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1.
Sci Rep ; 12(1): 3480, 2022 03 03.
Article in English | MEDLINE | ID: covidwho-1730307

ABSTRACT

The COVID-19 pandemic has resulted in significant diversion of human and material resources to COVID-19 diagnostics, to the extent that influenza viruses and co-infection in COVID-19 patients remains undocumented and pose serious public-health consequences. We optimized and validated a highly sensitive RT-PCR based multiplex-assay for the detection of SARS-CoV-2, influenza A and B viruses in a single-test. This study evaluated clinical specimens (n = 1411), 1019 saliva and 392 nasopharyngeal swab (NPS), tested using two-assays: FDA-EUA approved SARS-CoV-2 assay that targets N and ORF1ab gene, and the PKamp-RT-PCR based assay that targets SARS-CoV-2, influenza viruses A and B. Of the 1019 saliva samples, 17.0% (174/1019) tested positive for SARS-CoV-2 using either assay. The detection rate for SARS-CoV-2 was higher with the multiplex assay compared to SARS-specific assay [91.9% (160/174) vs. 87.9% (153/174)], respectively. Of the 392 NPS samples, 10.4% (41/392) tested positive for SARS-CoV-2 using either assay. The detection rate for SARS-CoV-2 was higher with the multiplex assay compared to SARS-specific assay [97.5% (40/41) vs. 92.1% (39/41)], respectively. This study presents clinical validation of a multiplex-PCR assay for testing SARS-CoV-2, influenza A and B viruses, using NPS and saliva samples, and demonstrates the feasibility of implementing the assay without disrupting the existing laboratory workflow.


Subject(s)
Influenza A virus/isolation & purification , Influenza B virus/isolation & purification , Multiplex Polymerase Chain Reaction/methods , Nasopharynx/virology , SARS-CoV-2/isolation & purification , Saliva/virology , Humans , Limit of Detection , Reproducibility of Results
2.
Microbiol Spectr ; 10(1): e0109021, 2022 02 23.
Article in English | MEDLINE | ID: covidwho-1673362

ABSTRACT

The rapid emergence of the coronavirus disease 2019 (COVID-19) pandemic has introduced a new challenge in diagnosing and differentiating respiratory infections. Accurate diagnosis of respiratory infections, including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is complicated by overlapping symptomology, and stepwise approaches to testing for each infection would lead to increased reagent usage and cost, as well as delays in clinical interventions. To avoid these issues, multiplex molecular assays have been developed to differentiate between respiratory viruses in a single test to meet clinical diagnostic needs. To evaluate the analytical performance of the FDA emergency use authorization (EUA)-approved Abbott Alinity m resp-4-plex assay (Alinity m) in testing for SARS-CoV-2, influenza A virus, influenza B virus, and respiratory syncytial virus (RSV), we compared its performance to those of both the EUA-approved Cepheid Xpert Xpress SARS-CoV-2, influenza A/B virus, and RSV assay (Xpert Xpress) and the EUA-approved Roche Cobas SARS-CoV-2 and influenza A/B virus assay (Cobas) in a single-center retrospective analysis. High concordance was observed among all three assays, with kappa statistics showing an almost perfect agreement (>0.90). The limit of detection (LOD) results for SARS-CoV-2 showed the Alinity m exhibiting the lowest LOD at 26 copies/mL, followed by the Cobas at 58 copies/mL and the Xpert Xpress at 83 copies/mL, with LOD results for the influenza A virus, influenza B virus, and RSV viral targets also showing equivalent or better performance on the Alinity m compared to the other two platforms. The Alinity m can be used as a high-volume testing platform for SARS-CoV-2, influenza A virus, influenza B virus, and RSV and exhibits analytical performance comparable to those of both the Xpert Xpress and Cobas assays. IMPORTANCE The rapid emergence of SARS-CoV-2 has introduced a new challenge in diagnosing and differentiating respiratory infections, especially considering the overlapping symptomology of many of these infections and differences in clinical interventions depending on the pathogen identified. To avoid these issues, multiplex molecular assays like the one described in this article need to be developed to differentiate between the most common respiratory pathogens in a single test and most effectively meet clinical diagnostic needs.


Subject(s)
Influenza A virus/isolation & purification , Influenza B virus/isolation & purification , Respiratory Syncytial Viruses/isolation & purification , Respiratory Tract Infections/diagnosis , SARS-CoV-2/isolation & purification , Diagnosis, Differential , Humans , Respiratory Tract Infections/virology , Sensitivity and Specificity , Time Factors
3.
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
4.
PLoS One ; 16(12): e0260947, 2021.
Article in English | MEDLINE | ID: covidwho-1556896

