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Golan-Tripto I, Danino D, De Waal L, Akel K, Dizitzer-Hillel Y, Tal A, Langman Y, Goldbart A. Viral load in hospitalized infants with respiratory syncytial virus bronchiolitis: a three-way comparative analysis. Eur J Pediatr 2024:10.1007/s00431-024-05614-3. [PMID: 38780651 DOI: 10.1007/s00431-024-05614-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Revised: 04/30/2024] [Accepted: 05/15/2024] [Indexed: 05/25/2024]
Abstract
Viral load measurement of Respiratory syncytial virus (RSV) in acute bronchiolitis depends on specimen collection, viral load quantification, and transport media. The aim of this study was to investigate viral load in three-way-comparative analyses; nasal swab versus nasal wash, quantitative real-time polymerase chain reaction (RT-PCR) versus cell tissue culture, and various transport media. A prospective cohort study of infants aged < 12 months, admitted to the Soroka Medical Center, due to acute bronchiolitis, was conducted. Two nasal swabs and two nasal wash samples (in UTM and VCM) were collected from each infant upon admission and after 48 h. Samples were immediately stored at -80 °C and tested at Viroclinics DDL (Rotterdam, Netherlands). Quantitative RT-PCR and quantitative virus culture were performed using tissue culture infective dose (TCID50). Spearman's correlation coefficient test assessed the correlation between the different methods, viral load, and clinical severity score. One hundred samples were collected from 13 infants (mean age 5.7 ± 3.8 months, 46% males). Twelve patients were RSV-A positive, and one was RSV-B positive. A high correlation was found between transport media- UTM and VCM (0.92, P < 0.001) and between nasal swabs and nasal wash samples (0.62, P = 0.02). RSV signals were higher in nasal wash than in swabs. PCR signals were lower in the second collection compared to the first. No correlation was found between viral load and clinical severity. Conclusion: RSV viral load is comparable across nasal wash, nasal swabs, and various transport media. However, it did not correlate with clinical severity, probably due to the limited sample size. Broader analyses are warranted. What is Known: • Viral load measurement in Respiratory Syncytial Virus (RSV) bronchiolitis depends on specimen collection, viral load quantification, and transport media. • The COVID-19 pandemic underscored the paramount significance of proper specimen collection, notably through nasal swabs. What is New: • RSV viral load was investigated in three-way-comparative analyses. • RSV viral load correlated well across PCR and tissue culture, nasal wash and swabs, and various transport media. RSV viral load did not correlate with clinical severity.
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Affiliation(s)
- Inbal Golan-Tripto
- Department of Pediatrics, Soroka University Medical Center, Beer Sheva, Israel.
- Pediatric Pulmonary Unit, Soroka University Medical Center, Beer Sheva, Israel.
- Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel.
| | - Dana Danino
- Department of Pediatrics, Soroka University Medical Center, Beer Sheva, Israel
- Infectious Disease Unit, Soroka University Medical Center, Beer Sheva, Israel
- Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Leon De Waal
- Viroclinics DDL, Cerba Research Company, Rotterdam, The Netherlands
| | - Khaled Akel
- Department of Pediatrics, Soroka University Medical Center, Beer Sheva, Israel
| | - Yotam Dizitzer-Hillel
- Department of Pediatrics 'C', Schneider's Children Medical Center of Israel, Petah Tikva, Israel
| | - Asher Tal
- Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Yasmine Langman
- Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Aviv Goldbart
- Department of Pediatrics, Soroka University Medical Center, Beer Sheva, Israel
- Pediatric Pulmonary Unit, Soroka University Medical Center, Beer Sheva, Israel
- Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
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2
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El Chaer F, Kaul DR, Englund JA, Boeckh M, Batista MV, Seo SK, Carpenter PA, Navarro D, Hirsch HH, Ison MG, Papanicolaou GA, Chemaly RF. American Society of Transplantation and Cellular Therapy Series: #7 - Management of Respiratory Syncytial Virus Infections in Hematopoietic Cell Transplant Recipients. Transplant Cell Ther 2023; 29:730-738. [PMID: 37783338 DOI: 10.1016/j.jtct.2023.09.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Accepted: 09/26/2023] [Indexed: 10/04/2023]
Abstract
The Practice Guidelines Committee of the American Society of Transplantation and Cellular Therapy (ASTCT) partnered with its Transplant Infectious Disease Special Interest Group (TID-SIG) to update the 2009 compendium-style infectious disease guidelines for hematopoietic cell transplantation (HCT). A new approach was adopted to better serve clinical providers by publishing each standalone topic in the infectious disease series in a concise format of frequently asked questions (FAQ), tables, and figures. Experts in HCT and infectious diseases identified FAQs and then provided answers based on the strength of the recommendation and the level of supporting evidence. In the seventh guideline in the series, we focus on the respiratory syncytial virus (RSV) with FAQs addressing epidemiology, clinical diagnosis, prophylaxis, and treatment. Special consideration was given to RSV in pediatric, cord blood, haploidentical, and T cell-depleted HCT and chimeric antigen receptor T cell therapy recipients, as well as to identify future research directions.
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Affiliation(s)
- Firas El Chaer
- Department of Medicine, Division of Hematology and Oncology, University of Virginia, Charlottesville, Virginia.
| | - Daniel R Kaul
- Division of Infectious Disease, University of Michigan Medical School, Ann Arbor, Michigan
| | - Janet A Englund
- Department of Pediatrics, University of Washington, Seattle Children's Research Institute, Seattle, Washington
| | - Michael Boeckh
- Clinical Research and Vaccine and Infectious Disease Divisions, Fred Hutchinson Cancer Center and Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington
| | - Marjorie V Batista
- Department of Infectious Diseases, AC Camargo Cancer Center, Sao Paulo, Brazil
| | - Susan K Seo
- Infectious Diseases Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York
| | - Paul A Carpenter
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - David Navarro
- Microbiology Service, Hospital Clínico Universitario, INCLIVA Research Institute, Valencia, and Department of Microbiology, School of Medicine, University of Valencia, Valencia & Centro de Investigación Biomédica en Red de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
| | - Hans H Hirsch
- Clinical Virology Laboratory, Laboratory Medicine, University Hospital Basel, Basel, Switzerland; Infectious Diseases & Hospital Epidemiology, University Hospital Basel, Basel, Switzerland; Transplantation & Clinical Virology, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Michael G Ison
- Respiratory Disease Branch, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland
| | - Genovefa A Papanicolaou
- Infectious Diseases Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York
| | - Roy F Chemaly
- Department of Infectious Diseases, Infection Control, and Employee Health, The University of Texas MD Anderson Cancer Center, Houston, Texas
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3
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Gallardo-Alfaro L, Lorente-Montalvo P, Cañellas M, Carandell E, Oliver A, Rojo E, Riera B, Llobera J, Bulilete O. Diagnostic accuracy of Panbio™ rapid antigen test for SARS-CoV-2 in paediatric population. BMC Pediatr 2023; 23:433. [PMID: 37644389 PMCID: PMC10463935 DOI: 10.1186/s12887-023-04201-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 07/21/2023] [Indexed: 08/31/2023] Open
Abstract
BACKGROUND Rapid antigen-detection tests (Ag-RDTs) are used to diagnose SARS-CoV-2 infection. Real-world studies of Ag-RDTs are necessary to evaluate their diagnostic yield in paediatric patients. Our aim was to evaluate the accuracy of the Panbio™ Rapid Antigen Test for SARS-CoV-2 in the setting of a primary health care centre (PHC), with use of the Reverse Transcription-Polymerase Chain Reaction (RT-PCR) as gold standard. METHODS This prospective diagnostic study was conducted at PHCs in Mallorca, Spain. Patients were ≤ 18 years-old that attended sites for RT-PCR testing due to symptoms suggestive of infection (fever, headache, nasal congestion and dry cough, among others) or epidemiological exposure (close contacts). Two samples were collected: a nasal mid-turbinate sample for Ag-RDTs and a nasopharyngeal swab for RT-PCR testing. The sensitivity, specificity, and predictive values of the AgRDT were calculated using the RT-PCR results as the reference. RESULTS We examined 1142 participants from 0 to 18 years (47.5% female, mean age 8.9 ± 4.8 years, median 9.0 [5.0-13.0]). There were 84 positive RT-PCR results (pre-test probability of 7.3%) and 52 positive Ag-RDT results. The sensitivity of the Ag-RDT was 59.5% (95% Confidence Interval (CI): 48.2-69.9%), the specificity was 99.8% (95%CI: 99.2-99.9%), the positive predictive value was 96.1% (95%CI: 85.6-99.4%), and the negative predictive value was 96.8% (95%CI: 95.6-97.7%). The sensitivity for individuals referred by a general practitioner (GP) or paediatrician due to symptoms was 71.4% (95%CI: 51.5-86.0%) and for asymptomatic individuals was 50.0% (95%CI: 9.1-90.8%). The specificity was greater than 98.9% overall and in all subgroups. The sensitivity was 73.0% (95%CI: 52.0-87.5%) for referred patients due to symptoms and who were tested within 5 days since symptom onset. No significant statistical differences between any groups were found. There were 34 false-negative Ag-RDT results (40.5%) and 2 false-positive Ag-RDT results (0.2%). CONCLUSION The sensitivity of the Panbio™ Test in paediatric individuals is below the minimum of 80% recommended by the World Health Organization for Ag-RDTs. This test had better accuracy in individuals referred by a GP or paediatrician due to symptoms, rather than those who were asymptomatic or referred due to epidemiological exposure. The RT-PCR test using a nasopharyngeal swab is accurate, but a less invasive alternative that has better sensitivity than the Panbio™ Test is needed for paediatric populations.
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Affiliation(s)
- Laura Gallardo-Alfaro
- Primary Health Care Research Unit, Balearic Public Health Service (Ib-Salut), Escola Graduada n9, 07002, Palma, Illes Balears, Spain
- Balearic Islands Health Research Institute (IdISBa), Carretera de Valldemossa, 79, 07120, Palma, Illes Balears, Spain
- RICAPPS- Red de Investigación Cooperativa de Atención Primaria Y Promoción de La Salud - Carlos III Health Institute (ISCIII), Madrid, Spain
| | - Patricia Lorente-Montalvo
- Primary Health Care Research Unit, Balearic Public Health Service (Ib-Salut), Escola Graduada n9, 07002, Palma, Illes Balears, Spain.
- RICAPPS- Red de Investigación Cooperativa de Atención Primaria Y Promoción de La Salud - Carlos III Health Institute (ISCIII), Madrid, Spain.
- Santa Ponça Primary Health Care Center, Balearic Public Health Service (Ib-Salut), Carrer del Riu Síl, 25, 07180, Santa Ponça, Illes Balears, Spain.
| | - Margarita Cañellas
- Son Llatzer University Hospital, Ctra. de Manacor, 07198, Palma, Illes Balears, Spain
| | - Eugenia Carandell
- Balearic Islands Health Research Institute (IdISBa), Carretera de Valldemossa, 79, 07120, Palma, Illes Balears, Spain
- RICAPPS- Red de Investigación Cooperativa de Atención Primaria Y Promoción de La Salud - Carlos III Health Institute (ISCIII), Madrid, Spain
- Directorate of General Health Service, Balearic Public Health Service (Ib-Salut), Reina Esclaramunda n9, 07005, Palma, Illes Balears, Spain
| | - Antonio Oliver
- Balearic Islands Health Research Institute (IdISBa), Carretera de Valldemossa, 79, 07120, Palma, Illes Balears, Spain
- Microbiology Service, Son Espases University Hospital, Balearic Public Health Service (Ib-Salut), Carretera de Valldemossa, 79, 07120, Palma, Illes Balears, Spain
| | - Estrella Rojo
- Balearic Islands Health Research Institute (IdISBa), Carretera de Valldemossa, 79, 07120, Palma, Illes Balears, Spain
- Microbiology Service, Son Espases University Hospital, Balearic Public Health Service (Ib-Salut), Carretera de Valldemossa, 79, 07120, Palma, Illes Balears, Spain
| | - Beatriz Riera
- Son Llatzer University Hospital, Ctra. de Manacor, 07198, Palma, Illes Balears, Spain
| | - Joan Llobera
- Primary Health Care Research Unit, Balearic Public Health Service (Ib-Salut), Escola Graduada n9, 07002, Palma, Illes Balears, Spain
- Balearic Islands Health Research Institute (IdISBa), Carretera de Valldemossa, 79, 07120, Palma, Illes Balears, Spain
- RICAPPS- Red de Investigación Cooperativa de Atención Primaria Y Promoción de La Salud - Carlos III Health Institute (ISCIII), Madrid, Spain
| | - Oana Bulilete
- Primary Health Care Research Unit, Balearic Public Health Service (Ib-Salut), Escola Graduada n9, 07002, Palma, Illes Balears, Spain
- Balearic Islands Health Research Institute (IdISBa), Carretera de Valldemossa, 79, 07120, Palma, Illes Balears, Spain
- RICAPPS- Red de Investigación Cooperativa de Atención Primaria Y Promoción de La Salud - Carlos III Health Institute (ISCIII), Madrid, Spain
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4
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Fourie E, Bording ES, Euser SM, Badoux P, Haverkort ME, van Houten MA. Nasal discharge: A unique enhanced alternative for the detection of respiratory pathogens in adults. J Med Virol 2023; 95:e29047. [PMID: 37621163 DOI: 10.1002/jmv.29047] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 07/26/2023] [Accepted: 08/12/2023] [Indexed: 08/26/2023]
Abstract
Upper respiratory tract infections are a significant cause of social- and disease burden worldwide. Currently, invasive and uncomfortable molecular detection methods are used for respiratory pathogen detection. We aimed to assess the ability and bearability of a rhinorrhea swab (RS) to detect respiratory pathogens in comparison to the combined nasopharyngeal and oropharyngeal swab (NP/OP). This study was performed at a Public Health Service severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) testing facility between November and December 2022 in the Netherlands. Adults aged 16 years and older, being subjected to a standard of care NP/OP swab with nasal discharge, were included and received an additional RS. Respiratory pathogen detection was evaluated using SARS-CoV-2 polymerase chain reaction (PCR) and multiplex ligation-dependent probe amplification (MLPA) PCR. Bearability was evaluated using visual analog scale (VAS) scores and a questionnaire. A total of 100 adults with a mean age ± SD of 46 ± 16 years were included. The NP/OP swab detected 104 pathogens, the RS 83 pathogens (p < 0.001), and in total 108 respiratory pathogens were identified in 89 adults (89%). The ability to detect respiratory pathogens compared between the RS and the combined NP/OP swab revealed a sensitivity of 82% (95% CI 73%-89%) and specificity of 100% (95% CI 72%-100%). RS were significantly more bearable than the combined NP/OP swab (p value < 0.001). Therefore, nasal discharge found in adults can be used as an adequate reliable medium for respiratory pathogen detection using SARS-CoV-2 PCR and MLPA PCR.
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Affiliation(s)
- Elandri Fourie
- Spaarne Gasthuis Academy, Spaarne Gasthuis, Hoofddorp, The Netherlands
| | - Eva S Bording
- Public Health Services Kennemerland, Haarlem, The Netherlands
| | - Sjoerd M Euser
- Regional Public Health Laboratory Kennemerland, Haarlem, The Netherlands
| | - Paul Badoux
- Regional Public Health Laboratory Kennemerland, Haarlem, The Netherlands
| | | | - Marlies A van Houten
- Spaarne Gasthuis Academy, Spaarne Gasthuis, Hoofddorp, The Netherlands
- Department of Pediatrics, Spaarne Gasthuis, Haarlem and Hoofddorp, The Netherlands
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5
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Lowry SA, Wolfe MK, Boehm AB. Respiratory virus concentrations in human excretions that contribute to wastewater: a systematic review and meta-analysis. JOURNAL OF WATER AND HEALTH 2023; 21:831-848. [PMID: 37387346 PMCID: wh_2023_057 DOI: 10.2166/wh.2023.057] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/01/2023]
Abstract
Concentrations of nucleic acids from a range of respiratory viruses in wastewater solids collected from wastewater treatment plants correlate to clinical data on disease occurrence in the community contributing to the wastewater. Viral nucleic acids enter wastewater from excretions deposited in toilets or drains. To relate measured concentrations in wastewater at a treatment plant to the number of community infections, viral nucleic-acid concentrations in human excretions are needed as inputs to a mass balance model. Here, we carried out a systematic review and meta-analysis to characterize the concentrations and presence of influenza A and B, respiratory syncytial virus, metapneumovirus, parainfluenza virus, rhinovirus, and seasonal coronaviruses in stool, urine, mucus, sputum, and saliva. We identified 220 data sets from 50 articles and reported viral concentrations and presence in these excretions. Data were unevenly distributed across virus type (with the most available for influenza) and excretion type (with the most available for respiratory excretions). Most articles only reported the presence or absence of the virus in a cross-sectional study design. There is a need for more concentration data, including longitudinal data, across all respiratory virus and excretion types. Such data would allow quantitatively linking virus wastewater concentrations to numbers of infected individuals.
