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Riccò M, Cascio A, Corrado S, Bottazzoli M, Marchesi F, Gili R, Giuri PG, Gori D, Manzoni P. Efficacy of Respiratory Syncytial Virus Vaccination to Prevent Lower Respiratory Tract Illness in Older Adults: A Systematic Review and Meta-Analysis of Randomized Controlled Trials. Vaccines (Basel) 2024; 12:500. [PMID: 38793751 PMCID: PMC11126042 DOI: 10.3390/vaccines12050500] [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: 04/10/2024] [Revised: 05/01/2024] [Accepted: 05/03/2024] [Indexed: 05/26/2024] Open
Abstract
A systematic review and meta-analysis was designed in order to ascertain the effectiveness of respiratory syncytial virus (RSV) vaccination in preventing lower respiratory tract diseases (LRTD) in older adults (age ≥ 60 years). Studies reporting on randomized controlled trials (RCTs) were searched for in three databases (PubMed, Embase, and Scopus) and the preprint repository medRxiv until 31 March 2024. A total of nine studies were eventually included, two of which were conference proceedings. Our analysis included five RCTs on five RSV vaccines (RSVpreF, RSVPreF3, Ad26.RSV.preF, MEDI7510, and mRNA-1345). The meta-analysis documented a pooled vaccine efficacy of 81.38% (95% confidence interval (95% CI) 70.94 to 88.06) for prevention of LRTD with three or more signs/symptoms during the first RSV season after the delivery of the vaccine. Follow-up data were available for RSVPreF3 (2 RSV seasons), RSVpreF (mid-term estimates of second RSV season), and mRNA-1345 (12 months after the delivery of the primer), with a pooled VE of 61.15% (95% CI 45.29 to 72.40). After the first season, the overall risk for developing RSV-related LRTD was therefore substantially increased (risk ratio (RR) 4.326, 95% CI 2.415; 7.748). However, all estimates were affected by substantial heterogeneity, as suggested by the 95% CI of I2 statistics, which could be explained by inconsistencies in the design of the parent studies, particularly when dealing with case definition. In conclusion, adult RSV vaccination was quite effective in preventing LRTD in older adults, but the overall efficacy rapidly decreased in the second season after the delivery of the vaccine. Because of the heterogenous design of the parent studies, further analyses are required before tailoring specific public health interventions.
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Affiliation(s)
- Matteo Riccò
- AUSL–IRCCS di Reggio Emilia, Servizio di Prevenzione e Sicurezza Negli Ambienti di Lavoro (SPSAL), Local Health Unit of Reggio Emilia, 42122 Reggio Emilia, Italy
| | - Antonio Cascio
- Infectious and Tropical Diseases Unit, Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties, “G D’Alessandro”, University of Palermo, AOUP P. Giaccone, 90127 Palermo, Italy;
| | - Silvia Corrado
- ASST Rhodense, Dipartimento della donna e Area Materno-Infantile, UOC Pediatria, 20024 Milano, Italy
| | - Marco Bottazzoli
- Department of Otorhinolaryngology, APSS Trento, 38122 Trento, Italy
| | - Federico Marchesi
- Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy
| | - Renata Gili
- Department of Prevention, Turin Local Health Authority, 10125 Torino, Italy
| | | | - Davide Gori
- Department of Biomedical and Neuromotor Sciences, University of Bologna, 40126 Bologna, Italy;
| | - Paolo Manzoni
- Department of Public Health and Pediatric Sciences, University of Torino School of Medicine, 10125 Turin, Italy;
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2
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Mattila S, Honkila M, Paalanne N, Mäki-Koivisto V, Halt K, Jartti T, Ruuskanen O, Waris M, Pokka T, Tapiainen T. Clinical Outcomes of Acutely Ill Children According to Cycle Threshold Values of Respiratory Viruses Detected by Multiplex PCR Testing. J Pediatric Infect Dis Soc 2023; 12:549-552. [PMID: 37738173 DOI: 10.1093/jpids/piad071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 09/18/2023] [Indexed: 09/24/2023]
Abstract
In this cohort study of 800 children attending a pediatric emergency department at Oulu University Hospital, Finland with fever or respiratory symptoms, the cycle threshold values of point-of-care multiplex polymerase chain reaction testing for respiratory viruses were not associated with hospitalization, respiratory support, or need for intensive care.
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Affiliation(s)
- Suvi Mattila
- Department of Pediatrics and Adolescent Medicine, Oulu University Hospital, Oulu, Finland
- Research Unit of Clinical Medicine and Medical Research Center Oulu, University of Oulu, Oulu, Finland
| | - Minna Honkila
- Department of Pediatrics and Adolescent Medicine, Oulu University Hospital, Oulu, Finland
- Research Unit of Clinical Medicine and Medical Research Center Oulu, University of Oulu, Oulu, Finland
| | - Niko Paalanne
- Department of Pediatrics and Adolescent Medicine, Oulu University Hospital, Oulu, Finland
- Research Unit of Clinical Medicine and Medical Research Center Oulu, University of Oulu, Oulu, Finland
| | | | - Kimmo Halt
- Department of Pediatrics and Adolescent Medicine, Oulu University Hospital, Oulu, Finland
- Research Unit of Clinical Medicine and Medical Research Center Oulu, University of Oulu, Oulu, Finland
| | - Tuomas Jartti
- Department of Pediatrics and Adolescent Medicine, Oulu University Hospital, Oulu, Finland
- Research Unit of Clinical Medicine and Medical Research Center Oulu, University of Oulu, Oulu, Finland
- Department of Pediatrics and Adolescent Medicine, Turku University Hospital and University of Turku, Turku, Finland
| | - Olli Ruuskanen
- Department of Pediatrics and Adolescent Medicine, Turku University Hospital and University of Turku, Turku, Finland
| | - Matti Waris
- Institute of Biomedicine, University of Turku, Turku, Finland
| | - Tytti Pokka
- Research Unit of Clinical Medicine and Medical Research Center Oulu, University of Oulu, Oulu, Finland
- Research Service Unit, Oulu University Hospital, Oulu, Finland
| | - Terhi Tapiainen
- Department of Pediatrics and Adolescent Medicine, Oulu University Hospital, Oulu, Finland
- Research Unit of Clinical Medicine and Medical Research Center Oulu, University of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
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Biškup UG, Steyer A, Lusa L, Strle F, Pokorn M, Mrvič T, Grosek Š, Petrovec M, Jevšnik Virant M. Molecular Typing of Mastadenoviruses in Simultaneously Collected Nasopharyngeal Swabs and Stool Samples from Children Hospitalized for Acute Bronchiolitis, Acute Gastroenteritis, and Febrile Seizures. Microorganisms 2023; 11:microorganisms11030780. [PMID: 36985353 PMCID: PMC10058226 DOI: 10.3390/microorganisms11030780] [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: 01/24/2023] [Revised: 02/23/2023] [Accepted: 03/15/2023] [Indexed: 03/30/2023] Open
Abstract
This study determines and compares the frequency of human mastadenovirus (HAdV) presence in children with acute bronchiolitis (AB), acute gastroenteritis (AGE), and febrile seizures (FS), ascertains types of HAdVs associated with each individual syndrome and contrasts the findings with a control group of children. The presence of HAdVs was ascertained in simultaneously collected nasopharyngeal (NP) swabs and stool samples amplifying the hexon gene by RT-PCR; these were sequenced to determine the types of HAdVs. HAdVs were grouped into eight different genotypes. Of these, three (F40, F41, and A31) were found solely in stool samples, whereas the others (B3, C1, C2, C5, and C6) were found in both stool samples and NP swabs. The most common genotypes in NP swabs were C2 (found in children with AGE and FS) and C1 (only in children with FS), whereas in stool samples genotypes F41 (in children with AGE) and C2 (in children with AGE and FS) prevailed, and C2 was simultaneously present in both samples. HAdVs were more often detected in stool samples than in NP swabs in patients (with the highest estimated viral load in stool samples in children with AB and AGE) and healthy controls and were more common in NP swabs in children with AGE than in children with AB. In most patients, the characterized genotypes in NP swabs and stool samples were in concordance.
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Affiliation(s)
- Urška Glinšek Biškup
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška 4, 1000 Ljubljana, Slovenia
| | - Andrej Steyer
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška 4, 1000 Ljubljana, Slovenia
- National Laboratory of Health, Environment and Food, Prvomajska 1, 2000 Maribor, Slovenia
| | - Lara Lusa
- Department of Mathematics, Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška 8, 6000 Koper, Slovenia
- Institute for Biostatistics and Medical Informatics, Faculty of Medicine, University of Ljubljana, Vrazov trg 2, 1104 Ljubljana, Slovenia
| | - Franc Strle
- Department of Infectious Diseases, University Medical Centre Ljubljana, Japljeva 2, 1525 Ljubljana, Slovenia
| | - Marko Pokorn
- Department of Infectious Diseases, University Medical Centre Ljubljana, Japljeva 2, 1525 Ljubljana, Slovenia
- Division of Pediatrics, Ljubljana University Medical Center, Bohoričeva 20, 1000 Ljubljana, Slovenia
- Department of Paediatrics, Faculty of Medicine, University of Ljubljana, Bohoričeva 20, 1000 Ljubljana, Slovenia
| | - Tatjana Mrvič
- Department of Infectious Diseases, University Medical Centre Ljubljana, Japljeva 2, 1525 Ljubljana, Slovenia
| | - Štefan Grosek
- Department of Paediatrics, Faculty of Medicine, University of Ljubljana, Bohoričeva 20, 1000 Ljubljana, Slovenia
- Neonatology Section, Department of Perinatology, Division of Obstetrics and Gynecology, University Medical Centre Ljubljana, Šlajmerjeva 3, 1000 Ljubljana, Slovenia
- Department of Pediatric Intensive Therapy, Division of Pediatrics, University Medical Centre Ljubljana, Bohoričeva 20, 1000 Ljubljana, Slovenia
| | - Miroslav Petrovec
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška 4, 1000 Ljubljana, Slovenia
| | - Monika Jevšnik Virant
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška 4, 1000 Ljubljana, Slovenia
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Gsenger J, Bruckner T, Ihling CM, Rehbein RM, Schnee SV, Hoos J, Manuel B, Pfeil J, Schnitzler P, Tabatabai J. RSV-CLASS -Clinical Assessment Severity Score: An easy-to-use clinical disease severity score for respiratory syncytial virus infection in hospitalized children. J Med Virol 2023; 95:e28541. [PMID: 36727642 DOI: 10.1002/jmv.28541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 01/24/2023] [Accepted: 01/30/2023] [Indexed: 02/03/2023]
Abstract
Respiratory syncytial virus (RSV) is the most common cause of acute respiratory tract infection in infants and young children often leading to severe disease requiring hospitalization. However, validated tools for systematic assessment of disease severity are lacking. This study aimed at creating and validating a standardized, simple-to-use disease severity score for RSV infection in children-the RSV-CLASS (Clinical Assessment Severity Score). Therefore, data from over 700 RSV-infected children over six winter seasons (2014-2020) was analyzed using univariate and multiple regression analyses for the prediction of lower respiratory tract infection (LRTI) as a proxy for a severe course of the disease. Testing a broad range of respiratory symptoms, they eventually yielded seven items. Performing stepwise selection, these were reduced to the final four items: cough, tachypnea, rales, and wheezing, each receiving one point in the proposed score named RSV-CLASS. The score was calculated for children in two cohorts A and B, one for development and one for validation, with an area under the curve of 0.90 and 0.87, respectively. With a score value of 3 or 4, 97.8% and 100% of the children, respectively, were admitted with LRTI and classified correctly. The RSV-CLASS is a disease severity score based on a neutral, analytical approach using prospective data from a large study cohort. It will contribute to systematically assessing the disease severity of RSV infection and can be used for evidence-based clinical decision-making as well as for research settings.
