Self-Sampling of Oropharyngeal Swabs Among Healthcare Workers for Molecular Detection of Respiratory Viruses: A Valuable Approach for Epidemiological Studies and Surveillance Programs

This study aimed at assessing the validity of self-collected (self-sampled) oropharyngeal (OP) swabs among healthcare workers compared to those collected by trained sentinel general practitioners (GP-sampled) from individuals with influenza-like illness (ILI), to be implemented in epidemiological studies and/or surveillance programs of viral pathogens involved in community respiratory infections. In our study, OP swabs were collected from adults (>18 years) with ILI during the 2018–2019 influenza season. Two groups of samples were considered: group 1−131 self-sampled OP swabs collected by healthcare workers after being trained on the sampling procedure; group 2−131 GP-sampled OP swabs collected from outpatients by sentinel GPs operating within the Italian Influenza Surveillance Network. To assess swabbing quality, following RNA extraction, each sample was tested for the presence of the human ribonuclease P gene (RNP) by in-house real-time reverse transcriptase–polymerase chain reaction (RT-PCR). Samples with a cycle threshold (Ct) <35 were considered adequate for further virological analysis. Influenza viruses (IVs), respiratory syncytial virus (RSV), and rhinovirus (RV) genomes were detected by in-house real-time RT-PCR. All samples were positive to RNP detection with Ct <35. The mean Ct value was similar in the two groups (group 1 vs. group 2: 25.93 ± 2.22 vs. 25.46 ± 2.40; p = 0.10). IVs, RSV, and RV positivity rates were 26.7 vs. 52.7% (p < 0.01), 7.6 vs. 9.9% (p = 0.52), and 21.4 vs. 19.9% (p = 0.76), respectively. Self-sampled OP swabs resulted as valid as GP-sampled OP swabs for molecular detection of respiratory viruses. Self-swabbing can thus be a worthwhile strategy for sample collection to implement molecular surveillance of respiratory pathogens and carry out epidemiological studies, easily reaching a larger population size.

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Abstract 43: Real Time Polymerase Chain Reaction Assays For Detection Of Respiratory Viruses In Kawasaki Disease Patients

Circulation ◽

10.1161/circ.131.suppl_2.43 ◽

2015 ◽

Vol 131 (suppl_2) ◽

Author(s):

Young Mi Hong ◽

Seul Bee Lee ◽

Han Seul Choi ◽

Jung Hyun Kwon ◽

Hae Soon Kim ◽

...

Keyword(s):

Polymerase Chain Reaction ◽

Respiratory Symptoms ◽

Respiratory Viruses ◽

Rt Pcr ◽

Chain Reaction ◽

Coronary Artery Diameter ◽

Group 3 ◽

Polymerase Chain ◽

Group 2 ◽

Group 1

Purpose: Respiratory symptoms are frequently observed in children with Kawasaki disease (KD) during the acute phase. The association rate of KD with antecedent respiratory illness has been reported to range from 56 to 83%. Clinical and epidemiologic features of KD support an infectious cause, but the etiology remains unknown. We investigated the association of respiratory viruses in children with KD using multiplex reverse transcriptase-polymerase chain reaction (RT-PCR). Methods: 138 KD patients were enrolled from January 2010 to June 2013. Two study groups (Group 1; n=94, KD without respiratory symptoms, Group 2; n=44, KD with respiratory symptoms) were compared with a control group (Group 3; n=5, febrile patients with respiratory symptoms). Laboratory data were obtained from each patient including complete blood count (CBC), erythrocyte sedimentation rate (ESR), platelet count, alanine aminotransferase (ALT), aspartate aminotransferase (AST), serum total protein, albumin, C-reactive protein (CRP), NT-pro brain natriuretic peptide (BNP). Echocardiographic measurements were compared between the three groups. RT-PCR was performed using nasopharyngeal secretion to screen for the presence of 14 viruses (corona virus, parainfluenza virus 1, 2 and 3, influenza A and B, respiratory syncytial virus A and B, rhino virus A, B and C, metapneumo virus, adenovirus, and bocavirus) in groups 2 and 3. Results: The rate of KD with respiratory symptoms was 17.5%. The duration of fever was significantly longer and coronary artery diameter was significantly larger in group 2 than in group 1. Coronary artery diameter, CRP, platelet count, ALT, and NT-pro BNP were significantly higher and albumin lower in group 2 compared with group 3. Detection rate of adenovirus was 55.0% in group 2 and 28.6% in group 3. Conclusion: A positive RT-PCR for respiratory viruses may be helpful to elucidate the specific virus in KD patients with respiratory symptoms. NT-proBNP is a very important diagnostic tool in differentiating KD from other febrile viral respiratory infaction.

