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1.
Euro Surveill ; 27(1)2022 01.
Article in English | MEDLINE | ID: covidwho-1613508

ABSTRACT

BackgroundSince the onset of the COVID-19 pandemic, the disease has frequently been compared with seasonal influenza, but this comparison is based on little empirical data.AimThis study compares in-hospital outcomes for patients with community-acquired COVID-19 and patients with community-acquired influenza in Switzerland.MethodsThis retrospective multi-centre cohort study includes patients > 18 years admitted for COVID-19 or influenza A/B infection determined by RT-PCR. Primary and secondary outcomes were in-hospital mortality and intensive care unit (ICU) admission for patients with COVID-19 or influenza. We used Cox regression (cause-specific and Fine-Gray subdistribution hazard models) to account for time-dependency and competing events with inverse probability weighting to adjust for confounders.ResultsIn 2020, 2,843 patients with COVID-19 from 14 centres were included. Between 2018 and 2020, 1,381 patients with influenza from seven centres were included; 1,722 (61%) of the patients with COVID-19 and 666 (48%) of the patients with influenza were male (p < 0.001). The patients with COVID-19 were younger (median 67 years; interquartile range (IQR): 54-78) than the patients with influenza (median 74 years; IQR: 61-84) (p < 0.001). A larger percentage of patients with COVID-19 (12.8%) than patients with influenza (4.4%) died in hospital (p < 0.001). The final adjusted subdistribution hazard ratio for mortality was 3.01 (95% CI: 2.22-4.09; p < 0.001) for COVID-19 compared with influenza and 2.44 (95% CI: 2.00-3.00, p < 0.001) for ICU admission.ConclusionCommunity-acquired COVID-19 was associated with worse outcomes compared with community-acquired influenza, as the hazards of ICU admission and in-hospital death were about two-fold to three-fold higher.


Subject(s)
COVID-19 , Influenza, Human , Cohort Studies , Hospital Mortality , Hospitalization , Hospitals , Humans , Influenza, Human/diagnosis , Influenza, Human/epidemiology , Intensive Care Units , Male , Pandemics , Retrospective Studies , SARS-CoV-2 , Switzerland/epidemiology
2.
PLoS One ; 17(1): e0262258, 2022.
Article in English | MEDLINE | ID: covidwho-1606499

ABSTRACT

Although patients infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), influenza A, influenza B and respiratory syncytial virus (RSV) show comparable or very similar manifestations, the therapeutic approaches of these respiratory viral infections are different, which requires an accurate diagnosis. Recently, the novel multiplex real-time reverse transcription-polymerase chain reaction assay AMPLIQUICK® Respiratory Triplex (BioSynex SA, Illkirch-Graffenstaden, France) allows simultaneous detection and differentiation of SARS-CoV-2, influenza A, influenza B, and RSV in respiratory tract samples. We herein evaluated the performance of the AMPLIQUICK® Respiratory Triplex for the detection of the four viruses in respiratory specimens, using Allplex™ Respiratory Panel 1 and 2019-nCoV assays (Seegene, Seoul, Korea) as reference comparator assays. A total of 359 archived predetermined respiratory samples, including 83, 145, 19 and 95 positive specimens for SARS-CoV-2, influenza A, influenza B and RSV respectively, were included. The AMPLIQUICK® Respiratory Triplex showed high concordance with the reference assays, with an overall agreement for SARS-CoV-2, influenza A, influenza B, and RSV at 97.6%, 98.8%, 98.3% and 100.0%, respectively, and high κ values ranging from 0.93 to 1.00, indicating an almost perfect agreement between assays. Furthermore, high correlations of cycle threshold (Ct) values were observed for positive samples of the four viruses between the AMPLIQUICK® Respiratory Triplex and comparator assays, with an overall high agreement between Ct values assessed by Bland-Altman analyses. In conclusion, these observations demonstrate that the multiplex AMPLIQUICK® Respiratory Triplex is a reliable assay for the qualitative detection and differentiation of SARS-CoV-2, influenza A, influenza B, and RSV in respiratory specimens, which may prove useful for streamlining diagnostics during the winter influenza-seasons.


Subject(s)
COVID-19/diagnosis , Influenza, Human/diagnosis , Multiplex Polymerase Chain Reaction/methods , Real-Time Polymerase Chain Reaction/methods , Respiratory Syncytial Virus Infections/diagnosis , COVID-19/virology , Humans , Influenza, Human/virology , Molecular Diagnostic Techniques , Nasopharynx/virology , Respiratory Syncytial Virus Infections/virology , Retrospective Studies , Sensitivity and Specificity
3.
Euro Surveill ; 26(27)2021 07.
Article in English | MEDLINE | ID: covidwho-1577032