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Affiliation(s)
- Julia Gsenger
- Center for Infectious Diseases, Virology, University Hospital Heidelberg, Heidelberg, Germany
- German Center for Infectious Diseases (DZIF), Heidelberg, Germany
| | - Thomas Bruckner
- Institute for Medical Biometry and Informatics, University of Heidelberg, Heidelberg, Germany
| | - Clara Marlene Ihling
- Center for Infectious Diseases, Virology, University Hospital Heidelberg, Heidelberg, Germany
- German Center for Infectious Diseases (DZIF), Heidelberg, Germany
- Dr. von Haunersches Kinderspital, University Hospital of the LMU Munich, Munich, Germany
| | - Rebecca Marie Rehbein
- Center for Infectious Diseases, Virology, University Hospital Heidelberg, Heidelberg, Germany
- German Center for Infectious Diseases (DZIF), Heidelberg, Germany
- Center for Child and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - Sarah Valerie Schnee
- Center for Infectious Diseases, Virology, University Hospital Heidelberg, Heidelberg, Germany
- German Center for Infectious Diseases (DZIF), Heidelberg, Germany
| | - Johannes Hoos
- Center for Infectious Diseases, Virology, University Hospital Heidelberg, Heidelberg, Germany
- German Center for Infectious Diseases (DZIF), Heidelberg, Germany
- Center for Child and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | | | | | - Paul Schnitzler
- Center for Infectious Diseases, Virology, University Hospital Heidelberg, Heidelberg, Germany
| | - Julia Tabatabai
- Center for Infectious Diseases, Virology, University Hospital Heidelberg, Heidelberg, Germany
- German Center for Infectious Diseases (DZIF), Heidelberg, Germany
- Center for Child and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany
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5
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Papan C, Argentiero A, Adams O, Porwoll M, Hakim U, Farinelli E, Testa I, Pasticci MB, Mezzetti D, Perruccio K, Simon A, Liese JG, Knuf M, Stein M, Yacobov R, Bamberger E, Schneider S, Esposito S, Tenenbaum T. Association of viral load with TRAIL, IP-10, CRP biomarker signature and disease severity in children with respiratory tract infection or fever without source: A prospective, multicentre cohort study. J Med Virol 2023; 95:e28113. [PMID: 36043485 DOI: 10.1002/jmv.28113] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 08/25/2022] [Accepted: 08/27/2022] [Indexed: 01/11/2023]
Abstract
BACKGROUND To investigate the association of viral load (VL) with (i) tumor necrosis factor-related apoptosis-inducing ligand (TRAIL), interferon gamma-induced protein-10, C-reactive protein, and a combinatorial score (BV score), and (ii) clinical severity. STUDY DESIGN In this prospective, multicentre cohort substudy, children with respiratory tract infection or fever without source were enrolled. VL for influenza virus, rhinovirus, respiratory syncytial virus, and adenovirus was measured from nasopharyngeal swabs. The reference standard diagnosis was established based on expert panel adjudication. RESULTS Of 1140 recruited patients, 333 had a virus monodetection. VL for the aggregated data set correlated with TRAIL and IP-10 levels, with the length of oxygen therapy, and inversely with the BV score. At a single viral level, only the influenza VL yielded a correlation with TRAIL, IP-10 levels, and the BV score. Children with a viral reference standard diagnosis had significantly higher VL than those with bacterial infection (p = 0.0005). Low TRAIL (incidence rate ratio [IRR] 0.6, 95% confidence interval [CI] 0.39-0.91) and young age (IRR 0.62, 95% CI 0.49-0.79) were associated with a longer hospital stay, while young age (IRR 0.33, 95% CI 0.18-0.61), low TRAIL (IRR 0.25, 95% CI 0.08-0.76), and high VL (IRR 1.16, 95% CI 1.00-1.33) were predictive of longer oxygen therapy. CONCLUSION These findings indicate that VL correlates with biomarkers and may serve as a complementary tool pertaining to disease severity.
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Affiliation(s)
- Cihan Papan
- Paediatric Infectious Diseases, Department of Paediatrics, University Children's Hospital Mannheim, Heidelberg University, Mannheim, Germany.,Centre for Infectious Diseases, Institute of Medical Microbiology and Hygiene, Saarland University, Homburg, Germany
| | - Alberto Argentiero
- Department of Surgical and Biomedical Sciences, Santa Maria della Misericordia Hospital, Università degli Studi di Perugia, Perugia, Italy
| | - Ortwin Adams
- Institute of Virology, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Marian Porwoll
- Paediatric Infectious Diseases, Department of Paediatrics, University Children's Hospital Mannheim, Heidelberg University, Mannheim, Germany
| | - Ummaya Hakim
- Paediatric Infectious Diseases, Department of Paediatrics, University Children's Hospital Mannheim, Heidelberg University, Mannheim, Germany
| | - Edoardo Farinelli
- Department of Surgical and Biomedical Sciences, Santa Maria della Misericordia Hospital, Università degli Studi di Perugia, Perugia, Italy
| | - Ilaria Testa
- Department of Surgical and Biomedical Sciences, Santa Maria della Misericordia Hospital, Università degli Studi di Perugia, Perugia, Italy
| | - Maria B Pasticci
- Department of Surgical and Biomedical Sciences, Santa Maria della Misericordia Hospital, Università degli Studi di Perugia, Perugia, Italy
| | - Daniele Mezzetti
- Department of Surgical and Biomedical Sciences, Santa Maria della Misericordia Hospital, Università degli Studi di Perugia, Perugia, Italy
| | - Katia Perruccio
- Department of Surgical and Biomedical Sciences, Santa Maria della Misericordia Hospital, Università degli Studi di Perugia, Perugia, Italy
| | - Arne Simon
- Department of Paediatric Oncology and Haematology, Saarland University Hospital, Homburg, Germany
| | - Johannes G Liese
- Department of Paediatrics, University of Würzburg, Würzburg, Germany
| | - Markus Knuf
- Department of Paediatrics, Children's Hospital, Helios Dr. Horst Schmidt Klinik, Wiesbaden, Germany.,Department of Paediatrics, University Medicine, Mainz, Germany
| | | | | | - Ellen Bamberger
- Technion-Israel Institute of Technology, Ruth and Bruce Rappaport Faculty of Medicine, Haifa, Israel.,Department of Paediatrics, Bnai-Zion Medical Center, Haifa, Israel
| | - Sven Schneider
- Institute for Clinical Chemistry, University of Heidelberg, Mannheim, Germany
| | - Susanna Esposito
- Department of Medicine and Surgery, Pediatric Clinic, Pietro Barilla Children's Hospital, University of Parma, Parma, Italy
| | - Tobias Tenenbaum
- Paediatric Infectious Diseases, Department of Paediatrics, University Children's Hospital Mannheim, Heidelberg University, Mannheim, Germany.,Clinic for Child and Adolescent Medicine, Sana Klinikum Lichtenberg, Academic Teaching Hospital, Charité-Universitätsmedizin, Berlin, Germany
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Coyle PV, Al Molawi NH, Kacem MABH, El Kahlout RA, Al Kuwari E, Al Khal A, Gillani I, Jeremijenko A, Saeb H, Al Thani M, Bertollini R, Abdul Rahim HF, Chemaitelly H, Tang P, Latif AN, Al Kaabi S, Al Maslamani MARS, Morris BD, Al-Ansari N, Kaleeckal AH, Abu Raddad LJ. Reporting of RT-PCR cycle threshold (Ct) values during the first wave of COVID-19 in Qatar improved result interpretation in clinical and public health settings. J Med Microbiol 2022; 71. [PMID: 35576147 DOI: 10.1099/jmm.0.001499] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Introduction. The cycle threshold (Ct) value in real-time PCR (RT-PCR) is where a target-specific amplification signal becomes detectable and can infer viral load, risk of transmission and recovery. Use of Ct values in routine practice is uncommon.Gap Statement. There is a lack of routine use of Ct values when reporting RT-PCR results in routine practice.Aim. To automatically insert Ct values and interpretive comments when reporting SARS-CoV-2 RT-PCR to improve patient management.Methodology. Routine Ct values across three different RT-PCR platforms were reviewed for concordance at presentation and clearance in patients with COVID-19. An indicative threshold (IT) linked to viral clearance kinetics was defined at Ct30 to categorize Ct values as low and high, reflecting high and low viral loads respectively.Results. The different gene targets of each platform showed high correlation and kappa score agreement (P<0.001). Average Ct values were automatically generated with values ≤Ct30 reported as positive and >Ct30 as reactive; interpretive comments were added to all reports. The new reporting algorithm impacted on: physician interpretation of SARS-CoV-2 results; patient management and transfer; staff surveillance; length of stay in quarantine; and redefinition of patient recovery.Conclusion. Incorporation of Ct values into routine practice is possible across different RT-PCR platforms and adds useful information for patient management. The use of an IT with interpretive comments improves clinical interpretation and could be a model for reporting other respiratory infections. Withholding Ct values wastes useful clinical data and should be reviewed by the profession, accreditation bodies and regulators.
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Affiliation(s)
- Peter V Coyle
- Hamad Medical Corporation, Doha, Qatar.,Biomedical Research Center, Member of QU Health, Qatar University, Doha, Qatar.,Wellcome-Wolfson Institute for Experimental Medicine, Queen's University, Belfast, UK
| | | | | | | | | | | | | | | | | | | | | | | | - Hiam Chemaitelly
- Infectious Disease Epidemiology Group, Weill Cornell Medicine-Qatar, Cornell University, Doha, Qatar.,World Health Organization Collaborating Centre for Disease Epidemiology Analytics on HIV/AIDS, Sexually Transmitted Infections, and Viral Hepatitis, Weill Cornell Medicine-Qatar, Cornell University, Qatar Foundation - Education City, Doha, Qatar
| | | | | | | | | | | | | | | | - Laith J Abu Raddad
- Infectious Disease Epidemiology Group, Weill Cornell Medicine-Qatar, Cornell University, Doha, Qatar.,World Health Organization Collaborating Centre for Disease Epidemiology Analytics on HIV/AIDS, Sexually Transmitted Infections, and Viral Hepatitis, Weill Cornell Medicine-Qatar, Cornell University, Qatar Foundation - Education City, Doha, Qatar.,Department of Population Health Sciences, Weill Cornell Medicine, Cornell University, New York, NY, USA
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7
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Burstein R, Althouse BM, Adler A, Akullian A, Brandstetter E, Cho S, Emanuels A, Fay K, Gamboa L, Han P, Huden K, Ilcisin M, Izzo M, Jackson ML, Kim AE, Kimball L, Lacombe K, Lee J, Logue JK, Rogers J, Chung E, Sibley TR, Van Raay K, Wenger E, Wolf CR, Boeckh M, Chu H, Duchin J, Rieder M, Shendure J, Starita LM, Viboud C, Bedford T, Englund JA, Famulare M. Interactions among 17 respiratory pathogens: a cross-sectional study using clinical and community surveillance data. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2022:2022.02.04.22270474. [PMID: 35169816 PMCID: PMC8845514 DOI: 10.1101/2022.02.04.22270474] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Background Co-circulating respiratory pathogens can interfere with or promote each other, leading to important effects on disease epidemiology. Estimating the magnitude of pathogen-pathogen interactions from clinical specimens is challenging because sampling from symptomatic individuals can create biased estimates. Methods We conducted an observational, cross-sectional study using samples collected by the Seattle Flu Study between 11 November 2018 and 20 August 2021. Samples that tested positive via RT-qPCR for at least one of 17 potential respiratory pathogens were included in this study. Semi-quantitative cycle threshold (Ct) values were used to measure pathogen load. Differences in pathogen load between monoinfected and coinfected samples were assessed using linear regression adjusting for age, season, and recruitment channel. Results 21,686 samples were positive for at least one potential pathogen. Most prevalent were rhinovirus (33·5%), Streptococcus pneumoniae (SPn, 29·0%), SARS-CoV-2 (13.8%) and influenza A/H1N1 (9·6%). 140 potential pathogen pairs were included for analysis, and 56 (40%) pairs yielded significant Ct differences (p < 0.01) between monoinfected and co-infected samples. We observed no virus-virus pairs showing evidence of significant facilitating interactions, and found significant viral load decrease among 37 of 108 (34%) assessed pairs. Samples positive with SPn and a virus were consistently associated with increased SPn load. Conclusions Viral load data can be used to overcome sampling bias in studies of pathogen-pathogen interactions. When applied to respiratory pathogens, we found evidence of viral-SPn facilitation and several examples of viral-viral interference. Multipathogen surveillance is a cost-efficient data collection approach, with added clinical and epidemiological informational value over single-pathogen testing, but requires careful analysis to mitigate selection bias.
