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Zhang G, Wang K, Ba L, Dong S, Gao J. Dynamic changes in the circulation of respiratory pathogens in children during and after the containment of the 2019 coronavirus disease pandemic in Kunming, China. Eur J Clin Microbiol Infect Dis 2024:10.1007/s10096-024-04945-1. [PMID: 39292354 DOI: 10.1007/s10096-024-04945-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Accepted: 09/10/2024] [Indexed: 09/19/2024]
Abstract
PURPOSE We aimed to determine the changes in the frequency of respiratory pathogens and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) during containment of the 2019 coronavirus disease pandemic and elucidate the epidemiological interference that may have occurred after lifting pandemic measures. METHODS A total of 4,770 Nasopharyngeal swab samples were collected from children with ARTIs from the First People's Hospital of Yunnan Province between January 2022 and December 2023 and subjected to nucleic acid testing for 13 types of respiratory pathogens and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). RESULTS The frequency of pathogens among children from 2020 to 2022 was in the following order: HRV > Mp > HADV > H3N2 > HMPV and HRV > HRSV > HPIV > H1N1 > H3N2. In weeks 1 to 3 of 2023, the frequency of pathogens significantly declined, and then H1N1 rebounded significantly in 2023. HRV, HRSV, and H3N2 showed a shift in the season of high frequency. Patterns of multi-pathogen infections were more complex in 2023 than in 2022, with HRV having a higher frequency and co-infection rate than other pathogens. These changes may have been associated with interference caused by the resurgence of SARS-CoV-2 prevalence, in addition to being influenced by changes in pandemic containment and lifting measures. CONCLUSIONS The frequency rate of common respiratory pathogens among children was not significantly different and remained high. The study findings help elucidate the aforementioned unique historical period and effectively control respiratory tract infections to reduce the harm to pediatric health caused by respiratory pathogens.
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Affiliation(s)
- Guiqian Zhang
- Department of Clinical Laboratory, The First People's Hospital of Yunnan Province, The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan, China
- Institute of Basic and Clinical Medicine, Yunnan Provincial Key Laboratory of Clinical Virology, The First People's Hospital of Yunnan Province, The Affiliated Hospital of Kunming University of Science and Technology, 157 Jinbi Road, Kunming, 650100, China
| | - Kaimei Wang
- Department of Medical Technology, Yunnan University of Business Management, Kunming, Yunnan, China
| | - Limei Ba
- Department of Clinical Laboratory, The First People's Hospital of Yunnan Province, The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Shumei Dong
- Department of Medical Technology, Yunnan University of Business Management, Kunming, Yunnan, China
| | - Jianmei Gao
- Institute of Basic and Clinical Medicine, Yunnan Provincial Key Laboratory of Clinical Virology, The First People's Hospital of Yunnan Province, The Affiliated Hospital of Kunming University of Science and Technology, 157 Jinbi Road, Kunming, 650100, China.
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2
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van Roekel C, Poukka E, Turunen T, Nohynek H, Presser L, Meijer A, Heikkinen T, Kramer R, Begier E, Teirlinck AC, Knol MJ. Effectiveness of Immunization Products Against Medically Attended Respiratory Syncytial Virus Infection: Generic Protocol for a Test-Negative Case-Control Study. J Infect Dis 2024; 229:S92-S99. [PMID: 37935046 DOI: 10.1093/infdis/jiad483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 10/20/2023] [Accepted: 10/24/2023] [Indexed: 11/09/2023] Open
Abstract
Monitoring the real-life effectiveness of respiratory syncytial virus (RSV) products is of major public health importance. This generic protocol for a test-negative design study aims to address currently envisioned approaches for RSV prevention (monoclonal antibodies and vaccines) to study effectiveness of these products among target groups: children, older adults, and pregnant women. The generic protocol approach was chosen to allow for flexibility in adapting the protocol to a specific setting. This protocol includes severe acute respiratory infection (SARI) and acute respiratory infection (ARI), both due to RSV, as end points. These end points can be applied to studies in hospitals, primarily targeting patients with more severe disease, but also to studies in general practitioner clinics targeting ARI.