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Affiliation(s)
- Sarah A Lowry
- Department of Civil and Environmental Engineering, Stanford University, 473 Via Ortega, Stanford, CA 94305, USA E-mail:
| | - Marlene K Wolfe
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, 1518 Clifton Rd., Atlanta, GA 30322, USA
| | - Alexandria B Boehm
- Department of Civil and Environmental Engineering, Stanford University, 473 Via Ortega, Stanford, CA 94305, USA
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6
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Fourie E, Sijm YEE, Badoux P, Mérelle ME, Haverkort ME, Euser SM, van Houten MA. High detection rate of viral pathogens in nasal discharge in children aged 0 till 5 years. J Med Virol 2023; 95:e28415. [PMID: 36541735 DOI: 10.1002/jmv.28415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 11/28/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022]
Abstract
Respiratory tract infections (RTI) in children remain a cause of disease burden worldwide. Nasopharyngeal (NP) & oropharyngeal (OP) swabs are used for respiratory pathogen detection, but hold disadvantages particularly for children, highlighting the importance and preference for a child friendly detection method. We aimed to evaluate the performance and tolerability of a rhinorrhea swab (RS) in detecting viral pathogens when compared to a combined OP(/NP) or mid-turbinate (MT) nasal swab. This study was conducted between September 2021 and July 2022 in the Netherlands. Children aged 0-5 years, with an upper RTI and nasal discharge, were included and received a combined swab and a RS. Multiplex polymerase chain reaction (PCR) and severe acute respiratory syndrome coronavirus-2 PCR were used for viral pathogen detection. Tolerability was evaluated with a questionnaire and visual analog scale (VAS) scores. During 11 months 88 children were included, with a median age of 1.00 year [interquartile range 0.00-3.00]. In total 122 viral pathogens were detected in 81 children (92%). Sensitivity and specificity of the RS compared to a combined swab were respectively 97% (95% confidence interval [CI] 91%-100%) and 78% (95% CI 45%-94%). Rhinorrhea samples detected more pathogens than the (combined) nasal samples, 112 versus 108 respectively. Median VAS scores were significantly lower for the RS in both children (2 vs. 6) and their parents (0 vs. 5). A RS can therefore just as effectively/reliably detect viral pathogens as the combined swab in young children and is better tolerated by both children and their parents/caregivers.
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Affiliation(s)
- Elandri Fourie
- Spaarne Gasthuis Academy, Spaarne Gasthuis, Hoofddorp, The Netherlands
| | - Yara E E Sijm
- Spaarne Gasthuis Academy, Spaarne Gasthuis, Hoofddorp, The Netherlands
| | - Paul Badoux
- Regional Public Health Laboratory Kennemerland, Haarlem, The Netherlands
| | - Marieke E Mérelle
- Department of Pediatrics, Spaarne Gasthuis, Hoofddorp, The Netherlands
| | | | - Sjoerd M Euser
- Regional Public Health Laboratory Kennemerland, Haarlem, The Netherlands
| | - Marlies A van Houten
- Spaarne Gasthuis Academy, Spaarne Gasthuis, Hoofddorp, The Netherlands.,Department of Pediatrics, Spaarne Gasthuis, Hoofddorp, The Netherlands
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7
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Using quantitative PCR to identify opportunities to strengthen soil-transmitted helminth control in Solomon Islands: A cross-sectional epidemiological survey. PLoS Negl Trop Dis 2022; 16:e0010350. [PMID: 35604904 PMCID: PMC9126411 DOI: 10.1371/journal.pntd.0010350] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 03/22/2022] [Indexed: 11/19/2022] Open
Abstract
Background The Kato-Katz microscopy technique is the global standard for assessment of soil-transmitted helminth (STH) burden. However, major limitations include its poor sensitivity, requirement for rapid sample processing, and inability to differentiate hookworm species nor detect Strongyloides spp. infections. We assessed the prevalence and intensity of STH species in Solomon Islands by conducting a province-wide survey using quantitative PCR (qPCR) for diagnosis, which can provide much better characterisation of STH burden than microscopy. Methodology/Principal findings We conducted a cross-sectional survey in 18 villages in Western Province to detect infections with six STH species and quantify intensity with three. We used linear mixed model regression to identify potential water, sanitation, and hygiene (WASH) and environmental risk factors for infection. We collected stool specimens from 830 village residents. Overall STH prevalence was 63.3% (range 27.5 to 91.5% across villages), led by Necator americanus (54.5% [range 17.5–89.4%]), followed by Ancylostoma ceylanicum (15.5% [range 2.8–45.8%]), Trichuris trichiura (9.1% [range 0–79.2%]), and Strongyloides spp. (3.2% [range 0–29.2%]). Most infections were of light intensity for N. americanus (85.7%) and T. trichiura (90.7%). Owning a household latrine was associated with a lower risk of N. americanus infection (AOR 0.41, 95% CI 0.24–0.68) while greater precipitation was linked to more common T. trichiura infection (AOR 1.14, 95% CI 1.04–1.25). Conclusion/Significance In this first large-scale population survey of STH in the Pacific using qPCR, we found evidence that ivermectin should be incorporated into STH control programmes because of the presence of T. trichiura and Strongyloides spp., both of which are poorly responsive to albendazole. Furthermore, One Health strategies are needed for improved A. ceylanicum and Strongyloides spp. control, WASH access and use should be improved to complement deworming programmes, and control efforts should ideally be expanded to entire communities. Trial registration ClinicalTrials.gov Australian and New Zealand Clinical Trials Registry ACTRN12618001086257. Routine assessments of the burden of intestinal worm infections rely on microscopy-based diagnostic methods, such as the Kato-Katz technique. However major limitations include its poor sensitivity, requirement for rapid sample processing, and inability to differentiate individual hookworm species and detect Strongyloides spp. infections. It is important to assess the burden of each of these infections to design control approaches beyond the current core strategy of albendazole preventive chemotherapy. Use of qPCR for diagnosis could address these gaps because it can distinguish all relevant intestinal worm species. We completed a province-wide intestinal worm infections prevalence survey using qPCR in Western Province, Solomon Islands. Overall prevalence was extremely high (62.5%). We identified a high burden of Necator americanus (54.5%) and detected Ancylostoma ceylanicum (15.5%), Trichuris trichiura (9.1%), and Strongyloides spp. (3.2%) infections. Increased age and precipitation were associated with higher prevalence of infection, while owning a household latrine was associated with lower odds of N. americanus infection. Our findings support the need to incorporate ivermectin into deworming programmes for Strongyloides spp. and T. trichiura control as these species are poorly responsive to albendazole, implement One Health strategies to address the zoonotic A. ceylanicum and Strongyloides spp., and expand control efforts to reach entire communities. WASH access should also be improved to complement deworming programmes.
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8
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Song Y, Hou J, Kwok JSL, Weng H, Tang MF, Wang MH, Leung ASY, Tao KP, Wong GWK, Chan RWY, Tsui SKW, Leung TF. Whole-Genome Shotgun Sequencing for Nasopharyngeal Microbiome in Pre-school Children With Recurrent Wheezing. Front Microbiol 2022; 12:792556. [PMID: 35250904 PMCID: PMC8889122 DOI: 10.3389/fmicb.2021.792556] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Accepted: 12/21/2021] [Indexed: 12/20/2022] Open
Abstract
Microbiome mediates early life immune deviation in asthma development. Recurrent wheeze (RW) in pre-school years is a risk factor for asthma diagnosis in school-age children. Dysbiosis exists in asthmatic airways, while its origin in pre-school years and relationship to RW is not clearly defined. This study investigated metagenomics of nasopharyngeal microbiome in pre-school children with RW. We applied whole-genome shotgun sequencing and human rhinovirus (HRV) detection on nasopharyngeal samples collected from three groups of pre-school children: (i) RW group: 16 children at-risk for asthma who were hospitalized for RW, (ii) inpatient control (IC): 18 subjects admitted for upper respiratory infection, and (iii) community control (CC): 36 children without respiratory syndromes. Sequence reads were analyzed by MetaPhlAn2 and HUMAnN2 algorithm for taxonomic and functional identification. Linear discriminant analysis effect size (LEfSe) analysis was used to identify discriminative features. We identified that Moraxella catarrhalis and Dolosigranulum pigrum were predominant species in nasopharynx. RW had lower alpha diversity (Shannon diversity index) than CC (0.48 vs. 1.07; Padj = 0.039), characterized by predominant Proteobacteria. LEfSe analysis revealed D. pigrum was the only discriminative species across groups (LDA = 5.57, P = 0.002), with its relative abundance in RW, IC, and CC being 9.6, 14.2, and 37.3%, respectively (P < 0.05). LEfSe identified five (ribo)nucleotides biosynthesis pathways to be group discriminating. Adjusting for HRV status, pre-school children with RW have lower nasopharyngeal biodiversity, which is associated with Proteobacteria predominance and lower abundance of D. pigrum. Along with discriminative pathways found in RW and CC, these microbial biomarkers help to understand RW pathogenesis.
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Affiliation(s)
- Yuping Song
- Department of Pediatrics, Prince of Wales Hospital, The Chinese University of Hong Kong, Sha Tin, Hong Kong SAR, China
| | - Jinpao Hou
- School of Biomedical Sciences, The Chinese University of Hong Kong, Sha Tin, Hong Kong SAR, China
| | - Jamie Sui Lam Kwok
- School of Biomedical Sciences, The Chinese University of Hong Kong, Sha Tin, Hong Kong SAR, China
| | - Haoyi Weng
- Jockey Club School of Public Health and Primary Care, Prince of Wales Hospital, The Chinese University of Hong Kong, Sha Tin, Hong Kong SAR, China
| | - Man Fung Tang
- Department of Pediatrics, Prince of Wales Hospital, The Chinese University of Hong Kong, Sha Tin, Hong Kong SAR, China.,Hong Kong Hub of Paediatric Excellence, The Chinese University of Hong Kong, Sha Tin, Hong Kong SAR, China
| | - Maggie Haitian Wang
- Jockey Club School of Public Health and Primary Care, Prince of Wales Hospital, The Chinese University of Hong Kong, Sha Tin, Hong Kong SAR, China
| | - Agnes Sze Yin Leung
- Department of Pediatrics, Prince of Wales Hospital, The Chinese University of Hong Kong, Sha Tin, Hong Kong SAR, China
| | - Kin Pong Tao
- Department of Pediatrics, Prince of Wales Hospital, The Chinese University of Hong Kong, Sha Tin, Hong Kong SAR, China.,The Chinese University of Hong Kong-University Medical Center Utrecht Joint Research Laboratory of Respiratory Virus and Immunobiology, The Chinese University of Hong Kong, Sha Tin, Hong Kong SAR, China
| | - Gary Wing Kin Wong
- Department of Pediatrics, Prince of Wales Hospital, The Chinese University of Hong Kong, Sha Tin, Hong Kong SAR, China
| | - Renee Wan Yi Chan
- Department of Pediatrics, Prince of Wales Hospital, The Chinese University of Hong Kong, Sha Tin, Hong Kong SAR, China.,Hong Kong Hub of Paediatric Excellence, The Chinese University of Hong Kong, Sha Tin, Hong Kong SAR, China.,The Chinese University of Hong Kong-University Medical Center Utrecht Joint Research Laboratory of Respiratory Virus and Immunobiology, The Chinese University of Hong Kong, Sha Tin, Hong Kong SAR, China
| | - Stephen Kwok Wing Tsui
- School of Biomedical Sciences, The Chinese University of Hong Kong, Sha Tin, Hong Kong SAR, China
| | - Ting Fan Leung
- Department of Pediatrics, Prince of Wales Hospital, The Chinese University of Hong Kong, Sha Tin, Hong Kong SAR, China.,Hong Kong Hub of Paediatric Excellence, The Chinese University of Hong Kong, Sha Tin, Hong Kong SAR, China.,The Chinese University of Hong Kong-University Medical Center Utrecht Joint Research Laboratory of Respiratory Virus and Immunobiology, The Chinese University of Hong Kong, Sha Tin, Hong Kong SAR, China
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9
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Walls S, Adhikari P, Reesha H, Baxter M. Sepsis Due to Haemophilus influenzae and Masked Influenza A Infection. Cureus 2022; 14:e22424. [PMID: 35371694 PMCID: PMC8947951 DOI: 10.7759/cureus.22424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/20/2022] [Indexed: 12/02/2022] Open
Abstract
Haemophilus influenzae (H. influenzae) is a facultative anaerobe, pleomorphic Gram-negative coccobacillus capable of causing various respiratory and blood stream infections. Introduction of childhood immunization against H. influenza type b has decreased its prevalence. Invasive infection with non-typeable H. influenzae is increasing specially in vulnerable population. We present a case of a 69-year-old female who developed septic shock due to H. influenzae infection. She was also found to have influenza A infection in bronchoalveolar lavage (BAL) sample although initial test with nasopharyngeal swab was negative. This case report highlights the fact that in patients with high clinical suspicion, negative nasopharyngeal swab with polymerase chain reaction may not rule out influenza infection and BAL may be necessary to confirm the diagnosis and H. influenzae can be causing bacterial superinfection in such patients. She was appropriately treated with third-generation cephalosporin for H. influenzae and with oseltamivir for influenza A. Her condition improved significantly with the treatment.
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10
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Gradisteanu Pircalabioru G, Iliescu FS, Mihaescu G, Cucu AI, Ionescu ON, Popescu M, Simion M, Burlibasa L, Tica M, Chifiriuc MC, Iliescu C. Advances in the Rapid Diagnostic of Viral Respiratory Tract Infections. Front Cell Infect Microbiol 2022; 12:807253. [PMID: 35252028 PMCID: PMC8895598 DOI: 10.3389/fcimb.2022.807253] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 01/04/2022] [Indexed: 12/16/2022] Open
Abstract
Viral infections are a significant public health problem, primarily due to their high transmission rate, various pathological manifestations, ranging from mild to severe symptoms and subclinical onset. Laboratory diagnostic tests for infectious diseases, with a short enough turnaround time, are promising tools to improve patient care, antiviral therapeutic decisions, and infection prevention. Numerous microbiological molecular and serological diagnostic testing devices have been developed and authorised as benchtop systems, and only a few as rapid miniaturised, fully automated, portable digital platforms. Their successful implementation in virology relies on their performance and impact on patient management. This review describes the current progress and perspectives in developing micro- and nanotechnology-based solutions for rapidly detecting human viral respiratory infectious diseases. It provides a nonexhaustive overview of currently commercially available and under-study diagnostic testing methods and discusses the sampling and viral genetic trends as preanalytical components influencing the results. We describe the clinical performance of tests, focusing on alternatives such as microfluidics-, biosensors-, Internet-of-Things (IoT)-based devices for rapid and accurate viral loads and immunological responses detection. The conclusions highlight the potential impact of the newly developed devices on laboratory diagnostic and clinical outcomes.
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Affiliation(s)
| | - Florina Silvia Iliescu
- National Institute for Research and Development in Microtechnologies—IMT, Bucharest, Romania
| | | | | | - Octavian Narcis Ionescu
- National Institute for Research and Development in Microtechnologies—IMT, Bucharest, Romania
- Petroleum-Gas University of Ploiesti, Ploiesti, Romania
| | - Melania Popescu
- National Institute for Research and Development in Microtechnologies—IMT, Bucharest, Romania
| | - Monica Simion
- National Institute for Research and Development in Microtechnologies—IMT, Bucharest, Romania
| | | | - Mihaela Tica
- Emergency University Hospital, Bucharest, Romania
| | - Mariana Carmen Chifiriuc
- Research Institute of the University of Bucharest, Bucharest, Romania
- Faculty of Biology, University of Bucharest, Bucharest, Romania
- Academy of Romanian Scientists, Bucharest, Romania
- The Romanian Academy, Bucharest, Romania
- *Correspondence: Mariana Carmen Chifiriuc, ; Ciprian Iliescu,
| | - Ciprian Iliescu
- National Institute for Research and Development in Microtechnologies—IMT, Bucharest, Romania
- Academy of Romanian Scientists, Bucharest, Romania
- Faculty of Applied Chemistry and Materials Science, University “Politehnica” of Bucharest, Bucharest, Romania
- *Correspondence: Mariana Carmen Chifiriuc, ; Ciprian Iliescu,
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11
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Mak GC, Ng AY, Lam ET, Chan RC, Tsang DN. Assessment of SARS-CoV-2 viral loads in combined nasal-and-throat swabs collected from COVID-19 individuals under the Universal Community Testing Programme in Hong Kong. J Virol Methods 2022; 300:114396. [PMID: 34856306 PMCID: PMC8629508 DOI: 10.1016/j.jviromet.2021.114396] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 10/24/2021] [Accepted: 11/29/2021] [Indexed: 12/20/2022]
Abstract
BACKGROUND Combined nasal-and-throat swabs (CNTS) is less invasive and easy to execute. CNTS also induces lower risk to healthcare workers upon collection. However, there is a lack of data on viral load assessment for population-wide testing. OBJECTIVE This study assessed if CNTS is suitable as an alternative specimen type for the detection of SARS-CoV-2. METHODS We assessed the viral load of SARS-CoV-2 in CNTS collected from COVID-19 individuals through the 2-week period of the Universal Community Testing Programme (UCTP) conducted in Hong Kong. In addition, we compared viral loads of SARS-CoV-2 for the paired CNTS and non-CNTS specimens among these individuals. RESULTS This UCTP identified 48 COVID-19 individuals from nearly 2 million specimens collected. The viral loads of SARS-CoV-2 varied widely, cycle threshold values Ct 16.28-36.94, among symptoms and asymptomatic individuals. The viral loads for the paired CNTS and non-CNTS specimens were comparable. CONCLUSIONS This study demonstrated that CNTS could be a specimen of choice for diagnosis of SARS-CoV-2.