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Affiliation(s)
- Roy Burstein
- Institute for Disease Modeling, Bill & Melinda Gates Foundation, Seattle WA USA
| | - Benjamin M. Althouse
- Institute for Disease Modeling, Bill & Melinda Gates Foundation, Seattle WA USA
- Institute for Disease Modeling, Bill & Melinda Gates Foundation, Seattle WA USA
- Department of Biology, New Mexico State University, Las Cruces, NM
| | - Amanda Adler
- Seattle Children’s Research Institute, Seattle WA USA
| | - Adam Akullian
- Institute for Disease Modeling, Bill & Melinda Gates Foundation, Seattle WA USA
| | | | - Shari Cho
- Brotman Baty Institute for Precision Medicine, Seattle WA USA
| | - Anne Emanuels
- Department of Medicine, University of Washington, Seattle WA USA
| | - Kairsten Fay
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle WA USA
| | - Luis Gamboa
- Brotman Baty Institute for Precision Medicine, Seattle WA USA
| | - Peter Han
- Brotman Baty Institute for Precision Medicine, Seattle WA USA
| | - Kristen Huden
- Department of Medicine, University of Washington, Seattle WA USA
| | - Misja Ilcisin
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle WA USA
| | - Mandy Izzo
- Institute for Disease Modeling, Bill & Melinda Gates Foundation, Seattle WA USA
| | | | - Ashley E. Kim
- Department of Medicine, University of Washington, Seattle WA USA
| | - Louise Kimball
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle WA USA
| | | | - Jover Lee
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle WA USA
| | | | - Julia Rogers
- Department of Medicine, University of Washington, Seattle WA USA
| | - Erin Chung
- Department of Pediatrics, University of Washington, Seattle Children’s Hospital, Seattle
| | - Thomas R. Sibley
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle WA USA
| | | | - Edward Wenger
- Institute for Disease Modeling, Bill & Melinda Gates Foundation, Seattle WA USA
| | - Caitlin R. Wolf
- Department of Medicine, University of Washington, Seattle WA USA
| | - Michael Boeckh
- Department of Medicine, University of Washington, Seattle WA USA
- Brotman Baty Institute for Precision Medicine, Seattle WA USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle WA USA
| | - Helen Chu
- Department of Medicine, University of Washington, Seattle WA USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle WA USA
| | - Jeff Duchin
- Department of Medicine, University of Washington, Seattle WA USA
- Public Health Seattle & King County, Seattle WA USA
| | - Mark Rieder
- Brotman Baty Institute for Precision Medicine, Seattle WA USA
| | - Jay Shendure
- Brotman Baty Institute for Precision Medicine, Seattle WA USA
- Department of Genome Sciences, University of Washington, Seattle WA USA
- Howard Hughes Medical Institute, Seattle WA USA
| | - Lea M. Starita
- Brotman Baty Institute for Precision Medicine, Seattle WA USA
- Department of Genome Sciences, University of Washington, Seattle WA USA
| | - Cecile Viboud
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
| | - Trevor Bedford
- Brotman Baty Institute for Precision Medicine, Seattle WA USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle WA USA
- Howard Hughes Medical Institute, Seattle WA USA
| | - Janet A. Englund
- Seattle Children’s Research Institute, Seattle WA USA
- Brotman Baty Institute for Precision Medicine, Seattle WA USA
| | - Michael Famulare
- Institute for Disease Modeling, Bill & Melinda Gates Foundation, Seattle WA USA
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8
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Mihala G, Grimwood K, Lambert SB, Ware RS. The Initial Timing and Burden of Viral Gastrointestinal Infections in Australian Infants: A Birth Cohort Study. J Pediatr Gastroenterol Nutr 2022; 74:e27-e30. [PMID: 34560725 DOI: 10.1097/mpg.0000000000003309] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
ABSTRACT The timing and nature of initial infections by potentially vaccine-preventable gastrointestinal viruses (group-F adenoviruses, classic human astrovirus, norovirus I/II, and sapovirus I/II/IV/V) was investigated in a community-based birth cohort. Weekly stool samples were collected from 158 children aged <2 years in an Australian subtropical city. Median age at initial infection was lowest for norovirus II (13.8 months) followed by sapovirus (14.3 months) and classic human astrovirus (17.6 months), and was >24 months for the remaining viruses. Norovirus II and sapovirus were most often associated with acute gastroenteritis symptoms (57% and 44%, respectively). Overall, healthcare was sought for 45% of symptomatic initial infections, which varied between 17% for norovirus I to 55% for norovirus II. Age at initial infection was lower when participants were exposed to other children. Norovirus II and sapovirus were the most important pathogens in this cohort, providing further evidence for them being priority targets for vaccine development.
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Affiliation(s)
- Gabor Mihala
- Menzies Health Institute Queensland and School of Medicine and Dentistry, Griffith University, Gold Coast, Australia
| | - Keith Grimwood
- Menzies Health Institute Queensland and School of Medicine and Dentistry, Griffith University, Gold Coast, Australia
- Departments of Infectious Diseases and Paediatrics, Gold Coast Health, Gold Coast, Australia
| | - Stephen Bernard Lambert
- Child Health Research Centre, School of Medicine, The University of Queensland, Brisbane, Australia
| | - Robert Stuart Ware
- Menzies Health Institute Queensland and School of Medicine and Dentistry, Griffith University, Gold Coast, Australia
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9
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Csadek I, Paulsen P, Weidinger P, Bak KH, Bauer S, Pilz B, Nowotny N, Smulders FJM. Nitrogen Accumulation in Oyster ( Crassostrea gigas) Slurry Exposed to Virucidal Cold Atmospheric Plasma Treatment. Life (Basel) 2021; 11:life11121333. [PMID: 34947864 PMCID: PMC8709485 DOI: 10.3390/life11121333] [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: 10/15/2021] [Revised: 11/26/2021] [Accepted: 11/28/2021] [Indexed: 11/22/2022] Open
Abstract
Viral contamination of edible bivalves is a major food safety issue. We studied the virucidal effect of a cold atmospheric plasma (CAP) source on two virologically different surrogate viruses [a double-stranded DNA virus (Equid alphaherpesvirus 1, EHV-1), and a single-stranded RNA virus (Bovine coronavirus, BCoV)] suspended in Dulbecco’s Modified Eagle’s Medium (DMEM). A 15 min exposure effectuated a statistically significant immediate reduction in intact BCoV viruses by 2.8 (ozone-dominated plasma, “low power”) or 2.3 log cycles (nitrate-dominated, “high power”) of the initial viral load. The immediate effect of CAP on EHV-1 was less pronounced, with “low power” CAP yielding a 1.4 and “high power” a 1.0 log reduction. We observed a decline in glucose contents in DMEM, which was most probably caused by a Maillard reaction with the amino acids in DMEM. With respect to the application of the virucidal CAP treatment in oyster production, we investigated whether salt water could be sanitized. CAP treatment entailed a significant decline in pH, below the limits acceptable for holding oysters. In oyster slurry (a surrogate for live oysters), CAP exposure resulted in an increase in total nitrogen, and, to a lower extent, in nitrate and nitrite; this was most probably caused by absorption of nitrate from the plasma gas cloud. We could not observe a change in colour, indicative for binding of NOx to haemocyanin, although this would be a reasonable assumption. Further studies are necessary to explore in which form this additional nitrogen is deposited in oyster flesh.
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Affiliation(s)
- Isabella Csadek
- Unit of Food Hygiene and Technology, Food Technology and Veterinary Public Health, Institute of Food Safety, University of Veterinary Medicine Vienna, Veterinärpl. 1, 1210 Vienna, Austria; (P.P.); (K.H.B.); (S.B.); (B.P.); (F.J.M.S.)
- Correspondence: ; Tel.: +43-1250-77-3325
| | - Peter Paulsen
- Unit of Food Hygiene and Technology, Food Technology and Veterinary Public Health, Institute of Food Safety, University of Veterinary Medicine Vienna, Veterinärpl. 1, 1210 Vienna, Austria; (P.P.); (K.H.B.); (S.B.); (B.P.); (F.J.M.S.)
| | - Pia Weidinger
- Viral Zoonoses, Emerging and Vector-Borne Infections Group, Institute of Virology, University of Veterinary Medicine Vienna, Veterinärpl. 1, 1210 Vienna, Austria; (P.W.); (N.N.)
| | - Kathrine H. Bak
- Unit of Food Hygiene and Technology, Food Technology and Veterinary Public Health, Institute of Food Safety, University of Veterinary Medicine Vienna, Veterinärpl. 1, 1210 Vienna, Austria; (P.P.); (K.H.B.); (S.B.); (B.P.); (F.J.M.S.)
| | - Susanne Bauer
- Unit of Food Hygiene and Technology, Food Technology and Veterinary Public Health, Institute of Food Safety, University of Veterinary Medicine Vienna, Veterinärpl. 1, 1210 Vienna, Austria; (P.P.); (K.H.B.); (S.B.); (B.P.); (F.J.M.S.)
| | - Brigitte Pilz
- Unit of Food Hygiene and Technology, Food Technology and Veterinary Public Health, Institute of Food Safety, University of Veterinary Medicine Vienna, Veterinärpl. 1, 1210 Vienna, Austria; (P.P.); (K.H.B.); (S.B.); (B.P.); (F.J.M.S.)
| | - Norbert Nowotny
- Viral Zoonoses, Emerging and Vector-Borne Infections Group, Institute of Virology, University of Veterinary Medicine Vienna, Veterinärpl. 1, 1210 Vienna, Austria; (P.W.); (N.N.)
- Department of Basic Medical Sciences, College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai Healthcare City, Dubai, United Arab Emirates
| | - Frans J. M. Smulders
- Unit of Food Hygiene and Technology, Food Technology and Veterinary Public Health, Institute of Food Safety, University of Veterinary Medicine Vienna, Veterinärpl. 1, 1210 Vienna, Austria; (P.P.); (K.H.B.); (S.B.); (B.P.); (F.J.M.S.)