ABSTRACT

BACKGROUND: On 9th January 2020, China CDC reported a novel coronavirus (later named SARS-CoV-2) as the causative agent of the coronavirus disease 2019 (COVID-19). Identifying the first appearance of virus is of epidemiological importance to tracking and mapping the spread of SARS-CoV-2 in a country. We therefore conducted a retrospective observational study to detect SARS-CoV-2 in oropharyngeal samples collected from hospitalized patients with a Severe Acute Respiratory Infection (SARI) enrolled in the DRIVE (Development of Robust and Innovative Vaccine Effectiveness) study in five Italian hospitals (CIRI-IT BIVE hospitals network) (1st November 2019 - 29th February 2020). OBJECTIVES: To acquire new information on the real trend in SARS-CoV-2 infection during pandemic phase I and to determine the possible early appearance of the virus in Italy. MATERIALS AND METHODS: Samples were tested for influenza [RT-PCR assay (A/H1N1, A/H3N2, B/Yam, B/Vic)] in accordance with the DRIVE study protocol. Subsequently, swabs underwent molecular testing for SARS-COV-2. [one-step real-time multiplex retro-transcription (RT) PCR]. RESULTS: In the 1683 samples collected, no evidence of SARS-CoV-2 was found. Moreover, 28.3% (477/1683) of swabs were positive for influenza viruses, the majority being type A (358 vs 119 type B). A/H3N2 was predominant among influenza A viruses (55%); among influenza B viruses, B/Victoria was prevalent. The highest influenza incidence rate was reported in patients aged 0-17 years (40.3%) followed by those aged 18-64 years (24.4%) and ≥65 years (14.8%). CONCLUSIONS: In Italy, some studies have shown the early circulation of SARS-CoV-2 in northern regions, those most severely affected during phase I of the pandemic. In central and southern regions, by contrast no early circulation of the virus was registered. These results are in line with ours. These findings highlight the need to continue to carry out retrospective studies, in order to understand the epidemiology of the novel coronavirus, to better identify the clinical characteristics of COVID-19 in comparison with other acute respiratory illnesses (ARI), and to evaluate the real burden of COVID-19 on the healthcare system.


Subject(s)
Influenza, Human/epidemiology , Severe Acute Respiratory Syndrome/epidemiology , Adolescent , Adult , Aged , Aged, 80 and over , COVID-19/diagnosis , COVID-19/virology , Female , Hospitals , Humans , Influenza A Virus, H1N1 Subtype/genetics , Influenza A Virus, H1N1 Subtype/isolation & purification , Influenza A Virus, H3N2 Subtype/genetics , Influenza A Virus, H3N2 Subtype/isolation & purification , Influenza B virus/genetics , Influenza B virus/isolation & purification , Influenza, Human/pathology , Influenza, Human/virology , Italy/epidemiology , Male , Middle Aged , RNA, Viral/genetics , RNA, Viral/metabolism , Retrospective Studies , SARS-CoV-2/genetics , SARS-CoV-2/isolation & purification , Severe Acute Respiratory Syndrome/pathology , Severe Acute Respiratory Syndrome/virology , Young Adult
5.
J Med Virol ; 93(10): 5798-5804, 2021 Oct.
Article in English | MEDLINE | ID: covidwho-1432412

ABSTRACT

Rapid diagnostics for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are paramount for reducing the spread of the current pandemic. During additional seasonal epidemics with influenza A/B and respiratory syncytial virus (RSV), the clinical signs and symptoms cannot be distinguished easily from SARS-CoV-2. Therefore, a new assay combining four targets in the form of the new Xpert Xpress SARS-CoV-2/Flu/RSV assay was evaluated. The assay was compared to the Xpert Xpress SARS-CoV-2, Xpert Xpress Flu/RSV, Seegene Flu/RSV, influenza A/B r-gene® and RSV/hMPV r-gene®. A total of 295 nasopharyngeal and throat swabs were tested at four institutes throughout Europe including 72 samples positive for SARS-CoV-2, 65 for influenza A, 47 for influenza B, and 77 for RSV. The sensitivity of the new assay was above 95% for all targets, with the highest for SARS-CoV-2 (97.2%). The overall correlation of SARS-CoV-2 Ct values between Xpert Xpress SARS-CoV-2 assay and Xpert Xpress SARS-CoV-2/Flu/RSV assay was high. The agreement between Ct values above 30 showed the multiplex giving higher Ct values for SARS-CoV-2 on average than the singleplex assay. In conclusion, the new assay is a rapid and reliable alternative with less hands-on time for the detection of not one, but four upper respiratory tract pathogens that may circulate at the same time.


Subject(s)
Influenza A virus/isolation & purification , Influenza B virus/isolation & purification , Respiratory Syncytial Virus, Human/isolation & purification , Respiratory Tract Infections/diagnosis , SARS-CoV-2/isolation & purification , COVID-19/diagnosis , COVID-19 Nucleic Acid Testing , Europe/epidemiology , Humans , Influenza, Human/diagnosis , Molecular Diagnostic Techniques , Multiplex Polymerase Chain Reaction , Nasopharynx/virology , Respiratory Syncytial Virus Infections/diagnosis , Respiratory Tract Infections/virology , SARS-CoV-2/genetics , Sensitivity and Specificity
6.
Arch Virol ; 166(11): 3085-3092, 2021 Nov.
Article in English | MEDLINE | ID: covidwho-1391877