ABSTRACT

BackgroundInfluenza virus presents a considerable challenge to public health by causing seasonal epidemics and occasional pandemics. Nanopore metagenomic sequencing has the potential to be deployed for near-patient testing, providing rapid infection diagnosis, rationalising antimicrobial therapy, and supporting infection-control interventions.AimTo evaluate the applicability of this sequencing approach as a routine laboratory test for influenza in clinical settings.MethodsWe conducted Oxford Nanopore Technologies (Oxford, United Kingdom (UK)) metagenomic sequencing for 180 respiratory samples from a UK hospital during the 2018/19 influenza season, and compared results to routine molecular diagnostic standards (Xpert Xpress Flu/RSV assay; BioFire FilmArray Respiratory Panel 2 assay). We investigated drug resistance, genetic diversity, and nosocomial transmission using influenza sequence data.ResultsCompared to standard testing, Nanopore metagenomic sequencing was 83% (75/90) sensitive and 93% (84/90) specific for detecting influenza A viruses. Of 59 samples with haemagglutinin subtype determined, 40 were H1 and 19 H3. We identified an influenza A(H3N2) genome encoding the oseltamivir resistance S331R mutation in neuraminidase, potentially associated with an emerging distinct intra-subtype reassortant. Whole genome phylogeny refuted suspicions of a transmission cluster in a ward, but identified two other clusters that likely reflected nosocomial transmission, associated with a predominant community-circulating strain. We also detected other potentially pathogenic viruses and bacteria from the metagenome.ConclusionNanopore metagenomic sequencing can detect the emergence of novel variants and drug resistance, providing timely insights into antimicrobial stewardship and vaccine design. Full genome generation can help investigate and manage nosocomial outbreaks.


Subject(s)
Cross Infection , Influenza, Human , Nanopores , Antiviral Agents/therapeutic use , Cross Infection/diagnosis , Cross Infection/drug therapy , Drug Resistance , Drug Resistance, Viral/genetics , Humans , Influenza A Virus, H3N2 Subtype/genetics , Influenza, Human/diagnosis , Influenza, Human/drug therapy , Influenza, Human/epidemiology , Metagenome , Neuraminidase/genetics , Seasons , United Kingdom
4.
Aging (Albany NY) ; 13(23): 24931-24942, 2021 12 12.
Article in English | MEDLINE | ID: covidwho-1573020

ABSTRACT

Since the Coronavirus 19 (COVID-19) pandemic, several SARS-CoV-2 variants of concern (SARS-CoV-2 VOC) have been reported. The B.1.1.7 variant has been associated with increased mortality and transmission risk. Furthermore, cluster and possible co-infection cases could occur in the next influenza season or COVID-19 pandemic wave, warranting efficient diagnosis and treatment decision making. Here, we aimed to detect SARS-CoV-2 and other common respiratory viruses using multiplex RT-PCR developed on the LabTurbo AIO 48 open system. We performed a multicenter study to evaluate the performance and analytical sensitivity of the LabTurbo AIO 48 system for SARS-CoV-2, influenza A/B, and respiratory syncytial virus (RSV) using 652 nasopharyngeal swab clinical samples from patients. The LabTurbo AIO 48 system demonstrated a sensitivity of 9.4 copies/per PCR for N2 of SARS-CoV-2; 24 copies/per PCR for M of influenza A and B; and 24 copies/per PCR for N of RSV. The assay presented consistent performance in the multicenter study. The multiplex RT-PCR applied on the LabTurbo AIO 48 open platform provided highly sensitive, robust, and accurate results and enabled high-throughput detection of B.1.1.7, influenza A/B, and RSV with short turnaround times. Therefore, this automated molecular diagnostic assay could enable streamlined testing if COVID-19 becomes a seasonal disease.


Subject(s)
COVID-19 Nucleic Acid Testing/methods , COVID-19/diagnosis , Influenza, Human/diagnosis , Multiplex Polymerase Chain Reaction/methods , Respiratory Syncytial Virus Infections/diagnosis , Adult , Aged , COVID-19/virology , Female , Humans , Influenza A virus/genetics , Influenza A virus/isolation & purification , Influenza, Human/virology , Influenzavirus B/genetics , Influenzavirus B/isolation & purification , Male , Middle Aged , Respiratory Syncytial Virus Infections/virology , Respiratory Syncytial Viruses/genetics , Respiratory Syncytial Viruses/isolation & purification , SARS-CoV-2/genetics , SARS-CoV-2/isolation & purification , Sensitivity and Specificity , Young Adult
5.
Med Sci Monit ; 27: e934862, 2021 12 12.
Article in English | MEDLINE | ID: covidwho-1572935

ABSTRACT

BACKGROUND This population study aimed to investigate influenza and influenza-like respiratory virus infections in children during the 2019/20 influenza season and the coronavirus disease 2019 (COVID-19) pandemic in Poland. MATERIAL AND METHODS This study analyzed data from the National Influenza Centre, the Department of Influenza Research at the National Institute of Public Health, and 16 Voivodeship Sanitary and Epidemiological Stations in Poland. Nose and throat swabs were obtained from children during the 2019/20 influenza season and the COVID-19 pandemic. Viral RNA detection was performed using quantitative reverse transcription-polymerase chain reaction (qRT-PCR) to diagnose influenza virus infection and viral subtypes. RESULTS In the analyzed group, both cases of influenza A and B and infections with influenza-like viruses were confirmed. Among all cases caused by influenza viruses, influenza A was more frequent than B, with predominance of the A/H1N1/pdm09 subtype. The flu-like virus which infected most children was the human respiratory syncytial virus (RSV). The greatest number of cases with RSV was registered in the group of the youngest children (0-4 years). CONCLUSIONS This population study from Poland showed that during the COVID-19 pandemic, and during the winter influenza season of 2019/20, influenza and influenza-like viral infections in children showed some differences from previous influenza seasons. The findings highlight the importance of viral infection surveillance and influenza vaccination in the pediatric population.