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Affiliation(s)
- Gannon C.K. Mak
- Corresponding author at: 9/F, Public Health Laboratory Centre, 382 Nam Cheong Street, Shek Kip Mei, Kowloon, Hong Kong Special Administrative Region
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12
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Chaves SS, Park JH, Prill MM, Whitaker B, Park R, Chew GL. Side-by-side comparison of parent vs. technician-collected respiratory swabs in low-income, multilingual, urban communities in the United States. BMC Public Health 2022; 22:103. [PMID: 35031041 PMCID: PMC8760092 DOI: 10.1186/s12889-022-12523-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 12/23/2021] [Indexed: 11/30/2022] Open
Abstract
Background Home-based swabbing has not been widely used. The objective of this analysis was to compare respiratory swabs collected by mothers of 7–12-year-olds living in low-income, multilingual communities in the United States with technician collected swabs. Methods Retrospective data analysis of respiratory samples collected at home by mothers compared to technicians. Anterior nasal and throat specimens collected using flocked swabs were combined in dry tubes. Test was done using TaqMan array cards for viral and bacterial pathogens. Cycle threshold (Ct) values of ribonuclease P (RNP) gene were used to assess specimen quality. Ct < 40 was interpreted as a positive result. Concordance of pathogen yield from mother versus technician collected swabs were analyzed using Cohen’s Kappa coefficients. Correlation analysis, paired t-test, and Wilcoxon signed-rank test for paired samples were used for RNP Ct values. Results We enrolled 36 households in Cincinnati (African American) and 44 (predominately Chinese or Latino) in Boston. In Cincinnati, eight of 32 (25%) mothers did not finish high school, and 11 (34%) had finished high school only. In Boston, 13 of 44 (30%) mothers had less than a high school diploma, 23 (52%) had finished high school only. Mother versus technician paired swabs (n = 62) had similar pathogen yield (paired t-test and Wilcoxon signed rank test p-values = 0.62 and 0.63, respectively; 95% confidence interval of the difference between the two measurements = − 0.45–0.75). Median Ct value for RNP was 22.6 (interquartile range, IQR = 2.04) for mother-collected and 22.4 (IQR = 2.39) for technician-collected swabs (p = 0.62). Agreement on pathogen yield between samples collected by mothers vs. technicians was higher for viruses than for bacterial pathogens, with high concordance for rhinovirus/enterovirus, human metapneumovirus, and adenovirus (Cohen’s kappa coefficients ≥80%, p < 0.0001). For bacterial pathogens, concordance was lower to moderate, except for Chlamydia pneumoniae, for which kappa coefficient indicated perfect agreement. Conclusion Mothers with a range of education levels from low-income communities were able to swab their children equally well as technicians. Home-swabbing using dry tubes, and less invasive collection procedures, could enhance respiratory disease surveillance. Supplementary Information The online version contains supplementary material available at 10.1186/s12889-022-12523-3.
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Affiliation(s)
- Sandra S Chaves
- CDC, National Center for Immunization and Respiratory Diseases, Influenza Division, Atlanta, USA.
| | - Ju-Hyeong Park
- CDC, National Institute for Occupational Safety and Health, Respiratory Health Division, Morgantown, USA
| | - Mila M Prill
- CDC, National Center for Immunization and Respiratory Diseases, Division of Viral Diseases, Atlanta, USA
| | - Brett Whitaker
- CDC, National Center for Immunization and Respiratory Diseases, Division of Viral Diseases, Atlanta, USA
| | - Reena Park
- Marshall University Joan C. Edwards School of Medicine, Huntington, USA
| | - Ginger L Chew
- CDC, National Center for Environmental Health, Division of Environmental Health Science and Practice, Atlanta, USA
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13
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Pereira LA, Lapinscki BA, Debur MC, Santos JS, Petterle RR, Nogueira MB, Vidal LRR, De Almeida SM, Raboni SM. Standardization of a high-performance RT-qPCR for viral load absolute quantification of influenza A. J Virol Methods 2021; 301:114439. [PMID: 34942203 DOI: 10.1016/j.jviromet.2021.114439] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 12/13/2021] [Accepted: 12/17/2021] [Indexed: 12/26/2022]
Abstract
Influenza is an acute viral infectious respiratory disease worldwide, presenting in different clinical forms, from influenza-like illness (ILI) to severe acute respiratory infection (SARI). Although real-time quantitative polymerase chain reaction (qPCR) is already an important tool for both diagnosis and treatment monitoring of several viral infections, the correlation between the clinical aspects and the viral load of influenza is still unclear. This lack of clarity is primarily due to the low accuracy and reproducibility of the methodologies developed to quantify the influenza virus. Thus, this study aimed to develop and standardize a universal absolute quantification for influenza A by reverse transcription-quantitative PCR (RT-qPCR), using a plasmid DNA. The assay showed efficiency (Eff%) 98.6, determination coefficient (R2) 0.998, linear range 10^1 to 10^10, limit of detection (LOD) 6.77, limit of quantification (LOQ) 20.52 copies/reaction. No inter and intra assay variability was shown, and neither was the matrix effect observed. Serial measurements of clinical samples collected at a 72h interval showed no change in viral load. By contrast, immunocompetent patients have a significantly lower viral load than immunosuppressed ones. Absolute quantification in clinical samples showed some predictors associated with increased viral load: (H1N1)pdm09 (0.045); women (p = 0.049) and asthmatics (p = 0.035). The high efficiency, precision, and previous performance in clinical samples suggest the assay can be used as an accurate universal viral load quantification of influenza A. Its applicability in predicting severity and response to antivirals needs to be evaluated.
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Affiliation(s)
- L A Pereira
- Graduate Program in Internal Medicine and Health Science, Universidade Federal, do Paraná, Curitiba, Brazil
| | - B A Lapinscki
- Graduate Program in Internal Medicine and Health Science, Universidade Federal, do Paraná, Curitiba, Brazil
| | - M C Debur
- Public Health Laboratory, Curitiba, Brazil
| | - J S Santos
- Virology Laboratory, Hospital de Clínicas, Universidade Federal do Paraná, Brazil
| | - R R Petterle
- Sector of Health Sciences, Medical School, Universidade Federal do Paraná, Curitiba, Brazil
| | - M B Nogueira
- Virology Laboratory, Hospital de Clínicas, Universidade Federal do Paraná, Brazil
| | - L R R Vidal
- Virology Laboratory, Hospital de Clínicas, Universidade Federal do Paraná, Brazil
| | - S M De Almeida
- Virology Laboratory, Hospital de Clínicas, Universidade Federal do Paraná, Brazil
| | - S M Raboni
- Virology Laboratory, Hospital de Clínicas, Universidade Federal do Paraná, Brazil; Infectious Diseases Division, Hospital de Clínicas, Universidade Federal do Paraná, Brazil.
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14
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Prospective Study of the Performance of Parent-Collected Nasal and Saliva Swab Samples, Compared with Nurse-Collected Swab Samples, for the Molecular Detection of Respiratory Microorganisms. Microbiol Spectr 2021; 9:e0016421. [PMID: 34756077 PMCID: PMC8579848 DOI: 10.1128/spectrum.00164-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Respiratory tract infections (RTIs) are ubiquitous among children in the community. A prospective observational study was performed to evaluate the diagnostic performance and quality of at-home parent-collected (PC) nasal and saliva swab samples, compared to nurse-collected (NC) swab samples, from children with RTI symptoms. Children with RTI symptoms were swabbed at home on the same day by a parent and a nurse. We compared the performance of PC swab samples as the test with NC swab samples as the reference for the detection of respiratory pathogen gene targets by reverse transcriptase PCR, with quality assessment using a human gene. PC and NC paired nasal and saliva swab samples were collected from 91 and 92 children, respectively. Performance and interrater agreement (Cohen's κ) of PC versus NC nasal swab samples for viruses combined showed sensitivity of 91.6% (95% confidence interval [CI], 85.47 to 95.73%) and κ of 0.84 (95% CI, 0.79 to 0.88), respectively; the respective values for bacteria combined were 91.4% (95% CI, 86.85 to 94.87%) and κ of 0.85 (95% CI, 0.80 to 0.89). In saliva samples, viral and bacterial sensitivities were lower at 69.0% (95% CI, 57.47 to 79.76%) and 78.1% (95% CI, 71.60 to 83.76%), as were κ values at 0.64 (95% CI, 0.53 to 0.72) and 0.70 (95% CI, 0.65 to 0.76), respectively. Quality assessment for human biological material (18S rRNA) indicated perfect interrater agreement. At-home PC nasal swab samples performed comparably to NC swab samples, whereas PC saliva swab samples lacked sensitivity for the detection of respiratory microbes. IMPORTANCE RTIs are ubiquitous among children. Diagnosis involves a swab sample being taken by a health professional, which places a considerable burden on community health care systems, given the number of cases involved. The coronavirus disease 2019 (COVID-19) pandemic has seen an increase in the at-home self-collection of upper respiratory tract swab samples without the involvement of health professionals. It is advised that parents conduct or supervise swabbing of children. Surprisingly, few studies have addressed the quality of PC swab samples for subsequent identification of respiratory pathogens. We compared NC and PC nasal and saliva swab samples taken from the same child with RTI symptoms, for detection of respiratory pathogens. The PC nasal swab samples performed comparably to NC samples, whereas saliva swab samples lacked sensitivity for the detection of respiratory microbes. Collection of swab samples by parents would greatly reduce the burden on community nurses without reducing the effectiveness of diagnoses.
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15
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Detection of six soil-transmitted helminths in human stool by qPCR- a systematic workflow. PLoS One 2021; 16:e0258039. [PMID: 34591904 PMCID: PMC8483301 DOI: 10.1371/journal.pone.0258039] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 09/16/2021] [Indexed: 11/19/2022] Open
Abstract
Soil-transmitted helminths (STH) infect up to one-quarter of the global population, with a significant associated disease burden. The main human STH are: Ancylostoma spp. and Necator americanus (hookworms); Ascaris lumbricoides, Trichuris trichiura, and Strongyloides stercoralis. The aim of this study was to establish a scalable system for stool STH multiplex quantitative real-time polymerase chain reactions (qPCR). Stool samples collected in Fiji and preserved in potassium dichromate were transferred to Melbourne at ambient temperature. Samples were washed to remove potassium dichromate and DNA was extracted with the Mini-Beadbeater-24 and a column-based kit. A SYBR green qPCR to detect the vertebrate mitochondrial gene was used as a DNA extraction control. Samples were tested using a probe-based multiplex qPCR targeting A. lumbricoides, T. trichiura and S. stercoralis, and in a second multiplex reaction to detect hookworms to the species level (A. duodenale, A. ceylanicum, N. americanus). An internal amplification control in both multiplex assays was included to prevent false-negative results due to PCR inhibitors. Samples were homogenised for a single cycle of 40 seconds to release STH DNA and washed stool was stored for up to 15 weeks at -30°C without compromising DNA. Our multiplex qPCR detected multiple species of STH without reduced sensitivity compared to singleplex. qPCR data from 40 stools was validated against STH-positive stools determined by microscopy. We have developed and validated an efficient and staged system for detecting six clinically important STH affecting humans that could be easily implemented without advanced automation in any qPCR-capable laboratory.
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16
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Suntarattiwong P, Mott JA, Mohanty S, Sinthuwattanawibool C, Srisantiroj N, Patamasingh Na Ayudhaya O, Klungthong C, Fernandez S, Kim L, Hunt D, Hombroek D, Brummer T, Chotpitayasunondh T, Dawood FS, Kittikraisak W. Feasibility and Performance of Self-Collected Nasal Swabs for Detection of Influenza Virus, Respiratory Syncytial Virus, and Human Metapneumovirus. J Infect Dis 2021; 224:831-838. [PMID: 34467984 DOI: 10.1093/infdis/jiab023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 01/14/2021] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND We assessed performance of participant-collected midturbinate nasal swabs compared to study staff-collected midturbinate nasal swabs for the detection of respiratory viruses among pregnant women in Bangkok, Thailand. METHODS We enrolled pregnant women aged ≥18 years and followed them throughout the 2018 influenza season. Women with acute respiratory illness self-collected midturbinate nasal swabs at home for influenza viruses, respiratory syncytial viruses (RSV), and human metapneumoviruses (hMPV) real-time RT-PCR testing and the study nurse collected a second midturbinate nasal swab during home visits. Paired specimens were processed and tested on the same day. RESULTS The majority (109, 60%) of 182 participants were 20-30 years old. All 200 paired swabs had optimal specimen quality. The median time from symptom onsets to participant-collected swabs was 2 days and to staff-collected swabs was also 2 days. The median time interval between the 2 swabs was 2 hours. Compared to staff-collected swabs, the participant-collected swabs were 93% sensitive and 99% specific for influenza virus detection, 94% sensitive and 99% specific for RSV detection, and 100% sensitive and 100% specific for hMPV detection. CONCLUSIONS Participant-collected midturbinate nasal swabs were a valid alternative approach for laboratory confirmation of influenza-, RSV-, and hMPV-associated illnesses among pregnant women in a community setting.
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Affiliation(s)
| | - Joshua A Mott
- Influenza Program, Thailand Ministry of Public Health-US Centers for Disease Control and Prevention Collaboration, Nonthaburi, Thailand
- Influenza Division, US Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Sarita Mohanty
- Influenza Division, US Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Chalinthorn Sinthuwattanawibool
- Influenza Program, Thailand Ministry of Public Health-US Centers for Disease Control and Prevention Collaboration, Nonthaburi, Thailand
| | | | | | - Chonticha Klungthong
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Stefan Fernandez
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Lindsay Kim
- Division of Viral Diseases, US Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | | | | | | | | | - Fatimah S Dawood
- Influenza Division, US Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Wanitchaya Kittikraisak
- Influenza Program, Thailand Ministry of Public Health-US Centers for Disease Control and Prevention Collaboration, Nonthaburi, Thailand
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17
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Zimmerman PA, King CL, Ghannoum M, Bonomo RA, Procop GW. Molecular Diagnosis of SARS-CoV-2: Assessing and Interpreting Nucleic Acid and Antigen Tests. Pathog Immun 2021; 6:135-156. [PMID: 34405126 PMCID: PMC8360705 DOI: 10.20411/pai.v6i1.422] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 04/23/2021] [Indexed: 12/11/2022] Open
Abstract
In this review, we summarize the current status of nucleic acid and antigen testing required for diagnosing SARS-CoV-2 infection and COVID-19 disease. Nucleic acid amplification (NAAT) and antigen-detection (Ag) tests occupy a critically important frontline of defense against SARS-CoV-2 in clinical and public health settings. In early stages of this outbreak, we observed that identifying the causative agent of a new illness of unknown origin was greatly accelerated by characterizing the nucleic acid signature of the novel coronavirus. Results from nucleic acid sequencing led to the development of highly sensitive RT-PCR testing for use in clinical settings and to informing best practices for patient care, and in public health settings to the development of strategies for protecting populations. As the current COVID-19 pandemic has evolved, we have seen how NAAT performance has been used to guide and optimize specimen collection, inform patient triage decisions, reveal unexpected clinical symptoms, clarify risks of transmission within patient care facilities, and guide appropriate treatment strategies. For public health settings during the earliest stages of the pandemic, NAATs served as the only tool available for studying the epidemiology of this new disease by identifying infected individuals, studying transmission patterns, modeling population impacts, and enabling disease control organizations and governments to make challenging disease mitigation recommendations to protect the expanding breadth of populations at risk. With time, the nucleic acid signature has provided the information necessary to understand SARS-CoV-2 protein expression for further development of antigen-based point-of-care (POC) diagnostic tests. The advent of massive parallel sequencing (ie, next generation sequencing) has afforded the characterization of this novel pathogen, informed the sequences best adapted for RT-PCR assays, guided vaccine production, and is currently used for tracking and monitoring SARS-CoV-2 variants.
