polymerase chain reaction) technique was used to detect respiratory viruses from nasal swabs. RESULTS: We detected viruses in 48 patients during exacerbation (80%), the most common virus was rhinovirus in 43.4% of patients, followed by bocavirus in 20%, adenovirus in 13.3%, enterovirus in 10% and human metapneumovirus in 6.7%. Co-infection with double viruses was detected in 10 patients. Bacterial infection was present in 56.7% of patients; the most common organism was Pseudomonas in 20% of patients, followed by Staphylococcus aureus, methicillin resistant Staphylococcus aureus, Klebsiella and Haemophilus influenzae. CRP was positive in 53.3% of patients. There was a significant relationship between sputum positive bacterial culture and each of influenza A virus, enterovirus and human metapneumovirus. CONCLUSIONS: This study demonstrated that exacerbation in cystic fibrosis may be exaggerated by viral infections such as influenza A and enterovirus necessitating hospitalization which shows the important protective role of vaccination. Also, a strong relationship was detected between some viruses such as enterovirus, human metapneumovirus and influenza and between bacterial infection.


Subject(s)
Bacterial Infections , Cystic Fibrosis , Influenza, Human , Methicillin-Resistant Staphylococcus aureus , Respiratory Tract Infections , Virus Diseases , Viruses , Bacteria , Bacterial Infections/complications , Bacterial Infections/epidemiology , Child , Cross-Sectional Studies , Cystic Fibrosis/complications , Humans , Infant , Influenza, Human/complications , Influenza, Human/diagnosis , Prospective Studies , Respiratory Tract Infections/complications , Respiratory Tract Infections/epidemiology , Virus Diseases/complications , Virus Diseases/epidemiology
19.
Influenza Other Respir Viruses ; 16(5): 937-941, 2022 09.
Article in English | MEDLINE | ID: covidwho-1973654

ABSTRACT

INTRODUCTION: The use of rapid molecular testing for influenza diagnosis is becoming increasingly popular. Used at the point of care or in a clinical laboratory, these tests detect influenza A and B viruses, though many do not distinguish between influenza A subtypes. The UK Severe Influenza Surveillance System (USISS) collects surveillance data on laboratory-confirmed influenza admissions to secondary care in England. This study set out to understand how rapid influenza molecular testing was being used and how it might influence the availability of subtyping data collected on influenza cases admitted to secondary care in England. METHODS: At the end of the 2017/2018 and 2018/2019 influenza seasons, a questionnaire was sent to all National Health Service Hospital Trusts in England to evaluate the use of rapid influenza testing. Surveillance data collected through USISS was analysed from 2011/2012 to 2020/2021. RESULTS: Of responding trusts, 42% (13/31) in 2017/2018 and 55% (9/17) in 2018/2019 used rapid influenza molecular tests, either alone or in combination with other testing. The majority of rapid tests used did not subtype the influenza A result, and limited follow-up testing occurred. Surveillance data showed significant proportions of influenza A hospital and intensive care unit/high dependency unit admissions without subtyping information, increasing by approximately 35% between 2012/2013 and 2020/2021. CONCLUSIONS: The use of rapid influenza molecular tests is a likely contributing factor to the large proportion of influenza A hospitalisations in England that were unsubtyped. Given their clear clinical advantages, further work must be done to reinforce these data for public health through integrated genomic surveillance.


Subject(s)
Influenza, Human , England/epidemiology , Humans , Influenza, Human/diagnosis , Influenza, Human/epidemiology , Molecular Diagnostic Techniques , Seasons , Secondary Care , State Medicine
20.
Methods Mol Biol ; 2511: 53-65, 2022.
Article in English | MEDLINE | ID: covidwho-1941366

ABSTRACT

COVID-19 disease caused by the novel SARS-CoV-2 virus represents a new challenge for healthcare systems. The molecular confirmation of infection is crucial to guide public health decision-making. This task could be made more difficult during the next influenza season. Thus, a rapid and user-friendly diagnostic test to discriminate SARS-CoV-2 from influenza viruses is urgently needed. Here, we present a multiplex quantitative polymerase chain reaction (qPCR) assay capable of distinguishing SARS-CoV-2 from influenza A and B cases. This assay benefits from the use of an inhibitor tolerant PCR mix which obviates the need for the rate-limiting extraction step, allowing for a more rapid and accurate analysis.


Subject(s)
COVID-19 , Herpesvirus 1, Cercopithecine , Influenza A virus , Influenza, Human , COVID-19/diagnosis , Diagnostic Tests, Routine , Humans , Influenza A virus/genetics , Influenza B virus , Influenza, Human/diagnosis , Multiplex Polymerase Chain Reaction , Real-Time Polymerase Chain Reaction , SARS-CoV-2/genetics , Sensitivity and Specificity
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