Subject(s)
COVID-19 , Influenza, Human/epidemiology , Academies and Institutes , Age Distribution , Child , Child, Preschool , Humans , Infant , Influenza, Human/diagnosis , Male , Pandemics , Poland/epidemiology , Polymerase Chain Reaction , SARS-CoV-2
6.
J Korean Med Sci ; 36(48): e328, 2021 Dec 13.
Article in English | MEDLINE | ID: covidwho-1572278

ABSTRACT

BACKGROUND: In the coronavirus disease 2019 (COVID-19) pandemic era, the simultaneous detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), influenza virus (Flu), and respiratory syncytial virus (RSV) is important in the rapid differential diagnosis in patients with respiratory symptoms. Three multiplex real-time reverse transcription polymerase chain reaction (rRT-PCR) assays have been recently developed commercially in Korea: PowerChek™ SARS-CoV-2, Influenza A&B Multiplex Real-time PCR Kit (PowerChek; KogeneBiotech); STANDARD™ M Flu/SARS-CoV-2 Real-time Detection Kit (STANDARD M; SD BioSensor); and Allplex™ SARS-CoV-2/FluA/FluB/RSV Assay (Allplex; Seegene). We evaluated the analytical and clinical performances of these kits. METHODS: A limit of detection tests were performed and cross-reactivity analysis was executed using clinical respiratory samples. Ninety-seven SARS-CoV-2-positive, 201 SARS-CoV-2-negative, 71 influenza A-positive, 50 influenza B-positive, 78 RSV-positive, and 207 other respiratory virus-positive nasopharyngeal swabs were tested using the three assays. The AdvanSure™ respiratory viruses rRT-PCR assay (AdvanSure; LG Life Sciences) was used as a comparator assay for RSV. RESULTS: Except in influenza B, in SARS-CoV-2 and influenza A, there were no significant differences in detecting specific genes of the viruses among the three assays. All three kits did not cross-react with common respiratory viruses. All three kits had greater than 92% positive percent agreement and negative percent agreement and ≥ 0.95 kappa value in the detection of SARS-CoV-2 and flu A/B. Allplex detected RSV more sensitively than AdvanSure. CONCLUSION: The overall performance of three multiplex rRT-PCR assays for the concurrent detection of SARS-CoV-2, influenza A/B, and RSV was comparable. These kits will promote prompt differential diagnosis of COVID-19, influenza, and RSV infection in the COVID-19 pandemic era.


Subject(s)
COVID-19/diagnosis , Influenza, Human/diagnosis , Multiplex Polymerase Chain Reaction/methods , Nasopharynx/virology , RNA, Viral/analysis , Respiratory Syncytial Virus Infections/diagnosis , COVID-19/virology , Cross Reactions , Humans , Influenza A virus/genetics , Influenza A virus/isolation & purification , Influenza B virus/genetics , Influenza B virus/isolation & purification , Influenza, Human/virology , Limit of Detection , Nucleocapsid Proteins/genetics , Polyproteins/genetics , RNA, Viral/metabolism , Reagent Kits, Diagnostic , Republic of Korea , Respiratory Syncytial Virus Infections/virology , Respiratory Syncytial Virus, Human/genetics , Respiratory Syncytial Virus, Human/isolation & purification , SARS-CoV-2/genetics , SARS-CoV-2/isolation & purification , Viral Matrix Proteins/genetics , Viral Proteins/genetics
7.
Biosens Bioelectron ; 197: 113771, 2022 Feb 01.
Article in English | MEDLINE | ID: covidwho-1536447

ABSTRACT

Due to the similar clinical symptoms of influenza (Flu) and coronavirus disease 2019 (COVID-19), there is a looming infection threat of concurrent Flu viruses and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In this work, we introduce a customized isothermal amplification integrated lateral flow strip (LFS) that is capable performing duplex reverse transcription-recombinase polymerase amplification (RT-RPA) and colorimetric LFS in a sequential manner. With customized amplification primer sets targeted to SARS-CoV-2 (opening reading frame 1a/b and nucleoprotein genes) and Flu viruses (Flu A and Flu B), the platform allows the rapid and simultaneous visual screening of SARS-CoV-2 and Flu viruses (Flu A and Flu B) without cross reactivity, false positives, and false negatives. Moreover, it maximally eases the detection, reduces the detection time (1 h), and improves the assay performance to detect as low as 10 copies of the viral RNA. Its clinical application is powerfully demonstrated with 100% accuracy for evaluating 15 SARS-CoV-2-positive clinical samples, 10 Flu viruses-positive clinical samples, and 5 negative clinical samples, which were pre-confirmed by standard qRT-PCR. We envision this portable device can meet the increasing need of online monitoring the serious infectious diseases that substantially affects health care systems worldwide.