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Affiliation(s)
- Peter A Zimmerman
- Center for Global Health and Diseases, Case Western Reserve University, Cleveland, Ohio
| | - Christopher L King
- Center for Global Health and Diseases, Case Western Reserve University, Cleveland, Ohio
| | - Mahmoud Ghannoum
- Center for Medical Mycology and Integrated Microbiome Core, Case Western Reserve University and University Hospitals Cleveland Medical Center, Cleveland, Ohio
| | - Robert A Bonomo
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio; Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio; Departments of Pharmacology, Molecular Biology and Microbiology, Biochemistry, and Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, Cleveland, Ohio; and the CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES) Cleveland, Ohio
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18
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Wang X, Li Y, Deloria-Knoll M, Madhi SA, Cohen C, Arguelles VL, Basnet S, Bassat Q, Brooks WA, Echavarria M, Fasce RA, Gentile A, Goswami D, Homaira N, Howie SRC, Kotloff KL, Khuri-Bulos N, Krishnan A, Lucero MG, Lupisan S, Mathisen M, McLean KA, Mira-Iglesias A, Moraleda C, Okamoto M, Oshitani H, O'Brien KL, Owor BE, Rasmussen ZA, Rath BA, Salimi V, Sawatwong P, Scott JAG, Simões EAF, Sotomayor V, Thea DM, Treurnicht FK, Yoshida LM, Zar HJ, Campbell H, Nair H. Global burden of acute lower respiratory infection associated with human parainfluenza virus in children younger than 5 years for 2018: a systematic review and meta-analysis. Lancet Glob Health 2021; 9:e1077-e1087. [PMID: 34166626 PMCID: PMC8298256 DOI: 10.1016/s2214-109x(21)00218-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 04/16/2021] [Accepted: 04/22/2021] [Indexed: 12/17/2022]
Abstract
BACKGROUND Human parainfluenza virus (hPIV) is a common virus in childhood acute lower respiratory infections (ALRI). However, no estimates have been made to quantify the global burden of hPIV in childhood ALRI. We aimed to estimate the global and regional hPIV-associated and hPIV-attributable ALRI incidence, hospital admissions, and mortality for children younger than 5 years and stratified by 0-5 months, 6-11 months, and 12-59 months of age. METHODS We did a systematic review of hPIV-associated ALRI burden studies published between Jan 1, 1995, and Dec 31, 2020, found in MEDLINE, Embase, Global Health, Cumulative Index to Nursing and Allied Health Literature, Web of Science, Global Health Library, three Chinese databases, and Google search, and also identified a further 41 high-quality unpublished studies through an international research network. We included studies reporting community incidence of ALRI with laboratory-confirmed hPIV; hospital admission rates of ALRI or ALRI with hypoxaemia in children with laboratory-confirmed hPIV; proportions of patients with ALRI admitted to hospital with laboratory-confirmed hPIV; or in-hospital case-fatality ratios (hCFRs) of ALRI with laboratory-confirmed hPIV. We used a modified Newcastle-Ottawa Scale to assess risk of bias. We analysed incidence, hospital admission rates, and hCFRs of hPIV-associated ALRI using a generalised linear mixed model. Adjustment was made to account for the non-detection of hPIV-4. We estimated hPIV-associated ALRI cases, hospital admissions, and in-hospital deaths using adjusted incidence, hospital admission rates, and hCFRs. We estimated the overall hPIV-associated ALRI mortality (both in-hospital and out-hospital mortality) on the basis of the number of in-hospital deaths and care-seeking for child pneumonia. We estimated hPIV-attributable ALRI burden by accounting for attributable fractions for hPIV in laboratory-confirmed hPIV cases and deaths. Sensitivity analyses were done to validate the estimates of overall hPIV-associated ALRI mortality and hPIV-attributable ALRI mortality. The systematic review protocol was registered on PROSPERO (CRD42019148570). FINDINGS 203 studies were identified, including 162 hPIV-associated ALRI burden studies and a further 41 high-quality unpublished studies. Globally in 2018, an estimated 18·8 million (uncertainty range 12·8-28·9) ALRI cases, 725 000 (433 000-1 260 000) ALRI hospital admissions, and 34 400 (16 400-73 800) ALRI deaths were attributable to hPIVs among children younger than 5 years. The age-stratified and region-stratified analyses suggested that about 61% (35% for infants aged 0-5 months and 26% for 6-11 months) of the hospital admissions and 66% (42% for infants aged 0-5 months and 24% for 6-11 months) of the in-hospital deaths were in infants, and 70% of the in-hospital deaths were in low-income and lower-middle-income countries. Between 73% and 100% (varying by outcome) of the data had a low risk in study design; the proportion was 46-65% for the adjustment for health-care use, 59-77% for patient groups excluded, 54-93% for case definition, 42-93% for sampling strategy, and 67-77% for test methods. Heterogeneity in estimates was found between studies for each outcome. INTERPRETATION We report the first global burden estimates of hPIV-associated and hPIV-attributable ALRI in young children. Globally, approximately 13% of ALRI cases, 4-14% of ALRI hospital admissions, and 4% of childhood ALRI mortality were attributable to hPIV. These numbers indicate a potentially notable burden of hPIV in ALRI morbidity and mortality in young children. These estimates should encourage and inform investment to accelerate the development of targeted interventions. FUNDING Bill & Melinda Gates Foundation.
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Affiliation(s)
- Xin Wang
- Centre for Global Health, Usher Institute, Edinburgh Medical School, University of Edinburgh, Edinburgh, UK
| | - You Li
- Centre for Global Health, Usher Institute, Edinburgh Medical School, University of Edinburgh, Edinburgh, UK
| | - Maria Deloria-Knoll
- Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Shabir A Madhi
- South African Medical Research Council, Vaccines and Infectious Diseases Analytical Research Unit, Soweto, South Africa; Department of Science and Technology, National Research Foundation, Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Cheryl Cohen
- Centre for Respiratory Disease and Meningitis, National Institute for Communicable Diseases, Johannesburg, South Africa; School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Vina Lea Arguelles
- Research Institute for Tropical Medicine, Muntinlupa, Metro Manila, Philippines
| | - Sudha Basnet
- Department of Child Health, Tribhuvan University, Katmandu, Nepal; the Centre for International Health, University of Bergen, Bergen, Norway
| | - Quique Bassat
- Barcelona Global Health Institute, Hospital Clínic-University of Barcelona, Barcelona, Spain; Centro de Investigação em Saúde de Manhiça, Maputo, Mozambique; Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain; Paediatric Infectious Diseases Unit, Pediatrics Department, Hospital Sant Joan de Déu, University of Barcelona, Barcelona, Spain; Consorcio de Investigación Biomédica en Red de Epidemiología y Salud Pública, Madrid, Spain
| | - W Abdullah Brooks
- Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Marcela Echavarria
- Clinical Virology Unit, Centro de Educación Médica e Investigaciones Clínicas, Argentina
| | - Rodrigo A Fasce
- Public Health Institute of Chile, Región Metropolitana, Chile
| | - Angela Gentile
- Ricardo Gutierrez Children Hospital, Buenos Aires, Argentina
| | - Doli Goswami
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Nusrat Homaira
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh; Discipline of Paediatrics, School of Women's and Children's Health, The University of New South Wales, Sydney, NSW, Australia
| | - Stephen R C Howie
- Medical Research Council Unit, The Gambia at London School of Hygiene & Tropical Medicine, London, UK; Department of Paediatrics, Child & Youth Health, University of Auckland, Auckland, New Zealand
| | - Karen L Kotloff
- Department of Pediatrics and Department of Medicine, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Najwa Khuri-Bulos
- Department of Pediatrics, University of Jordan, School of Medicine, Amman, Jordan
| | - Anand Krishnan
- Centre for Community Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Marilla G Lucero
- Research Institute for Tropical Medicine, Muntinlupa, Philippines
| | - Socorro Lupisan
- Research Institute for Tropical Medicine, Muntinlupa, Philippines
| | - Maria Mathisen
- Department of Medical Microbiology, Vestre Viken Hospital Trust, Drammen, Norway
| | - Kenneth A McLean
- Centre for Global Health, Usher Institute, Edinburgh Medical School, University of Edinburgh, Edinburgh, UK
| | - Ainara Mira-Iglesias
- Área de Investigación en Vacunas, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana, Salud Pública, Valencia, Spain
| | - Cinta Moraleda
- Barcelona Global Health Institute, Hospital Clínic-University of Barcelona, Barcelona, Spain; Infectious Pediatric Diseases Section, Hospital Universitario de Octubre, Universidad Complutense, Research Institute Hospital de Octubre, Madrid, Spain
| | - Michiko Okamoto
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Histoshi Oshitani
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Katherine L O'Brien
- Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Betty E Owor
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Zeba A Rasmussen
- Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
| | - Barbara A Rath
- Vienna Vaccine Safety Initiative, Berlin, Germany; Université Bourgogne-Franche Comté, Besançon, France
| | - Vahid Salimi
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Pongpun Sawatwong
- Division of Global Health Protection, Thailand Ministry of Public Health and US Centers for Disease Control and Prevention Collaboration, Nonthaburi, Thailand
| | - J Anthony G Scott
- KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research, Kilifi, Kenya; Nuffield Department of Tropical Medicine, Oxford University, Oxford, UK; Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK
| | - Eric A F Simões
- Department of Pediatrics, Section of Infectious Diseases, University of Colorado, School of Medicine, Aurora, CO, USA; Department of Epidemiology and Center for Global Health, Colorado School of Public Health, Aurora, CO, USA
| | | | - Donald M Thea
- Department of Global Health and Development, Boston University School of Public Health, Boston, MA, USA
| | - Florette K Treurnicht
- Department of Medical Virology, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Lay-Myint Yoshida
- Department of Pediatric Infectious Diseases, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Heather J Zar
- Department of Paediatrics & Child Health, Medical Research Council Unit on Child & Adolescent Health, University of Cape Town, Cape Town, South Africa
| | - Harry Campbell
- Centre for Global Health, Usher Institute, Edinburgh Medical School, University of Edinburgh, Edinburgh, UK
| | - Harish Nair
- Centre for Global Health, Usher Institute, Edinburgh Medical School, University of Edinburgh, Edinburgh, UK.
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Li M, Wei R, Yang Y, He T, Shen Y, Qi T, Han T, Song Z, Zhu Z, Ma X, Lin Y, Yuan Y, Zhao K, Lu H, Zhou X. Comparing SARS-CoV-2 Testing in Anterior Nasal Vestibular Swabs vs. Oropharyngeal Swabs. Front Cell Infect Microbiol 2021; 11:653794. [PMID: 34307187 PMCID: PMC8293915 DOI: 10.3389/fcimb.2021.653794] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 06/16/2021] [Indexed: 12/18/2022] Open
Abstract
Purpose To investigate the sensitivity of SARS-CoV-2 testing in specimens collected from the anterior nasal vestibules of COVID-19 patients. Methods A cross-sectional analysis was performed on 30 patients with a confirmed diagnosis of COVID-19 at the Shanghai Public Health Clinical Center from March 14, 2020 to March 21, 2020. Paired specimens were collected from both the anterior nasal vestibule and the oropharynx from all patients. All specimens were tested for SARS-CoV-2 using reverse transcription-polymerase chain reaction (RT-PCR) assays. Results Of the 30 patients with confirmed COVID-19, 17 patients (56.7%) tested positive for SARS-CoV-2 when oropharyngeal specimens were used, while 20 patients (66.7%) tested positive when nasal swab specimens were used. There was no statistically significant difference in sensitivity between the two methods. Conclusions Respiratory swabs collected from the nasal vestibule offer a less invasive alternative to oropharyngeal swabs for specimen collection in the detection of SARS-CoV-2 infection, and have adequate sensitivity.
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Affiliation(s)
- Meiyan Li
- Department of Ophthalmology and Optometry, Eye and ENT Hospital, Fudan University, Shanghai, China
- NHC Key Laboratory of Myopia, Fudan University, Shanghai, China
- Shanghai Research Center of Ophthalmology and Optometry, Shanghai, China
| | - Ruoyan Wei
- Department of Ophthalmology and Optometry, Eye and ENT Hospital, Fudan University, Shanghai, China
- NHC Key Laboratory of Myopia, Fudan University, Shanghai, China
- Shanghai Research Center of Ophthalmology and Optometry, Shanghai, China
| | - Yaling Yang
- Department of Ophthalmology, Shanghai Public Health Clinical Center, Shanghai, China
| | - Taiwen He
- Department of Ophthalmology, Shanghai Public Health Clinical Center, Shanghai, China
| | - Yinzhong Shen
- Department of Infectious Diseases and Immunology, Shanghai Public Health Clinical Center, Shanghai, China
| | - Tangkai Qi
- Department of Infectious Diseases and Immunology, Shanghai Public Health Clinical Center, Shanghai, China
| | - Tian Han
- Department of Ophthalmology and Optometry, Eye and ENT Hospital, Fudan University, Shanghai, China
- NHC Key Laboratory of Myopia, Fudan University, Shanghai, China
- Shanghai Research Center of Ophthalmology and Optometry, Shanghai, China
| | - Zhigang Song
- Department of Pathogen Diagnosis and Biosafety, Shanghai Public Health Clinical Center, Shanghai, China
| | - Zhaoqin Zhu
- Department of Laboratory Medicine, Shanghai Public Health Clinical Center, Shanghai, China
| | - Xiaopeng Ma
- Shanghai Research Institute of Acupuncture and Meridian, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yixiao Lin
- Department of Infectious Diseases and Immunology, Shanghai Public Health Clinical Center, Shanghai, China
| | - Yasheng Yuan
- Department of Otolaryngology, Eye and ENT Hospital, Fudan University, Shanghai, China
| | - Keqing Zhao
- Department of Otolaryngology, Eye and ENT Hospital, Fudan University, Shanghai, China
| | - Hongzhou Lu
- Department of Infectious Diseases and Immunology, Shanghai Public Health Clinical Center, Shanghai, China
| | - Xingtao Zhou
- Department of Ophthalmology and Optometry, Eye and ENT Hospital, Fudan University, Shanghai, China
- NHC Key Laboratory of Myopia, Fudan University, Shanghai, China
- Shanghai Research Center of Ophthalmology and Optometry, Shanghai, China
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20
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Rodrigues J, Gouveia C, Santos MA, Costa O, Côrte‐Real R, Brito MJ. Comparison of nasopharyngeal samples for SARS-CoV-2 detection in a paediatric cohort. J Paediatr Child Health 2021; 57:1078-1081. [PMID: 33605504 PMCID: PMC8013390 DOI: 10.1111/jpc.15405] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 01/22/2021] [Accepted: 02/04/2021] [Indexed: 01/10/2023]
Abstract
AIM The diagnosis of coronavirus disease 2019 (COVID-19) depends on accurate and rapid testing. Choosing an appropriate sample may impact diagnosis. Naso-oropharyngeal swabs (NOS) are most frequently used, despite several limitations. Since studies suggest nasopharyngeal aspirate (NPA) as a superior alternative in children, we hypothesised collecting both nasopharyngeal swab and aspirate would improve our diagnostic accuracy. METHODS Observational, longitudinal, prospective study from 7 March to 7 May in a tertiary paediatric hospital in Lisbon. The objective was to compare the rate of detection of SARS-CoV-2 between NOS and NPA samples collected simultaneously. RESULTS A total of 438 samples collected from 85 patients with confirmed COVID-19. There were 47.7% overall positive specimens - 32% (70/219) positive NOS and 63.5% (139/219) positive NPA. The tests were 67.6% concordant (k = 0.45). 50.3% had positive NPA with negative NOS, while 1.3% had positive NOS with negative NPA. NPA proved to be more sensitive (98.6% with 95% confidence interval 91.2-99.9% vs. 49.6% with 95% confidence interval 41.1-58.2%, P < 0.001). Additionally, the difference between NPA and NOS positive samples was statistically significant across all population groups (age, health condition, clinical presentation, contact with COVID-19 patients or need for hospitalisation), meaning NPA is more sensitive overall. CONCLUSIONS Nasopharyngeal aspirates had greater sensitivity than naso-oropharyngeal swabs in detecting SARS-CoV-2. Our results suggest paediatric patients would benefit from collecting nasopharyngeal aspirates in hospital settings, whenever feasible, to improve diagnosis of COVID-19.
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Affiliation(s)
- Jorge Rodrigues
- Infectious Diseases Unit, Department of Pediatrics, Hospital Dona EstefâniaCentro Hospitalar Universitário Lisboa Central, EPELisbonPortugal
| | - Catarina Gouveia
- Infectious Diseases Unit, Department of Pediatrics, Hospital Dona EstefâniaCentro Hospitalar Universitário Lisboa Central, EPELisbonPortugal,Nova Medical SchoolFaculdade de Ciências MédicasLisbonPortugal
| | - Madalena Almeida Santos
- Molecular Biology Laboratory, Department of Clinical PathologyCentro Hospitalar Universitário Lisboa Central, EPELisbonPortugal
| | - Olga Costa
- Molecular Biology Laboratory, Department of Clinical PathologyCentro Hospitalar Universitário Lisboa Central, EPELisbonPortugal
| | - Rita Côrte‐Real
- Molecular Biology Laboratory, Department of Clinical PathologyCentro Hospitalar Universitário Lisboa Central, EPELisbonPortugal
| | - Maria João Brito
- Infectious Diseases Unit, Department of Pediatrics, Hospital Dona EstefâniaCentro Hospitalar Universitário Lisboa Central, EPELisbonPortugal
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21
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Tsuneki-Tokunaga A, Kanai K, Itagaki A, Tsuchie H, Okada T, Kasagi M, Tanaka K, Aoki M, Hinay AJA, Kageyama S. Growth capability of epidemic influenza viruses in Japan since the 2009 H1N1 pandemic. Arch Virol 2021; 166:1193-1196. [PMID: 33580378 PMCID: PMC7880649 DOI: 10.1007/s00705-021-04976-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 12/17/2020] [Indexed: 11/26/2022]
Abstract
The correlation of viral growth capability (n = 156) with the viral load in nasopharyngeal swabs (n = 76) was assessed. Epidemic influenza A/H1N1, A/H3N2, and B viruses showed a wide range of growth capability (104-1011 copies/mL) in Madin-Darby canine kidney cells. The growth was correlated with the nasopharyngeal viral load (r = 0.53). Six selected strains showed growth-dependent cell death (r = 0.96) in a growth kinetics assay. Epidemic influenza viruses exhibit a wide range of growth capability. Growth capability should be considered one of the key factors in disease prognosis.
