Respiratory Specimen Collection Research Articles

Bronchoscopy-guided antimicrobial therapy for cystic fibrosis.

Bronchoscopy-guided antimicrobial therapy for cystic fibrosis.

More common RNAemia in the early stage of severe SARS-CoV-2 BF.7.14 infections in pediatric patients

The risk factors of severe infections in children during the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreak in Beijing remain elusive. SARS-CoV-2-positive children admitted to the intensive care unit (ICU) with collected plasma specimens were enrolled and screened for common pathogens using capillary electrophoresis-based multiplex PCR from December 12, 2022, to January 24, 2023. The SARS-CoV-2 sub-variants were identified using next-generation sequencing. Plasma was positive for two (positive; P), one (suspicious; S), or no (negative; N) SARS-CoV-2 genes were classified as plasmatic RNA-positive (RNAemia; P + S) or without RNAemia (N). Clinical and laboratory data of the enrolled cases were then collected and analyzed. The 34 enrolled children included 26 males and 24 younger than three years. All were negative for other respiratory pathogens. BF.7.14 (18/29) was the predominant subvariant. Viral loads in respiratory specimens, hours from symptom onset to the first respiratory specimen collection (time-variable), with comorbidities and BF.7.14 and BA.5.2 distributions were significantly different in P vs. N and RNAemia vs. without RNAemia group. Among most cases, the T lymphocyte ratios decreased, while the cytokine level and the B lymphocyte ratio increased. The time variables were 2.22 ± 2.05 and 4.00 ± 2.49 days in BF.7.14 and BA.5.2 infections, respectively. In conclusion, SARS-CoV-2 was more likely to cause severe infections among males aged ≤ 3 years old with comorbidities during the SARS-CoV-2 outbreak in Beijing, while RNAemia is more common in children at the early stage of severe BF.7.14 infections, and most had high cytokine levels and B-cell activation.

SG-APSIC1011: Factors associated with improved knowledge of COVID-19 prevention and control following a training of healthcare workers in Vietnam

Objectives: SARS-CoV-2 is a novel and highly infectious virus. An effective response requires rapid training of healthcare workers (HCWs). We measured the change in knowledge related to COVID-19 and associated factors before and after training of HCWs in Vietnam. Methods: A quasi-experimental design was used to evaluate HCW knowledge related to prevention and control of SARS-CoV-2 before and after attending a 2-day training-of-trainers course. Between June and September 2020, 963 HCWs from 194 hospitals in 21 provinces received the training. HCW knowledge was assessed using a 20-item questionnaire consisting of multiple-choice questions at the beginning and closing of the training course. A participant received 1 point for each correct answer. He or she was considered to have improved knowledge the posttest score was higher than the pretest score with a score ≥15 on the posttest. We applied the McNemar test and logistic regression model to test the level of association between demographic factors and change in knowledge of COVID-19. Results: Overall, 100% of HCWs completed both the pretest and posttest. At baseline, only 14.7% scored ≥15. Following the training, 78.4% scored ≥15 and 64.3% had improved knowledge according to the predetermined definition. Questions related to the order of PPE donning and doffing and respiratory specimen collection procedures were identified as having the greatest improvement (44.6% and 60.7%, respectively). Being female (OR, 1.5; 95% CI, 1.1–2.0), having a postgraduate degree (OR, 2.5; 95% CI, 1.4–4.4), working in a nonmanager position (OR, 1.5; 95% CI, 1.1–2.1), previous contact with a COVID-19 patient (OR, 1.5; 95% CI, 1.1–2.0), and working in northern Vietnam (OR, 2.0; 95% CI, 1.4–2.6), were associated with greater knowledge improvement. Conclusions: Most HCWs demonstrated improved knowledge of COVID-19 prevention and control after attending the training. Particular groups may benefit from additional training: those who are male, leaders and managers, those who hold an undergraduate degree, and those who work in the southern provinces.