ABSTRACT

Adenovirus, respiratory syncytial virus, and influenza virus are common causes of respiratory infections. The COVID-19 pandemic had a significant impact on their prevalence. The aim of this study was to analyze the epidemic changes of common respiratory viruses in the Affiliated Hospital of Hangzhou Normal University in Hangzhou, China, from October of 2017 to February of 2021. We collected statistics from 121,529 patients in the outpatient and inpatient departments of the hospital who had throat or nose swabs collected for testing for four virus antigens by the colloidal gold method. Of these, 13,200 (10.86%) were positive for influenza A virus, 8,402 (6.91%) were positive for influenza B virus, 6,056 (4.98%) were positive for adenovirus, and 4,739 (3.90%) were positive for respiratory syncytial virus. The positivity rates of the influenza A virus (0-14 years old, P = 0.376; over 14 years old, P = 0.197) and respiratory syncytial virus (0-14 years old, P = 0.763; over 14 years old, P = 0.465) did not differ significantly by gender. After January of 2020, influenza virus infection decreased significantly. The positivity rate of respiratory syncytial virus remained high, and its epidemic season was similar to before. Strict respiratory protection and regulation of crowd activities have a great impact on the epidemic characteristics of viruses. After major changes in the public health environment, virus epidemics and their mutations should be monitored closely, extensively, and continuously.


Subject(s)
Respiratory Tract Infections/epidemiology , Respiratory Tract Infections/virology , Adenoviridae/isolation & purification , Adolescent , Adult , Age Factors , Aged , Aged, 80 and over , COVID-19/epidemiology , COVID-19/prevention & control , Child , Child, Preschool , China/epidemiology , Female , Humans , Infant , Infant, Newborn , Influenza A virus/isolation & purification , Influenza B virus/isolation & purification , Male , Middle Aged , Prevalence , Respiratory Syncytial Virus, Human/isolation & purification , SARS-CoV-2 , Seasons , Sex Factors , Young Adult
7.
Eur J Clin Microbiol Infect Dis ; 40(8): 1743-1748, 2021 Aug.
Article in English | MEDLINE | ID: covidwho-1323942

ABSTRACT

We evaluated a novel transcription-reverse transcription concerted reaction (TRC) assay that can detect influenza A and B within 15 min using nasopharyngeal swab and gargle samples obtained from patients with influenza-like illness, between January and March 2018 and between January and March 2019. Based on the combined RT-PCR and sequencing results, in the nasal swabs, the sensitivity and specificity of TRC for detecting influenza were calculated as 1.000 and 1.000, respectively. In the gargle samples, the sensitivity and specificity of TRC were 0.946 and 1.000, respectively. The TRC assay showed comparable performance to RT-PCR in the detection of influenza viruses.


Subject(s)
Influenza A virus/isolation & purification , Influenza B virus/isolation & purification , Influenza, Human/diagnosis , Influenza, Human/virology , Nasopharynx/virology , Adult , Aged , Diagnostic Tests, Routine , Female , Humans , Male , Middle Aged , Prospective Studies , Sensitivity and Specificity
8.
Rev. bras. ter. intensiva ; 33(2): 320-324, abr.-jun. 2021. tab, graf
Article in English, Portuguese | WHO COVID, LILACS (Americas) | ID: covidwho-1299683

ABSTRACT

RESUMO Apresentação de um caso de infecção por Influenza B e doença de Kawasaki em adolescente ocorrido durante a pandemia da COVID-19. Adolescente asmática evoluiu com febre e síndrome gripal por 7 dias e deu entrada com quadro de insuficiência respiratória aguda, necessitando de intubação orotraqueal. Evoluiu também com instabilidade hemodinâmica respondedora ao uso de droga vasoativa. Foram introduzidas antibioticoterapia e medidas de suporte. Apresentou melhora hemodinâmica e respiratória progressiva, porém mantinha febre e alteração de provas inflamatórias. Durante internação, evoluiu com conjuntivite não purulenta bilateral, descamação de mão e pés, língua em framboesa e linfonodomegalia cervical, recebendo diagnóstico de doença de Kawasaki. Recebeu gamaglobulina e, por conta de quadro clínico refratário, foi administrado também corticoide, evoluindo afebril 24 horas após. Não apresentou alterações coronarianas. O único agente isolado foi Influenza B, mesmo realizando painel viral e investigação para COVID-19 com reação em cadeia da polimerase e sorologia. Durante internação, apresentou tromboembolismo pulmonar, e, em investigação de coagulopatias, foi diagnosticada com mutação em heterozigose de fator V de Leiden. Há uma potencial associação entre doença de Kawasaki e infecção por Influenza B ou outros vírus, como o coronavírus e, por isso, esses diagnósticos devem ser investigados nos pacientes pediátricos, incluindo adolescentes, com quadros febris prolongados.