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10
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Hwang H, Lim JS, Song SA, Achangwa C, Sim W, Kim G, Ryu S. Transmission dynamics of the Delta variant of SARS-CoV-2 infections in South Korea. J Infect Dis 2021; 225:793-799. [PMID: 34865022 DOI: 10.1093/infdis/jiab586] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 11/29/2021] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND The Delta variant of SARS-CoV-2 is now the predominant variant worldwide. However, its transmission dynamics remain unclear. METHODS We analyzed 405 local case-patients infected with the Delta variant of SARS-CoV-2 and temporal patterns of viral shedding identified between 22 June and 31 July 2021 in Daejeon, South Korea. RESULTS Overall, 20% were presymptomatic at the time of epidemiological investigation. We identified six clustered outbreaks, and all were associated with indoor facilities. In 23 household contacts, the secondary attack rate was 63%. We estimated the mean serial interval as 3.26 days (95% credible interval, 2.92-3.60), and 15% (95% confidence interval, 13-18%) of cases seeded 80% of all local transmission. Analysis of the nasopharyngeal swab samples identified virus shedding from the presymptomatic patients, and the highest viral load was observed two days after symptom onset. CONCLUSIONS Our findings suggest that the Delta variant is highly transmissible in indoor settings and households. Rapid contact tracing, isolation of the asymptomatic contacts, strict adherence to public health measures, and increased uptake of COVID-19 vaccination including booster doses are needed to reduce the community transmission of the Delta variant.
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Affiliation(s)
- Hari Hwang
- Department of Infectious Disease Control, Daejeon Metropolitan Government, Daejeon, South Korea
| | - Jun-Sik Lim
- Department of Preventive Medicine, Konyang University College of Medicine, Daejeon, South Korea.,Onehealth Research Institute, Konyang University College of Medicine, Daejeon, South Korea
| | - Sun-Ah Song
- Department of Infectious Disease Research, Health and Environmental Research Institute, Daejeon Metropolitan Government, Daejeon, South Korea
| | - Chiara Achangwa
- Department of Preventive Medicine, Konyang University College of Medicine, Daejeon, South Korea.,Onehealth Research Institute, Konyang University College of Medicine, Daejeon, South Korea
| | - Woobeom Sim
- Department of Infectious Disease Control, Daejeon Metropolitan Government, Daejeon, South Korea
| | - Giho Kim
- Department of Infectious Disease Control, Daejeon Metropolitan Government, Daejeon, South Korea
| | - Sukhyun Ryu
- Department of Preventive Medicine, Konyang University College of Medicine, Daejeon, South Korea.,Onehealth Research Institute, Konyang University College of Medicine, Daejeon, South Korea
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11
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Polese-Bonatto M, Sartor ITS, Varela FH, Giannini GLT, Azevedo TR, Kern LB, Fernandes IR, Zavaglia GO, de David CN, Santos AP, de Almeida WAF, Porto VBG, Scotta MC, Stein RT. Children Have Similar Reverse Transcription Polymerase Chain Reaction Cycle Threshold for Severe Acute Respiratory Syndrome Coronavirus 2 in Comparison With Adults. Pediatr Infect Dis J 2021; 40:e413-e417. [PMID: 34596626 PMCID: PMC8505158 DOI: 10.1097/inf.0000000000003300] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/29/2021] [Indexed: 12/23/2022]
Abstract
BACKGROUND The viral dynamics and the role of children in the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are not completely understood. Our aim was to evaluate reverse transcription polymerase chain reaction (RT-PCR) cycle threshold (Ct) values among children with confirmed SARS-CoV-2 compared with that of adult subjects. METHODS Patients (from 2 months to ≤18 years of age and adults) with signs and symptoms of acute SARS-CoV-2 infection for less than 7 days were prospectively enrolled in the study from May to November 2020. All participants performed RT-PCR assay for SARS-CoV-2 detection; Ct values of ORF1ab, N and S gene targets and the average of all the 3 probes were used as surrogates of viral load. RESULTS There were 21 infants (2 months to <2 years), 40 children (≥2 to <12 years), 22 adolescents (≥12 to <18 years) and 293 adults of 376 participants with confirmed SARS-CoV-2 infections. RT-PCR Ct values from all participants less than 18 years of age, as well as from all childhood subgroups, were not significantly different from adults, comparing ORF1ab, N, S and all the gene targets together (P = 0.453). CONCLUSIONS Ct values for children were comparable with that of adults. Although viral load is not the only determinant of SARS-CoV-2 transmission, children may play a role in the spread of coronavirus disease 2019 in the community.
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Affiliation(s)
| | | | - Fernanda Hammes Varela
- From the Social Responsibility – PROADI-SUS, Hospital Moinhos de Vento
- School of Medicine, Pontifícia Universidade Católica do Rio Grande do Sul
| | | | | | | | | | | | | | - Amanda Paz Santos
- From the Social Responsibility – PROADI-SUS, Hospital Moinhos de Vento
| | | | | | - Marcelo Comerlato Scotta
- From the Social Responsibility – PROADI-SUS, Hospital Moinhos de Vento
- School of Medicine, Pontifícia Universidade Católica do Rio Grande do Sul
| | - Renato T. Stein
- From the Social Responsibility – PROADI-SUS, Hospital Moinhos de Vento
- School of Medicine, Pontifícia Universidade Católica do Rio Grande do Sul
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12
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Knudtzen FC, Jensen TG, Lindvig SO, Rasmussen LD, Madsen LW, Hoegh SV, Bek-Thomsen M, Laursen CB, Nielsen SL, Johansen IS. SARS-CoV-2 viral load as a predictor for disease severity in outpatients and hospitalised patients with COVID-19: A prospective cohort study. PLoS One 2021; 16:e0258421. [PMID: 34637459 PMCID: PMC8509867 DOI: 10.1371/journal.pone.0258421] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 09/27/2021] [Indexed: 01/01/2023] Open
Abstract
Introduction We aimed to examine if severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) polymerase chain reaction (PCR) cycle quantification (Cq) value, as a surrogate for SARS-CoV-2 viral load, could predict hospitalisation and disease severity in adult patients with coronavirus disease 2019 (COVID-19). Methods We performed a prospective cohort study of adult patients with PCR positive SARS-CoV-2 airway samples including all out-patients registered at the Department of Infectious Diseases, Odense University Hospital (OUH) March 9-March 17 2020, and all hospitalised patients at OUH March 10-April 21 2020. To identify associations between Cq-values and a) hospital admission and b) a severe outcome, logistic regression analyses were used to compute odds ratios (OR) and 95% Confidence Intervals (CI), adjusting for confounding factors (aOR). Results We included 87 non-hospitalised and 82 hospitalised patients. The median baseline Cq-value was 25.5 (interquartile range 22.3–29.0). We found a significant association between increasing Cq-value and hospital-admission in univariate analysis (OR 1.11, 95% CI 1.04–1.19). However, this was due to an association between time from symptom onset to testing and Cq-values, and no association was found in the adjusted analysis (aOR 1.08, 95% CI 0.94–1.23). In hospitalised patients, a significant association between lower Cq-values and higher risk of severe disease was found (aOR 0.89, 95% CI 0.81–0.98), independent of timing of testing. Conclusions SARS-CoV-2 PCR Cq-values in outpatients correlated with time after symptom onset, but was not a predictor of hospitalisation. However, in hospitalised patients lower Cq-values were associated with higher risk of severe disease.
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Affiliation(s)
- Fredrikke Christie Knudtzen
- Department of Infectious Diseases, Odense University Hospital, Odense, Denmark.,Department of Clinical Research, University of Southern Denmark, Odense, Denmark.,Clinical Center of Emerging and Vector-borne Infections, Odense University Hospital, Odense, Denmark.,OPEN, Open Patient Data Explorative Network, Odense University Hospital, University of Southern Denmark, Odense, Denmark
| | - Thøger Gorm Jensen
- Clinical Center of Emerging and Vector-borne Infections, Odense University Hospital, Odense, Denmark.,Department of Clinical Microbiology, Odense University Hospital, Odense, Denmark.,Research Unit for Clinical Microbiology, University of Southern Denmark, Odense, Denmark
| | - Susan Olaf Lindvig
- Department of Infectious Diseases, Odense University Hospital, Odense, Denmark
| | | | - Lone Wulff Madsen
- Department of Infectious Diseases, Odense University Hospital, Odense, Denmark.,Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Silje Vermedal Hoegh
- Department of Clinical Microbiology, Odense University Hospital, Odense, Denmark.,Research Unit for Clinical Microbiology, University of Southern Denmark, Odense, Denmark
| | | | - Christian B Laursen
- Department of Clinical Research, University of Southern Denmark, Odense, Denmark.,Department of Respiratory Medicine, Odense University Hospital, Odense, Denmark
| | | | - Isik Somuncu Johansen
- Department of Infectious Diseases, Odense University Hospital, Odense, Denmark.,Department of Clinical Research, University of Southern Denmark, Odense, Denmark
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13
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Bouzid D, Vila J, Hansen G, Manissero D, Pareja J, Rao SN, Visseaux B. Systematic review on the association between respiratory virus real-time PCR cycle threshold values and clinical presentation or outcomes. J Antimicrob Chemother 2021; 76:iii33-iii49. [PMID: 34555159 PMCID: PMC8460103 DOI: 10.1093/jac/dkab246] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Objectives It is unclear whether real-time (rt)-PCR cycle threshold (Ct) values can be utilized to guide clinical and infection-control decisions. This systematic review assesses the association between respiratory pathogen rt-PCR Ct values and clinical presentation or outcomes. Methods We searched MEDLINE, EMBASE and Cochrane library databases on 14–17 January 2020 for studies reporting the presence or absence of an association between Ct values and clinical presentation or outcomes, excluding animal studies, reviews, meta-analyses, and non-English language studies. Results Among 33 studies identified (reporting on between 9 and 4918 participants by pathogen), influenza (n = 11 studies; 4918 participants), human rhinovirus (HRV, n = 11; 2012) and respiratory syncytial virus (RSV, n = 8; 3290) were the most-studied pathogens. Low influenza Ct values were associated with mortality in 1/3 studies, with increased disease severity/duration or ICU admission in 3/9, and with increased hospitalization or length of hospital stay (LOS) in 1/6. Low HRV Ct values were associated with increased disease severity/duration or ICU admission in 3/10 studies, and with increased hospitalization or LOS in 1/3. Low RSV Ct values were associated with increased disease severity/duration or ICU admission in 3/6 studies, and with increased hospitalization or LOS in 4/4. Contradictory associations were also identified for other respiratory pathogens. Conclusions Respiratory infection Ct values may inform clinical and infection-control decisions. However, the study heterogeneity observed in this review highlights the need for standardized workflows to utilize Ct values as a proxy of genomic load and confirm their value for respiratory infection management.
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Affiliation(s)
- Donia Bouzid
- Université de Paris, IAME, INSERM, Paris, France.,Université de Paris, Service d'Accueil des Urgences, Hôpital Bichat Claude Bernard, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Jordi Vila
- Department of Clinical Microbiology, Biomedical Diagnostic Centre, Hospital Clinic, School of Medicine, University of Barcelona, Institute of Global Health, Barcelona, Spain
| | - Glen Hansen
- Microbiology and Molecular Diagnostics, Hennepin County Medical Center, Department of Infectious Diseases, University of Minnesota School of Medicine, Minneapolis, MN, USA.,Department of Pathology & Laboratory Medicine, University of Minnesota, School of Medicine, Minneapolis, MN, USA
| | | | - Josep Pareja
- STAT-Dx Life, S.L. (a QIAGEN Company), Medical Affairs, Barcelona, Spain
| | - Sonia N Rao
- QIAGEN Inc., Medical Affairs, Germantown, MD, USA
| | - Benoit Visseaux
- Université de Paris, IAME, INSERM, Paris, France.,Université de Paris, Laboratoire de Virologie, Hôpital Bichat Claude Bernard, Assistance Publique-Hôpitaux de Paris, Paris, France
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14
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Cassidy H, Van Genne M, Lizarazo-Forero E, Gard L, Niesters HGM. A discussion of syndromic molecular testing for clinical care. J Antimicrob Chemother 2021; 76:iii58-iii66. [PMID: 34555161 PMCID: PMC8460109 DOI: 10.1093/jac/dkab243] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Current molecular detection methods for single or multiplex pathogens by real-time PCR generally offer great sensitivity and specificity. However, many infectious pathogens often result in very similar clinical presentations, complicating the test-order for physicians who have to narrow down the causative agent prior to in-house PCR testing. As a consequence, the intuitive response is to start empirical therapy to treat a broad spectrum of possible pathogens. Syndromic molecular testing has been increasingly integrated into routine clinical care, either to provide diagnostic, epidemiological or patient management information. These multiplex panels can be used to screen for predefined infectious disease pathogens simultaneously within a 1 h timeframe, creating opportunities for rapid diagnostics. Conversely, syndromic panels have their own challenges and must be adaptable to the evolving demands of the clinical setting. Firstly, questions have been raised regarding the clinical relevance of some of the targets included in the panels and secondly, there is the added expense of integration into the clinical laboratory. Here, we aim to discuss some of the factors that should be considered before performing syndromic testing rather than traditional low-plex in-house PCR.