IMPACT OF SOCIAL DISTANCING DURING THE SARS-COV-2 PANDEMIC ON THE ASSOCIATION BETWEEN VIRAL RESPIRATORY ILLNESS AND CARDIOVASCULAR-RELATED EVENTS

IMPACT OF SOCIAL DISTANCING DURING THE SARS-COV-2 PANDEMIC ON THE ASSOCIATION BETWEEN VIRAL RESPIRATORY ILLNESS AND CARDIOVASCULAR-RELATED EVENTS

Metagenomic prediction of antimicrobial resistance in critically ill patients with lower respiratory tract infections

BackgroundAntimicrobial resistance (AMR) is rising at an alarming rate and complicating the management of infectious diseases including lower respiratory tract infections (LRTI). Metagenomic next-generation sequencing (mNGS) is a recently established method for culture-independent LRTI diagnosis, but its utility for predicting AMR has remained unclear. We aimed to assess the performance of mNGS for AMR prediction in bacterial LRTI and demonstrate proof of concept for epidemiological AMR surveillance and rapid AMR gene detection using Cas9 enrichment and nanopore sequencing.MethodsWe studied 88 patients with acute respiratory failure between 07/2013 and 9/2018, enrolled through a previous observational study of LRTI. Inclusion criteria were age ≥ 18, need for mechanical ventilation, and respiratory specimen collection within 72 h of intubation. Exclusion criteria were decline of study participation, unclear LRTI status, or no matched RNA and DNA mNGS data from a respiratory specimen. Patients with LRTI were identified by clinical adjudication. mNGS was performed on lower respiratory tract specimens. The primary outcome was mNGS performance for predicting phenotypic antimicrobial susceptibility and was assessed in patients with LRTI from culture-confirmed bacterial pathogens with clinical antimicrobial susceptibility testing (n = 27 patients, n = 32 pathogens). Secondary outcomes included the association between hospital exposure and AMR gene burden in the respiratory microbiome (n = 88 patients), and AMR gene detection using Cas9 targeted enrichment and nanopore sequencing (n = 10 patients).ResultsCompared to clinical antimicrobial susceptibility testing, the performance of respiratory mNGS for predicting AMR varied by pathogen, antimicrobial, and nucleic acid type sequenced. For gram-positive bacteria, a combination of RNA + DNA mNGS achieved a sensitivity of 70% (95% confidence interval (CI) 47–87%) and specificity of 95% (CI 85–99%). For gram-negative bacteria, sensitivity was 100% (CI 87–100%) and specificity 64% (CI 48–78%). Patients with hospital-onset LRTI had a greater AMR gene burden in their respiratory microbiome versus those with community-onset LRTI (p = 0.00030), or those without LRTI (p = 0.0024). We found that Cas9 targeted sequencing could enrich for low abundance AMR genes by > 2500-fold and enabled their rapid detection using a nanopore platform.ConclusionsmNGS has utility for the detection and surveillance of resistant bacterial LRTI pathogens.

Evaluation of selected aspects of influenza surveillance system and describing influenza surveillance data collected during 2014-2018 of district general hospital Matara, Sri Lanka

Background: Influenza is one of the diseases which have the pandemic potential. Influenza surveillance as part of the pandemic preparedness activities was initiated in Sri Lanka in 2005. This study would help in evaluating, strengthening influenza surveillance system of DGH Matara, and taking targeted preventive measures and contribute to more efficient resource allocation in the future.Methods: This was a cross sectional analytical study.Results: Case definitions for ILI and SARI used were consistent with the epidemiology unit Sri Lanka prescribed definitions. Though the site collected data on cases daily and sampled weekly, sampling technique was not random. Respiratory specimen collection, packaging, storage and transport were consistent with the guidelines of epidemiology Unit, Sri Lanka. Refrigerator temperature monitoring, analyzing surveillance data on site as well as supervisory visits made by central level were not satisfactory. No clear pattern of ILI and SARI was observed among different age groups during 2014-2018. Influenza viral activity was detected except for “untyped” from respiratory samples sent by DGH, Matara during 2014-2018. Pandemic preparedness by the site was not at optimal level.Conclusions: Representativeness of data obtained from respiratory specimen collection and data analyzing were not satisfactory. Temperature monitoring inside storage refrigerators of the site was not possible as no written records were available. Supervision from the central level was not satisfactory.