Subject(s)
Biosensing Techniques , COVID-19 , Influenza, Human , Humans , Influenza, Human/diagnosis , Nucleic Acid Amplification Techniques , SARS-CoV-2 , Sensitivity and Specificity
8.
J Clin Microbiol ; 59(6)2021 05 19.
Article in English | MEDLINE | ID: covidwho-1511414

ABSTRACT

The threat posed by novel pandemics in the future remains active. Equipping our routine laboratory with clinical metagenomics to detect unknown threats early on offers a considerable advantage and may be feasible and scalable with the ability to identify complicated infectious diseases in routine care. Though several technical and regulatory challenges still exist, clinical metagenomics may improve individual patient outcomes and provide earlier warning signs to improve pandemic preparedness.


Subject(s)
Communicable Diseases , Influenza, Human , Communicable Diseases/diagnosis , Communicable Diseases/epidemiology , Humans , Influenza, Human/diagnosis , Influenza, Human/epidemiology , Metagenomics , Pandemics
9.
BMC Cardiovasc Disord ; 21(1): 528, 2021 11 08.
Article in English | MEDLINE | ID: covidwho-1505900

ABSTRACT

BACKGROUND: The value of mechanical circulatory support (MCS) in cardiogenic shock, especially the combination of the ECMELLA approach (Impella combined with ECMO), remains controversial. CASE PRESENTATION: A previously healthy 33-year-old female patient was submitted to a local emergency department with a flu-like infection and febrile temperatures up to 39 °C. The patient was tested positive for type-A influenza, however negative for SARS-CoV-2. Despite escalated invasive ventilation, refractory hypercapnia (paCO2: 22 kPa) with severe respiratory acidosis (pH: 6.9) and a rising norepinephrine rate occurred within a few hours. Due to a Horovitz-Index < 100, out-of-centre veno-venous extracorporeal membrane oxygenation (vv-ECMO)-implantation was performed. A CT-scan done because of anisocoria revealed an extended dissection of the right vertebral artery. While the initial left ventricular function was normal, echocardiography revealed severe global hypokinesia. After angiographic exclusion of coronary artery stenoses, we geared up LV unloading by additional implantation of an Impella CP and expanded the vv-ECMO to a veno-venous-arterial ECMO (vva-ECMO). Clinically relevant bleeding from the punctured femoral arteries resulted in massive transfusion and was treated by vascular surgery later on. Under continued MCS, LVEF increased to approximately 40% 2 days after the initiation of ECMELLA. After weaning, the Impella CP was explanted at day 5 and the vva-ECMO was removed on day 9, respectively. The patient was discharged in an unaffected neurological condition to rehabilitation 25 days after the initial admission. CONCLUSIONS: This exceptional case exemplifies the importance of aggressive MCS in severe cardiogenic shock, which may be especially promising in younger patients with non-ischaemic cardiomyopathy and potentially reversible causes of cardiogenic shock. This case impressively demonstrates that especially young patients may achieve complete neurological restoration, even though the initial prognosis may appear unfavourable.


Subject(s)
Extracorporeal Membrane Oxygenation/methods , Heart-Assist Devices , Influenza A virus/isolation & purification , Influenza, Human , Respiration, Artificial/methods , Respiratory Insufficiency , Ventricular Dysfunction, Left , Adult , COVID-19/diagnosis , Clinical Deterioration , Critical Care/methods , Echocardiography/methods , Female , Heart Failure/physiopathology , Heart Failure/therapy , Humans , Influenza, Human/complications , Influenza, Human/diagnosis , Influenza, Human/physiopathology , Respiratory Insufficiency/etiology , Respiratory Insufficiency/physiopathology , Respiratory Insufficiency/therapy , SARS-CoV-2 , Serologic Tests/methods , Severity of Illness Index , Shock, Cardiogenic/etiology , Shock, Cardiogenic/physiopathology , Shock, Cardiogenic/therapy , Treatment Outcome , Ventricular Dysfunction, Left/etiology , Ventricular Dysfunction, Left/physiopathology , Ventricular Dysfunction, Left/therapy
10.
Influenza Other Respir Viruses ; 15(3): 381-388, 2021 05.
Article in English | MEDLINE | ID: covidwho-1452868