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Affiliation(s)
- Hayley Cassidy
- The University of Groningen, University Medical Centre Groningen, Department of Medical Microbiology and Infection Prevention, Division of Clinical Virology, Groningen, The Netherlands
| | - Mart Van Genne
- The University of Groningen, University Medical Centre Groningen, Department of Medical Microbiology and Infection Prevention, Division of Clinical Virology, Groningen, The Netherlands
| | - Erley Lizarazo-Forero
- The University of Groningen, University Medical Centre Groningen, Department of Medical Microbiology and Infection Prevention, Division of Clinical Virology, Groningen, The Netherlands
| | - Lilli Gard
- The University of Groningen, University Medical Centre Groningen, Department of Medical Microbiology and Infection Prevention, Division of Clinical Virology, Groningen, The Netherlands
| | - Hubert G M Niesters
- The University of Groningen, University Medical Centre Groningen, Department of Medical Microbiology and Infection Prevention, Division of Clinical Virology, Groningen, The Netherlands
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15
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Rabaan AA, Tirupathi R, Sule AA, Aldali J, Mutair AA, Alhumaid S, Muzaheed, Gupta N, Koritala T, Adhikari R, Bilal M, Dhawan M, Tiwari R, Mitra S, Emran TB, Dhama K. Viral Dynamics and Real-Time RT-PCR Ct Values Correlation with Disease Severity in COVID-19. Diagnostics (Basel) 2021; 11:1091. [PMID: 34203738 PMCID: PMC8232180 DOI: 10.3390/diagnostics11061091] [Citation(s) in RCA: 109] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 06/02/2021] [Accepted: 06/10/2021] [Indexed: 01/08/2023] Open
Abstract
Real-time RT-PCR is considered the gold standard confirmatory test for coronavirus disease 2019 (COVID-19). However, many scientists disagree, and it is essential to understand that several factors and variables can cause a false-negative test. In this context, cycle threshold (Ct) values are being utilized to diagnose or predict SARS-CoV-2 infection. This practice has a significant clinical utility as Ct values can be correlated with the viral load. In addition, Ct values have a strong correlation with multiple haematological and biochemical markers. However, it is essential to consider that Ct values might be affected by pre-analytic, analytic, and post-analytical variables such as collection technique, specimen type, sampling time, viral kinetics, transport and storage conditions, nucleic acid extraction, viral RNA load, primer designing, real-time PCR efficiency, and Ct value determination method. Therefore, understanding the interpretation of Ct values and other influential factors could play a crucial role in interpreting viral load and disease severity. In several clinical studies consisting of small or large sample sizes, several discrepancies exist regarding a significant positive correlation between the Ct value and disease severity in COVID-19. In this context, a revised review of the literature has been conducted to fill the knowledge gaps regarding the correlations between Ct values and severity/fatality rates of patients with COVID-19. Various databases such as PubMed, Science Direct, Medline, Scopus, and Google Scholar were searched up to April 2021 by using keywords including "RT-PCR or viral load", "SARS-CoV-2 and RT-PCR", "Ct value and viral load", "Ct value or COVID-19". Research articles were extracted and selected independently by the authors and included in the present review based on their relevance to the study. The current narrative review explores the correlation of Ct values with mortality, disease progression, severity, and infectivity. We also discuss the factors that can affect these values, such as collection technique, type of swab, sampling method, etc.
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Affiliation(s)
- Ali A. Rabaan
- Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, Dhahran 31311, Saudi Arabia;
| | - Raghavendra Tirupathi
- Department of Medicine Keystone Health, Penn State University School of Medicine, Hershey, PA 16801, USA;
- Department of Medicine, Wellspan Chambersburg and Waynesboro Hospitals, Chambersburg, PA 17201, USA
| | - Anupam A Sule
- Department of Informatics and Outcomes, St Joseph Mercy Oakland, Pontiac, MI 48341, USA;
| | - Jehad Aldali
- Pathology Organization, Imam Mohammed Ibn Saud Islamic University, Riyadh 13317, Saudi Arabia;
| | - Abbas Al Mutair
- Research Center, Almoosa Specialist Hospital, Al-Ahsa 36342, Saudi Arabia;
- College of Nursing, Princess Norah Bint Abdulrahman University, Riyadh 11564, Saudi Arabia
- School of Nursing, Wollongong University, Wollongong, NSW 2522, Australia
| | - Saad Alhumaid
- Administration of Pharmaceutical Care, Al-Ahsa Health Cluster, Ministry of Health, Al-Ahsa 31982, Saudi Arabia;
| | - Muzaheed
- Department of Clinical Laboratory Science, College of Applied Medical Sciences, Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia;
| | - Nitin Gupta
- Department of Infectious Diseases, Kasturba Medical College, Manipal Academy of Higher Education, Manipal 576104, India;
| | - Thoyaja Koritala
- Department of Internal Medicine, Mayo Clinic Health System Mankato, Mayo Clinic College of Medicine and Science, Mankato, MN 56001, USA;
| | - Ramesh Adhikari
- Department of Hospital Medicine, Franciscan Health Lafayette, Lafayette, IN 47905, USA;
| | - Muhammad Bilal
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China;
| | - Manish Dhawan
- Department of Microbiology, Punjab Agricultural University, Ludhiana 141004, India;
- The Trafford Group of Colleges, Manchester WA14 5PQ, UK
| | - Ruchi Tiwari
- Department of Veterinary Microbiology and Immunology, College of Veterinary Sciences, Uttar Prade Pandit Deen Dayal Upadhyaya Pashu Chikitsa Vigyan Vishwavidyalaya Evam Go Anusandha Sansthan (DUVASU), Mathura 281001, India;
| | - Saikat Mitra
- Department of Pharmacy, Faculty of Pharmacy, University of Dhaka, Dhaka 1000, Bangladesh;
| | - Talha Bin Emran
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong 4381, Bangladesh
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, India
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16
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Karger AB, Ferrieri P, Nelson AC. Viral Loads of SARS-CoV-2 in Young Children. JAMA Pediatr 2021; 175:528-529. [PMID: 33523095 DOI: 10.1001/jamapediatrics.2020.5542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Amy B Karger
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis
| | - Patricia Ferrieri
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis
| | - Andrew C Nelson
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis
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17
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Romero-Alvarez D, Garzon-Chavez D, Espinosa F, Ligña E, Teran E, Mora F, Espin E, Albán C, Galarza JM, Reyes J. Cycle Threshold Values in the Context of Multiple RT-PCR Testing for SARS-CoV-2. Risk Manag Healthc Policy 2021; 14:1311-1317. [PMID: 33824608 PMCID: PMC8018360 DOI: 10.2147/rmhp.s282962] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Accepted: 12/28/2020] [Indexed: 12/17/2022] Open
Abstract
Purpose Discharge or follow up of confirmed coronavirus disease 2019 (COVID-19) cases depend on accurate interpretation of RT-PCR. Currently, positive/negative interpretations are based on amplification instead of quantification of cycle threshold (Ct) values, which could be used as proxies of patient infectiousness. Here, we measured Ct values in hospitalized confirmed COVID-19 patients at different times and its implications in diagnosis and follow up. Patients and Methods Observational study between March 17th-May 12th, 2020 using multiple RT-PCR testing. A cohort of 118 Hispanic hospitalized patients with confirmed COVID-19 diagnosis in a reference hospital in Quito, Ecuador. Multiple RT-PCR tests were performed using deep nasal swab samples and the assessment of SARS-CoV-2 genes N, RdRP, and E. Results Patients’ median age was of 49 years (range: 24–91) with a male majority (62.7%). We found increasing levels of Ct values in time, with a mean Ct value of 29.13 (n = 61, standard deviation (sd) = 5.55) for the first test and 34.38 (n = 60, sd = 4), 35.52 (n = 20, sd = 2.85), and 36.12 (n = 6, sd = 3.28), for the second, third, and fourth tests, respectively. Time to RT-PCR lack of amplification for all tests was of 34 days while time to RT-PCR Ct values >33 was of 30 days. Conclusion Cycle thresholds can potentially be used to improve diagnosis, management and control. We found that turnover time for negativity can be large for hospitalized patients and that 11% cases persisted with infectious Ct values for more time than the current isolation recommendations. ![]()
Point your SmartPhone at the code above. If you have a QR code reader the video abstract will appear. Or use: https://youtu.be/KjdapC4SGeE
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Affiliation(s)
- Daniel Romero-Alvarez
- Biodiversity Institute and Department of Ecology & Evolutionary Biology, University of Kansas, Lawrence, KS, USA
| | - Daniel Garzon-Chavez
- Colegio de Ciencias de la Salud, Universidad San Francisco de Quito, Quito, Ecuador
| | - Franklin Espinosa
- Departamento Microbiología Médica, Hospital IESS Quito Sur, Quito, Ecuador
| | - Edison Ligña
- Departamento Microbiología Médica, Hospital IESS Quito Sur, Quito, Ecuador
| | - Enrique Teran
- Colegio de Ciencias de la Salud, Universidad San Francisco de Quito, Quito, Ecuador
| | - Francisco Mora
- Departamento Microbiología Médica, Hospital IESS Quito Sur, Quito, Ecuador
| | - Emilia Espin
- Hospital IESS Carlos Andrade Marin, Quito, Ecuador
| | | | | | - Jorge Reyes
- Departamento Microbiología Médica, Hospital IESS Quito Sur, Quito, Ecuador.,Universidad Central del Ecuador, Quito, Ecuador
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18
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Fox-Lewis A, Fox-Lewis S, Beaumont J, Drinković D, Harrower J, Howe K, Jackson C, Rahnama F, Shilton B, Qiao H, Smith KK, Morpeth SC, Taylor S, Blakiston M, Roberts S, McAuliffe G. SARS-CoV-2 viral load dynamics and real-time RT-PCR cycle threshold interpretation in symptomatic non-hospitalised individuals in New Zealand: a multicentre cross sectional observational study. Pathology 2021; 53:530-535. [PMID: 33838922 PMCID: PMC7980174 DOI: 10.1016/j.pathol.2021.01.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 12/14/2020] [Accepted: 01/15/2021] [Indexed: 12/27/2022]
Abstract
We conducted a multicentre cross sectional observational study of laboratory, public health and hospitalisation data for PCR-confirmed COVID-19 cases within the New Zealand Northern Region, between 12 February and 8 June 2020. The aim of this study was to describe population level SARS-CoV-2 upper respiratory tract (URT) viral load dynamics by stratifying positivity rates and polymerase chain reaction (PCR) cycle threshold (Ct) values of URT samples from COVID-19 cases by days since symptom onset, and to explore utility of Ct values in determining length of time post-infection and thus potential infectivity. Of 123,124 samples tested for SARS-CoV-2 by PCR, 579 samples (407 positive and 172 negative) from 368 symptomatic non-hospitalised individuals with PCR-confirmed infection were included. Sample positivity rate was 61.5% (8/13) for pre-symptomatic samples, rising to 93.2% (317/340) for samples collected during the purported symptomatic infectious period (days 0–10 post-symptom onset), and dropping to 36.3% (82/226) for post-infectious period samples (day 11 onwards). URT viral load peaked shortly after symptom onset, with median Ct values ranging 20.00–29.99 until 15 days post-symptom onset, and >30.00 after this time. Of samples with a Ct value of <20.00, 96.1% were collected during the symptomatic infectious period. However, of samples with a Ct value ≥30.00 and ≥35.00, 46.9% and 18.5%, respectively, were also collected during the symptomatic infectious period. The findings of this study indicate that at or soon after symptom onset represents the optimum time to test for SARS-CoV-2 in the URT, with median Ct values suggesting the useful testing window extends until around 15 days post-symptom onset. In asymptomatic individuals or those with unknown dates of symptom onset, Ct values <20.00 imply recent onset/potential infectivity, but Ct values ≥30.00 or ≥35.00 do not exclude recent onset/potential infectivity. Individual sample Ct values should not be used as an absolute marker of length of time post-infection or to exclude infectivity where date of symptom onset is unavailable.