ABSTRACT We report a case of Influenza B infection and Kawasaki disease in an adolescent, diagnosed during the COVID-19 pandemic. An asthmatic female adolescent presented with fever and flu-like symptoms for 7 days and was admitted with acute respiratory failure requiring mechanical ventilation. She progressed with hemodynamic instability responsive to vasoactive drugs. Antibiotic therapy and support measures were introduced, showing progressive hemodynamics and respiratory improvement, however with persistent fever and increased inflammatory markers. During the hospitalization, she developed bilateral non-purulent conjunctivitis, hand and feet desquamation, strawberry tongue, and cervical adenopathy, and was diagnosed with Kawasaki disease. She was prescribed intravenous immunoglobulin and, due to the refractory clinical conditions, corticosteroid therapy was added; 24 hours later, the patient was afebrile. No coronary changes were found. A full viral panel including COVID-19 C-reactive protein and serology could only isolate the Influenza B virus. During the hospitalization, she was diagnosed with pulmonary thromboembolism; coagulopathies were investigated, and she was diagnosed with heterozygous factor V Leiden mutation. There is a potential association between Kawasaki disease and infection with Influenza B or with other viruses such as coronavirus. Therefore, this association should be considered in pediatric patients, adolescents included, with prolonged febrile conditions.


Subject(s)
Humans , Female , Adolescent , Respiratory Insufficiency/diagnosis , Influenza, Human/diagnosis , COVID-19 , Mucocutaneous Lymph Node Syndrome/diagnosis , Influenza B virus/isolation & purification , Respiration, Artificial , Respiratory Insufficiency/etiology , Influenza, Human/therapy , Hospitalization , Mucocutaneous Lymph Node Syndrome/complications
9.
J Med Virol ; 93(7): 4392-4398, 2021 07.
Article in English | MEDLINE | ID: covidwho-1263103

ABSTRACT

With the arrival of coronavirus disease 2019 (COVID-19) in Brazil in February 2020, several preventive measures were taken by the population aiming to avoid severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection including the use of masks, social distancing, and frequent hand washing then, these measures may have contributed to preventing infection also by other respiratory viruses. Our goal was to determine the frequencies of Influenza A and B viruses (FLUAV/FLUBV), human mastadenovirus C (HAdV-C), Enterovirus 68 (EV-68), and rhinovirus (RV) besides SARS-CoV-2 among hospitalized patients suspect of COVID-19 with cases of acute respiratory disease syndrome (ARDS) in the period of March to December 2020 and to detect possible coinfections among them. Nucleic acid detection was performed using reverse-transcription quantitative polymerase chain reaction (RT-qPCR) in respiratory samples using naso-oropharyngeal swabs and bronchoalveolar lavage. A total of 418 samples of the 987 analyzed (42.3%) were positive for SARS-CoV-2, 16 (1.62%) samples were positive for FLUAV, no sample was positive for FLUBV or EV-68, 67 (6.78%) samples were positive for HAdV-C, 55 samples were positive for RV 1/2 (26.3%) and 37 for RV 2/2 (13.6%). Coinfections were also detected, including a triple coinfection with SARS-CoV-2, FLUAV, and HAdV-C. In the present work, a very low frequency of FLUV was reported among hospitalized patients with ARDS compared to the past years, probably due to preventive measures taken to avoid COVID-19 and the high influenza vaccination coverage in the region in which this study was performed.


Subject(s)
Adenoviridae Infections/epidemiology , COVID-19/epidemiology , Common Cold/epidemiology , Enterovirus Infections/epidemiology , Influenza, Human/epidemiology , Physical Distancing , Adenoviridae Infections/prevention & control , Adolescent , Adult , Aged , Aged, 80 and over , Brazil/epidemiology , COVID-19/prevention & control , Child , Child, Preschool , Coinfection/epidemiology , Coinfection/virology , Common Cold/prevention & control , Enterovirus D, Human/genetics , Enterovirus D, Human/isolation & purification , Enterovirus Infections/prevention & control , Female , Humans , Infant , Influenza A virus/genetics , Influenza A virus/isolation & purification , Influenza B virus/genetics , Influenza B virus/isolation & purification , Influenza, Human/prevention & control , Male , Masks , Mastadenovirus/genetics , Mastadenovirus/isolation & purification , Middle Aged , Nucleic Acid Amplification Techniques/methods , Reverse Transcriptase Polymerase Chain Reaction/methods , Rhinovirus/genetics , Rhinovirus/isolation & purification , SARS-CoV-2/genetics , SARS-CoV-2/isolation & purification , Young Adult
10.
Int J Infect Dis ; 105: 763-768, 2021 Apr.
Article in English | MEDLINE | ID: covidwho-1201502

ABSTRACT

OBJECTIVE: We aimed to evaluate the clinical and epidemiological behavior of influenza type A versus type B and analyze if there was any correlation or differences between the characteristics of both groups. METHODS: An observational, retrospective, descriptive, and population-based study based of children who were hospitalized at the only national pediatric hospital of Costa Rica from January 1, 2010 to December 31, 2018 and had a confirmed influenza virus infection. RESULTS: 336 patients were analyzed. Mean age was 35,6 ± 36,7 months (3,0 ± 3,1 years). The only significant variables at 25% in relation to influenza type A or B virus were: sex, month of diagnosis, fever, vomiting, cough, use of antibiotics and admission to the PICU. The hospitalization rate at our hospital increased between the months of October to December, with a higher percentage of cases in November and December, which reveals that the "real peak" in our population begins between 3 to 4 months after the end of the vaccination campaign. Patients with influenza A virus had a 2.5 times greater risk of being admitted to the PICU. Mortality rate was 0.6% and 0% among influenza A and B children, respectively. CONCLUSIONS: Variables in which a causality was found with type A or B virus were: admission to the PICU, month of diagnosis, and cough. However, influenza B clinical behavior continues to be unpredictable.