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Affiliation(s)
- Caren van Roekel
- Centre for Infectious Disease Control, National Institute for Public Health and Environment, Bilthoven, the Netherlands
| | - Eero Poukka
- Infectious Disease Control and Vaccinations Unit, Department of Health Security, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Topi Turunen
- Infectious Disease Control and Vaccinations Unit, Department of Health Security, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Hanna Nohynek
- Infectious Disease Control and Vaccinations Unit, Department of Health Security, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Lance Presser
- Centre for Infectious Disease Control, National Institute for Public Health and Environment, Bilthoven, the Netherlands
| | - Adam Meijer
- Centre for Infectious Disease Control, National Institute for Public Health and Environment, Bilthoven, the Netherlands
| | - Terho Heikkinen
- Department of Pediatrics, University of Turku and Turku University Hospital, Turku, Finland
| | | | | | - Anne C Teirlinck
- Centre for Infectious Disease Control, National Institute for Public Health and Environment, Bilthoven, the Netherlands
| | - Mirjam J Knol
- Centre for Infectious Disease Control, National Institute for Public Health and Environment, Bilthoven, the Netherlands
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3
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Jahn K, Karakioulaki M, Schumann DM, Hirsch HH, Leuzinger K, Grize L, Aliberti S, Sotgiu G, Tamm M, Stolz D. Impact of bronchoalveolar lavage on the management of immunocompromised hosts. Eur J Intern Med 2024; 120:52-61. [PMID: 37722932 DOI: 10.1016/j.ejim.2023.09.007] [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: 08/05/2023] [Revised: 08/25/2023] [Accepted: 09/07/2023] [Indexed: 09/20/2023]
Abstract
BACKGROUND Respiratory infections are an important cause of morbidity and mortality in immunocompromised individuals. Fiberoptic bronchoscopy with bronchoalveolar lavage (BAL) is an important tool to detect infectious agents in immunocompromised patients with low respiratory tract infections (LRTI). RESEARCH QUESTION BAL changes the management of immunocompromised patients with suspected LRTI. STUDY DESIGN AND METHODS Immunocompromised patients with a suspicion of LRTI underwent diagnostic BAL. The primary composite outcome consisted of pre-defined modifications in the management of the immunocompromised patients following BAL. We quantified the impact of bronchoscopy up to 30 days after the procedure. RESULTS A total of 2666 visits from 1301 patients were included in the study and immunosuppression was classified as haematological (n = 1040; 544 patients), solid organ transplantation (n = 666; 107 patients) and other causes (n = 960; 650 patients). BAL led to a change in management in 52.36% (n = 1396) of all cases. This percentage, as well as the 30-day mortality differed significantly amongst the three groups. Age, C-reactive protein and aetiology of infection determined significantly the risk of 30-day mortality in all patients. In 1.89% (n = 50) of all cases, a combination of 2 respiratory viral agents was identified and 24.23% (n = 646) were diagnosed with a single respiratory viral agent. INTERPRETATION BAL leads to changes in management in the majority of immunosuppressed patients. There is a high prevalence of multimicrobial infections and respiratory viral infections in immunocompromised patients with respiratory symptoms. Individual virus infection is associated with diverse risk of a negative outcome.
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Affiliation(s)
- Kathleen Jahn
- Clinic of Respiratory Medicine and Pulmonary Cell Research, University Hospital, Basel, Switzerland
| | - Meropi Karakioulaki
- Clinic of Respiratory Medicine and Pulmonary Cell Research, University Hospital, Basel, Switzerland; Clinic of Respiratory Medicine, Faculty of Medicine, University of Freiburg, Germany
| | - Desiree M Schumann
- Clinic of Respiratory Medicine and Pulmonary Cell Research, University Hospital, Basel, Switzerland
| | - Hans H Hirsch
- Clinical Virology, Laboratory Medicine, University Hospital Basel, Basel, Switzerland University Hospital, Basel, Switzerland; Transplantation & Clinical Virology, Department Biomedicine, University of Basel, Basel Switzerland; Division of Infectious Diseases & Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
| | - Karoline Leuzinger
- Clinical Virology, Laboratory Medicine, University Hospital Basel, Basel, Switzerland University Hospital, Basel, Switzerland; Transplantation & Clinical Virology, Department Biomedicine, University of Basel, Basel Switzerland
| | - Leticia Grize
- Clinic of Respiratory Medicine and Pulmonary Cell Research, University Hospital, Basel, Switzerland
| | - Stefano Aliberti
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Italy; IRCCS Humanitas Research Hospital, Respiratory Unit, Rozzano, Italy
| | - Giovanni Sotgiu
- Clinical Epidemiology and Medical Statistics Unit, Department of Medicine, Surgery and Pharmacy, University of Sassari, Sassari, Italy
| | - Michael Tamm
- Clinic of Respiratory Medicine and Pulmonary Cell Research, University Hospital, Basel, Switzerland
| | - Daiana Stolz
- Clinic of Respiratory Medicine and Pulmonary Cell Research, University Hospital, Basel, Switzerland; Clinic of Respiratory Medicine, Faculty of Medicine, University of Freiburg, Germany.