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Affiliation(s)
- Akeno Tsuneki-Tokunaga
- Division of Virology, Department of Microbiology and Immunology, Tottori University Faculty of Medicine, Yonago, Japan
- Tottori Infectious Diseases Forum, Tottori prefecture, Japan
| | - Kyosuke Kanai
- Division of Virology, Department of Microbiology and Immunology, Tottori University Faculty of Medicine, Yonago, Japan
- Tottori Infectious Diseases Forum, Tottori prefecture, Japan
| | - Asao Itagaki
- Division of Virology, Department of Microbiology and Immunology, Tottori University Faculty of Medicine, Yonago, Japan
- Tottori Infectious Diseases Forum, Tottori prefecture, Japan
| | - Hideaki Tsuchie
- Tottori Infectious Diseases Forum, Tottori prefecture, Japan
- Tsuchie Internal Medicine and Pediatric Clinic, Sakaiminato, Japan
| | - Takayoshi Okada
- Tottori Infectious Diseases Forum, Tottori prefecture, Japan
- Department of Pediatrics, Tottori Prefectural Kousei Hospital, Kurayoshi, Japan
| | - Masaaki Kasagi
- Tottori Infectious Diseases Forum, Tottori prefecture, Japan
- Kasagi Children's Clinic for Health Service, Yonago, Japan
| | - Kiyoshi Tanaka
- Tottori Infectious Diseases Forum, Tottori prefecture, Japan
- Tanaka Pediatric Clinic, Tottori, Japan
| | - Miho Aoki
- Division of Virology, Department of Microbiology and Immunology, Tottori University Faculty of Medicine, Yonago, Japan
| | - Alfredo Jr A Hinay
- Division of Virology, Department of Microbiology and Immunology, Tottori University Faculty of Medicine, Yonago, Japan
| | - Seiji Kageyama
- Division of Virology, Department of Microbiology and Immunology, Tottori University Faculty of Medicine, Yonago, Japan.
- Tottori Infectious Diseases Forum, Tottori prefecture, Japan.
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22
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Di Pietro GM, Capecchi E, Luconi E, Lunghi G, Bosis S, Bertolozzi G, Cantoni B, Marano G, Boracchi P, Biganzoli E, Castaldi S, Marchisio P. Diagnosis of SARS-CoV-2 in children: accuracy of nasopharyngeal swab compared to nasopharyngeal aspirate. Eur J Clin Microbiol Infect Dis 2021; 40:1155-1160. [PMID: 33411175 PMCID: PMC7788172 DOI: 10.1007/s10096-020-04131-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 12/14/2020] [Indexed: 11/26/2022]
Abstract
The tests currently used for the identification of SARS-CoV-2 include specimens taken from the upper and lower respiratory tract. Although recommendations from the World Health Organization prioritise the usage of a nasopharyngeal swab (NS), nasopharyngeal aspirates (NPA) are thought to be superior in identifying SARS-CoV-2 in children. To our knowledge, however, no paediatric study has been published on the subject. The aim of this study is to evaluate the diagnostic performances of NS referred to NPA for SARS-CoV-2 in children. We calculated the sensitivity and specificity of the NS referred to the NPA of the whole sample and considered both age and collection period as covariates in different analyses. We collected 300 paired samples. The NS had a specificity of 97.7% and a sensitivity of 58.1%. We found similar results for the group of subjects ≥ 6 years old, while for subjects < 6 years old, the sensitivity was 66.7% and the specificity 97.8%. Considering period as a covariate, the sensitivity and specificity for patients hospitalised in March (31 patients, 52 records) were 70.0% and 97.6%, while for patients involved in the follow-up (16 patients, 57 records), they were 57.2% and 89.7%. The NS has a low sensitivity in detecting SARS-CoV-2 in children when referred to the NPA, whereas its specificity is high. Our results suggest that in children under 6 years of age, NSs should be preferred whenever possible. Though statistically not significant, the sensitivity of the NS rises when performed before the NPA.
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Affiliation(s)
| | - Ester Capecchi
- University of Milan, Via della Commenda 9, 20122, Milan, Italy
| | - Ester Luconi
- Foundation IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | - Giovanna Lunghi
- University of Milan, Via della Commenda 9, 20122, Milan, Italy
- Foundation IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | - Samantha Bosis
- Foundation IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | | | - Barbara Cantoni
- Foundation IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | - Giuseppe Marano
- Department of Clinical Sciences and Community Health & DSRC, University of Milan, Milan, Italy
| | - Patrizia Boracchi
- Department of Clinical Sciences and Community Health & DSRC, University of Milan, Milan, Italy
| | - Elia Biganzoli
- University of Milan, Via della Commenda 9, 20122, Milan, Italy
- Department of Clinical Sciences and Community Health & DSRC, University of Milan, Milan, Italy
| | - Silvana Castaldi
- University of Milan, Via della Commenda 9, 20122, Milan, Italy
- Foundation IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | - Paola Marchisio
- University of Milan, Via della Commenda 9, 20122, Milan, Italy
- Foundation IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy
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23
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Guo WL, Jiang Q, Ye F, Li SQ, Hong C, Chen LY, Li SY. Effect of Throat Washings on Detection of 2019 Novel Coronavirus. Clin Infect Dis 2020; 71:1980-1981. [PMID: 32271374 PMCID: PMC7184513 DOI: 10.1093/cid/ciaa416] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 04/08/2020] [Indexed: 11/13/2022] Open
Abstract
The 2019 novel coronavirus was detected in the self-collected throat washings. Positive testing rate of throat washing was much higher than that of Nasopharyngeal swabs. Throat washing is a promising candidate for 2019-nCoV screening and monitoring due to its noninvasive and reliability.
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Affiliation(s)
- Wen-Liang Guo
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Qian Jiang
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Feng Ye
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Shao-Qiang Li
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Cheng Hong
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Li-Yan Chen
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Shi-Yue Li
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
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24
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Hou N, Wang K, Zhang H, Bai M, Chen H, Song W, Jia F, Zhang Y, Han S, Xie B. Comparison of detection rate of 16 sampling methods for respiratory viruses: a Bayesian network meta-analysis of clinical data and systematic review. BMJ Glob Health 2020; 5:bmjgh-2020-003053. [PMID: 33168521 PMCID: PMC7654123 DOI: 10.1136/bmjgh-2020-003053] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 09/18/2020] [Accepted: 10/14/2020] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Respiratory viruses (RVs) is a common cause of illness in people of all ages, at present, different types of sampling methods are available for respiratory viral diagnosis. However, the diversity of available sampling methods and the limited direct comparisons in randomised controlled trials (RCTs) make decision-making difficult. We did a network meta-analysis, which accounted for both direct and indirect comparisons, to determine the detection rate of different sampling methods for RVs. METHODS Relevant articles were retrieved comprehensively by searching the online databases of PubMed, Embase and Cochrane published before 25 March 2020. With the help of R V.3.6.3 software and 'GeMTC V.0.8.2' package, network meta-analysis was performed within a Bayesian framework. Node-splitting method and I 2 test combined leverage graphs and Gelman-Rubin-Brooks plots were conducted to evaluate the model's accuracy. The rank probabilities in direct and cumulative rank plots were also incorporated to rank the corresponding sampling methods for overall and specific virus. RESULTS 16 sampling methods with 54 438 samples from 57 literatures were ultimately involved in this study. The model indicated good consistency and convergence but high heterogeneity, hence, random-effect analysis was applied. The top three sampling methods for RVs were nasopharyngeal wash (NPW), mid-turbinate swab (MTS) and nasopharyngeal swab (NPS). Despite certain differences, the results of virus-specific subanalysis were basically consistent with RVs: MTS, NPW and NPS for influenza; MTS, NPS and NPW for influenza-a and b; saliva, NPW and NPS for rhinovirus and parainfluenza; NPW, MTS and nasopharyngeal aspirate for respiratory syncytial virus; saliva, NPW and MTS for adenovirus and sputum; MTS and NPS for coronavirus. CONCLUSION This network meta-analysis provides supporting evidences that NPW, MTS and NPS have higher diagnostic value regarding RVs infection, moreover, particular preferred methods should be considered in terms of specific virus pandemic. Of course, subsequent RCTs with larger samples are required to validate our findings.
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Affiliation(s)
- Nianzong Hou
- Department of Hand and Foot Surgery, Zibo Central Hospital,Shandong First Medical University, Zibo, Shandong, China
| | - Kai Wang
- Department of Critical Care Medicine, Zibo central hospital, Zibo, Shandong, China
| | - Haiyang Zhang
- Department of Hand and Foot Surgery, Zibo Central Hospital,Shandong First Medical University, Zibo, Shandong, China
| | - Mingjian Bai
- Department of Clinical Laboratory, Aerospace Central Hospital, Beijing, China
| | - Hao Chen
- Department of spine Surgery, Renji Hospital, Shanghai, China
| | - Weidong Song
- Department of Orthopedic Surgery, Sun Yat-Sen Memorial Hospital, Guangzhou, Guangdong, China
| | - Fusen Jia
- Department of Hand and Foot Surgery, Zibo Central Hospital,Shandong First Medical University, Zibo, Shandong, China
| | - Yi Zhang
- Department of Hand and Foot Surgery, Zibo Central Hospital,Shandong First Medical University, Zibo, Shandong, China
| | - Shiliang Han
- Department of Hand and Foot Surgery, Zibo Central Hospital,Shandong First Medical University, Zibo, Shandong, China
| | - Bing Xie
- Department of Hand and Foot Surgery, Zibo Central Hospital,Shandong First Medical University, Zibo, Shandong, China
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25
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Leong NKC, Chu DKW, Chu JTS, Tam YH, Ip DKM, Cowling BJ, Poon LLM. A six-plex droplet digital RT-PCR assay for seasonal influenza virus typing, subtyping, and lineage determination. Influenza Other Respir Viruses 2020; 14:720-729. [PMID: 32519796 PMCID: PMC7578307 DOI: 10.1111/irv.12769] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Revised: 05/19/2020] [Accepted: 05/21/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND There are two influenza A subtypes (H1 and H3) and two influenza B lineages (Victoria and Yamagata) that currently co-circulate in humans. In this study, we report the development of a six-plex droplet digital RT-PCR (ddRT-PCR) assay that can detect HA and M segments of influenza A (H1, H3, and M) and influenza B (Yamagata HA, Victoria HA, and M) viruses in a single reaction mixture. It can simultaneously detect six different nucleic acid targets in a ddRT-PCR platform. METHODS The six-plex ddRT-PCR used in this study is an amplitude-based multiplex assay. The analytical performance of the assay was evaluated. Correlation with standard qRT-PCR methodology was assessed using 55 clinical samples. RESULTS The assay has a wide dynamic range, and it has good reproducibility within and between runs. The limit of quantification of each target in this assay ranged from 15 copies/reaction for influenza B Victoria M gene to 45 copies/reaction for influenza B Yamagata M gene. In addition, this assay can accurately quantify each of these targets in samples containing viral RNAs from two different viruses that were mixed in a highly skewed ratio. Typing, subtyping, and lineage differentiation data of 55 tested clinical respiratory specimens were found to be identical to those deduced from standard monoplex qRT-PCR assays. CONCLUSIONS The six-plex ddRT-PCR test was demonstrated to be highly suitable for detecting dual influenza infection cases. This assay is expected to be a useful diagnostic tool for clinical and research use.
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Affiliation(s)
- Nathaniel K. C. Leong
- School of Public HealthLKS Faculty of MedicineThe University of Hong KongHong KongChina
| | - Daniel K. W. Chu
- School of Public HealthLKS Faculty of MedicineThe University of Hong KongHong KongChina
| | - Julie T. S. Chu
- School of Public HealthLKS Faculty of MedicineThe University of Hong KongHong KongChina
| | - Yat H. Tam
- School of Public HealthLKS Faculty of MedicineThe University of Hong KongHong KongChina
| | - Dennis K. M. Ip
- School of Public HealthLKS Faculty of MedicineThe University of Hong KongHong KongChina
| | - Benjamin J. Cowling
- School of Public HealthLKS Faculty of MedicineThe University of Hong KongHong KongChina
| | - Leo L. M. Poon
- School of Public HealthLKS Faculty of MedicineThe University of Hong KongHong KongChina
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26
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Malosh RE, Petrie JG, Callear AP, Monto AS, Martin ET. Home collection of nasal swabs for detection of influenza in the Household Influenza Vaccine Evaluation Study. Influenza Other Respir Viruses 2020; 15:227-234. [PMID: 33107200 PMCID: PMC7902250 DOI: 10.1111/irv.12822] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 10/05/2020] [Accepted: 10/07/2020] [Indexed: 01/25/2023] Open
Abstract
Background Community‐based studies of influenza and other respiratory viruses (eg, SARS‐CoV‐2) require laboratory confirmation of infection. During the current COVID‐19 pandemic, social distancing guidelines require alternative data collection in order to protect both research staff and participants. Home‐collected respiratory specimens are less resource‐intensive, can be collected earlier after symptom onset, and provide a low‐contact means of data collection. A prospective, multi‐year, community‐based cohort study is an ideal setting to examine the utility of home‐collected specimens for identification of influenza. Methods We describe the feasibility and reliability of home‐collected specimens for the detection of influenza. We collected data and specimens between October 2014 and June 2017 from the Household Influenza Vaccine Evaluation (HIVE) Study. Cohort participants were asked to collect a nasal swab at home upon onset of acute respiratory illness. Research staff also collected nose and throat swab specimens in the study clinic within 7 days of onset. We estimated agreement using Cohen's kappa and calculated sensitivity and specificity of home‐collected compared to staff‐collected specimens. Results We tested 336 paired staff‐ and home‐collected respiratory specimens for influenza by RT‐PCR; 150 staff‐collected specimens were positive for influenza A/H3N2, 23 for influenza A/H1N1, 14 for influenza B/Victoria, and 31 for influenza B/Yamagata. We found moderate agreement between collection methods for influenza A/H3N2 (0.70) and B/Yamagata (0.69) and high agreement for influenza A/H1N1 (0.87) and B/Victoria (0.86). Sensitivity ranged from 78% to 86% for all influenza types and subtypes. Specificity was high for influenza A/H1N1 and both influenza B lineages with a range from 96% to 100%, and slightly lower for A/H3N2 infections (88%). Conclusions Collection of nasal swab specimens at home is both feasible and reliable for identification of influenza virus infections.
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Affiliation(s)
- Ryan E Malosh
- Department of Epidemiology, University of Michigan School of Public Health, 1415 Washingon Heights, Ann Arbor, MI, 48109, USA
| | - Joshua G Petrie
- Department of Epidemiology, University of Michigan School of Public Health, 1415 Washingon Heights, Ann Arbor, MI, 48109, USA
| | - Amy P Callear
- Department of Epidemiology, University of Michigan School of Public Health, 1415 Washingon Heights, Ann Arbor, MI, 48109, USA
| | - Arnold S Monto
- Department of Epidemiology, University of Michigan School of Public Health, 1415 Washingon Heights, Ann Arbor, MI, 48109, USA
| | - Emily T Martin
- Department of Epidemiology, University of Michigan School of Public Health, 1415 Washingon Heights, Ann Arbor, MI, 48109, USA
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27
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Arnold MT, Temte JL, Barlow SK, Bell CJ, Goss MD, Temte EG, Checovich MM, Reisdorf E, Scott S, Guenther K, Wedig M, Shult P, Uzicanin A. Comparison of participant-collected nasal and staff-collected oropharyngeal specimens for human ribonuclease P detection with RT-PCR during a community-based study. PLoS One 2020; 15:e0239000. [PMID: 33027284 PMCID: PMC7540885 DOI: 10.1371/journal.pone.0239000] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 08/27/2020] [Indexed: 11/24/2022] Open
Abstract
We analyzed 4,352 participant- and staff-collected respiratory specimens from 2,796 subjects in the Oregon Child Absenteeism due to Respiratory Disease Study. Trained staff collected oropharyngeal specimens from school-aged children with acute respiratory illness while household participants of all ages collected their own midturbinate nasal specimens in year one and anterior nasal specimens in year two. Human ribonuclease P levels were measured using RT-PCR for all staff- and participant-collected specimens to determine adequacy, defined as Cycle threshold less than 38. Overall, staff- and participant-collected specimens were 99.9% and 96.4% adequate, respectively. Participant-collected midturbinate specimens were 95.2% adequate in year one, increasing to 97.2% in year two with anterior nasal collection. The mean human ribonuclease P Cycle threshold for participant-collected specimens was 31.18 in year one and 28.48 in year two. The results from this study suggest that community-based participant collection of respiratory specimens is comparable to staff-collected oropharyngeal specimens, is feasible, and may be optimal with anterior nasal collection.