Subject(s)
Influenza A virus/isolation & purification , Influenza B virus/isolation & purification , Influenza, Human/epidemiology , Child , Child, Preschool , Costa Rica/epidemiology , Female , Hospitalization/statistics & numerical data , Hospitals, Pediatric/statistics & numerical data , Humans , Infant , Infant, Newborn , Influenza Vaccines/therapeutic use , Influenza, Human/mortality , Influenza, Human/prevention & control , Influenza, Human/virology , Intensive Care Units, Pediatric/statistics & numerical data , Male , Retrospective Studies
11.
J Glob Health ; 11: 05007, 2021 Mar 01.
Article in English | MEDLINE | ID: covidwho-1168061

ABSTRACT

BACKGROUND: Respiratory syncytial virus (RSV) and influenza are prevalent seasonal community viruses. Although not completely understood, SARS-CoV-2 may have the same means of transmission. Preventive social measures aimed at preventing SARS-CoV-2 spread could impact transmission of other respiratory viruses as well. The aim of this study is to report the detection of RSV and influenza during the period of social distancing due to COVID-19 pandemic in a heavily affected community. METHODS: Prospective study with pediatric and adult populations seeking care for COVID-19-like symptoms during the fall and winter of 2020 at two hospitals in Southern Brazil. RT-PCR tests for SARS-CoV-2, influenza A (Flu A), influenza B (Flu B) and respiratory syncytial virus (RSV) was performed for all participants. RESULTS: 1435 suspected COVID-19 participants (1137 adults, and 298 children). were included between May and August. Median age was 37.7 years (IQR = 29.6-47.7), and 4.92 years (IQR = 1.96-9.53), for the adult and child cohorts, respectively. SARS-CoV-2 was positive in 469 (32.7%) while influenza and RSV were not detected at all. CONCLUSIONS: Measures to reduce SARS-CoV-2 transmission likely exerted a huge impact in the spread of alternate respiratory pathogens. These findings contribute to the knowledge about the dynamics of virus spread. Further, it may be considered for guiding therapeutic choices for these other viruses.


Subject(s)
COVID-19/prevention & control , Influenza A virus/isolation & purification , Influenza B virus/isolation & purification , Influenza, Human/diagnosis , Respiratory Syncytial Virus Infections/diagnosis , Respiratory Syncytial Viruses/isolation & purification , Adolescent , Adult , Aged , Aged, 80 and over , Brazil/epidemiology , COVID-19/diagnosis , COVID-19/epidemiology , Child , Child, Preschool , Female , Hospitals , Humans , Infant , Influenza, Human/transmission , Male , Middle Aged , Physical Distancing , Prospective Studies , Respiratory Syncytial Virus Infections/transmission , SARS-CoV-2/isolation & purification , Seasons , Young Adult
12.
Euro Surveill ; 25(44)2020 11.
Article in English | MEDLINE | ID: covidwho-1110208

ABSTRACT

BackgroundPoint-of-care tests (POCT) for influenza A and B viruses and respiratory syncytial virus (RSV) were implemented in emergency departments of all hospitals in the Capital Region of Denmark in 2018.AimTo establish whether POC testing for influenza viruses or RSV is based on a valid respiratory symptom indication, whether changes in patient management based on a positive result are safe and whether syndromic POC testing may benefit patients with influenza or RSV.MethodsSamples from 180 children (< 18 years) and 375 adults tested using POCT between February and July 2018 were retested for 26 respiratory pathogens. Diagnosis, indication for POC testing, hospitalisation time, antimicrobial therapy and readmission or death within one month of testing were obtained from patient records.ResultsA valid indication for POC testing was established in 168 (93.3%) of children and 334 (89.1%) of adults. A positive POCT result significantly reduced antibiotic prescription and median hospitalisation time by 44.3 hours for adults and 14.2 hours for children, and significantly increased antiviral treatment in adults. Risk of readmission or death was not significantly altered by a positive result. Testing for 26 respiratory pathogens established that risk of coinfection is lower with increasing age and that POCT for adults should be restricted to the influenza and RSV season.ConclusionPositive POCT resulted in changed patient management for both children and adults, and was deemed safe. POCT for additional pathogens may be beneficial in children below 5 years of age and outside the influenza and RSV season.