ABSTRACT

BACKGROUND: Reliable diagnostics are a key to identifying influenza infections. OBJECTIVES: Our objectives were to describe the detection of influenza among severe acute respiratory infection (SARI) cases, to compare test results from the Fast Track Diagnostics (FTD) Kit for influenza detection to the Centers for Disease Control (CDC) human influenza virus detection and characterization panel, and to assess seasonality of influenza in Burkina Faso. METHODS: Nasopharyngeal and oropharyngeal specimens from SARI cases (hospitalized patients with fever, cough, and onset in the previous 10 days) were tested using the FTD-33 Kit and the CDC rRT-PCR influenza assays. We assessed sensitivity and specificity of the FTD-33 Kit for detecting influenza A, influenza B, and the influenza A(H1N1)pdm09 strain using the CDC human influenza rRT-PCR panel as the gold standard. RESULTS: From December 2016 to February 2019, 1706 SARI cases were identified, 1511 specimens were tested, and 211 were positive for influenza A (14.0%) and 100 for influenza B (6.6%) by either assay. Higher influenza circulation occurred between November and April with varying peaks of influenza A and influenza B. Sensitivity of the FTD-33 assay was 91.9% for influenza A, 95.7% for influenza B, and 93.8% for A(H1N1)pdm09 subtype. Specificity was over 99% for all three tests. CONCLUSIONS: Our study indicates that Burkina Faso has one peak of influenza each year which is similar to the Northern Hemisphere and differs from other countries in West Africa. We found high concordance of influenza results between the two assays indicating FTD-33 can be used to reliably detect influenza among SARI cases.


Subject(s)
Influenza A Virus, H1N1 Subtype , Influenza, Human , Centers for Disease Control and Prevention, U.S. , Humans , Influenza A Virus, H1N1 Subtype/genetics , Influenza, Human/diagnosis , Influenza, Human/epidemiology , Laboratories , Reverse Transcriptase Polymerase Chain Reaction , United States
11.
Influenza Other Respir Viruses ; 15(1): 34-44, 2021 01.
Article in English | MEDLINE | ID: covidwho-1452865

ABSTRACT

BACKGROUND: Severe acute respiratory infection (SARI) accounts for a large burden of illness in Indonesia. However, epidemiology of SARI in tertiary hospitals in Indonesia is unknown. This study sought to assess the burden, clinical characteristics, and etiologies of SARI and concordance of clinical diagnosis with confirmed etiology. METHODS: Data and samples were collected from subjects presenting with SARI as part of the acute febrile Illness requiring hospitalization study (AFIRE). In tertiary hospitals, clinical diagnosis was ascertained from chart review. Samples were analyzed to determine the "true" etiology of SARI at hospitals and Indonesia Research Partnership on Infectious Diseases (INA-RESPOND) laboratory. Distribution and characteristics of SARI by true etiology and accuracy of clinical diagnosis were assessed. RESULTS: Four hundred and twenty of 1464 AFIRE subjects presented with SARI; etiology was identified in 242 (57.6%), including 121 (28.8%) viruses and bacteria associated with systemic infections, 70 (16.7%) respiratory bacteria and viruses other than influenza virus, and 51 (12.1%) influenza virus cases. None of these influenza patients were accurately diagnosed as having influenza during hospitalization. CONCLUSIONS: Influenza was misdiagnosed among all patients presenting with SARI to Indonesian tertiary hospitals in the AFIRE study. Diagnostic approaches and empiric management should be guided by known epidemiology. Public health strategies to address the high burden of influenza should include broad implementation of SARI screening, vaccination programs, clinician education and awareness campaigns, improved diagnostic capacity, and support for effective point-of-care tests.


Subject(s)
Influenza, Human , Orthomyxoviridae , Respiratory Tract Infections , Diagnostic Errors , Hospitalization , Humans , Indonesia/epidemiology , Infant , Influenza, Human/diagnosis , Influenza, Human/epidemiology , Respiratory Tract Infections/diagnosis , Respiratory Tract Infections/epidemiology
12.
Infect Control Hosp Epidemiol ; 41(5): 499-504, 2020 05.
Article in English | MEDLINE | ID: covidwho-1452452

ABSTRACT

OBJECTIVE: Older adults often have atypical presentation of illness and are particularly vulnerable to influenza and its sequelae, making the validity of influenza case definitions particularly relevant. We sought to assess the performance of influenza-like illness (ILI) and severe acute respiratory illness (SARI) criteria in hospitalized older adults. DESIGN: Prospective cohort study. SETTING: The Serious Outcomes Surveillance Network of the Canadian Immunization Research Network undertakes active surveillance for influenza among hospitalized adults. METHODS: Data were pooled from 3 influenza seasons: 2011/12, 2012/13, and 2013/14. The ILI and SARI criteria were defined clinically, and influenza was laboratory confirmed. Frailty was measured using a validated frailty index. RESULTS: Of 11,379 adult inpatients (7,254 aged ≥65 years), 4,942 (2,948 aged ≥65 years) had laboratory-confirmed influenza. Their median age was 72 years (interquartile range [IQR], 58-82) and 52.6% were women. The sensitivity of ILI criteria was 51.1% (95% confidence interval [CI], 49.6-52.6) for younger adults versus 44.6% (95% CI, 43.6-45.8) for older adults. SARI criteria were met by 64.1% (95% CI, 62.7-65.6) of younger adults versus 57.1% (95% CI, 55.9-58.2) of older adults with laboratory-confirmed influenza. Patients with influenza who were prefrail or frail were less likely to meet ILI and SARI case definitions. CONCLUSIONS: A substantial proportion of older adults, particularly those who are frail, are missed by standard ILI and SARI case definitions. Surveillance using these case definitions is biased toward identifying younger cases, and does not capture the true burden of influenza. Because of the substantial fraction of cases missed, surveillance definitions should not be used to guide diagnosis and clinical management of influenza.