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Affiliation(s)
- Mitchell T. Arnold
- Department of Family Medicine and Community Health, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI, United States of America
- * E-mail:
| | - Jonathan L. Temte
- Department of Family Medicine and Community Health, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI, United States of America
| | - Shari K. Barlow
- Department of Family Medicine and Community Health, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI, United States of America
| | - Cristalyne J. Bell
- Department of Family Medicine and Community Health, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI, United States of America
| | - Maureen D. Goss
- Department of Family Medicine and Community Health, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI, United States of America
| | - Emily G. Temte
- Department of Family Medicine and Community Health, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI, United States of America
| | - Mary M. Checovich
- Department of Family Medicine and Community Health, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI, United States of America
| | - Erik Reisdorf
- Wisconsin State Laboratory of Hygiene, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Samantha Scott
- Wisconsin State Laboratory of Hygiene, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Kyley Guenther
- Wisconsin State Laboratory of Hygiene, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Mary Wedig
- Wisconsin State Laboratory of Hygiene, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Peter Shult
- Wisconsin State Laboratory of Hygiene, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Amra Uzicanin
- US Centers for Disease Control and Prevention, Atlanta, GA, United States of America
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28
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Pham J, Meyer S, Nguyen C, Williams A, Hunsicker M, McHardy I, Gendlina I, Goldstein DY, Fox AS, Hudson A, Darby P, Hovey P, Morales J, Mitchell J, Harrington K, Majlessi M, Moberly J, Shah A, Worlock A, Walcher M, Eaton B, Getman D, Clark C. Performance Characteristics of a High-Throughput Automated Transcription-Mediated Amplification Test for SARS-CoV-2 Detection. J Clin Microbiol 2020; 58:e01669-20. [PMID: 32727828 PMCID: PMC7512162 DOI: 10.1128/jcm.01669-20] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 07/27/2020] [Indexed: 01/12/2023] Open
Abstract
The COVID-19 pandemic caused by the new SARS-CoV-2 coronavirus has imposed severe challenges on laboratories in their effort to achieve sufficient diagnostic testing capability for identifying infected individuals. In this study, we report the analytical and clinical performance characteristics of a new, high-throughput, fully automated nucleic acid amplification test system for the detection of SARS-CoV-2. The assay utilizes target capture, transcription-mediated amplification, and acridinium ester-labeled probe chemistry on the automated Panther system to directly amplify and detect two separate target sequences in the open reading frame 1ab (ORF1ab) region of the SARS-CoV-2 RNA genome. The probit 95% limit of detection of the assay was determined to be 0.004 50% tissue culture infective dose (TCID50)/ml using inactivated virus and 25 copies/ml (c/ml) using synthetic in vitro transcript RNA targets. Analytical sensitivity (100% detection) was confirmed to be 83 to 194 c/ml using three commercially available SARS-CoV-2 nucleic acid controls. No cross-reactivity or interference was observed with testing of six related human coronaviruses, as well as 24 other viral, fungal, and bacterial pathogens, at high titers. Clinical nasopharyngeal swab specimen testing (n = 140) showed 100%, 98.7%, and 99.3% positive, negative, and overall agreement, respectively, with a validated reverse transcription-PCR nucleic acid amplification test (NAAT) for SARS-CoV-2 RNA. These results provide validation evidence for a sensitive and specific method for pandemic-scale automated molecular diagnostic testing for SARS-CoV-2.
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Affiliation(s)
| | | | | | | | | | - Ian McHardy
- Scripps Health, Microbiology Laboratory, San Diego California, USA
| | - Inessa Gendlina
- Montefiore Medical Center, Department of Pathology, Bronx, New York, USA
| | | | - Amy S Fox
- Montefiore Medical Center, Department of Pathology, Bronx, New York, USA
| | | | - Paul Darby
- Hologic, Inc., San Diego California, USA
| | - Paul Hovey
- Hologic, Inc., San Diego California, USA
| | | | | | | | | | | | - Ankur Shah
- Hologic, Inc., San Diego California, USA
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29
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Value of swab types and collection time on SARS-COV-2 detection using RT-PCR assay. J Virol Methods 2020; 286:113974. [PMID: 32949663 PMCID: PMC7493793 DOI: 10.1016/j.jviromet.2020.113974] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 07/27/2020] [Accepted: 09/14/2020] [Indexed: 01/09/2023]
Abstract
The value of swab types on the detection of SARS-CoV-2 from patients during infection late stage is studied. The effect of specimen collection time on the detection rate of novel coronavirus was explored. Nasopharyngeal /nasal swabs collected before washing in the morning are more suitable for screening of large-scale specimens.
Objective Low viral load from patients infected with SARS-CoV-2 during infection late stage easily lead to false negative nucleic acid testing results, thus having great challenges to the prevention and control of the current pandemic. In present study, we mainly aimed to evaluate specimen types and specimen collection timepoint on the positive detection of 2019 novel coronavirus from patients at infection late stage based on RT-PCR testing. Methods Paired nasopharyngeal swabs, nasal swabs, oropharyngeal swabs and anal swabs were collected from patients infected with SARS-CoV-2 during infection late stage before washing in the morning and afternoon on the same day. Then virus RNA was extracted and tested for 2019-nCoV identification by RT-PCR within 24 h. Results Viral load was low at late infection stage. Specimens collected before washing in the morning would increase the detection ratio of 2019-nCoV. Detection ratio of nasopharyngeal swab [65 (95 % CI: 49.51–77.87) vs 42.5(95 % CI: 28.51–57.8)] or nasal swab [57.5 (95 % CI: 42.2–71.49) vs 35 (95 % CI: 22.13–50.49)] is higher not only than oropharyngeal swab[22.5 (95 % CI: 12.32–37.5) vs 7.5 (95 % CI: 2.58–19.86)], but also anal swab[2.5 (95 % CI: 0.44–12.88) vs 5 (95 % CI: 1.38–16.5)]. Conclusions In summary, our research discovers that nasopharyngeal or nasal swab collected before washing in the morning might be more suitable for detecting of large-scale specimens from patients infected with low SARS-CoV-2 load during infection late stage. Those results could facilitate other laboratories in collecting appropriate specimens for improving detection of SARS-CoV-2 from patients during infection late stage as well as initially screening.
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30
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Evaluation of Lateral-Flow Assay for Rapid Detection of Influenza Virus. BIOMED RESEARCH INTERNATIONAL 2020; 2020:3969868. [PMID: 32964030 PMCID: PMC7495160 DOI: 10.1155/2020/3969868] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 08/11/2020] [Indexed: 12/22/2022]
Abstract
Background Influenza virus mainly causes acute respiratory infections in humans. However, the diagnosis of influenza is not accurate based on clinical evidence, as the symptoms of flu are similar to other respiratory virus. The lateral-flow assay is a rapid method to detect influenza virus. But the effectiveness of the technique in detecting flu viruses is unclear. Hence, a meta-analysis would be performed to evaluate the accuracy of LFA in detecting influenza virus. Methods Relevant literature was searched out in PubMed, Embase, Web of Science, and Cochrane Library databases with the keywords "lateral flow assay" and "flu virus". By Meta-DiSc software, pooled sensitivity, pooled specificity, positive likelihood ratio (PLR), negative likelihood ratio (NLR), diagnostic odds ratio (DOR), summary receiver operating characteristic curve (SROC), and area under the curve (AUC) can be calculated. Results This meta-analysis contains 13 studies and 24 data. The pooled sensitivity and specificity of the influenza virus detected by LFA were 0.84 (95% CI: 0.82-0.86) and 0.97 (95% CI: 0.97-0.98), respectively. The pooled values of PLR, NLR, DOR, and SROC were 32.68 (17.16-62.24), 0.17 (0.13-0.24), 334.07 (144.27-773.53), and 0.9877. No publication bias was found. Conclusions LFA exhibited high sensitivity and specificity in diagnosing influenza virus. It is a valuable alternative method which can diagnose influenza virus quickly. However, more evidence is required to confirm whether LFA is comparable to traditional methods for detecting the virus.
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31
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Is Nasopharyngeal Swab Comparable With Nasopharyngeal Aspirate to Detect SARS-CoV-2 in Children? Pediatr Infect Dis J 2020; 39:e288-e289. [PMID: 32740453 DOI: 10.1097/inf.0000000000002824] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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32
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Nasal Swab Sampling for SARS-CoV-2: a Convenient Alternative in Times of Nasopharyngeal Swab Shortage. J Clin Microbiol 2020; 58:JCM.00721-20. [PMID: 32295896 PMCID: PMC7269411 DOI: 10.1128/jcm.00721-20] [Citation(s) in RCA: 109] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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33
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Uyeki TM, Bernstein HH, Bradley JS, Englund JA, File TM, Fry AM, Gravenstein S, Hayden FG, Harper SA, Hirshon JM, Ison MG, Johnston BL, Knight SL, McGeer A, Riley LE, Wolfe CR, Alexander PE, Pavia AT. Clinical Practice Guidelines by the Infectious Diseases Society of America: 2018 Update on Diagnosis, Treatment, Chemoprophylaxis, and Institutional Outbreak Management of Seasonal Influenzaa. Clin Infect Dis 2020; 68:e1-e47. [PMID: 30566567 DOI: 10.1093/cid/ciy866] [Citation(s) in RCA: 332] [Impact Index Per Article: 83.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 10/05/2018] [Indexed: 12/19/2022] Open
Abstract
These clinical practice guidelines are an update of the guidelines published by the Infectious Diseases Society of America (IDSA) in 2009, prior to the 2009 H1N1 influenza pandemic. This document addresses new information regarding diagnostic testing, treatment and chemoprophylaxis with antiviral medications, and issues related to institutional outbreak management for seasonal influenza. It is intended for use by primary care clinicians, obstetricians, emergency medicine providers, hospitalists, laboratorians, and infectious disease specialists, as well as other clinicians managing patients with suspected or laboratory-confirmed influenza. The guidelines consider the care of children and adults, including special populations such as pregnant and postpartum women and immunocompromised patients.
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Affiliation(s)
- Timothy M Uyeki
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Henry H Bernstein
- Division of General Pediatrics, Cohen Children's Medical Center, New Hyde Park, New York
| | - John S Bradley
- Division of Infectious Diseases, Rady Children's Hospital.,University of California, San Diego
| | - Janet A Englund
- Department of Pediatrics, University of Washington, Seattle Children's Hospital
| | - Thomas M File
- Division of Infectious Diseases Summa Health, Northeast Ohio Medical University, Rootstown
| | - Alicia M Fry
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Stefan Gravenstein
- Providence Veterans Affairs Medical Center and Center for Gerontology and Healthcare Research, Brown University, Providence, Rhode Island
| | - Frederick G Hayden
- Division of Infectious Diseases and International Health, University of Virginia Health System, Charlottesville
| | - Scott A Harper
- Office of Public Health Preparedness and Response, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Jon Mark Hirshon
- Department of Emergency Medicine, Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore
| | - Michael G Ison
- Divisions of Infectious Diseases and Organ Transplantation, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - B Lynn Johnston
- Department of Medicine, Dalhousie University, Nova Scotia Health Authority, Halifax, Canada
| | - Shandra L Knight
- Library and Knowledge Services, National Jewish Health, Denver, Colorado
| | - Allison McGeer
- Division of Infection Prevention and Control, Sinai Health System, University of Toronto, Ontario, Canada
| | - Laura E Riley
- Department of Maternal-Fetal Medicine, Massachusetts General Hospital, Boston
| | - Cameron R Wolfe
- Division of Infectious Diseases, Duke University Medical Center, Durham, North Carolina
| | - Paul E Alexander
- McMaster University, Hamilton, Ontario, Canada.,Infectious Diseases Society of America, Arlington, Virginia
| | - Andrew T Pavia
- Division of Pediatric Infectious Diseases, University of Utah, Salt Lake City
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34
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Brealey JC, Young PR, Sloots TP, Ware RS, Lambert SB, Sly PD, Grimwood K, Chappell KJ. Bacterial colonization dynamics associated with respiratory syncytial virus during early childhood. Pediatr Pulmonol 2020; 55:1237-1245. [PMID: 32176838 DOI: 10.1002/ppul.24715] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 02/24/2020] [Indexed: 12/21/2022]
Abstract
Respiratory syncytial virus (RSV) is an important cause of early life acute respiratory infections. Potentially pathogenic respiratory bacteria, including Streptococcus pneumoniae, Moraxella catarrhalis, and Haemophilus influenzae are frequently detected during RSV infections and associated with increased illness severity. However, the temporal dynamics of bacterial colonization associated with RSV infection remain unclear. We used weekly nasal swab data from a prospective longitudinal birth cohort in Brisbane, Australia, to investigate bacterial colonization patterns within children aged less than 2 years in the 4-week period before and after an RSV infection. During 54 RSV infection episodes recorded in 47 children, both S. pneumoniae and M. catarrhalis were detected frequently (in 33 [61.1%] and 26 [48.1%] RSV infections, respectively). In most cases, S. pneumoniae and M. catarrhalis colonization preceded the viral infection, with the nasal load of each increasing during RSV infection. Generally, the dominant serotype of S. pneumoniae remained consistent in the 1 to 2 weeks immediately before and after RSV infection. Little evidence was found to indicate that prior colonization with either bacteria predisposed participants to developing RSV infection during the annual seasonal epidemic. Possible coacquisition events, where the bacteria species was first detected with RSV and not in the preceding 4 weeks, were observed in approximately 20% of RSV/S. pneumoniae and RSV/M. catarrhalis codetections. Taken together our results indicate that RSV generally triggered an outgrowth, rather than a new acquisition, of S. pneumoniae and M. catarrhalis from the resident microbial community.
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Affiliation(s)
- Jaelle C Brealey
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia
| | - Paul R Young
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia.,Australian Infectious Diseases Research Centre, The University of Queensland, St Lucia, Queensland, Australia
| | - Theo P Sloots
- Child Health Research Centre, The University of Queensland, South Brisbane, Queensland, Australia.,Queensland Paediatric Infectious Diseases Laboratory, Infection Management and Prevention Service, Children's Health Queensland, South Brisbane, Queensland, Australia
| | - Robert S Ware
- School of Medicine and Infection and Immunology Division, Menzies Health Institute Queensland, Griffith University, Southport, Queensland, Australia
| | - Stephen B Lambert
- Child Health Research Centre, The University of Queensland, South Brisbane, Queensland, Australia
| | - Peter D Sly
- Australian Infectious Diseases Research Centre, The University of Queensland, St Lucia, Queensland, Australia.,Child Health Research Centre, The University of Queensland, South Brisbane, Queensland, Australia
| | - Keith Grimwood
- School of Medicine and Infection and Immunology Division, Menzies Health Institute Queensland, Griffith University, Southport, Queensland, Australia.,Departments of Infectious Diseases and Paediatrics, Gold Coast Health, Southport, Queensland, Australia
| | - Keith J Chappell
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia.,Australian Infectious Diseases Research Centre, The University of Queensland, St Lucia, Queensland, Australia
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35
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Acquired Immunodeficiency from Maternal Chemotherapy and Severe Primary Pneumocystis Infection in an Infant. Case Rep Pediatr 2020; 2020:5740304. [PMID: 32257491 PMCID: PMC7102488 DOI: 10.1155/2020/5740304] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Accepted: 02/12/2020] [Indexed: 12/12/2022] Open
Abstract
Pneumocystis jirovecii is recognized as an opportunistic pathogen in immunosuppressed patients. We report a case of severe Pneumocystis pneumonia (PCP) in an infant with acquired combined immunodeficiency secondary to maternal chemotherapy exposure during the second and third trimesters of pregnancy. The infant required cardiorespiratory support with veno-venous extracorporeal membrane oxygenation (VV-ECMO) for severe respiratory failure. This case highlights the potential for severe acquired immunodeficiency in this patient cohort and further postnatal surveillance is highly recommended.