Subject(s)
Emergency Service, Hospital , Influenza A virus , Influenza B virus , Influenza, Human , Point-of-Care Testing , Respiratory Syncytial Virus Infections , Respiratory Syncytial Viruses , Adolescent , Adult , Aged , Child , Child, Preschool , Denmark/epidemiology , Female , Humans , Infant , Infant, Newborn , Influenza A virus/isolation & purification , Influenza B virus/isolation & purification , Influenza, Human/diagnosis , Influenza, Human/epidemiology , Influenza, Human/therapy , Male , Middle Aged , Respiratory Syncytial Virus Infections/diagnosis , Respiratory Syncytial Virus Infections/epidemiology , Respiratory Syncytial Virus Infections/therapy , Respiratory Syncytial Viruses/isolation & purification , Risk Assessment , Young Adult
13.
Int J Biol Sci ; 17(2): 539-548, 2021.
Article in English | MEDLINE | ID: covidwho-1090199

ABSTRACT

Rationale: Coronavirus disease 2019 (COVID-19) has caused a global pandemic. A classifier combining chest X-ray (CXR) with clinical features may serve as a rapid screening approach. Methods: The study included 512 patients with COVID-19 and 106 with influenza A/B pneumonia. A deep neural network (DNN) was applied, and deep features derived from CXR and clinical findings formed fused features for diagnosis prediction. Results: The clinical features of COVID-19 and influenza showed different patterns. Patients with COVID-19 experienced less fever, more diarrhea, and more salient hypercoagulability. Classifiers constructed using the clinical features or CXR had an area under the receiver operating curve (AUC) of 0.909 and 0.919, respectively. The diagnostic efficacy of the classifier combining the clinical features and CXR was dramatically improved and the AUC was 0.952 with 91.5% sensitivity and 81.2% specificity. Moreover, combined classifier was functional in both severe and non-serve COVID-19, with an AUC of 0.971 with 96.9% sensitivity in non-severe cases, which was on par with the computed tomography (CT)-based classifier, but had relatively inferior efficacy in severe cases compared to CT. In extension, we performed a reader study involving three experienced pulmonary physicians, artificial intelligence (AI) system demonstrated superiority in turn-around time and diagnostic accuracy compared with experienced pulmonary physicians. Conclusions: The classifier constructed using clinical and CXR features is efficient, economical, and radiation safe for distinguishing COVID-19 from influenza A/B pneumonia, serving as an ideal rapid screening tool during the COVID-19 pandemic.


Subject(s)
COVID-19 Testing/methods , COVID-19/diagnostic imaging , Influenza, Human/diagnostic imaging , Pneumonia, Viral/diagnostic imaging , Radiography, Thoracic , Aged , COVID-19/epidemiology , COVID-19/physiopathology , COVID-19/virology , Deep Learning , Diagnosis, Differential , Humans , Influenza A virus/isolation & purification , Influenza B virus/isolation & purification , Influenza, Human/physiopathology , Influenza, Human/virology , Male , Middle Aged , Pandemics , Pneumonia , Pneumonia, Viral/physiopathology , Pneumonia, Viral/virology , ROC Curve , Retrospective Studies , SARS-CoV-2/isolation & purification , Sensitivity and Specificity
14.
J Med Microbiol ; 70(2)2021 Feb.
Article in English | MEDLINE | ID: covidwho-1010700

ABSTRACT

Introduction. Laboratories worldwide are facing high demand for molecular testing during the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, which might be further aggravated by the upcoming influenza season in the northern hemisphere.Gap Statement. Given that the symptoms of influenza are largely indistinguishable from those of coronavirus disease 2019 (COVID-19), both SARS-CoV-2 and the influenza viruses require concurrent testing by RT-PCR in patients presenting with symptoms of respiratory tract infection.Aim. We adapted and evaluated a laboratory-developed multiplex RT-PCR assay for simultaneous detection of SARS-CoV-2 (dual target), influenza A and influenza B (SC2/InflA/InflB-UCT) on a fully automated high-throughput system (cobas6800).Methodology. Analytical performance was assessed by serial dilution of quantified reference material and cell culture stocks in transport medium, including pretreatment for chemical inactivation. For clinical evaluation, residual portions of 164 predetermined patient samples containing SARS-CoV-2 (n=52), influenza A (n=43) or influenza B (n=19), as well as a set of negative samples, were subjected to the novel multiplex assay.Results. The assay demonstrated comparable analytical performance to currently available commercial tests, with limits of detection of 94.9 cp ml-1 for SARS-CoV-2, 14.6 cp ml-1 for influenza A and 422.3 cp ml-1 for influenza B. Clinical evaluation showed excellent agreement with the comparator assays (sensitivity of 98.1, 97.7 and 100 % for Sars-CoV-2 and influenza A and B, respectively).Conclusion. The SC2/InflA/InflB-UCT allows for efficient high-throughput testing for all three pathogens and thus provides streamlined diagnostics while conserving resources during the influenza season.