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Investigations, actions and learning from an outbreak of SARS-CoV-2 infection among healthcare workers in the United Kingdom

Journal of Infection Prevention ◽

10.1177/1757177420976798 ◽

2020 ◽

pp. 175717742097679

Author(s):

Kordo Saeed ◽

Emanuela Pelosi ◽

Nitin Mahobia ◽

Nicola White ◽

Christopher Labdon ◽

...

Keyword(s):

Real Time ◽

Healthcare Workers ◽

Healthcare Facility ◽

Rt Pcr ◽

Serum Samples ◽

The United Kingdom ◽

Key Issues ◽

Current Infection ◽

Polymerase Chain ◽

A Current

Background: We report an outbreak of SARS coronavirus-2 (SARS-CoV-2) infection among healthcare workers (HCW) in an NHS elective healthcare facility. Methodology: A narrative chronological account of events after declaring an outbreak of SARS-CoV-2 among HCWs. As part of the investigations, HCWs were offered testing during the outbreak. These were: (1) screening by real-time reverse transcriptase polymerase chain reaction (RT- PCR) to detect a current infection; and (2) serum samples to determine seroprevalence. Results: Over 180 HCWs were tested by real-time RT-PCR for SARS-CoV-2 infection. The rate of infection was 15.2% (23.7% for clinical or directly patient-facing HCWs vs. 4.8% in non-clinical non-patient-facing HCWs). Of the infected HCWs, 57% were asymptomatic. Seroprevalence (SARS-CoV-2 IgG) among HCWs was 13%. It was challenging to establish an exact source for the outbreak. The importance of education, training, social distancing and infection prevention practices were emphasised. Additionally, avoidance of unnecessary transfer of patients and minimising cross-site working for staff and early escalation were highlighted. Establishing mass and regular screening for HCWs are also crucial to enabling the best care for patients while maintaining the wellbeing of staff. Conclusion: To our knowledge, this is the first UK outbreak report among HCWs and we hope to have highlighted some key issues and learnings that can be considered by other NHS staff and HCWs globally when dealing with such a task in future.

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A New Multiplex Real-Time RT-PCR for Simultaneous Detection and Differentiation of Avian Bornaviruses

Viruses ◽

10.3390/v13071358 ◽

2021 ◽

Vol 13 (7) ◽

pp. 1358

Author(s):

Brigitte Sigrist ◽

Jessica Geers ◽

Sarah Albini ◽

Dennis Rubbenstroth ◽

Nina Wolfrum

Keyword(s):

Real Time ◽

Simultaneous Detection ◽

Epidemiological Studies ◽

Virus Species ◽

Rt Pcr ◽

P Gene ◽

Field Samples ◽

Causative Agents ◽

Species Specific ◽

Proventricular Dilatation Disease

Avian bornaviruses were first described in 2008 as the causative agents of proventricular dilatation disease (PDD) in parrots and their relatives (Psittaciformes). To date, 15 genetically highly diverse avian bornaviruses covering at least five viral species have been discovered in different bird orders. Currently, the primary diagnostic tool is the detection of viral RNA by conventional or real-time RT-PCR (rRT-PCR). One of the drawbacks of this is the usage of either specific assays, allowing the detection of one particular virus, or of assays with a broad detection spectrum, which, however, do not allow for the simultaneous specification of the detected virus. To facilitate the simultaneous detection and specification of avian bornaviruses, a multiplex real-time RT-PCR assay was developed. Whole-genome sequences of various bornaviruses were aligned. Primers were designed to recognize conserved regions within the overlapping X/P gene and probes were selected to detect virus species-specific regions within the target region. The optimization of the assay resulted in the sensitive and specific detection of bornaviruses of Psittaciformes, Passeriformes, and aquatic birds. Finally, the new rRT-PCR was successfully employed to detect avian bornaviruses in field samples from various avian species. This assay will serve as powerful tool in epidemiological studies and will improve avian bornavirus detection.