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4
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Laxton CS, Peno C, Hahn AM, Allicock OM, Perniciaro S, Wyllie AL. The potential of saliva as an accessible and sensitive sample type for the detection of respiratory pathogens and host immunity. THE LANCET. MICROBE 2023; 4:e837-e850. [PMID: 37516121 DOI: 10.1016/s2666-5247(23)00135-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 04/19/2023] [Accepted: 04/24/2023] [Indexed: 07/31/2023]
Abstract
Despite its prominence in early scientific records, the usefulness of saliva as a respiratory specimen has been de-emphasised over the past century. However, due to its low cost and reliance on specific supply chains and the non-invasive nature of its collection, its benefits over swab-based specimens are again becoming increasingly recognised. These benefits were highlighted over the course of the COVID-19 pandemic, where saliva emerged as a more practical, clinically non-inferior sample type for the detection of SARS-CoV-2 and saw numerous saliva-based diagnostic tests approved for clinical use. Looking forward, as saliva uniquely contains both respiratory secretions and immunological components, it has potentially wide applications, ranging from clinical diagnostics to post-vaccine disease burden and immunity surveillance. This Personal View seeks to summarise the existing evidence for the use of saliva in detecting respiratory pathogens, beyond SARS-CoV-2, as well as detailing methodological factors that can influence sample quality and thus, clinical utility.
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Affiliation(s)
- Claire S Laxton
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Chikondi Peno
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Anne M Hahn
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Orchid M Allicock
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Stephanie Perniciaro
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Anne L Wyllie
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA.
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5
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Teirlinck AC, Johannesen CK, Broberg EK, Penttinen P, Campbell H, Nair H, Reeves RM, Bøås H, Brytting M, Cai W, Carnahan A, Casalegno JS, Danis K, De Gascun C, Ellis J, Emborg HD, Gijon M, Guiomar R, Hirve SS, Jiřincová H, Nohynek H, Oliva JA, Osei-Yeboah R, Paget J, Pakarna G, Pebody R, Presser L, Rapp M, Reiche J, Rodrigues AP, Seppälä E, Socan M, Szymanski K, Trebbien R, Večeřová J, van der Werf S, Zambon M, Meijer A, Fischer TK. New perspectives on respiratory syncytial virus surveillance at the national level: lessons from the COVID-19 pandemic. Eur Respir J 2023; 61:2201569. [PMID: 37012081 PMCID: PMC10069872 DOI: 10.1183/13993003.01569-2022] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 02/10/2023] [Indexed: 04/05/2023]
Abstract
The emergence of SARS-CoV-2 and the resulting coronavirus disease 2019 (COVID-19) pandemic has led to the reconsideration of surveillance strategies for respiratory syncytial virus (RSV) and other respiratory viruses. The COVID-19 pandemic and the non-pharmaceutical interventions for COVID-19 had a substantial impact on RSV transmission in many countries, with close to no transmission detected during parts of the usual season of 2020–2021. Subsequent relaxation of social restrictions has resulted in unusual out-of-season resurgences of RSV in several countries, causing a higher healthcare burden and often a higher proportion of hospitalisations than usual among children older than 1 year in age [1]. In case of an emerging infectious disease with pandemic potential, preparedness to scale up surveillance for the emerging disease while continuing the maintenance of surveillance activities of pre-existing seasonal diseases is necessary. Learning from the COVID-19 pandemic and considering the effects of this pandemic, we provide recommendations that can guide towards sustainable RSV surveillance with the potential to be integrated into the broader perspective of respiratory surveillance. https://bit.ly/40TsO0G
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Affiliation(s)
- Anne C Teirlinck
- National Institute for Public Health and the Environment (RIVM) - Centre for Infectious Disease Control, Bilthoven, The Netherlands
| | - Caroline K Johannesen
- Statens Serum Institut, Copenhagen, Denmark
- Department of Clinical Research, Nordsjaellands Hospital, and University of Copenhagen, Department of Public Health, Copenhagen, Denmark
| | - Eeva K Broberg
- European Centre for Disease Prevention and Control, Stockholm, Sweden
| | - Pasi Penttinen