Subject(s)
Influenza, Human/diagnosis , Influenza, Human/epidemiology , Aged , Aged, 80 and over , Bias , Canada/epidemiology , Female , Frail Elderly , Hospitalization , Humans , Immunization , Laboratories, Hospital , Male , Prospective Studies , Research , Sensitivity and Specificity , Sentinel Surveillance
13.
J Infect Public Health ; 14(11): 1567-1570, 2021 Nov.
Article in English | MEDLINE | ID: covidwho-1461377

ABSTRACT

The emerging of the COVID-19 pandemic is currently challenging for the public health system globally. Beyond SARS-CoV-2 pathogenicity, co-infections with recycling respiratory pathogens, whether bacterial, viral, or fungal, might increase disease symptoms, morbidity, and mortality. In this study, we reported two COVID-19 cases in the early phase of the virus spread in Saudi Arabia with underdiagnosed respiratory viruses' co-infections, influenza B and Parainfluenza-2, detected retrospectively. Fortunately, both patients recovered and were discharged home. Underestimation of co-infection among COVID19 patients might lead to hospital stay prolongation and increases morbidity and mortality. Therefore, it is crucial to consider and screen for co-infecting pathogens among COVID-19 patients and those with risk factors.


Subject(s)
COVID-19 , Coinfection , Influenza, Human , Paramyxoviridae Infections , Coinfection/diagnosis , Coinfection/epidemiology , Humans , Influenza, Human/diagnosis , Influenza, Human/epidemiology , Pandemics , Retrospective Studies , SARS-CoV-2 , Saudi Arabia/epidemiology
14.
Med Microbiol Immunol ; 210(5-6): 277-282, 2021 Dec.
Article in English | MEDLINE | ID: covidwho-1449965

ABSTRACT

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has forced the implementation of unprecedented public health measures strategies which might also have a significant impact on the spreading of other viral pathogens such as influenza and Respiratory Syncytial Virus (RSV) . The present study compares the incidences of the most relevant respiratory viruses before and during the SARS-CoV-2 pandemic in emergency room patients. We analyzed the results of in total 14,946 polymerase chain reaction point-of-care tests (POCT-PCR) for Influenza A, Influenza B, RSV and SARS-CoV-2 in an adult and a pediatric emergency room between December 1, 2018 and March 31, 2021. Despite a fivefold increase in the number of tests performed, the positivity rate for Influenza A dropped from 19.32% (165 positives of 854 tests in 2018/19), 14.57% (149 positives of 1023 in 2019-20) to 0% (0 positives of 4915 tests) in 2020/21. In analogy, the positivity rate for Influenza B and RSV dropped from 0.35 to 1.47%, respectively, 10.65-21.08% to 0% for both in 2020/21. The positivity rate for SARS-CoV2 reached 9.74% (110 of 1129 tests performed) during the so-called second wave in December 2020. Compared to the two previous years, seasonal influenza and RSV incidence was eliminated during the COVID-19 pandemic. Corona-related measures and human behavior patterns could lead to a significant decline or even complete suppression of other respiratory viruses such as influenza and RSV.


Subject(s)
COVID-19/epidemiology , Influenza, Human/diagnosis , Point-of-Care Testing/statistics & numerical data , Respiratory Syncytial Virus Infections/diagnosis , COVID-19/virology , Hospitals/statistics & numerical data , Humans , Incidence , Influenza, Human/epidemiology , Influenza, Human/virology , Orthomyxoviridae/genetics , Orthomyxoviridae/isolation & purification , Orthomyxoviridae/physiology , Pandemics , Polymerase Chain Reaction , Respiratory Syncytial Virus Infections/epidemiology , Respiratory Syncytial Virus Infections/virology , Respiratory Syncytial Virus, Human/genetics , Respiratory Syncytial Virus, Human/isolation & purification , Respiratory Syncytial Virus, Human/physiology , Retrospective Studies
16.
Chem Pharm Bull (Tokyo) ; 69(10): 984-988, 2021.
Article in English | MEDLINE | ID: covidwho-1445702

ABSTRACT

Membrane-based rapid test reagents including immunochromatography are widely used in clinical practice. Recently, high-sensitive reagents based on the immunochromatography method, such as silver amplification method and time resolved fluorescence method for influenza testing, has been developed and early confirmation of infection can be achieved. Furthermore, genetic testing, automated all the steps from extraction till detection, is getting popular. Genetic testing of mycoplasma by Smart Gene Myco system and Coronavirus disease 2019 (COVID-19) test is a good example of membrane-based rapid test reagents. This system uses silica particle-containing membrane filter and enable to shorten the assay time by automates pre-treatment process for removing contamination substances in the sample which affect polymerase-chain-reaction amplification. We hope utilized genetic testing application will help quick confirmation of COVID-19 positive patient and prevent the collapse of medical system under COVID-19 development.