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36
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Ma ZY, Deng H, Hua LD, Lei W, Zhang CB, Dai QQ, Tao WJ, Zhang L. Suspension microarray-based comparison of oropharyngeal swab and bronchoalveolar lavage fluid for pathogen identification in young children hospitalized with respiratory tract infection. BMC Infect Dis 2020; 20:168. [PMID: 32087697 PMCID: PMC7036252 DOI: 10.1186/s12879-020-4900-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 02/18/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Respiratory tract infection (RTI) in young children is a leading cause of morbidity and hospitalization worldwide. There are few studies assessing the performance for bronchoalveolar lavage fluid (BALF) versus oropharyngeal swab (OPS) specimens in microbiological findings for children with RTI. The primary purpose of this study was to compare the detection rates of OPS and paired BALF in detecting key respiratory pathogens using suspension microarray. METHODS We collected paired OPS and BALF specimens from 76 hospitalized children with respiratory illness. The samples were tested simultaneously for 8 respiratory viruses and 5 bacteria by suspension microarray. RESULTS Of 76 paired specimens, 62 patients (81.6%) had at least one pathogen. BALF and OPS identified respiratory pathogen infections in 57 (75%) and 49 (64.5%) patients, respectively (P > 0.05). The etiology analysis revealed that viruses were responsible for 53.7% of the patients, whereas bacteria accounted for 32.9% and Mycoplasma pneumoniae for 13.4%. The leading 5 pathogens identified were respiratory syncytial virus, Streptococcus pneumoniaee, Haemophilus influenzae, Mycoplasma pneumoniae and adenovirus, and they accounted for 74.2% of etiological fraction. For detection of any pathogen, the overall detection rate of BALF (81%) was marginally higher than that (69%) of OPS (p = 0.046). The differences in the frequency distribution and sensitivity for most pathogens detected by two sampling methods were not statistically significant. CONCLUSIONS In this study, BALF and OPS had similar microbiological yields. Our results indicated the clinical value of OPS testing in pediatric patients with respiratory illness.
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Affiliation(s)
- Zhan-Ying Ma
- Dongguan Maternal and Child Health Care Hospital, Dongguan, 523120, China
| | - Hua Deng
- Translational Medicine Center, Guangdong Women and Children Hospital, Guangzhou, 511400, China
| | - Li-Dong Hua
- Translational Medicine Center, Guangdong Women and Children Hospital, Guangzhou, 511400, China
| | - Wen Lei
- Translational Medicine Center, Guangdong Women and Children Hospital, Guangzhou, 511400, China
| | - Chang-Bin Zhang
- Prenatal Diagnosis Centre, Guangdong Women and Children Hospital, Guangzhou, 511400, China
| | - Qi-Qiang Dai
- Guangzhou DaAn Clinical Laboratory Center, YunKang Group, Guangzhou, 51000, China
| | - Wei-Jing Tao
- Guangzhou DaAn Clinical Laboratory Center, YunKang Group, Guangzhou, 51000, China
| | - Liang Zhang
- Translational Medicine Center, Guangdong Women and Children Hospital, Guangzhou, 511400, China.
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37
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Hii SF, Senevirathna D, Llewellyn S, Inpankaew T, Odermatt P, Khieu V, Muth S, McCarthy J, Traub RJ. Development and Evaluation of a Multiplex Quantitative Real-Time Polymerase Chain Reaction for Hookworm Species in Human Stool. Am J Trop Med Hyg 2019; 99:1186-1193. [PMID: 30226132 PMCID: PMC6221243 DOI: 10.4269/ajtmh.18-0276] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Hookworm disease caused by Necator americanus, Ancylostoma duodenale, and Ancylostoma ceylanicum affects half a billion people worldwide. The prevalence and intensity of infection of individual hookworm species are vital for assessing morbidity and generating targeted intervention programs for their control. The present study aims to evaluate a multiplex real-time quantitative PCR (qPCR) assay to determine the prevalence and egg intensity of all three hookworm species and compare this with standard microscopy and published genus-based conventional and real-time multiplex qPCRs. Performance of the diagnostic assays was evaluated using DNA extracted from 192 fecal samples collected as part of a soil-transmitted helminth (STH) survey in northern Cambodia. The prevalence of hookworms as detected by the multiplex hookworm qPCR of 84/192 (43.8%) was significantly higher than that using microscopy of 49/192 (25.5%). The hookworm multiplex qPCR showed very good agreement for the detection of both N. americanus (Kappa 0.943) and Ancylostoma spp. (Kappa 0.936) with a multiplex STH qPCR. A strong and moderate quantitative correlation between cycle threshold and eggs per gram (EPG) feces was obtained for the hookworm qPCR for seeded DNA egg extracts (R 2 ≥ 0.9004) and naturally egg-infected individuals (R 2 = 0.6848), respectively. The newly developed hookworm quantitative multiplex qPCR has the potential for application in anthelmintic efficacy trials and for monitoring the success of mass deworming programs targeting individual species of anthroponotic and zoonotic hookworms.
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Affiliation(s)
- Sze Fui Hii
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Australia
| | - Dammika Senevirathna
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Australia
| | - Stacey Llewellyn
- Clinical Tropical Medicine Laboratory, QIMR Berghofer Medical Research Institute, Herston, Australia
| | - Tawin Inpankaew
- Department of Parasitology, Faculty of Veterinary Medicine, Kasetsart University, Bangkok, Thailand
| | - Peter Odermatt
- University of Basel, Basel, Switzerland.,Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Basel, Switzerland
| | - Virak Khieu
- National Centre for Parasitology, Entomology, and Malaria Control, Phnom Penh, Cambodia
| | - Sinoun Muth
- National Centre for Parasitology, Entomology, and Malaria Control, Phnom Penh, Cambodia
| | - James McCarthy
- Clinical Tropical Medicine Laboratory, QIMR Berghofer Medical Research Institute, Herston, Australia
| | - Rebecca J Traub
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Australia
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38
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Comparison of Respiratory Specimen Collection Methods for Detection of Influenza Virus Infection by Reverse Transcription-PCR: a Literature Review. J Clin Microbiol 2019; 57:JCM.00027-19. [PMID: 31217267 DOI: 10.1128/jcm.00027-19] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The detection of influenza virus in respiratory specimens from ill individuals is the most commonly used method to identify influenza virus infection. A number of respiratory specimen types may be used, including swabs, brush, aspirate, and wash, and specimens may be collected from numerous sites, including the anterior and posterior nasopharynx, oropharynx, and nares. Traditionally, respiratory specimens from the nasopharynx have been considered to have the highest sensitivity for viral detection. However, as molecular assays such as reverse transcription-PCR (RT-PCR) have increased the sensitivity of viral detection from respiratory specimens, the use of less-invasive and easier-to-obtain specimens has increased for the detection of influenza virus. This review presents and evaluates the sensitivities of respiratory specimen methods used in epidemiologic studies that used RT-PCR to detect influenza virus in respiratory specimens from ill patients. This literature review suggested that a combination of two less-invasive swabbing methods, such as nasal and oropharyngeal swabs, had about the same sensitivity as did nasopharyngeal specimens for influenza virus detection by RT-PCR. By combining two less-invasive collection methods, it may be possible to reduce barriers to enrollment without compromising influenza virus detection sensitivity.
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Seaman CP, Tran LTT, Cowling BJ, Sullivan SG. Self-collected compared with professional-collected swabbing in the diagnosis of influenza in symptomatic individuals: A meta-analysis and assessment of validity. J Clin Virol 2019; 118:28-35. [PMID: 31400670 DOI: 10.1016/j.jcv.2019.07.010] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 06/20/2019] [Accepted: 07/29/2019] [Indexed: 11/29/2022]
Abstract
Self-collected nasal swabs offer a cheaper alternative to professional-collected swabs for influenza testing. However, the diagnostic accuracy of self-collection has not been quantitatively reviewed. We identified 14 studies that compared diagnostic accuracy of self-collected to professional-collected swabs in influenza symptomatic individuals. Self-collected swabs were found to be highly acceptable, simple and comfortable to use. Data from nine studies were meta-analyzed. Pooled sensitivity was 87% (95% CI: 80%, 92%) and specificity was 99% (95% CI: 98%, 100%), compared to professional-collected swabs in the diagnosis of influenza. Pooled sensitivity and specificity estimates were used to assess the potential bias that would be introduced in studies had self-collected rather than professional-collected samples been used. While self-collected swabbing should not replace the role of clinical testing, our findings support the use of self-collected swabs for influenza research and surveillance. This method will be an important tool for evaluating novel influenza vaccines and vaccination strategies.
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Affiliation(s)
- Christopher P Seaman
- School of Population and Global Health, University of Melbourne, Melbourne, Australia
| | - Luong Thi Tuyet Tran
- School of Population and Global Health, University of Melbourne, Melbourne, Australia
| | - Benjamin J Cowling
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, The University of Hong Kong, Hong Kong Special Administrative Region
| | - Sheena G Sullivan
- School of Population and Global Health, University of Melbourne, Melbourne, Australia; WHO Collaborating Centre for Reference and Research on Influenza, Royal Melbourne Hospital, and the Doherty Department, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia; Department of Epidemiology, Fielding School of Public Health, University of California, Los Angeles, USA.
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40
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Wang L, Yang S, Yan X, Liu T, Feng Z, Li G. Comparing the yield of oropharyngeal swabs and sputum for detection of 11 common pathogens in hospitalized children with lower respiratory tract infection. Virol J 2019; 16:84. [PMID: 31234918 PMCID: PMC6591818 DOI: 10.1186/s12985-019-1177-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 05/07/2019] [Indexed: 12/01/2022] Open
Abstract
Background Advances in molecular laboratory techniques are changing the prospects for the diagnosis of viral infectious diseases. Multiplex polymerase chain reaction assay (multiplex-PCR) can detect dozens of pathogens simultaneously, greatly reducing turnaround time (TAT) and improving detection sensitivity. But as a double-edged sword, due to the high sensitivity of PCR, the type of respiratory specimens is critical to diagnosis. In this work, we performed a head-to-head comparison to evaluate the multiplex-PCR yields between two samples, sputum and flocked oropharyngeal swabs (OPS). Methods Eleven common respiratory pathogens were tested in hospitalized children< 13 years of age who met the criteria for lower respiratory tract infection by GeXP-based multiplex-PCR of paired OPS and sputum. Results From January to June 2018, 440 children with paired OPS and sputum were tested. The positive rate was 84% (369/440) for OPS and 88% (386/440) for sputum (p = .007). The frequency of detection of HRV, RSV, Influenza A virus, HMPV, parainfluenza virus, adenovirus, M. pneumoniae, coronavirus, bocavirus and C. pneumoniae in sputa was higher than that of OPSs (all p < .001). Both types of specimens had similarly very good kappa values for most of pathogens, except for Mycoplasma pneumonia (κ = 0.61) and Chlamydia pneumoniae (κ = 0.24). Additionally, 79.3% (349/440) of cases showed consistent results between the two types of samples, and they were significantly younger than patients with inconsistent results (p = .002). Conclusions Flocked oropharyngeal swabs and sputum performed similarly for the detection of common respiratory pathogens in hospitalized children by multiplex-PCR, except for Mycoplasma pneumoniae and Chlamydia pneumoniae. Young patients are likely to have consistent results between the two specimens. Electronic supplementary material The online version of this article (10.1186/s12985-019-1177-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Le Wang
- Institute of Pediatric Research, Children's Hospital of Hebei Province, Shijiazhuang, 050031, China
| | - Shuo Yang
- Institute of Pediatric Research, Children's Hospital of Hebei Province, Shijiazhuang, 050031, China
| | - Xiaotong Yan
- Institute of Pediatric Research, Children's Hospital of Hebei Province, Shijiazhuang, 050031, China
| | - Teng Liu
- Institute of Pediatric Research, Children's Hospital of Hebei Province, Shijiazhuang, 050031, China
| | - Zhishan Feng
- Hebei General Hospital, Shijiazhuang, 050000, China.
| | - Guixia Li
- Institute of Pediatric Research, Children's Hospital of Hebei Province, Shijiazhuang, 050031, China.
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Sarna M, Ware RS, Lambert SB, Sloots TP, Nissen MD, Grimwood K. Timing of First Respiratory Virus Detections in Infants: A Community-Based Birth Cohort Study. J Infect Dis 2019; 217:418-427. [PMID: 29165576 PMCID: PMC7107408 DOI: 10.1093/infdis/jix599] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 11/16/2017] [Indexed: 11/13/2022] Open
Abstract
Background Determining timing of first virus detection episodes (fVDEs) for different respiratory viruses in infants identifies risk periods and informs preventive interventions, including vaccination. We describe the ages and nature of fVDEs in an infant birth cohort and explore factors associated with increased odds of symptomatic fVDEs. Methods The Observational Research in Childhood Infectious Diseases (ORChID) study is a community-based birth cohort describing acute respiratory infections in infants until their second birthday. Parents recorded daily symptoms and collected nose swabs weekly, which were batch-tested using polymerase chain reaction assays for 17 respiratory viruses. Results One hundred fifty-eight infants participated in ORChID. The median age for fVDEs was 2.9 months for human rhinovirus (HRV) but was ≥13.9 months for other respiratory viruses. Overall, 52% of HRV fVDEs were symptomatic, compared with 57%–83% of other fVDEs. Respiratory syncytial virus and human metapneumovirus fVDEs were more severe than HRV fVDEs. Older age and the winter season were associated with symptomatic episodes. Conclusions Infants do not always experience respiratory symptoms with their fVDE. Predominance of early HRV detections highlights the need for timing any intervention early in life. fVDEs from other respiratory viruses most commonly occur when maternal vaccines may no longer provide protection.
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Affiliation(s)
- Mohinder Sarna
- School of Public Health, University of Queensland, Brisbane.,UQ Child Health Research Centre, School of Medicine, University of Queensland, Brisbane
| | - Robert S Ware
- UQ Child Health Research Centre, School of Medicine, University of Queensland, Brisbane.,Menzies Health Institute Queensland, Griffith University, Gold Coast
| | - Stephen B Lambert
- UQ Child Health Research Centre, School of Medicine, University of Queensland, Brisbane
| | - Theo P Sloots
- UQ Child Health Research Centre, School of Medicine, University of Queensland, Brisbane
| | - Michael D Nissen
- UQ Child Health Research Centre, School of Medicine, University of Queensland, Brisbane
| | - Keith Grimwood
- School of Medicine and Menzies Health Institute Queensland, Griffith University, Gold Coast.,Departments of Infectious Diseases and Paediatrics, Gold Coast Health, Queensland, Australia
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Fisher CE, Boeckh M, Jerome KR, Englund J, Kuypers J. Evaluating addition of self-collected throat swabs to nasal swabs for respiratory virus detection. J Clin Virol 2019; 115:43-46. [PMID: 30978619 PMCID: PMC6587583 DOI: 10.1016/j.jcv.2019.04.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 03/28/2019] [Accepted: 04/03/2019] [Indexed: 10/27/2022]
Abstract
BACKGROUND Early and accurate detection of respiratory viruses (RV) is important for patient management. We have previously shown that self-collected nasal swabs (NS) are feasible and as sensitive as clinician-collected nasal washes for detection of RV, but the additive benefit of self-collected throat swabs is unknown. OBJECTIVES To evaluate the added yield of self-collected nasal to throat swabs for detection of RV by PCR in patients with upper respiratory tract infection (URTI) symptoms. STUDY DESIGN Patients with URTI symptoms self-collected paired polyurethane foam NS and nylon flocked throat swabs and completed a symptom survey. Swabs were tested for 12 RV by real-time reverse transcription (RT)-PCR. Descriptive, McNemar's, and Wilcoxon signed rank statistical tests were used. RESULTS 115 paired nasal and throat swabs were collected from 63 individuals, with 71/115 (62%) positive for a RV by at least one specimen, including 51 positive by both, 17 positive by NS only, and 3 positive by throat swab only. The sensitivity of NS was 96% (95%CI: 88-99) versus 76% (95% CI: 65-85) in throat swabs, p<0.001. The median PCR cycle threshold (Ct) in 51 concordant samples was lower (indicating higher viral concentration) in NS (25.1) versus throat swabs (32.0). The three samples positive only by throat swab had high Ct values (33.8, 36.2, and 38.8, all rhinovirus). CONCLUSION Self-collection of NS was significantly more sensitive than self collection of throat swabs for detection of RV by RT-PCR. The addition of throat sampling does not appear to increase the diagnostic load in the self-testing setting.
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Affiliation(s)
- Cynthia E Fisher
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA, United States; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States.
| | - Michael Boeckh
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA, United States; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States; Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Keith R Jerome
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States; Department of Laboratory Medicine, University of Washington, United States
| | - Janet Englund
- Seattle Children's Hospital, Seattle, WA, United States
| | - Jane Kuypers
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States; Department of Laboratory Medicine, University of Washington, United States
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Uyeki TM, Bernstein HH, Bradley JS, Englund JA, File TM, Fry AM, Gravenstein S, Hayden FG, Harper SA, Hirshon JM, Ison MG, Johnston BL, Knight SL, McGeer A, Riley LE, Wolfe CR, Alexander PE, Pavia AT. Clinical Practice Guidelines by the Infectious Diseases Society of America: 2018 Update on Diagnosis, Treatment, Chemoprophylaxis, and Institutional Outbreak Management of Seasonal Influenzaa. Clin Infect Dis 2019; 68. [PMID: 30566567 PMCID: PMC6653685 DOI: 10.1093/cid/ciy866 10.1093/cid/ciz044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/30/2023] Open
Abstract
These clinical practice guidelines are an update of the guidelines published by the Infectious Diseases Society of America (IDSA) in 2009, prior to the 2009 H1N1 influenza pandemic. This document addresses new information regarding diagnostic testing, treatment and chemoprophylaxis with antiviral medications, and issues related to institutional outbreak management for seasonal influenza. It is intended for use by primary care clinicians, obstetricians, emergency medicine providers, hospitalists, laboratorians, and infectious disease specialists, as well as other clinicians managing patients with suspected or laboratory-confirmed influenza. The guidelines consider the care of children and adults, including special populations such as pregnant and postpartum women and immunocompromised patients.