- European Centre for Disease Prevention and Control, Stockholm, Sweden
| | | | - Harish Nair
- Usher Institute, University of Edinburgh, Edinburgh, UK
| | | | - Håkon Bøås
- Norwegian Institute of Public Health, Oslo, Norway
| | - Mia Brytting
- Public Health Agency of Sweden, Stockholm, Sweden
| | - Wei Cai
- Robert Koch Institute, Berlin, Germany
| | | | - Jean-Sebastien Casalegno
- Centre National de Référence des virus des infections respiratoires dont la grippe, Hospices Civils de Lyon, Lyon, France
| | - Kostas Danis
- European Centre for Disease Prevention and Control, Stockholm, Sweden
| | | | | | | | | | - Raquel Guiomar
- National Institute of Health Ricardo Jorge, Lisbon, Portugal
| | | | | | - Hanna Nohynek
- Finnish National Institute for Health and Welfare, Helsinki, Finland
| | - Jesus Angel Oliva
- Instituto de Salud Carlos III Madrid, CIBER de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | | | - John Paget
- Netherlands Institute for Health Services Research (Nivel), Utrecht, The Netherlands
| | | | - Richard Pebody
- World Health Organization Regional Office for Europe, Copenhagen, Denmark
| | - Lance Presser
- National Institute for Public Health and the Environment (RIVM) - Centre for Infectious Disease Control, Bilthoven, The Netherlands
| | - Marie Rapp
- Public Health Agency of Sweden, Stockholm, Sweden
| | | | | | | | - Maja Socan
- National Institute of Public Health, Ljubljana, Slovenia
| | - Karol Szymanski
- National Institute of Public Health NIH National Research Institute, Warsaw, Poland
| | | | | | | | | | - Adam Meijer
- National Institute for Public Health and the Environment (RIVM) - Centre for Infectious Disease Control, Bilthoven, The Netherlands
| | - Thea K Fischer
- Statens Serum Institut, Copenhagen, Denmark
- Department of Clinical Research, Nordsjaellands Hospital, and University of Copenhagen, Department of Public Health, Copenhagen, Denmark
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6
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Kurai D, Song J, Huang YC, Jie Z, Atanasov P, Jiang X, Hernandez-Pastor L, Huang THW, Park S, Lim K, Richmond PC. Targeted Literature Review of the Burden of Respiratory Syncytial Infection among High-Risk and Elderly Patients in Asia Pacific Region. Infect Dis Ther 2023; 12:807-828. [PMID: 36869266 PMCID: PMC10017894 DOI: 10.1007/s40121-023-00777-2] [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: 11/30/2022] [Accepted: 02/09/2023] [Indexed: 03/05/2023] Open
Abstract
INTRODUCTION The burden of respiratory syncytial virus (RSV), which causes acute respiratory illness, is well recognized among the pediatric population but also imposes a significant risk to the elderly (age ≥ 60) and those with underlying comorbidities. The study aimed to review the most recent data on epidemiology and burden (clinical and economic) of RSV in the elderly/high-risk populations in China, Japan, South Korea, Taiwan, and Australia. METHODS A targeted review was conducted of English, Japanese, Korean, and Chinese language articles published from 1 January 2010 to 7 October 2020 relevant for the purpose. RESULTS A total of 881 studies were identified, and 41 were included. The median proportion of elderly patients with RSV in all adult patients with acute respiratory infection (ARI) or community acquired pneumonia was 79.78% (71.43-88.12%) in Japan, 48.00% (3.64-80.00%) in China, 41.67% (33.33-50.00%) in Taiwan, 38.61% in Australia, and 28.57% (22.76-33.33%) in South Korea. RSV was associated with a high clinical burden on those patients with comorbidities such as asthma and chronic obstructive pulmonary disease. In China, inpatients with ARI showed a significantly higher rate of RSV-related hospitalization than outpatients (13.22% versus 4.08%, p < 0.01). The median length of hospital stay among elderly patients with RSV was longest in Japan (30 days) and shortest in China (7 days). Mortality data varied by region with some studies reporting rates as high as 12.00% (9/75) in hospitalized elderly patients. Finally, data on the economic burden was only available for South Korea, with the median cost of a medical admission for an elderly patient with RSV being US dollar (USD) 2933. CONCLUSION RSV infection is a major source of disease burden among elderly patients, especially in regions with aging populations. It also complicates the management of those with underlying diseases. Appropriate prevention strategies are required to reduce the burden among the adult, especially the elderly, population. Data gaps regarding economic burden of RSV infection in the Asia Pacific region indicates the need for further research to increase our understanding on the burden of this disease in this region.