Subject(s)
Chromatography, Affinity/methods , Point-of-Care Systems , COVID-19/diagnosis , COVID-19/virology , COVID-19 Testing , Genetic Testing , Humans , Influenza, Human/diagnosis , Influenza, Human/virology , Orthomyxoviridae/genetics , Orthomyxoviridae/isolation & purification , Polymerase Chain Reaction , SARS-CoV-2/genetics , SARS-CoV-2/isolation & purification
17.
JAMA Netw Open ; 4(9): e2128534, 2021 09 01.
Article in English | MEDLINE | ID: covidwho-1441922

ABSTRACT

Importance: Currently, there are no presymptomatic screening methods to identify individuals infected with a respiratory virus to prevent disease spread and to predict their trajectory for resource allocation. Objective: To evaluate the feasibility of using noninvasive, wrist-worn wearable biometric monitoring sensors to detect presymptomatic viral infection after exposure and predict infection severity in patients exposed to H1N1 influenza or human rhinovirus. Design, Setting, and Participants: The cohort H1N1 viral challenge study was conducted during 2018; data were collected from September 11, 2017, to May 4, 2018. The cohort rhinovirus challenge study was conducted during 2015; data were collected from September 14 to 21, 2015. A total of 39 adult participants were recruited for the H1N1 challenge study, and 24 adult participants were recruited for the rhinovirus challenge study. Exclusion criteria for both challenges included chronic respiratory illness and high levels of serum antibodies. Participants in the H1N1 challenge study were isolated in a clinic for a minimum of 8 days after inoculation. The rhinovirus challenge took place on a college campus, and participants were not isolated. Exposures: Participants in the H1N1 challenge study were inoculated via intranasal drops of diluted influenza A/California/03/09 (H1N1) virus with a mean count of 106 using the median tissue culture infectious dose (TCID50) assay. Participants in the rhinovirus challenge study were inoculated via intranasal drops of diluted human rhinovirus strain type 16 with a count of 100 using the TCID50 assay. Main Outcomes and Measures: The primary outcome measures included cross-validated performance metrics of random forest models to screen for presymptomatic infection and predict infection severity, including accuracy, precision, sensitivity, specificity, F1 score, and area under the receiver operating characteristic curve (AUC). Results: A total of 31 participants with H1N1 (24 men [77.4%]; mean [SD] age, 34.7 [12.3] years) and 18 participants with rhinovirus (11 men [61.1%]; mean [SD] age, 21.7 [3.1] years) were included in the analysis after data preprocessing. Separate H1N1 and rhinovirus detection models, using only data on wearble devices as input, were able to distinguish between infection and noninfection with accuracies of up to 92% for H1N1 (90% precision, 90% sensitivity, 93% specificity, and 90% F1 score, 0.85 [95% CI, 0.70-1.00] AUC) and 88% for rhinovirus (100% precision, 78% sensitivity, 100% specificity, 88% F1 score, and 0.96 [95% CI, 0.85-1.00] AUC). The infection severity prediction model was able to distinguish between mild and moderate infection 24 hours prior to symptom onset with an accuracy of 90% for H1N1 (88% precision, 88% sensitivity, 92% specificity, 88% F1 score, and 0.88 [95% CI, 0.72-1.00] AUC) and 89% for rhinovirus (100% precision, 75% sensitivity, 100% specificity, 86% F1 score, and 0.95 [95% CI, 0.79-1.00] AUC). Conclusions and Relevance: This cohort study suggests that the use of a noninvasive, wrist-worn wearable device to predict an individual's response to viral exposure prior to symptoms is feasible. Harnessing this technology would support early interventions to limit presymptomatic spread of viral respiratory infections, which is timely in the era of COVID-19.


Subject(s)
Biometry/methods , Common Cold/diagnosis , Influenza A Virus, H1N1 Subtype , Influenza, Human/diagnosis , Rhinovirus , Severity of Illness Index , Wearable Electronic Devices , Adult , Area Under Curve , Biological Assay , Biometry/instrumentation , Cohort Studies , Common Cold/virology , Early Diagnosis , Feasibility Studies , Female , Humans , Influenza A Virus, H1N1 Subtype/growth & development , Influenza, Human/virology , Male , Mass Screening , Models, Biological , Rhinovirus/growth & development , Sensitivity and Specificity , Virus Shedding , Young Adult
18.
J Virol Methods ; 298: 114304, 2021 12.
Article in English | MEDLINE | ID: covidwho-1440233