Subject(s)
COVID-19 Testing/methods , COVID-19/diagnosis , Influenza A virus/genetics , Influenza B virus/genetics , Influenza, Human/diagnosis , SARS-CoV-2/genetics , High-Throughput Screening Assays/methods , Humans , Influenza A virus/isolation & purification , Influenza B virus/isolation & purification , Influenza, Human/virology , Limit of Detection , Molecular Diagnostic Techniques/methods , Multiplex Polymerase Chain Reaction , Reverse Transcriptase Polymerase Chain Reaction , SARS-CoV-2/isolation & purification , Sensitivity and Specificity
15.
Int J Infect Dis ; 103: 517-524, 2021 Feb.
Article in English | MEDLINE | ID: covidwho-974116

ABSTRACT

OBJECTIVE: To develop a novel quadruplex real-time reverse transcription polymerase chain reaction (rRT-PCR) assay for the diagnosis of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection, differential diagnosis and detection of co-infections. METHODS: A one-step quadruplex rRT-PCR assay was developed for simultaneous detection and differentiation of SARS-CoV-2 ORF1ab and N genes, influenza A virus (hIAV) and influenza B virus (hIBV). RESULTS: The quadruplex rRT-PCR assay had good sensitivity and specificity. Correlation coefficients and amplification efficiencies of all singleplex and quadruplex rRT-PCR reactions were within acceptable ranges. The 95% lower limits of detection for plasmid standards and positive nucleic acid extracts of the quadruplex rRT-PCR assay were 57.38-95.11 copies/µL and 114.65-154.25 copies/µL, respectively. Excellent results were attained for inter- and intra-assay reproducibility. Among these clinical samples, only four samples showed results inconsistent with the singleplex rRT-PCR assays. CONCLUSIONS: To the authors' knowledge, this is the first study to report a quadruplex rRT-PCR assay for the detection of two SARS-CoV-2 genes, hIAV and hIBV with perfect clinical performance.


Subject(s)
COVID-19/diagnosis , Influenza A virus/isolation & purification , Influenza B virus/isolation & purification , Real-Time Polymerase Chain Reaction/methods , Reverse Transcriptase Polymerase Chain Reaction/methods , SARS-CoV-2/isolation & purification , Humans , Sensitivity and Specificity
16.
Euro Surveill ; 25(46)2020 11.
Article in English | MEDLINE | ID: covidwho-937369

ABSTRACT

The COVID-19 pandemic negatively impacted the 2019/20 WHO European Region influenza surveillance. Compared with previous 4-year averages, antigenic and genetic characterisations decreased by 17% (3,140 vs 2,601) and 24% (4,474 vs 3,403). Of subtyped influenza A viruses, 56% (26,477/47,357) were A(H1)pdm09, 44% (20,880/47,357) A(H3). Of characterised B viruses, 98% (4,585/4,679) were B/Victoria. Considerable numbers of viruses antigenically differed from northern hemisphere vaccine components. In 2020/21, maintaining influenza virological surveillance, while supporting SARS-CoV-2 surveillance is crucial.


Subject(s)
Coronavirus Infections/epidemiology , Disease Notification/statistics & numerical data , Epidemiological Monitoring , Influenza A virus/isolation & purification , Influenza B virus/isolation & purification , Influenza, Human/epidemiology , Influenza, Human/virology , Antigens, Viral/genetics , Betacoronavirus , COVID-19 , Humans , Influenza A Virus, H1N1 Subtype/genetics , Influenza A Virus, H1N1 Subtype/isolation & purification , Influenza A Virus, H3N2 Subtype/genetics , Influenza A Virus, H3N2 Subtype/isolation & purification , Influenza A virus/genetics , Influenza B virus/genetics , Pandemics , Pneumonia, Viral , Population Surveillance , RNA, Viral/genetics , SARS-CoV-2 , Sequence Analysis, DNA
17.
J Infect ; 81(6): 966-972, 2020 12.
Article in English | MEDLINE | ID: covidwho-922066

ABSTRACT

OBJECTIVES: The effect of SARS-CoV-2 on existing respiratory viruses in circulation and the overall burden of viral respiratory disease remains uncertain. Traditionally, severe viral respiratory disease disproportionally affects those with underlying chronic lung diseases. This study aimed to assess the impact of SARS-CoV-2 on the prevalence and clinical characteristics of respiratory virus disease in hospitalised adults. METHODS: Data for this cohort study were from hospitalised adults who had multiplex PCR testing for respiratory viruses over several seasons in Hampshire, UK. Respiratory virus detection during the first epidemic peak of SARS-CoV-2 was compared to detection during the same time period across previous years. RESULTS: 856 patients had multiplex PCR for respiratory viruses between March and May over 5 years. Before 2020, a non-SARS-CoV-2 virus was detected in 54% patients (202/371) compared to 4.1% (20/485) in 2020 (p < 0.0001). SARS-CoV-2 was associated with asthma or COPD exacerbations in a smaller proportion of infected patients compared to other viruses (1.0% vs 37%, p < 0.0001). CONCLUSIONS: The emergence of SARS-CoV-2 was associated with substantial reductions in the circulation of seasonal respiratory viruses and large differences in the characteristics of viral-associated disease, including illness in a greater proportion of patients without underlying lung disease.