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Affiliation(s)
- Andrew Fox-Lewis
- Microbiology Department, LabPLUS, Auckland City Hospital, Auckland District Health Board, Auckland, New Zealand
| | - Shivani Fox-Lewis
- Virology-Immunology Department, LabPLUS, Auckland City Hospital, Auckland District Health Board, Auckland, New Zealand.
| | - Jenna Beaumont
- Microbiology Department, Middlemore Hospital, Counties Manukau District Health Board, Auckland, New Zealand
| | - Dragana Drinković
- Microbiology Department, North Shore Hospital, Waitematā District Health Board, Auckland, New Zealand
| | - Jay Harrower
- Auckland Regional Public Health Service, Auckland District Health Board, Auckland, New Zealand
| | - Kevin Howe
- Auckland Regional Public Health Service, Auckland District Health Board, Auckland, New Zealand
| | - Catherine Jackson
- Nga Tai Ora Public Health Northland, Northland District Health Board, Whangarei, New Zealand
| | - Fahimeh Rahnama
- Virology-Immunology Department, LabPLUS, Auckland City Hospital, Auckland District Health Board, Auckland, New Zealand
| | | | - Helen Qiao
- Microbiology Department, Middlemore Hospital, Counties Manukau District Health Board, Auckland, New Zealand
| | - Kevin K Smith
- Microbiology Department, North Shore Hospital, Waitematā District Health Board, Auckland, New Zealand
| | - Susan C Morpeth
- Microbiology Department, Middlemore Hospital, Counties Manukau District Health Board, Auckland, New Zealand
| | - Susan Taylor
- Microbiology Department, Middlemore Hospital, Counties Manukau District Health Board, Auckland, New Zealand
| | - Matthew Blakiston
- Microbiology Department, LabPLUS, Auckland City Hospital, Auckland District Health Board, Auckland, New Zealand; Labtests, Auckland, New Zealand
| | - Sally Roberts
- Microbiology Department, LabPLUS, Auckland City Hospital, Auckland District Health Board, Auckland, New Zealand
| | - Gary McAuliffe
- Virology-Immunology Department, LabPLUS, Auckland City Hospital, Auckland District Health Board, Auckland, New Zealand; Labtests, Auckland, New Zealand
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19
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Schnuriger A, Perrier M, Marinho V, Michel Y, Saloum K, Boukli N, Lambert-Niclot S, Amiel C, Fofana DB, Gozlan J, Morand-Joubert L. Caution in interpretation of SARS-CoV-2 quantification based on RT-PCR cycle threshold value. Diagn Microbiol Infect Dis 2021; 100:115366. [PMID: 33756311 PMCID: PMC7929791 DOI: 10.1016/j.diagmicrobio.2021.115366] [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: 12/08/2020] [Revised: 02/15/2021] [Accepted: 02/27/2021] [Indexed: 12/15/2022]
Abstract
RT-PCR is the reference method for diagnosis of a Severe Acute Respiratory Syndrome-Coronavirus-2 (SARS-CoV-2) infection. During the setting up of 6 SARS-CoV-2 RT-PCR assays in our laboratory, comparative evaluations were systematically undertaken and allowed to evidence major discrepancies on cycle threshold RT-PCR results between techniques. These tendencies were confirmed in routine application when analyzing sequential samples from the same patients. Our aim was to examine the impact of the technique among factors influencing RT-PCR result, a far surrogate of ‘viral load’ in the heterogeneous environment of respiratory specimens.
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Affiliation(s)
- Aurélie Schnuriger
- Department of virology, St Antoine - Tenon - Trousseau university hospitals, Assistance Publique - Hôpitaux de Paris, France; Sorbonne Université, INSERM UMR_S 938, Centre de Recherche Saint-Antoine (CRSA), Paris, France.
| | - Marine Perrier
- Department of virology, St Antoine - Tenon - Trousseau university hospitals, Assistance Publique - Hôpitaux de Paris, France
| | - Valérie Marinho
- Department of virology, St Antoine - Tenon - Trousseau university hospitals, Assistance Publique - Hôpitaux de Paris, France
| | - Yanne Michel
- Department of virology, St Antoine - Tenon - Trousseau university hospitals, Assistance Publique - Hôpitaux de Paris, France
| | - Kenda Saloum
- Department of virology, St Antoine - Tenon - Trousseau university hospitals, Assistance Publique - Hôpitaux de Paris, France
| | - Narjis Boukli
- Department of virology, St Antoine - Tenon - Trousseau university hospitals, Assistance Publique - Hôpitaux de Paris, France
| | - Sidonie Lambert-Niclot
- Department of virology, St Antoine - Tenon - Trousseau university hospitals, Assistance Publique - Hôpitaux de Paris, France; Sorbonne Université, INSERM UMR_S 1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), Paris, France
| | - Corinne Amiel
- Department of virology, St Antoine - Tenon - Trousseau university hospitals, Assistance Publique - Hôpitaux de Paris, France
| | - Djeneba Bocar Fofana
- Department of virology, St Antoine - Tenon - Trousseau university hospitals, Assistance Publique - Hôpitaux de Paris, France
| | - Joël Gozlan
- Department of virology, St Antoine - Tenon - Trousseau university hospitals, Assistance Publique - Hôpitaux de Paris, France; Sorbonne Université, INSERM UMR_S 938, Centre de Recherche Saint-Antoine (CRSA), Paris, France
| | - Laurence Morand-Joubert
- Department of virology, St Antoine - Tenon - Trousseau university hospitals, Assistance Publique - Hôpitaux de Paris, France; Sorbonne Université, INSERM UMR_S 1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), Paris, France
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20
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Poon KS, Tee NWS. Caveats of Reporting Cycles Threshold from SARS-CoV-2 Qualitative PCR Assays: A Molecular Diagnostic Laboratory Perspective. Clin Infect Dis 2020; 73:e2851-e2852. [PMID: 32929464 PMCID: PMC7543341 DOI: 10.1093/cid/ciaa1399] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Affiliation(s)
- Kok-Siong Poon
- Molecular Diagnosis Centre, Department of Laboratory Medicine, National University Hospital, Singapore
| | - Nancy Wen-Sim Tee
- Molecular Diagnosis Centre, Department of Laboratory Medicine, National University Hospital, Singapore.,Division of Microbiology, Department of Laboratory Medicine, National University Hospital, Singapore
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21
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Vazquez F, Fernández J. Resistance-Guided Therapy for Mycoplasma genitalium Infections. Clin Infect Dis 2020; 71:1469-1471. [PMID: 31629367 DOI: 10.1093/cid/ciz1035] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 10/14/2019] [Indexed: 11/13/2022] Open
Affiliation(s)
- Fernando Vazquez
- Servicio de Microbiología, Hospital Universitario Central de Asturias, Oviedo, Asturias, Spain.,Departamento de Biología Funcional, Área de Microbiología, Facultad de Medicina, Universidad de Oviedo, Oviedo, Spain.,Grupo de Microbiología Translacional, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain.,Grupo de Estudio de Infecciones de Transmisión Sexual, Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica, Spain.,Instituto Universitario Fernández Vega y Fundación de Investigación Oftalmológica, Oviedo, Spain
| | - Javier Fernández
- Servicio de Microbiología, Hospital Universitario Central de Asturias, Oviedo, Asturias, Spain.,Grupo de Microbiología Translacional, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
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22
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Rao SN, Manissero D, Steele VR, Pareja J. A Systematic Review of the Clinical Utility of Cycle Threshold Values in the Context of COVID-19. Infect Dis Ther 2020; 9:573-586. [PMID: 32725536 PMCID: PMC7386165 DOI: 10.1007/s40121-020-00324-3] [Citation(s) in RCA: 252] [Impact Index Per Article: 63.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND The ability to predict likely prognosis and infectiousness for patients with COVID-19 would aid patient management decisions. Diagnosis is usually via real-time PCR, and it is unclear whether the semi-quantitative capability of this method, determining viral load through cycle threshold (Ct) values, can be leveraged. OBJECTIVES We aim to review available knowledge on correlations between SARS-COV-2 Ct values and patient- or healthcare-related outcomes to determine whether Ct values provide useful clinical information. SOURCES A PubMed search was conducted on 1 June 2020 based on a search strategy of (Ct value OR viral load) AND SARS-CoV-2. Data were extracted from studies reporting on the presence or absence of an association between Ct values, or viral loads determined via Ct value, and clinical outcomes. CONTENT Data from 18 studies were relevant for inclusion. One study reported on the correlation between Ct values and mortality and one study reported on the correlation between Ct values and progression to severe disease; both reported a significant association (p < 0.001 and p = 0.008, respectively). Fourteen studies reported on the correlation between Ct value or viral loads determined via Ct value and disease severity, and an association was observed in eight (57%) studies. Studies reporting on the correlation of viral load with biochemical and haematological markers showed an association with at least one marker, including increased lactate dehydrogenase (n = 4), decreased lymphocytes (n = 3) and increased high-sensitivity troponin I (n = 2). Two studies reporting on the correlation with infectivity showed that lower Ct values were associated with higher viral culture positivity. IMPLICATIONS Data suggest that lower Ct values may be associated with worse outcomes and that Ct values may be useful in predicting the clinical course and prognosis of patients with COVID-19; however, further studies are warranted to confirm clinical value.
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Affiliation(s)
| | | | | | - Josep Pareja
- STAT-Dx Life, S.L. (a QIAGEN Company), Barcelona, Spain.
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23
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Lumby CK, Zhao L, Breuer J, Illingworth CJR. A large effective population size for established within-host influenza virus infection. eLife 2020; 9:e56915. [PMID: 32773034 PMCID: PMC7431133 DOI: 10.7554/elife.56915] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 07/30/2020] [Indexed: 12/13/2022] Open
Abstract
Strains of the influenza virus form coherent global populations, yet exist at the level of single infections in individual hosts. The relationship between these scales is a critical topic for understanding viral evolution. Here we investigate the within-host relationship between selection and the stochastic effects of genetic drift, estimating an effective population size of infection Ne for influenza infection. Examining whole-genome sequence data describing a chronic case of influenza B in a severely immunocompromised child we infer an Ne of 2.5 × 107 (95% confidence range 1.0 × 107 to 9.0 × 107) suggesting that genetic drift is of minimal importance during an established influenza infection. Our result, supported by data from influenza A infection, suggests that positive selection during within-host infection is primarily limited by the typically short period of infection. Atypically long infections may have a disproportionate influence upon global patterns of viral evolution.