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Evaluation of Influenza Patients Admitted in 2019–2020 Flu Season

Journal of Pediatric Infectious Diseases ◽

10.1055/s-0041-1741003 ◽

2022 ◽

Author(s):

Bahar Öztelcan Gündüz ◽

Erman Ataş ◽

Bülent Ünay ◽

Halit Halil

Keyword(s):

Physical Examination ◽

Chronic Diseases ◽

Influenza A ◽

Influenza Infection ◽

Febrile Seizures ◽

Influenza Viruses ◽

Influenza B ◽

Close Monitoring ◽

Group 2 ◽

Group 1

Abstract Objective Influenza viruses are among the most common respiratory pathogens for all age groups, and may cause seasonal outbreaks. The aim of our study was to describe the clinical characteristics of influenza cases in the 2019–2020 flu season and to study the risk factors for hospital admission and complications. Methods This was a retrospective study in 251 children (group 1: nonhospitalized; group 2: hospitalized) with influenza in the 2019–2020 flu season. Data on demographic features, influenza type, complaints, complications, and hospitalization length were collected and recorded. Results Influenza A was detected in 199 (79.3%) patients, and influenza B was detected in 52 (20.7%); 43.4% of patients were girls and 56.6% were boys. The mean age of the patients was 3.91 ± 3.3 years (16 days to 18 years). A total of 52 (20.7%) patients were hospitalized. The age of the patients in group 2 was lower than that in group 1 (3.1 vs. 4.2 years, p = 0.03). Group 2 patients were more likely to have creatine kinase (CK) elevation, febrile seizures, and physical examination abnormalities. Group 2 patients were also more likely to have influenza A. Patients with febrile seizures, chronic diseases, abnormal physical examination findings, developed complications, and additional drug use apart from oseltamivir in the treatment were also more likely to require hospitalization. Conclusion Infants and children with chronic diseases, history of febrile seizures, complications, and the use of drugs other than antiviral drugs should be carefully evaluated in case they need hospitalization. Increasing vaccination rates, initiation of antiviral treatment for selected patients, and close monitoring of patients in risk groups can decrease morbidity and mortality. Myalgias are a common complaint in patients with acute influenza infection. Previous studies suggest CK measurement be part of the work-up for the hospitalized patient with acute influenza infection.

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Real-time RT-PCR assay to differentiate clades of H5N1 avian influenza viruses circulating in Vietnam

Journal of Virological Methods ◽

10.1016/j.jviromet.2013.06.023 ◽

2013 ◽

Vol 193 (2) ◽

pp. 452-458 ◽

Cited By ~ 8

Author(s):

Z. Kis ◽

J. Jones ◽

A. Creanga ◽

K. Ferdinand ◽

K. Inui ◽

...

Keyword(s):

Avian Influenza ◽

Real Time ◽

Influenza Viruses ◽

Rt Pcr ◽

Avian Influenza Viruses ◽

Pcr Assay ◽

H5n1 Avian Influenza

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Short-Time Estimation of Fractionation in Atrial Fibrillation with Coarse-Grained Correlation Dimension for Mapping the Atrial Substrate

Entropy ◽

10.3390/e22020232 ◽

2020 ◽

Vol 22 (2) ◽

pp. 232

Author(s):

Aikaterini Vraka ◽

Fernando Hornero ◽

Vicente Bertomeu-González ◽

Joaquín Osca ◽

Raúl Alcaraz ◽

...

Keyword(s):

Atrial Fibrillation ◽

Real Time ◽

Correlation Dimension ◽

Coarse Grained ◽

Long Term Results ◽

Operating Characteristics ◽

Type Iv ◽

Group 2 ◽

Short Time ◽

Group 1

Atrial fibrillation (AF) is currently the most common cardiac arrhythmia, with catheter ablation (CA) of the pulmonary veins (PV) being its first line therapy. Ablation of complex fractionated atrial electrograms (CFAEs) outside the PVs has demonstrated improved long-term results, but their identification requires a reliable electrogram (EGM) fractionation estimator. This study proposes a technique aimed to assist CA procedures under real-time settings. The method has been tested on three groups of recordings: Group 1 consisted of 24 highly representative EGMs, eight of each belonging to a different AF Type. Group 2 contained the entire dataset of 119 EGMs, whereas Group 3 contained 20 pseudo-real EGMs of the special Type IV AF. Coarse-grained correlation dimension (CGCD) was computed at epochs of 1 s duration, obtaining a classification accuracy of 100% in Group 1 and 84.0–85.7% in Group 2, using 10-fold cross-validation. The receiver operating characteristics (ROC) analysis for highly fractionated EGMs, showed 100% specificity and sensitivity in Group 1 and 87.5% specificity and 93.6% sensitivity in Group 2. In addition, 100% of the pseudo-real EGMs were correctly identified as Type IV AF. This method can consistently express the fractionation level of AF EGMs and provides better performance than previous works. Its ability to compute fractionation in short-time can agilely detect sudden changes of AF Types and could be used for mapping the atrial substrate, thus assisting CA procedures under real-time settings for atrial substrate modification.

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