Subject(s)
COVID-19/epidemiology , Respiratory Tract Infections/epidemiology , Respiratory Tract Infections/virology , SARS-CoV-2/isolation & purification , Adult , Aged , Aged, 80 and over , COVID-19/diagnosis , Cohort Studies , Female , Hospitalization , Humans , Influenza A virus/isolation & purification , Influenza B virus/isolation & purification , Male , Middle Aged , Multiplex Polymerase Chain Reaction , Prospective Studies , Respiratory Syncytial Virus, Human/isolation & purification , Respiratory Tract Infections/diagnosis , Seasons , United Kingdom/epidemiology , Virus Diseases/epidemiology
18.
Exp Biol Med (Maywood) ; 246(4): 400-405, 2021 02.
Article in English | MEDLINE | ID: covidwho-913987

ABSTRACT

Due to the common symptoms of COVID-19, patients are similar to influenza-like illness. Therefore, the detection method would be crucial to discriminate between SARS-CoV-2 and influenza virus-infected patients. In this study, CRISPR-Cas12a-based detection was applied for detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), influenza A virus, and influenza B virus which would be a practical and attractive application for screening of patients with COVID-19 and influenza in areas with limited resources. The limit of detection for SARS-CoV-2, influenza A, and influenza B detection was 10, 103, and 103 copies/reaction, respectively. Moreover, the assays yielded no cross-reactivity against other respiratory viruses. The results revealed that the detection of influenza virus and SARS-CoV-2 by using RT-RPA and CRISPR-Cas12a technology reaches 96.23% sensitivity and 100% specificity for SARS-CoV-2 detection. The sensitivity for influenza virus A and B detections was 85.07% and 94.87%, respectively. In addition, the specificity for influenza virus A and B detections was approximately 96%. In conclusion, the RT-RPA with CRISPR-Cas12a assay was an effective method for the screening of influenza viruses and SARS-CoV-2 which could be applied to detect other infectious diseases in the future.


Subject(s)
COVID-19/diagnosis , Influenza A virus/genetics , Influenza B virus/genetics , Influenza, Human/diagnosis , Molecular Diagnostic Techniques , Nucleic Acid Amplification Techniques , SARS-CoV-2/genetics , CRISPR-Cas Systems , Clustered Regularly Interspaced Short Palindromic Repeats , Humans , Influenza A virus/isolation & purification , Influenza B virus/isolation & purification , Limit of Detection , RNA, Viral/analysis , RNA, Viral/genetics , SARS-CoV-2/isolation & purification
19.
Pediatr Infect Dis J ; 40(3): 191-198, 2021 03 01.
Article in English | MEDLINE | ID: covidwho-889612

ABSTRACT

BACKGROUND: Severe complications of influenza in children are uncommon but may result in admission to hospital or an intensive care unit (ICU) and death. METHODS: Active prospective surveillance using the Australian Paediatric Surveillance Unit with monthly reporting by pediatricians of national demographic and clinical data on children with <15 years of age hospitalized with severe complications of laboratory-confirmed influenza during ten influenza seasons 2008-2017. RESULTS: Of 722 children notified, 613 had laboratory-confirmed influenza and at least one severe complication. Most (60%) were <5 years of age; 10% were <6 months, hence ineligible for vaccination. Almost half of all cases were admitted to ICU and 30 died. Most children were previously healthy: 40.3% had at least one underlying medical condition. Sixty-five different severe complications were reported; pneumonia was the most common, occurring in over half of all cases. Influenza A accounted for 68.6% hospitalizations; however, influenza B was more often associated with acute renal failure (P = 0.014), rhabdomyolysis (P = 0.019), myocarditis (P = 0.015), pericarditis (P = 0.013), and cardiomyopathy (P = 0.035). Children who died were more likely to be older (5-14 years), have underlying medical conditions, be admitted to ICU, and have encephalitis, acute renal failure, or myocarditis. Only 36.1% of all children reported received antiviral medications, and 8.5% were known to be vaccinated for seasonal influenza. CONCLUSIONS: Severe influenza complications cause morbidity and mortality in children, which may increase if coinfection with COVID-19 occurs in the 2020 season and beyond. Increased vaccination rates, even in healthy children, early diagnosis and timely antiviral treatment are needed to reduce severe complications and death.


Subject(s)
COVID-19/epidemiology , Influenza A virus/isolation & purification , Influenza B virus/isolation & purification , Influenza, Human/epidemiology , SARS-CoV-2/isolation & purification , Vaccination , Adolescent , Antiviral Agents/therapeutic use , Australia/epidemiology , COVID-19/complications , COVID-19/mortality , COVID-19/virology , Child , Child, Preschool , Coinfection , Epidemiological Monitoring , Female , Hospitalization , Humans , Infant , Influenza, Human/complications , Influenza, Human/mortality , Influenza, Human/virology , Intensive Care Units , Male , Prospective Studies , Seasons
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