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Affiliation(s)
| | - JoonYoung Song
- Korea University College of Medicine, Seoul, South Korea
| | | | - Zhijun Jie
- Department of Pulmonary and Critical Care Medicine, Shanghai Fifth People's Hospital, Fudan University, Shanghai, China
| | - Petar Atanasov
- Health Economics and Market Access, Amaris Consulting, Barcelona, Spain
| | - Xiaobin Jiang
- Health Economics and Market Access, Amaris Consulting, Shanghai, China
| | | | | | | | - KyungHwa Lim
- Asia Pacific Market Access, Janssen Pharmaceuticals, Seoul, South Korea
| | - Peter C Richmond
- University of Western Australia Medical School, 35 Stirling Highway, Perth, WA, 6009, Australia.
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7
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Vereecke N, Woźniak A, Pauwels M, Coppens S, Nauwynck H, Cybulski P, Theuns S, Stadejek T. Successful Whole Genome Nanopore Sequencing of Swine Influenza A Virus (swIAV) Directly from Oral Fluids Collected in Polish Pig Herds. Viruses 2023; 15:435. [PMID: 36851649 PMCID: PMC9962634 DOI: 10.3390/v15020435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 01/20/2023] [Accepted: 01/31/2023] [Indexed: 02/09/2023] Open
Abstract
Influenza A virus (IAV) is a single-stranded, negative-sense RNA virus and a common cause of seasonal flu in humans. Its genome comprises eight RNA segments that facilitate reassortment, resulting in a great variety of IAV strains. To study these processes, the genetic code of each segment should be unraveled. Fortunately, new third-generation sequencing approaches allow for cost-efficient sequencing of IAV segments. Sequencing success depends on various factors, including proper sample storage and processing. Hence, this work focused on the effect of storage of oral fluids and swIAV sequencing. Oral fluids (n = 13) from 2017 were stored at -22 °C and later transferred to -80 °C. Other samples (n = 21) were immediately stored at -80 °C. A reverse transcription quantitative PCR (RT-qPCR) pre- and post-storage was conducted to assess IAV viral loads. Next, samples were subjected to two IAV long-read nanopore sequencing methods to evaluate success in this complex matrix. A significant storage-associated loss of swIAV loads was observed. Still, a total of 17 complete and 6 near-complete Polish swIAV genomes were obtained. Genotype T, (H1avN2, seven herds), P (H1N1pdm09, two herds), U (H1avN1, three herds), and A (H1avN1, 1 herd) were circulated on Polish farms. In conclusion, oral fluids can be used for long-read swIAV sequencing when considering appropriate storage and segment amplification protocols, which allows us to monitor swIAV in an animal-friendly and cost-efficient manner.