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Affiliation(s)
- Timothy M Uyeki
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Henry H Bernstein
- Division of General Pediatrics, Cohen Children's Medical Center, New Hyde Park, New York
| | - John S Bradley
- Division of Infectious Diseases, Rady Children's Hospital
- University of California, San Diego
| | - Janet A Englund
- Department of Pediatrics, University of Washington, Seattle Children's Hospital
| | - Thomas M File
- Division of Infectious Diseases Summa Health, Northeast Ohio Medical University, Rootstown
| | - Alicia M Fry
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Stefan Gravenstein
- Providence Veterans Affairs Medical Center and Center for Gerontology and Healthcare Research, Brown University, Providence, Rhode Island
| | - Frederick G Hayden
- Division of Infectious Diseases and International Health, University of Virginia Health System, Charlottesville
| | - Scott A Harper
- Office of Public Health Preparedness and Response, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Jon Mark Hirshon
- Department of Emergency Medicine, Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore
| | - Michael G Ison
- Divisions of Infectious Diseases and Organ Transplantation, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - B Lynn Johnston
- Department of Medicine, Dalhousie University, Nova Scotia Health Authority, Halifax, Canada
| | - Shandra L Knight
- Library and Knowledge Services, National Jewish Health, Denver, Colorado
| | - Allison McGeer
- Division of Infection Prevention and Control, Sinai Health System, University of Toronto, Ontario, Canada
| | - Laura E Riley
- Department of Maternal-Fetal Medicine, Massachusetts General Hospital, Boston
| | - Cameron R Wolfe
- Division of Infectious Diseases, Duke University Medical Center, Durham, North Carolina
| | - Paul E Alexander
- McMaster University, Hamilton, Ontario, Canada
- Infectious Diseases Society of America, Arlington, Virginia
| | - Andrew T Pavia
- Division of Pediatric Infectious Diseases, University of Utah, Salt Lake City
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Abstract
A wide variety of microorganisms are potential respiratory pathogens, and the spectrum of known pathogens for each respiratory infection syndrome has not changed markers over recent years. Detection of likely etiologic agents of respiratory infections can help direct management and can also play an important role in disease surveillance. For this purpose, we are still reliant on many traditional diagnostic tools that have been used for decades in order to determine the microbial etiology of respiratory infections. However, these tools have been increasingly supplemented by newer methods, particular molecular diagnostic techniques, which have enabled the more rapid detection of many pathogens that were previously difficult to detect. These advances have particularly lead to improvements in the ability to detect respiratory viruses and also other microorganisms that do not normally colonize the respiratory tract. Recognition of the existence of the lung microbiome has challenged the traditional views of pneumonia pathogenesis and may provide the opportunity for new diagnostic tools that are focused on more than just detection of specific known pathogens. Continued liaison between clinicians and laboratory staff is vital in order to facilitate the most cost-effective use of laboratory diagnostics.
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Goggin RK, Bennett CA, Bassiouni A, Bialasiewicz S, Vreugde S, Wormald PJ, Psaltis AJ. Comparative Viral Sampling in the Sinonasal Passages; Different Viruses at Different Sites. Front Cell Infect Microbiol 2018; 8:334. [PMID: 30283747 PMCID: PMC6156342 DOI: 10.3389/fcimb.2018.00334] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 08/29/2018] [Indexed: 12/12/2022] Open
Abstract
Background: With the emergence of the microbiome as an important factor in health and disease in the respiratory tract standardised, validated techniques are required for its accurate characterisation. No standardised technique has been reported specifically for viral sampling in the sinonasal passages. Aim: To optimise viral sampling techniques from the sinonasal cavity. Methods: Sterile cytology brushes were used under endoscopic guidance to sample the sinonasal mucosa at time of endoscopic sinus surgery at both the middle and inferior meatuses (MM and IM). DNA and RNA were extracted from the samples and underwent PCR or RT-PCR testing, respectively, for a panel of 15 common upper respiratory tract viruses. Results: Twenty-four adult patients were recruited for this study. 18/24 (75%) patients were positive for virus in at least one site, while 8/24 (33%) were positive for virus at both sites. The mean number of viruses identified at the two sites were similar (0.875 ± 0.899 at the MM vs. 0.750 ± 1.032 at the IM). 6/24 (25%) of patients showed no virus at either site, while 3/24 (12.5%) demonstrated the same viral species at both sites. Conclusion: Although the number of viruses present at different sites with the nasal cavity are similar, discord exists in the viral species between sites. It is therefore recommended that both sites are sampled in the clinical and research setting better to characterise the viral species within the nasal cavity.
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Affiliation(s)
- Rachel K Goggin
- Department of Surgery - Otolaryngology, University of Adelaide, Adelaide, SA, Australia
| | - Catherine A Bennett
- Department of Surgery - Otolaryngology, University of Adelaide, Adelaide, SA, Australia
| | - Ahmed Bassiouni
- Department of Surgery - Otolaryngology, University of Adelaide, Adelaide, SA, Australia
| | - Seweryn Bialasiewicz
- Queensland Paediatric Infectious Diseases Laboratory, Children's Health Queensland, Brisbane, QLD, Australia.,Child Health Research Centre, The University of Queensland, Brisbane, QLD, Australia
| | - Sarah Vreugde
- Department of Surgery - Otolaryngology, University of Adelaide, Adelaide, SA, Australia
| | - Peter-John Wormald
- Department of Surgery - Otolaryngology, University of Adelaide, Adelaide, SA, Australia
| | - Alkis J Psaltis
- Department of Surgery - Otolaryngology, University of Adelaide, Adelaide, SA, Australia
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Praznik A, Vinšek N, Prodan A, Erčulj V, Pokorn M, Mrvič T, Paro D, Krivec U, Strle F, Petrovec M, Žnidaršič Eržen M, Grosek Š. Risk factors for bronchiolitis severity: A retrospective review of patients admitted to the university hospital from central region of Slovenia. Influenza Other Respir Viruses 2018; 12:765-771. [PMID: 29944781 PMCID: PMC6185887 DOI: 10.1111/irv.12587] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 06/11/2018] [Indexed: 12/01/2022] Open
Abstract
Aim Study's objective was to identify risk factors associated with bronchiolitis severity. Methods A retrospective chart review of all children <2 years old diagnosed with bronchiolitis at the University Medical Centre Ljubljana between May 2014 and April 2015, who were treated as outpatients (paediatric emergency department, PED group) or as inpatients in the standard hospital setting (WARD group) or in the paediatric intensive care unit (PICU group). Detection of respiratory viruses in nasopharyngeal swab was accomplished by RT‐PCR. Severity was assessed by Wang Respiratory Score and hospitalization longer than 24 hours. Results The study included 761 children. The three most frequently detected viruses were respiratory syncytial virus (RSV), human rhinovirus (hRV) and human bocavirus (hBoV) (57.5%, 272/473; 25.6%, 121/473; 18.4%, 87/473). Patient groups differed in Wang Respiratory Score for the severity of bronchiolitis (P < 0.001). No differences regarding the causative viruses were found. There was a lower proportion of children with the presence of more than one virus in PICU group compared to other two groups (P = 0.017). The three groups significantly differed in age, birthweight, comorbidities, bronchodilator treatment and antibiotic usage. However, multiple regression analysis revealed that younger age and the use of antibiotics were associated with bronchiolitis severity defined as hospitalization for >24 hours. Conclusions Respiratory syncytial virus, hRV and hBoV were the most frequently detected viruses. The majority of patients admitted to the PICU had only one virus detected. Younger age and the use of antibiotics were associated with bronchiolitis severity.
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Affiliation(s)
- Ajda Praznik
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Neža Vinšek
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Ana Prodan
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | | | - Marko Pokorn
- Department of Infectious Diseases, University Medical Centre Ljubljana, Ljubljana, Slovenia.,Chair of Infectious Diseases, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Tatjana Mrvič
- Department of Infectious Diseases, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Darja Paro
- Department of Neonatology, University Children's Hospital, University Medical Centre, Ljubljana, Slovenia.,Chair of Pediatrics, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Uroš Krivec
- Pulmonology Department, University Children's Hospital, University Medical Centre, Ljubljana, Slovenia
| | - Franc Strle
- Department of Infectious Diseases, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Miroslav Petrovec
- Chair of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia.,Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Marta Žnidaršič Eržen
- Pediatric Clinical Department, Community Health Centre Ljubljana, Ljubljana, Slovenia
| | - Štefan Grosek
- Chair of Pediatrics, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia.,Department of Pediatric Surgery and Intensive Care, University Medical Centre Ljubljana, Ljubljana, Slovenia
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Saliva as a diagnostic specimen for testing respiratory virus by a point-of-care molecular assay: a diagnostic validity study. Clin Microbiol Infect 2018; 25:372-378. [PMID: 29906597 DOI: 10.1016/j.cmi.2018.06.009] [Citation(s) in RCA: 128] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 06/01/2018] [Accepted: 06/02/2018] [Indexed: 11/20/2022]
Abstract
OBJECTIVES Automated point-of-care molecular assays have greatly shortened the turnaround time of respiratory virus testing. One of the major bottlenecks now lies at the specimen collection step, especially in a busy clinical setting. Saliva is a convenient specimen type that can be provided easily by adult patients. This study assessed the diagnostic validity, specimen collection time and cost associated with the use of saliva. METHODS This was a prospective diagnostic validity study comparing the detection rate of respiratory viruses between saliva and nasopharyngeal aspirate (NPA) among adult hospitalized patients using Xpert® Xpress Flu/RSV. The cost and time associated with the collection of saliva and nasopharyngeal specimens were also estimated. RESULTS Between July and October 2017, 214 patients were recruited. The overall agreement between saliva and NPA was 93.3% (196/210, κ 0.851, 95% CI 0.776-0.926). There was no significant difference in the detection rate of respiratory viruses between saliva and NPA (32.9% (69/210) versus 35.7% (75/210); p 0.146). The overall sensitivity and specificity were 90.8% (81.9%-96.2%) and 100% (97.3%-100%), respectively, for saliva, and were 96.1% (88.9%-99.2%) and 98.5% (94.7%-99.8%), respectively, for NPA. The time and cost associated with the collection of saliva were 2.26-fold and 2.59-fold lower, respectively, than those of NPA. CONCLUSIONS Saliva specimens have high sensitivity and specificity in the detection of respiratory viruses by an automated multiplex Clinical Laboratory Improvement Amendments-waived point-of-care molecular assay when compared with those of NPA. The use of saliva also reduces the time and cost associated with specimen collection.
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Lunardi F, Vuljan SE, Perissinotto E, Pezzuto F, Malacrida S, Bugin S, Bertozzi I, Snijders D, Rizzo S, Barbato A, Calabrese F. Nasopharyngeal aspirate value in paediatric chronic lower respiratory tract illness. Eur Respir J 2018; 51:13993003.01783-2017. [DOI: 10.1183/13993003.01783-2017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 03/12/2018] [Indexed: 11/05/2022]
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Jennings L, Huang QS, Barr I, Lee PI, Kim WJ, Buchy P, Sanicas M, Mungall BA, Chen J. Literature review of the epidemiology of influenza B disease in 15 countries in the Asia-Pacific region. Influenza Other Respir Viruses 2018; 12:383-411. [PMID: 29127742 PMCID: PMC5907823 DOI: 10.1111/irv.12522] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/26/2017] [Indexed: 01/06/2023] Open
Abstract
Influenza control strategies focus on the use of trivalent influenza vaccines containing two influenza A virus subtypes and one of the two circulating influenza type B lineages (Yamagata or Victoria). Mismatches between the vaccine B lineage and the circulating lineage have been regularly documented in many countries, including those in the Asia‐Pacific region. We conducted a literature review with the aim of understanding the relative circulation of influenza B viruses in Asia‐Pacific countries. PubMed and Western Pacific Region Index Medicus were searched for relevant articles on influenza type B published since 1990 in English language for 15 Asia‐Pacific countries. Gray literature was also accessed. From 4834 articles identified, 121 full‐text articles were analyzed. Influenza was reported as an important cause of morbidity in the Asia‐Pacific region, affecting all age groups. In all 15 countries, influenza B was identified and associated with between 0% and 92% of laboratory‐confirmed influenza cases in any one season/year. Influenza type B appeared to cause more illness in children aged between 1 and 10 years than in other age groups. Epidemiological data for the two circulating influenza type B lineages remain limited in several countries in the Asia‐Pacific, although the co‐circulation of both lineages was seen in countries where strain surveillance data were available. Mismatches between circulating B lineages and vaccine strains were observed in all countries with available data. The data suggest that a shift from trivalent to quadrivalent seasonal influenza vaccines could provide additional benefits by providing broader protection.
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Affiliation(s)
- Lance Jennings
- Canterbury District Health Board, Christchurch, New Zealand
| | - Qiu Sue Huang
- WHO National Influenza Centre, Institute of Environmental Science and Research, Porirua, New Zealand
| | - Ian Barr
- WHO Collaborating Centre for Reference and Research on Influenza, Melbourne, VIC, Australia
| | - Ping-Ing Lee
- Department of Pediatrics, National Taiwan University Children's Hospital, Taipei, Taiwan
| | - Woo Joo Kim
- Department of Internal Medicine, Korea University Guro Hospital, Seoul, Korea
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50
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Nunes MC, Soofie N, Downs S, Tebeila N, Mudau A, de Gouveia L, Madhi SA. Comparing the Yield of Nasopharyngeal Swabs, Nasal Aspirates, and Induced Sputum for Detection of Bordetella pertussis in Hospitalized Infants. Clin Infect Dis 2017; 63:S181-S186. [PMID: 27838671 PMCID: PMC5106614 DOI: 10.1093/cid/ciw521] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Background. Advances in molecular laboratory techniques are changing the landscape of Bordetella pertussis illness diagnosis. Polymerase chain reaction (PCR) assays have greatly improved the sensitivity detection and the turnaround time to diagnosis compared to culture. Moreover, different respiratory specimens, such as flocked nasopharyngeal swabs (NPSs), nasopharyngeal aspirates (NPAs), and induced sputum, have been used for B. pertussis detection, although there is limited head-to-head comparison to evaluating the PCR yield from the 3 sampling methods. Methods. Hospitalized infants <6 months of age who fulfilled a broad syndromic criteria of respiratory illness were tested for B. pertussis infection by PCR on paired NPSs and NPAs; or paired NPSs and induced sputum. An exploratory analysis of B. pertussis culture was performed on induced sputum specimens and in a subset of NPSs. Results. From November 2014 to May 2015, 484 infants with paired NPSs and NPAs were tested; 15 (3.1%) PCR-confirmed pertussis cases were identified, 13 of which were PCR positive on both samples, while 1 each were positive only on NPS or NPA. From March to October 2015, 320 infants had NPSs and induced sputum collected, and 11 (3.4%) pertussis cases were identified by PCR, including 8 (72.7%) positive on both samples, 1 (9.1%) only positive on NPS, and 2 (18.2%) only positive on induced sputum. The 3 types of specimens had similar negative predictive value >99% and sensitivity >83%. Compared to PCR, culture sensitivity was 60% in induced sputum and 40% in NPSs. Conclusions. Flocked nasopharyngeal swabs, nasopharyngeal aspirates, and induced sputum performed similarly for the detection of B. pertussis infection in young infants by PCR.
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Affiliation(s)
- Marta C Nunes
- Department of Science and Technology/National Research Foundation, Vaccine Preventable Diseases.,Medical Research Council, Respiratory and Meningeal Pathogens Research Unit, University of the Witwatersrand
| | - Nasiha Soofie
- Department of Science and Technology/National Research Foundation, Vaccine Preventable Diseases.,Medical Research Council, Respiratory and Meningeal Pathogens Research Unit, University of the Witwatersrand
| | - Sarah Downs
- Department of Science and Technology/National Research Foundation, Vaccine Preventable Diseases.,Medical Research Council, Respiratory and Meningeal Pathogens Research Unit, University of the Witwatersrand
| | - Naume Tebeila
- Department of Science and Technology/National Research Foundation, Vaccine Preventable Diseases.,Medical Research Council, Respiratory and Meningeal Pathogens Research Unit, University of the Witwatersrand
| | - Azwi Mudau
- Department of Science and Technology/National Research Foundation, Vaccine Preventable Diseases.,Medical Research Council, Respiratory and Meningeal Pathogens Research Unit, University of the Witwatersrand
| | - Linda de Gouveia
- National Institute for Communicable Diseases, National Health Laboratory Service, Centre for Respiratory Diseases and Meningitis, Johannesburg, South Africa
| | - Shabir A Madhi
- Department of Science and Technology/National Research Foundation, Vaccine Preventable Diseases.,Medical Research Council, Respiratory and Meningeal Pathogens Research Unit, University of the Witwatersrand.,National Institute for Communicable Diseases, National Health Laboratory Service, Centre for Respiratory Diseases and Meningitis, Johannesburg, South Africa
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