375. High Laboratory-confirmed SARS-CoV-2 Attack Rate in Lima Health Care Personnel During August 2020-March 2021 Suggests Role for Improved Infection Control

BackgroundPeru has one of the highest per capita SARS-CoV-2 death rates in Latin America. Healthcare workers (HCW) are a critical workforce during the COVID-19 pandemic but are themselves often at increased risk of infection. We evaluated SARS-CoV-2 attack rate and risk factors among frontline HCWs.MethodsWe performed a prospective cohort study of HCW serving two acute care hospitals in Lima, Peru from Aug 2020 to Mar 2021. Participants had baseline SARS-CoV-2 serology using the CDC ELISA, active symptom monitoring, and weekly respiratory specimen collection with COVID-19 exposure/risk assessment for 16-weeks regardless of symptoms. Respiratory specimens were tested by real-time reverse transcriptase PCR (rRT-PCR).ResultsOf 783 eligible, 667 (85%) HCW were enrolled (33% nurse assistants, 29% non-clinical staff, 26% nurses, 7% physicians, and 6% other). At baseline and prior to COVID-19 vaccine introduction, 214 (32.1%; 214/667) were reactive for SARS-CoV-2 antibodies. In total, 72 (10.8%; 72/667) HCWs were found to be rRT-PCR positive during weekly follow-up. Of the rRT-PCR positive HCWs, 37.5% (27/72) did not report symptoms within 1-week of specimen collection. During follow up, HCW without detectable SARS-CoV-2 antibodies at baseline were significantly more likely to be rRT-PCR positive (65/453, 14.3%) compared to those with SARS-CoV-2 antibodies at baseline (4/214, 1.9%) (p-value: < 0.001). Three HCW were both serologically reactive and rRT-PCR positive at baseline. Looking only at HCW without SARS-CoV-2 antibodies, nurse assistants (rRT-PCR positive: 18.6%; 27/141) and non-clinical healthcare workers (16.5%; 21/127) were at greater risk of infection compared to nurses (8.5%; 10/118), physicians (7.9%; 3/38), and other staff (10.3%; 4/29) (RR 1.95;95%CI 1.2,3.3; p-value: 0.01).ConclusionBaseline SARS-CoV-2 prevalence and 16-week cumulative incidence were substantial in this pre-vaccination Peruvian HCW cohort. Almost 40% of new infections occurred in HCW without complaint of symptoms illustrating a limitation of symptom-based HCW screening for COVID-19 prevention. Nurse assistants and non-clinical healthcare workers were at greater risk of infection indicating a role for focused infection prevention and risk reduction strategies for some groups of HCW.Disclosures Fernanda C. Lessa, MD, MPH, Nothing to disclose

Valid and Reliable Assessment of Upper Respiratory Tract Specimen Collection Skills during the COVID-19 Pandemic.

Proper specimen collection is the most important step to ensure accurate testing for the coronavirus disease 2019 (COVID-19) and other infectious diseases. Assessment of healthcare workers’ upper respiratory tract specimen collection skills is needed to ensure samples of high-quality clinical specimens for COVID-19 testing. This study explored the validity evidence for a theoretical MCQ-test and checklists developed for nasopharyngeal (NPS) and oropharyngeal (OPS) specimen collection skills assessment. We found good inter-item reliability (Cronbach’s alpha = 0.76) for the items of the MCQ-test and high inter-rater reliability using the checklist for the assessment of OPS and NPS skills on 0.86 and 0.87, respectively. The MCQ scores were significantly different between experts (mean 98%) and novices (mean 66%), p < 0.001, and a pass/fail score of 91% was established. We found a significant discrimination between checklist scores of experts (mean 95% score for OPS and 89% for NPS) and novices (mean 50% score for OPS and 36% for NPS), p < 0.001, and a pass/fail score was established of 76% for OPS and 61% for NPS. Further, the results also demonstrated that a group of non-healthcare educated workers can perform upper respiratory tract specimen collection comparably to experts after a short and focused simulation-based training session. This study, therefore, provides validity evidence for the use of a theoretical and practical test for upper respiratory specimens’ collection skills that can be used for competency-based training of the workers in the COVID-19 test centers.