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Affiliation(s)
- Casper K Lumby
- Department of Genetics, University of CambridgeCambridgeUnited Kingdom
| | - Lei Zhao
- Department of Genetics, University of CambridgeCambridgeUnited Kingdom
| | - Judith Breuer
- Great Ormond Street HospitalLondonUnited Kingdom
- Division of Infection and Immunity, University College LondonLondonUnited Kingdom
| | - Christopher JR Illingworth
- Department of Genetics, University of CambridgeCambridgeUnited Kingdom
- Department of Applied Mathematics and Theoretical Physics, University of CambridgeCambridgeUnited Kingdom
- Department of Computer Science, Institute of Biotechnology, University of HelsinkiHelsinkiFinland
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24
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Detection of SARS-CoV-2 in nasal swabs using MALDI-MS. Nat Biotechnol 2020; 38:1168-1173. [PMID: 32733106 DOI: 10.1038/s41587-020-0644-7] [Citation(s) in RCA: 125] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 07/14/2020] [Indexed: 12/31/2022]
Abstract
Detection of SARS-CoV-2 using RT-PCR and other advanced methods can achieve high accuracy. However, their application is limited in countries that lack sufficient resources to handle large-scale testing during the COVID-19 pandemic. Here, we describe a method to detect SARS-CoV-2 in nasal swabs using matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) and machine learning analysis. This approach uses equipment and expertise commonly found in clinical laboratories in developing countries. We obtained mass spectra from a total of 362 samples (211 SARS-CoV-2-positive and 151 negative by RT-PCR) without prior sample preparation from three different laboratories. We tested two feature selection methods and six machine learning approaches to identify the top performing analysis approaches and determine the accuracy of SARS-CoV-2 detection. The support vector machine model provided the highest accuracy (93.9%), with 7% false positives and 5% false negatives. Our results suggest that MALDI-MS and machine learning analysis can be used to reliably detect SARS-CoV-2 in nasal swab samples.
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25
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See KC, Liew SM, Ng DCE, Chew EL, Khoo EM, Sam CH, Sheena D, Zahilah Filzah Z, Chin SY, Lee PY, Tan LP, Farah Najwa Z, Sabrina S, Them WW, Saipriya T, Muhammad Zamakhshari ZA, Cheah WK, Peariasamy K, Goh PP, Ibrahim H. COVID-19: Four Paediatric Cases in Malaysia. Int J Infect Dis 2020; 94:125-127. [PMID: 32304822 PMCID: PMC7158792 DOI: 10.1016/j.ijid.2020.03.049] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 03/18/2020] [Accepted: 03/20/2020] [Indexed: 11/22/2022] Open
Abstract
OBJECTIVE This is a brief report of 4 paediatric cases of COVID-19 infection in Malaysia BACKGROUND: COVID-19, a coronavirus, first detected in Wuhan, China has now spread rapidly to over 60 countries and territories around the world, infecting more than 85000 individuals. As the case count amongst children is low, there is need to report COVID-19 in children to better understand the virus and the disease. CASES In Malaysia, until end of February 2020, there were four COVID-19 paediatric cases with ages ranging from 20 months to 11 years. All four cases were likely to have contracted the virus in China. The children had no symptoms or mild flu-like illness. The cases were managed symptomatically. None required antiviral therapy. DISCUSSION There were 2 major issues regarding the care of infected children. Firstly, the quarantine of an infected child with a parent who tested negative was an ethical dilemma. Secondly, oropharyngeal and nasal swabs in children were at risk of false negative results. These issues have implications for infection control. Consequently, there is a need for clearer guidelines for child quarantine and testing methods in the management of COVID-19 in children.
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Affiliation(s)
- K C See
- Department of Paediatric, Hospital Sungai Buloh, Ministry of Health, Malaysia
| | - S M Liew
- Department of Primary Care Medicine, Faculty of Medicine, University of Malaya, Malaysia
| | - David C E Ng
- Department of Paediatric, Hospital Tuanku Jaafar, Seremban, Ministry of Health, Malaysia
| | - E L Chew
- Department of Paediatric, Hospital Sultanah Maliha, Langkawi, Ministry of Health, Malaysia
| | - E M Khoo
- Department of Primary Care Medicine, Faculty of Medicine, University of Malaya, Malaysia
| | - C H Sam
- Department of Paediatric, Hospital Sultanah Maliha, Langkawi, Ministry of Health, Malaysia
| | - D Sheena
- Department of Paediatric, Hospital Sungai Buloh, Ministry of Health, Malaysia
| | - Z Zahilah Filzah
- Department of Paediatric, Hospital Sungai Buloh, Ministry of Health, Malaysia
| | - S Y Chin
- Department of Paediatric, Hospital Sungai Buloh, Ministry of Health, Malaysia
| | - P Y Lee
- Department of Paediatric, Hospital Sungai Buloh, Ministry of Health, Malaysia
| | - L P Tan
- Department of Paediatric, Hospital Sungai Buloh, Ministry of Health, Malaysia
| | - Z Farah Najwa
- Department of Paediatric, Hospital Sungai Buloh, Ministry of Health, Malaysia
| | - S Sabrina
- Department of Paediatric, Hospital Sungai Buloh, Ministry of Health, Malaysia
| | - W W Them
- Department of Paediatric, Hospital Sungai Buloh, Ministry of Health, Malaysia
| | - T Saipriya
- Department of Paediatric, Hospital Sungai Buloh, Ministry of Health, Malaysia
| | | | - W K Cheah
- Department of Medicine, Hospital Taiping, Ministry of Health, Malaysia
| | - K Peariasamy
- Institute for Clinical Research, Block B, National Institute of Health, Setia Alam, Ministry of Health, Malaysia
| | - P P Goh
- Institute for Clinical Research, Block B, National Institute of Health, Setia Alam, Ministry of Health, Malaysia.
| | - H Ibrahim
- Division for Research and Technical Support, Ministry of Health, Malaysia
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26
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Raaymakers MJA, Brand PLP, Landstra AM, Brouwer ML, Balemans WAF, Niers LEM, Merkus PJFM, Boehmer ALM, Kluytmans JAJW, de Jongste JC, Pijnenburg MWH, Vaessen-Verberne AAPH. Episodic viral wheeze and multiple-trigger wheeze in preschool children are neither distinct nor constant patterns. A prospective multicenter cohort study in secondary care. Pediatr Pulmonol 2019; 54:1439-1446. [PMID: 31211525 DOI: 10.1002/ppul.24411] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 04/29/2019] [Accepted: 05/09/2019] [Indexed: 11/10/2022]
Abstract
OBJECTIVES To evaluate whether episodic viral wheeze (EVW) and multiple-trigger wheeze (MTW) are clinically distinguishable and stable preschool wheezing phenotypes. METHODS Children of age 1 to 4 year with recurrent, pediatrician-confirmed wheeze were recruited from secondary care; 189 were included. Respiratory and viral upper respiratory tract infection (URTI) symptoms were recorded weekly by parents in an electronic diary during 12 months. Every 3 months, diary-based symptoms were classified as EVW or MTW and compared to phenotypes assigned by pediatricians based on clinical history. We collected nasal samples for respiratory virus PCR during URTI, respiratory symptoms and in absence of symptoms. RESULTS Of 660 3-month periods, the diary-based phenotype was EVW in 11%, MTW in 54% and 35% were free from respiratory episodes. Pediatrician-based classification showed 59% EVW and 26% MTW. The Kappa measure of agreement between diary-based and pediatrician-assigned phenotypes was very low (0.12, 95%CI, 0.07-0.17). Phenotypic instability was observed in 32% of cases. PCR was positive in 71% during URTI symptoms, 66% during respiratory symptoms and 38% in the absence of symptoms. CONCLUSION This study shows that EVW and MTW are variable over time within patients. Pediatrician classification of these phenotypes based on clinical history does not correspond to prospectively recorded symptom patterns. The applicability of these phenotypes as a basis for therapeutic decisions and prognosis should be questioned.
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Affiliation(s)
| | - Paul L P Brand
- Department of Pediatrics, Isala Hospital, Zwolle, The Netherlands.,Department of Pediatrics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Anneke M Landstra
- Department of Pediatrics, Rijnstate Hospital, Arnhem, The Netherlands
| | - Marianne L Brouwer
- Department of Pediatrics, Canisius Wilhelmina Hospital, Nijmegen, The Netherlands
| | | | - Laetitia E M Niers
- Department of Pediatrics, Máxima Medical Centre, Veldhoven, The Netherlands
| | - Peter J F M Merkus
- Department of Pediatrics Pulmonology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Annemie L M Boehmer
- Department of Pediatrics, Maasstad Medical Center, Rotterdam, The Netherlands.,Department of Pediatrics Pulmonology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | | | - Johan C de Jongste
- Department of Pediatrics Pulmonology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Marielle W H Pijnenburg
- Department of Pediatrics Pulmonology, Erasmus University Medical Center, Rotterdam, The Netherlands
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27
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Busson L, Bartiaux M, Brahim S, Konopnicki D, Dauby N, Gérard M, De Backer P, Van Vaerenbergh K, Mahadeb B, De Foor M, Wautier M, Vandenberg O, Mols P, Levy J, Hallin M. Prospective evaluation of diagnostic tools for respiratory viruses in children and adults. J Virol Methods 2019; 266:1-6. [PMID: 30658123 PMCID: PMC7119678 DOI: 10.1016/j.jviromet.2019.01.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 01/11/2019] [Accepted: 01/15/2019] [Indexed: 12/30/2022]
Abstract
Molecular techniques have considerably improved sensitivity of viral diagnosis. Interpretation of results can be delicate as DNA or RNA traces can be detected. Their use is hindered by their cost and the difficulty to absorb high workloads. Their impact in management of patients still has to be demonstrated. Tertiary care hospitals should provide a testing algorithm to suit each case.
Aim To compare the performances of molecular and non-molecular tests to diagnose respiratory viral infections and to evaluate the pros and contras of each technique. Methods Two hundred ninety-nine respiratory samples were prospectively explored using multiplex molecular techniques (FilmArray Respiratory Panel, Clart Pneumovir), immunological techniques (direct fluorescent assay, lateral flow chromatography) and cell cultures. Findings Molecular techniques permitted the recovery of up to 50% more respiratory pathogens in comparison to non-molecular methods. FilmArray detected at least 30% more pathogens than Clart Pneumovir which could be explained by the differences in their technical designs. The turnaround time under 2 hours for the FilmArray permitted delivery of results when patients were still in the emergency room.