ABSTRACT

The potential co-circulation of SARS-CoV-2, influenza, and respiratory syncytial virus (RSV) could pose an unprecedented challenge to healthcare systems worldwide. Here, we compared the performance of the PowerChek SARS-CoV-2, Influenza A&B, RSV Multiplex Real-time PCR Kit (PowerChek) for simultaneous detection of SARS-CoV-2, influenza A and B, and respiratory syncytial virus with that of BioFire Respiratory Panel 2.1 (RP2.1) using 175 nasopharyngeal swab (NPS) specimens. Positive percent agreement and negative percent agreement of the PowerChek assay compared to RP2.1 were as follows: 100 % (40/40) and 100 % (135/135) for SARS-CoV-2; 100 % (39/39) and 100 % (136/136) for influenza A; 100 % (35/35) and 100 % (140/140) for influenza B; and 93.1 % (27/29) and 100 % (146/146) for RSV, respectively. The limit of detection (LOD) was accessed using RNA standards for each virus, and the LOD values of the PowerChek assay for SARS-CoV-2, influenza A and B, and RSV were 0.36, 1.24, 0.09, and 0.63 copies/µL, respectively. Our results demonstrate that the PowerChek assay is sensitive and accurate for detection of SARS-CoV-2, influenza A and B, and RSV, suggesting that this assay can be a valuable diagnostic tool when SARS-CoV-2, influenza, and RSV are co-circulating.


Subject(s)
COVID-19 , Influenza, Human , Respiratory Syncytial Virus Infections , Respiratory Syncytial Virus, Human , Humans , Influenza B virus/genetics , Influenza, Human/diagnosis , Nasopharynx , Real-Time Polymerase Chain Reaction , Respiratory Syncytial Virus Infections/diagnosis , Respiratory Syncytial Virus, Human/genetics , SARS-CoV-2 , Sensitivity and Specificity
19.
J Clin Virol ; 143: 104946, 2021 10.
Article in English | MEDLINE | ID: covidwho-1433478

ABSTRACT

BACKGROUND: COVID-19 and influenza (flu) share similar clinical symptoms. Therefore, differential detection of these viruses during the respiratory virus season will be an important component for proper patient triage, management, and treatment. OBJECTIVES: Establish the diagnostic performance related to SARS-CoV-2 and Flu A/B detection for the BD SARS-CoV-2/Flu for BD MAX™ System ("MAX SARS-CoV-2/Flu") multiplex assay. MATERIALS AND METHODS: Two hundred and thirty-five (235) retrospective nasopharyngeal specimens were obtained from external vendors. The BD BioGx SARS-CoV-2 Reagents for BD MAX™ System ("BioGx SARS-CoV-2″) and the Cepheid Xpert® Xpress Flu/RSV ("Xpert Flu/RSV") were utilized as reference methods. RESULTS: By reference methods, 52 specimens were SARS-CoV-2-positive, 59 were Flu A-positive, and 60 were Flu B-positive. MAX SARS-CoV-2/Flu had positive percent agreement (PPA) and negative percent agreement (NPA) values for SARS-CoV-2 detection of 96.2% ([95%CI]:87.0-98.9) and 100% [95%CI:88.7-100], respectively; PPA values for Flu A and Flu B of 100% [95%CI:93.9-100] and 98.3% [95%CI:91.1-99.7], respectively, and NPA values for Flu A and Flu B of 98.9% [95%CI:94.0-99.8] and 100% [95%CI:95.9-100], respectively. CONCLUSIONS: The MAX SARS-CoV-2/Flu assay met FDA-EUA performance criteria for SARS-CoV-2 (≥95% for PPA and NPA) and FDA clearance criteria for Flu A/B (PPA ≥90%; lower bound of the 95%CI ≥80% and NPA ≥95%; lower bound of the 95%CI ≥90%).


Subject(s)
COVID-19 , Influenza, Human , Humans , Influenza, Human/diagnosis , Molecular Diagnostic Techniques , Nasopharynx , Retrospective Studies , SARS-CoV-2 , Sensitivity and Specificity
20.
J Med Virol ; 93(10): 5998-6007, 2021 10.
Article in English | MEDLINE | ID: covidwho-1432442

ABSTRACT

In the context of the coronavirus disease 2019 pandemic, we investigated the epidemiological and clinical characteristics of a young patient infected by avian influenza A (H5N6) virus in Anhui Province, East China, and analyzed genomic features of the pathogen in 2020. Through the cross-sectional investigation of external environment monitoring (December 29-31, 2020), 1909 samples were collected from Fuyang City. It was found that the positive rate of H5N6 was higher than other areas obviously in Tianma poultry market, where the case appeared. In addition, dual coinfections were detected with a 0.057% polymerase chain reaction positive rate the surveillance years. The virus was the clade 2.3.4.4, which was most likely formed by genetic reassortment between H5N6 and H9N2 viruses. This study found that the evolution rates of the hemagglutinin and neuraminidase genes of the virus were higher than those of common seasonal influenza viruses. The virus was still highly pathogenic to poultry and had a preference for avian receptor binding.


Subject(s)
COVID-19/epidemiology , Influenza A virus/isolation & purification , Influenza in Birds/virology , Influenza, Human/virology , Animals , Child, Preschool , China , Female , Genome, Viral/genetics , Humans , Influenza A virus/classification , Influenza A virus/genetics , Influenza, Human/diagnosis , Mutation , Phylogeny , Poultry/virology , Reassortant Viruses/classification , Reassortant Viruses/genetics , Reassortant Viruses/isolation & purification , SARS-CoV-2 , Viral Proteins/genetics
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