SARS-CoV-2 PCR and antibody testing for an entire rural community: methods and feasibility of high-throughput testing procedures

BackgroundEarly in the pandemic, inadequate SARS-CoV-2 testing limited understanding of transmission. Chief among barriers to large-scale testing was unknown feasibility, particularly in non-urban areas. Our objective was to report methods of high-volume, comprehensive SARS-CoV-2 testing, offering one model to augment disease surveillance in a rural community.MethodsA community-university partnership created an operational site used to test most residents of Bolinas, California regardless of symptoms in 4 days (April 20th – April 23rd, 2020). Prior to testing, key preparatory elements included community mobilization, pre-registration, volunteer recruitment, and data management. On day of testing, participants were directed to a testing lane after site entry. An administrator viewed the lane-specific queue and pre-prepared test kits, linked to participants’ records. Medical personnel performed sample collection, which included finger prick with blood collection to run laboratory-based antibody testing and respiratory specimen collection for polymerase chain reaction (PCR).ResultsUsing this 4-lane model, 1,840 participants were tested in 4 days. A median of 57 participants (IQR 47–67) were tested hourly. The fewest participants were tested on day 1 (n = 338 participants), an intentionally lower volume day, increasing to n = 571 participants on day 4. The number of testing teams was also increased to two per lane to allow simultaneous testing of multiple participants on days 2–4. Consistent staffing on all days helped optimize proficiency, and strong community partnership was essential from planning through execution.ConclusionsHigh-volume ascertainment of SARS-CoV-2 prevalence by PCR and antibody testing was feasible when conducted in a community-led, drive-through model in a non-urban area.

Rapid and Safe Detection of SARS-CoV-2 and Influenza Virus RNA Using Onsite Quantitative PCR Diagnostic Testing From Clinical Specimens Collected in Molecular Transport Medium.

BACKGROUNDThe ability to rapidly detect SARS-CoV-2 and influenza virus infection is vital for patient care due to overlap in clinical symptoms. Roche’s cobas® Liat® SARS-CoV-2 & Influenza A/B Nucleic Acid Test used on the cobas® Liat® was granted approval under FDA’s Emergency Use Authorization (EUA) for nasopharyngeal (NP) and nasal swabs collected in viral/universal transport medium (VTM/UTM). However, there is a critical need for media that inactivates the virus, especially when specimens are collected in decentralized settings. This study aimed to investigate the use of PrimeStore Molecular Transport Medium® (PS-MTM®), designed to inactivate/kill and stabilize RNA/DNA for ambient transport and pre-processing of collected samples.METHODSA limit of detection (LOD) using serially diluted SARS-CoV-2 RNA in PS-MTM® and routine UTM was established using standard qPCR. Additionally, a clinical panel of NP and oral swabs collected in PS-MTM® collected during the 2020 coronavirus disease 2019 (COVID-19) pandemic were evaluated on the cobas® Liat® and compared to ‘gold standard’ qPCR on an ABI-7500 instrument.RESULTSSARS-CoV-2 RNA LOD using standard qPCR was equivalent on the cobas® Liat® instrument. cobas® Liat® detection from oral/NP swabs in PS-MTM® media exhibited equivalent positive percent agreement (100%) and negative percent agreement (96.4%).CONCLUSIONPS-MTM® and the Roche cobas® Liat® are compatible and complimentary devices for respiratory specimen collection and rapid disease detection, respectively. PS-MTM® is equivalent to standard VTM/UTM with the added benefit of safe, non-infectious sample processing for near-patient testing.