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Affiliation(s)
- Nick Vereecke
- Laboratory of Virology, Faculty of Veterinary Medicine, Ghent University, 9820 Merelbeke, Belgium
- PathoSense BV, 2500 Lier, Belgium
| | - Aleksandra Woźniak
- Department of Pathology and Veterinary Diagnostic, Institute of Veterinary Medicine, Warsaw University of Life Sciences-SGGW, 02-776 Warsaw, Poland
| | | | | | - Hans Nauwynck
- Laboratory of Virology, Faculty of Veterinary Medicine, Ghent University, 9820 Merelbeke, Belgium
- PathoSense BV, 2500 Lier, Belgium
| | - Piotr Cybulski
- Goodvalley Agro S.A., Dworcowa 25, 77-320 Przechlewo, Poland
| | - Sebastiaan Theuns
- Laboratory of Virology, Faculty of Veterinary Medicine, Ghent University, 9820 Merelbeke, Belgium
- PathoSense BV, 2500 Lier, Belgium
| | - Tomasz Stadejek
- Department of Pathology and Veterinary Diagnostic, Institute of Veterinary Medicine, Warsaw University of Life Sciences-SGGW, 02-776 Warsaw, Poland
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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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9
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Chen H, Feng S, Zhou W, Li Z, Richard-Greenblatt M, Wang P. Pretreatment Methods for Human Nasopharyngeal Swabs to Increase the Signal to Noise Ratio of High Sensitivity Immunoassays. ACS MEASUREMENT SCIENCE AU 2022; 2:414-421. [PMID: 36785662 PMCID: PMC9885992 DOI: 10.1021/acsmeasuresciau.2c00024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Mucous samples collected through nasopharyngeal (NP) swabs are considered gold standard specimens for the detection of respiratory pathogens. Matrices of these highly viscous samples often cause significant background noises in immunoassays, especially immunoassays with high sensitivity. We demonstrated such nonspecific background signals in both a chemiluminescence enzyme-linked immunosorbent assay (ELISA) and a novel highly sensitive immunoassay called Microbubbling SARS-CoV-2 Antigen Assay (MSAA). We developed and demonstrated the effectiveness of two quick sample pretreatment methods, filtration and preadsorption, to decrease nonspecific signals and increase the signal-to-noise ratio (SNR). Using these pretreatment methods, the SNR (at 3.6 × 104 copies/mL of inactivated SARS-CoV-2) was increased by 42.4-fold (95% CI 41.0-43.8) and 67.1-fold (95% CI 57.9-76.3) in the MSAA, and 1.3-fold (95% CI 0.9-1.7) and 1.8-fold (95% CI 1.6-2.0) in the chemiluminescence ELISA assay. Sample pretreatment methods developed in this study are broadly adaptable for the development of immunoassays for highly viscous samples.
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10
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Jones RP, Ponomarenko A. Roles for Pathogen Interference in Influenza Vaccination, with Implications to Vaccine Effectiveness (VE) and Attribution of Influenza Deaths. Infect Dis Rep 2022; 14:710-758. [PMID: 36286197 PMCID: PMC9602062 DOI: 10.3390/idr14050076] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 09/15/2022] [Accepted: 09/15/2022] [Indexed: 08/29/2023] Open
Abstract
Pathogen interference is the ability of one pathogen to alter the course and clinical outcomes of infection by another. With up to 3000 species of human pathogens the potential combinations are vast. These combinations operate within further immune complexity induced by infection with multiple persistent pathogens, and by the role which the human microbiome plays in maintaining health, immune function, and resistance to infection. All the above are further complicated by malnutrition in children and the elderly. Influenza vaccination offers a measure of protection for elderly individuals subsequently infected with influenza. However, all vaccines induce both specific and non-specific effects. The specific effects involve stimulation of humoral and cellular immunity, while the nonspecific effects are far more nuanced including changes in gene expression patterns and production of small RNAs which contribute to pathogen interference. Little is known about the outcomes of vaccinated elderly not subsequently infected with influenza but infected with multiple other non-influenza winter pathogens. In this review we propose that in certain years the specific antigen mix in the seasonal influenza vaccine inadvertently increases the risk of infection from other non-influenza pathogens. The possibility that vaccination could upset the pathogen balance, and that the timing of vaccination relative to the pathogen balance was critical to success, was proposed in 2010 but was seemingly ignored. Persons vaccinated early in the winter are more likely to experience higher pathogen interference. Implications to the estimation of vaccine effectiveness and influenza deaths are discussed.
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Affiliation(s)
- Rodney P Jones
- Healthcare Analysis and Forecasting, Wantage OX12 0NE, UK
| | - Andrey Ponomarenko
- Department of Biophysics, Informatics and Medical Instrumentation, Odessa National Medical University, Valikhovsky Lane 2, 65082 Odessa, Ukraine
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Duncan DB, Mackett K, Ali MU, Yamamura D, Balion C. Performance of saliva compared with nasopharyngeal swab for diagnosis of COVID-19 by NAAT in cross-sectional studies: Systematic review and meta-analysis. Clin Biochem 2022; 117:84-93. [PMID: 35952732 PMCID: PMC9359767 DOI: 10.1016/j.clinbiochem.2022.08.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 07/14/2022] [Accepted: 08/05/2022] [Indexed: 11/03/2022]
Abstract
Nucleic acid amplification testing (NAAT) is the preferred method to diagnose coronavirus disease 2019 (COVID-19). Saliva has been suggested as an alternative to nasopharyngeal swabs (NPS), but previous systematic reviews were limited by the number and types of studies available. The objective of this systematic review and meta-analysis was to assess the diagnostic performance of saliva compared with NPS for COVID-19. We searched Ovid MEDLINE, Embase, Cochrane, and Scopus databases up to 24 April 2021 for studies that directly compared paired NPS and saliva specimens taken at the time of diagnosis. Meta-analysis was performed using an exact binomial rendition of the bivariate mixed-effects regression model. Risk of bias was assessed using the QUADAS-2 tool. Of 2683 records, we included 23 studies with 25 cohorts, comprising 11,582 paired specimens. A wide variety of NAAT assays and collection methods were used. Meta-analysis gave a pooled sensitivity of 87 % (95 % CI = 83-90 %) and specificity of 99 % (95 % CI = 98-99 %). Subgroup analyses showed the highest sensitivity when the suspected individual is tested in an outpatient setting and is symptomatic. Our results support the use of saliva NAAT as an alternative to NPS NAAT for the diagnosis of COVID-19.