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Affiliation(s)
- L Busson
- Department of Microbiology, Laboratoire des Hôpitaux Universitaires Bruxellois, Brussels, Belgium.
| | - M Bartiaux
- Department of Emergency Medicine, Centre Hospitalier Universitaire Saint-Pierre, Université Libre de Bruxelles, Brussels, Belgium
| | - S Brahim
- Department of Emergency Medicine, Centre Hospitalier Universitaire Saint-Pierre, Université Libre de Bruxelles, Brussels, Belgium
| | - D Konopnicki
- Department of Infectious Diseases, Centre Hospitalier Universitaire Saint-Pierre, Université Libre de Bruxelles, Brussels, Belgium
| | - N Dauby
- Department of Infectious Diseases, Centre Hospitalier Universitaire Saint-Pierre, Université Libre de Bruxelles, Brussels, Belgium
| | - M Gérard
- Department of Infectious Diseases, Centre Hospitalier Universitaire Saint-Pierre, Université Libre de Bruxelles, Brussels, Belgium
| | - P De Backer
- Pediatric Department, Centre Hospitalier Universitaire Saint-Pierre, Université Libre de Bruxelles, Brussels, Belgium
| | - K Van Vaerenbergh
- Pediatric Department, Centre Hospitalier Universitaire Saint-Pierre, Université Libre de Bruxelles, Brussels, Belgium
| | - B Mahadeb
- Department of Microbiology, Laboratoire des Hôpitaux Universitaires Bruxellois, Brussels, Belgium
| | - M De Foor
- Department of Microbiology, Laboratoire des Hôpitaux Universitaires Bruxellois, Brussels, Belgium
| | - M Wautier
- Department of Molecular Diagnostic, Laboratoire des Hôpitaux Universitaires Bruxellois, Brussels, Belgium
| | - O Vandenberg
- Department of Microbiology, Laboratoire des Hôpitaux Universitaires Bruxellois, Brussels, Belgium; Infectious Diseases Epidemiological Unit, Public Health School, Université Libre de Bruxelles, Brussels, Belgium
| | - P Mols
- Department of Emergency Medicine, Centre Hospitalier Universitaire Saint-Pierre, Université Libre de Bruxelles, Brussels, Belgium
| | - J Levy
- Pediatric Department, Centre Hospitalier Universitaire Saint-Pierre, Université Libre de Bruxelles, Brussels, Belgium
| | - M Hallin
- Department of Microbiology, Laboratoire des Hôpitaux Universitaires Bruxellois, Brussels, Belgium
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28
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Turi KN, Wu P, Escobar GJ, Gebretsadik T, Ding T, Walsh EM, Li SX, Carroll KN, Hartert TV. Prevalence of infant bronchiolitis-coded healthcare encounters attributable to RSV. Health Sci Rep 2018; 1:e91. [PMID: 30623050 PMCID: PMC6295609 DOI: 10.1002/hsr2.91] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 08/18/2018] [Accepted: 08/22/2018] [Indexed: 12/28/2022] Open
Abstract
AIM We sought to determine the proportion of bronchiolitis episodes attributable to respiratory syncytial virus (RSV) among ICD-9 coded infant bronchiolitis episodes which were tested for RSV. METHODS Bronchiolitis healthcare encounters were extracted from Kaiser Permanente Northern California databases for years 2006 to 2009. We used ICD-9 codes for bronchiolitis to capture bronchiolitis-related healthcare encounters including hospital admissions (Hospitalization), emergency department visits (EDV), and outpatient visits (OPV). We reported the monthly proportion of RSV-positive bronchiolitis episodes among tested bronchiolitis episodes. We used logistic regression to assess association between bronchiolitis episodes and patient demographic and health care characteristics. We also used logistic regression to assess association between decision to test and patient demographics and health care characteristics. RESULTS Among 10,411 ICD-9 coded infant bronchiolitis episodes, 29% were RSV tested. Fifty one percent of those tested were RSV positive. Between December and February, and in infants ≤6 months, the proportion of bronchiolitis episodes that were attributable to RSV was 77.2% among hospitalized episodes, 78.3% among EDV episodes, and 60.9% among OPV episodes, respectively. The proportion of RSV-positive bronchiolitis episodes varied based upon infant age at diagnosis, level of health care service used, and time of the year of the episode. CONCLUSION Estimation of the proportion of ICD-9 coded bronchiolitis episodes attributable to RSV is more specific when restricting to bronchiolitis episodes during peak months, younger infant age, and those requiring higher level of healthcare.
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Affiliation(s)
- Kedir N. Turi
- Department of MedicineVanderbilt University Medical CenterNashvilleTNUSA
| | - Pingsheng Wu
- Department of MedicineVanderbilt University Medical CenterNashvilleTNUSA
- Department of BiostatisticsVanderbilt University Medical CenterNashvilleTNUSA
| | - Gabriel J. Escobar
- Kaiser Permanente Northern California, Systems Research Initiative, Perinatal Research Unit, Division of ResearchKaiser PermanenteOaklandCAUSA
- Department of Inpatient PediatricsKaiser Permanente Medical CenterWalnut CreekCAUSA
| | - Tebeb Gebretsadik
- Department of BiostatisticsVanderbilt University Medical CenterNashvilleTNUSA
| | - Tan Ding
- Department of BiostatisticsVanderbilt University Medical CenterNashvilleTNUSA
| | - Eileen M. Walsh
- Department of Inpatient PediatricsKaiser Permanente Medical CenterWalnut CreekCAUSA
| | - Sherian X. Li
- Department of Inpatient PediatricsKaiser Permanente Medical CenterWalnut CreekCAUSA
| | - Kecia N. Carroll
- Department of PediatricsVanderbilt University Medical CenterNashvilleTNUSA
| | - Tina V. Hartert
- Department of MedicineVanderbilt University Medical CenterNashvilleTNUSA
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Fieldhouse JK, Toh TH, Lim WH, Ting J, Ha SJ, Hii KC, Kong CI, Wong TM, Wong SC, Warkentien TE, Gray GC. Surveillance for respiratory syncytial virus and parainfluenza virus among patients hospitalized with pneumonia in Sarawak, Malaysia. PLoS One 2018; 13:e0202147. [PMID: 30110367 PMCID: PMC6093684 DOI: 10.1371/journal.pone.0202147] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 07/27/2018] [Indexed: 12/26/2022] Open
Abstract
Background Respiratory syncytial virus (RSV) and parainfluenza virus (PIV) are frequent causes of pneumonia and death among children at Sibu and Kapit Hospitals in Sarawak, Malaysia. Objectives To determine the prevalence and risk factors for RSV subtypes A and B and PIV types 1–4 among patients hospitalized with pneumonia. Methods In a cross-sectional, pilot study nasopharyngeal swabs were studied with real-time reverse transcription polymerase chain reaction assays. Concurrently, we helped Sibu and Kapit Hospitals adapt their first molecular diagnostics for RSV and PIV. Results Of 129 specimens collected (June to July 2017), 39 tested positive for RSV-A (30.2%), two were positive for RSV B (1.6%), one was positive for PIV-3 (0.8%) and one was positive for PIV-4 (0.8%). No samples were positive for PIV-1 or PIV-2. Of the 39 RSV-A positive specimens, 46.2% were collected from children under one year of age and only 5.1% were from patients over the age of 18. A multivariable analysis found the odds of children <1 year of age testing positive for RSV-A were 32.7 (95% CI: 3.9, 276.2) times larger than >18 years of age, and the odds of patients hospitalized at Kapit Hospital testing positive for RSV-A were 3.2 (95% CI: 1.3, 7.8) times larger than patients hospitalized at Sibu Hospital. Conclusion This study found an unusually high prevalence of RSV-A among pneumonia patients admitted to the two hospitals. Subsequently, Sibu Hospital adapted the molecular assays with the goal of providing more directed care for such pneumonia patients.
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Affiliation(s)
- Jane K. Fieldhouse
- Duke Global Health Institute, Duke University, Durham, North Carolina, United States of America
- Division of Infectious Diseases, Duke University School of Medicine, Durham, North Carolina, United States of America
- * E-mail:
| | - Teck-Hock Toh
- Clinical Research Center, Sibu Hospital, Sibu, Sarawak, Malaysia
- Department of Paediatrics, Sibu Hospital, Sibu, Sarawak, Malaysia
- Faculty of Medicine, SEGi University Sibu Clinical Campus, Sibu Hospital, Sibu, Sarawak, Malaysia
| | - Wei-Honn Lim
- Clinical Research Center, Sibu Hospital, Sibu, Sarawak, Malaysia
| | - Jakie Ting
- Clinical Research Center, Sibu Hospital, Sibu, Sarawak, Malaysia
| | - Siaw-Jing Ha
- Clinical Research Center, Sibu Hospital, Sibu, Sarawak, Malaysia
- Department of Paediatrics, Sibu Hospital, Sibu, Sarawak, Malaysia
| | | | | | - Toh-Mee Wong
- Department of Medicine, Sibu Hospital, Sibu, Sarawak, Malaysia
| | - See-Chang Wong
- Department of Paediatrics, Sibu Hospital, Sibu, Sarawak, Malaysia
- Faculty of Medicine, SEGi University Sibu Clinical Campus, Sibu Hospital, Sibu, Sarawak, Malaysia
| | | | - Gregory C. Gray
- Duke Global Health Institute, Duke University, Durham, North Carolina, United States of America
- Division of Infectious Diseases, Duke University School of Medicine, Durham, North Carolina, United States of America
- Emerging Infectious Diseases Program, Duke-NUS Medical School, Singapore, Singapore
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Pathogen Clearance and New Respiratory Tract Infections Among Febrile Children in Zanzibar Investigated With Multitargeting Real-Time Polymerase Chain Reaction on Paired Nasopharyngeal Swab Samples. Pediatr Infect Dis J 2018; 37:643-648. [PMID: 29889810 DOI: 10.1097/inf.0000000000001876] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
BACKGROUND New molecular methods have revealed frequent and often polymicrobial respiratory infections in children in low-income settings. It is not known whether presence of multiple pathogens is due to prolonged infections or to frequent exposure. The aim of this study was to analyze short-term pathogen clearance from nasopharynx and the rate of new respiratory tract infections in febrile preschool children. METHODS Children (n = 207) with uncomplicated acute febrile illness 2-59 months of age presenting to a health center in Zanzibar, Tanzania, April-July 2011, were included. Paired nasopharyngeal swab samples, collected at enrolment and after 14 days, were analyzed by multiple real-time polymerase chain reaction for Adenovirus, bocavirus, Bordetella pertussis, Chlamydophila pneumoniae, Coronaviruses, Enterovirus, influenza A and B virus, metapneumovirus, measles virus, Mycoplasma pneumoniae, parainfluenza virus, Parechovirus, respiratory syncytial virus and Rhinovirus. An age-matched and geographically matched healthy control group (n = 166) underwent nasopharyngeal sampling on 1 occasion. RESULTS At baseline, 157/207 (76%) patients had at least 1 pathogen detected, in total 199 infections. At follow-up (day 14), 162/199 (81%) of these infections were not detected, including >95% of the previously detected infections with Enterovirus, influenza A virus, influenza B virus, metapneumovirus or parainfluenza virus. Still 115 (56%) children were positive for at least 1 pathogen at follow-up, of which 95/115 (83%) were not found at baseline. Detection of influenza B on day 14 was significantly associated with fever during follow-up. CONCLUSION The results suggest that children with acute febrile illness in Zanzibar rapidly clear respiratory tract infections but frequently acquire new infections within 14 days.
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A Virological and Phylogenetic Analysis of the Emergence of New Clades of Respiratory Syncytial Virus. Sci Rep 2017; 7:12232. [PMID: 28947776 PMCID: PMC5612963 DOI: 10.1038/s41598-017-12001-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 08/30/2017] [Indexed: 12/14/2022] Open
Abstract
The significant burden of Respiratory Syncytial Virus (RSV) in pediatric and elderly populations is well recognized. However, questions remain about transmission and evolution of RSV in the community, between seasons, and the role played by viral genetics in viral replication. Therefore, we integrated next generation sequencing, patient viral load, and viral replication analysis with surveillance of RSV to initiate a better understanding of viral adaptation in communities. RSV type-A and B infections were most closely related to RSV sequences from the USA and Asia, respectfully. The sample titres between RSV types-A and B were not significantly different. However, when the patient sample titre was compared to the phylogenetics of RSV, emergent clades were identified that we termed High Titre (HiT) clades of RSV. In conclusion, the correlation between patient viral load and replication kinetics of RSV patient isolates in culture indicated that viral genetics may determine virus replicative ability within patients. There was evolution or introduction of high-titre RSV type-A and B infections that seeded HiT clades in the subsequent year. Therefore, virological analysis of RSV isolates in conjunction with RSV phylogenetics may be a tool for predicting new clades of RSV in impending seasons.
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