Clinical evaluation of rapid point-of-care antigen tests for diagnosis of SARS-CoV-2 infection

The RT-qPCR in respiratory specimens is the gold standard for diagnosing acute COVID-19 infections. However, this test takes considerable time before test results become available, thereby delaying patients from being diagnosed, treated, and isolated immediately. Rapid antigen tests could overcome this problem. In the first study, clinical performances of five rapid antigen tests were compared to RT-qPCR in upper respiratory specimens from 40 patients with positive and 40 with negative RTq-PCR results. In the second study, the rapid antigen test with one of the best test characteristics (Romed) was evaluated in a large prospective collection of upper respiratory specimens from 900 different COVID-19-suspected patients (300 emergency room patients, 300 nursing home patients, and 300 health care workers). Test specificities ranged from 87.5 to 100.0%, and test sensitivities from 55.0 to 80.0%. The clinical specificity of the Romed test was 99.8% (95% CI 98.9–100). Overall clinical sensitivity in the study population was 73.3% (95% CI 67.9–78.2), whereas sensitivity in the different patient groups varied from 65.3 to 86.7%. Sensitivity was 83.0 to 86.7% in patients with short duration of symptoms. In a population with a COVID-19 prevalence of 1%, the negative predictive value in all patients was 99.7%. There is a large variability in diagnostic performance between rapid antigen tests. The Romed rapid antigen test showed a good clinical performance in patients with high viral loads (RT-qPCR cycle threshold ≤30), which makes this antigen test suitable for rapid identification of COVID-19-infected health care workers and patients.

Detection of bacterial pathogens using home oropharyngeal swab collection in children with cystic fibrosis.

Collection of respiratory cultures for airway microbiology surveillance is an essential component of routine clinical care in cystic fibrosis (CF). The COVID-19 global pandemic has necessitated increased use of telehealth, but one limitation of telehealth is the inability to collect respiratory specimens. We initiated a protocol for at-home collection of oropharyngeal (OP) swabs from children with CF. Home respiratory specimen collection was offered during telehealth encounters. Home OP swab kits were sent to participating families via mail with instructions for collection and return. Specimens were returned by overnight shipping or dropped off at a hospital lab for processing and culture. We evaluated demographic data and compared culture results from the home-collected specimen to the most recent specimen collected in clinic. We also tracked the frequency of newly identified Pseudomonas aeruginosa. Home OP swab kits were sent to families of 33 children with CF (range 1.5-19 years). OP swab kits were successfully returned from 19 children (range 1.5-19 years). One or more CF pathogens grew from 79% of the specimens. For four individuals, the home collected specimen demonstrated the new growth of P. aeruginosa. Home collection of OP swabs for bacterial culture is feasible in children with CF across a range of ages. Most home-collected specimens demonstrated growth of one or more CF pathogens and results were similar to recent in-clinic specimens, suggesting acceptable sample collection technique. Anti-pseudomonal therapy was initiated for four children based on the growth of P. aeruginosa from the home respiratory specimen.