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Affiliation(s)
- Donald Brody Duncan
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario L8S 4K1, Canada; Microbiology Department, Hamilton Regional Laboratory Medicine Program, Hamilton Health Sciences, Hamilton, Ontario L8L 2X2, Canada
| | - Katharine Mackett
- Department of Health Research Methods, Evidence and Impact, McMaster University, Hamilton, Ontario L8S 4K1, Canada
| | - Muhammad Usman Ali
- Department of Health Research Methods, Evidence and Impact, McMaster University, Hamilton, Ontario L8S 4K1, Canada
| | - Deborah Yamamura
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario L8S 4K1, Canada; Microbiology Department, Hamilton Regional Laboratory Medicine Program, Hamilton Health Sciences, Hamilton, Ontario L8L 2X2, Canada; Division of Infectious Diseases, Department of Medicine, McMaster University, Hamilton, Ontario L8V 1C3, Canada
| | - Cynthia Balion
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario L8S 4K1, Canada; Department of Health Research Methods, Evidence and Impact, McMaster University, Hamilton, Ontario L8S 4K1, Canada.
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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] [Key Words] [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
| | - 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
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13
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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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Couetil L, Ivester K, Barnum S, Pusterla N. Equine respiratory viruses, airway inflammation and performance in thoroughbred racehorses. Vet Microbiol 2021; 257:109070. [PMID: 33865081 DOI: 10.1016/j.vetmic.2021.109070] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 04/06/2021] [Indexed: 12/31/2022]
Abstract
Equine asthma is a common cause of poor performance in racehorses but it is unclear if respiratory viruses contribute to its etiology. The objective of the study was to determine if respiratory viruses were associated with clinical signs and bronchoalveolar lavage fluid (BALF) cytology in Thoroughbred racehorses. Equine herpesviruses (EHV-1, 2, 4, 5) and equine rhinitis A and B viruses (ERBV, ERAV) genomes were quantified by qPCR in nasopharyngeal, tracheal, and BALF samples collected after racing. The relationships between virus detection and load and clinical signs, performance, BALF cytology, and environmental exposures were examined with generalized linear mixed models. Ninety-two samples were collected from 31 horses. EHV-1 and ERAV were not found; EHV-4 was detected in only one sample. EHV-2, EHV-5 and ERBV were more likely to be detected in upper airway samples than in BALF (P < 0.0001). Neither respiratory virus detection nor load was associated with clinical signs or performance. Nasopharyngeal detection and load of ERBV and tracheal detection and load of EHV-5 were associated with increased proportions of neutrophils in BALF (P < 0.003). However, nasopharyngeal detection and load of EHV-5 was not (P = 0.11). Nasopharyngeal detection and load of EHV-2 were associated with decreased BALF mast cell proportions. Respirable dust exposures were significantly higher in horses with detection of ERBV when compared to horses with no detectable ERBV (P < 0.001). Our results suggest that ERBV, EHV-2 and EHV-5 are commonly present in upper airways of healthy racehorses; however, the role they play in the etiology of equine asthma remains unclear.
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Affiliation(s)
- Laurent Couetil
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Purdue University, West Lafayette, IN, 47907, USA.
| | - Kathleen Ivester
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Purdue University, West Lafayette, IN, 47907, USA
| | - Samantha Barnum
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, CA, 95616, USA
| | - Nicola Pusterla
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, CA, 95616, USA
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