STROKE FOLLOWING POSITIVE BIOMARKER FOR VIRAL RESPIRATORY ILLNESS

SESSION TITLE: Chest Infections Posters SESSION TYPE: Original Investigation Posters PRESENTED ON: October 18-21, 2020 PURPOSE: Several studies have established an association between acute viral respiratory infections and myocardial infarction. Comparatively, other vascular events, namely strokes, and their association with viral infections have been less established in literature. Additionally, studies that have been done to evaluate the association between strokes and viral respiratory infections have been limited by self-reported data or study designs susceptible to bias. Our aim is to determine whether patients with common acute viral respiratory infections have increased risk for stroke and to determine the risk interval between the infection and stroke. METHODS: A retrospective chart review was conducted on patients admitted to multiple affiliated Baylor Scott & White central Texas hospitals from February 1, 2014 through April 19, 2019. We investigated stroke risk associated with respiratory virus panel- PCR (RVP) positivity using a self-controlled case series. RVP positivity was reviewed to determine the presence or absence of increased risk interval. Risk intervals were identified as 7 days or 14 days after respiratory specimen collection and associated control intervals were one year before and one year after the risk intervals. RESULTS: Of the 241 patients, both groups were not different in age, gender, race or Charlson comorbidity index. 316 hospitalizations were identified for ischemic, hemorrhagic, or subarachnoid events that occurred 1 year before and 1 year after a RVP positivity. 23% of the strokes were hemorrhagic, 83% were ischemic. 31% of positive RVP were influenza, 32% were rhinovirus, 22% were human metapneumovirus, 12% were respiratory syncytial virus, and 9% were parainfluenza virus. Of the 319 hospitalizations, 26 occurred during the risk interval and 289 occurred during the control interval. The risk ratio of hospitalization for ischemic or hemorrhagic stroke during the risk interval (up to 1 week after positive RVP) compared to control interval is 2.26 (95% CI: 1.96 – 2.61). The risk ratio observed in the second week after the RVP positivity was not different from the control group. Using TOAST criteria to sub classify ischemic strokes, most strokes were cardioembolic or due to large artery atherosclerosis. CONCLUSIONS: In this multi-hospital study from central Texas, there is a significant association between respiratory viral infections (primarily rhinovirus and influenza) and stroke. CLINICAL IMPLICATIONS: Public health measures like social distancing, hand hygiene, and vaccinations that prevent the spread of viral respiratory illness could decrease vascular events like stroke. DISCLOSURES: no disclosure on file for Joey Carlin; No relevant relationships by Shekhar Ghamande, source=Web Response No relevant relationships by Meghan McGraw, source=Web Response No relevant relationships by Abirami Subramanian, source=Web Response No relevant relationships by Heath White, source=Web Response No relevant relationships by Kiumars Zolfaghari, source=Web Response

American Association for Bronchology and Interventional Pulmonology (AABIP) Statement on the Use of Bronchoscopy and Respiratory Specimen Collection in Patients With Suspected or Confirmed COVID-19 Infection.

American Association for Bronchology and Interventional Pulmonology (AABIP) Statement on the Use of Bronchoscopy and Respiratory Specimen Collection in Patients With Suspected or Confirmed COVID-19 Infection.

Development of positive/negative pressure booth generating airflow for protection of medical staff from contagious respiratory pathogens.

BackgroundThe pandemic of COVID-19 caused confusion in medical settings because of increased patient load, and caused many infections among medical staff which occurred through exposure to bio-particles discharged from patients. The risk of exposure became maximum at the examination of patients, particularly in the collection of respiratory specimens. Effective interventions to reduce the risk are needed.MethodsA one-person booth consisting of curtain walls, frames, and fan-HEPA filter-unit (FFU) was designed. Using the airstream from/to FFU, it has dual functions as a positive/negative pressure machine to prevent pathogens in patient’s cough to reach the medical staff inside/outside the booth, respectively. The curtain walls and positioning of the patient and staff were aerodynamically optimized for the best control of the airstream.ResultsThe positive pressure booth is to isolate a staff inside to safely deal with a surge in the number of patients in situations like influenza pandemics. The negative pressure booth is to isolate a patient inside to protect a staff outside from dangerous contagious respiratory infectious diseases including COVID-19. A calculated airflow of the positive pressure machine efficiently pushed back bio-particles discharged from a person outside the booth. The bio-particles of a cough from a person inside the negative pressure booth was sucked into the FFU for filtration immediately after the discharge. The booth needed a short front curtain of a stair-cut shape, and a patient and a staff facing each other needed to be positioned at an angle 45° to the airstream for optimization of the airflow.ConclusionsThe booth named Barriflow® would prevent the bioparticles of a patient’s cough to reach the medical staff due to an aerodynamically designed airstream from the FFU and curtains surrounding it. It could be applied to cases of not only COVID-19 or influenza but also of other dangerous, contagious respiratory diseases.

Variations in Seasonal Influenza Vaccine Effectiveness due to Study Characteristics: A Systematic Review and Meta-analysis of Test-Negative Design Studies.

BackgroundStudy characteristics influence vaccine effectiveness (VE) estimation. We examined the influence of some of these on seasonal influenza VE estimates from test-negative design (TND) studies.MethodsWe systematically searched bibliographic databases and websites for full-text publications of TND studies on VE against laboratory-confirmed seasonal influenza in outpatients after the 2009 pandemic influenza. We followed the Cochrane Handbook for Systematic Reviews of Interventions guidelines. We examined influence of source of vaccination information, respiratory specimen swab time, and covariate adjustment on VE. We calculated pooled adjusted VE against H1N1 and H3N2 influenza subtypes, influenza B, and all influenza using an inverse-variance random-effects model.ResultsWe included 70 full-text articles. Pooled VE against H1N1 and H3N2 influenza subtypes, influenza B, and all influenza was higher for studies that used self-reported vaccination than for those that used medical records. Pooled VE was higher with respiratory specimen collection within ≤7 days vs ≤4 days of symptom onset, but the opposite was observed for H1N1. Pooled VE was higher for studies that adjusted for age but not for medical conditions compared with those that adjusted for both. There was, however, a lack of statistical significance in almost all differences in pooled VE between compared groups.ConclusionsThe available evidence is not strong enough to conclude that influenza VE from TND studies varies by source of vaccination information, respiratory specimen swab time, or adjustment for age/medical conditions. The evidence is, however, indicative that these factors ought to be considered while designing or evaluating TND studies of influenza VE.

Acute flaccid myelitis - has it gone unrecognised in Australian children?

We have identified a previously unrecognised cluster of a newly recognised condition - acute flaccid myelitis (AFM) - among acute flaccid paralysis (AFP) cases identified by the Australian Paediatric Active Enhanced Disease Surveillance Network (PAEDS) 2007-2017. In the 12 months before and after detection of enterovirus D68 (EV-D68) from a single AFP case in April 2016, 24 of 97 notified cases of AFP were found to be clinically compatible with AFM; of these 24 cases, ten, clustered in early 2016, met magnetic resonance imaging (MRI) criteria for AFM. Detection of emerging enteroviruses requires collection of respiratory, cerebrospinal fluid and stool specimens, and should be routine practice for all AFP cases.

Respiratory Specimen Collection Booth for COVID-19 Test: Efficiency Based Newly Introduced Facility.

Hospitals need to find a safe and rapid method for respiratory specimen collection as the number of patients suspicious for coronavirus disease -2019 (COVID-19) rapidly grows. Applied with significant infection control and prevention measures, a respiratory specimen collection booth was newly designed. The new respiratory specimen collection booth not only increased COVID-19 testing cases but also decreased personal protective equipment consumption.

Bronchoscopy and respiratory specimen collection for COVID-19

The COVID-19 pandemic is the first and most challenging health condition in the 21st century. The number of patients confirmed with COVID-19 disease worldwide is now above one million, and the number of deaths is increasing day by day. Bronchoscopy is a procedure used for the diagnosis and treatment of various conditions, but it can also transmit disease if appropriate precautions are not followed. In this short review, the limited scientific knowledge about bronchoscopy in COVID-19 pneumonia and the precautions which should be performed are summarized.

Duplex real-time RT-PCR assay for detection and subgroup-specific identification of human respiratory syncytial virus

Human respiratory syncytial virus (HRSV) is a leading cause of acute respiratory illness in young children worldwide. Reliable detection and identification of HRSV subgroup A and B infections are essential for accurate disease burden estimates in anticipation of licensure of novel HRSV vaccines and immunotherapies. To ensure continued reliability, molecular assays must remain current with evolving virus strains. We have developed a HRSV subgroup-specific real-time RT-PCR (rRT-PCR) assay for detection and subgroup identification using primers and subgroup-specific probes targeting a conserved region of the nucleoprotein gene combined in a single duplex reaction using all genome sequence data currently available in GenBank. The assay was validated for analytical sensitivity, specificity, reproducibility, and clinical performance with a geographically diverse collection of viral isolates and respiratory specimens in direct comparison with an established pan-HRSV rRT-PCR reference test. The assay was sensitive, reproducibly detecting as few as 5–10 copies/reaction of target RNA. The assay was specific, showing no amplification with a panel of 16 other common respiratory pathogens or predicted by in silico primer/probe analysis. The duplex rRT-PCR assay based on the most current available genome sequence data permits rapid, sensitive and specific detection and subgroup identification of HRSV.