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Petat H, Corbet S, Leterrier B, Vabret A, Ar Gouilh M. Unravelling the acute respiratory infection landscape: virus type, viral load, health status and coinfection do matter. Front Cell Infect Microbiol 2024; 14:1380855. [PMID: 38803572 PMCID: PMC11128575 DOI: 10.3389/fcimb.2024.1380855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 04/24/2024] [Indexed: 05/29/2024] Open
Abstract
Introduction Acute respiratory infections (ARI) are the most common infections in the general population and are mainly caused by respiratory viruses. Detecting several viruses in a respiratory sample is common. To better understand these viral codetections and potential interferences, we tested for the presence of viruses and developed quantitative PCR (Polymerase Chain Reaction) for the viruses most prevalent in coinfections: human rhinovirus (HRV) and respiratory syncytial virus (RSV), and quantified their viral loads according to coinfections and health status, age, cellular abundance and other variables. Materials and methods Samples from two different cohorts were analyzed: one included hospitalized infants under 12 months of age with acute bronchiolitis (n=719) and the other primary care patients of all ages with symptoms of ARI (n=685). We performed Multiplex PCR on nasopharyngeal swabs, and quantitative PCR on samples positive for HRV or/and RSV to determine viral loads (VL). Cellular abundance (CA) was also estimated by qPCR targeting the GAPDH gene. Genotyping was performed either directly from first-line molecular panel or by PCR and sequencing for HRV. Results The risks of viral codetection were 4.1 (IC95[1.8; 10.0]) and 93.9 1 (IC95[48.7; 190.7]) higher in infants hospitalized for bronchiolitis than in infants in primary care for RSV and HRV respectively (p<0.001). CA was higher in samples positive for multiple viruses than in mono-infected or negative samples (p<0.001), and higher in samples positive for RSV (p<0.001) and HRV (p<0.001) than in negative samples. We found a positive correlation between CA and VL for both RSV and HRV. HRV VL was higher in children than in the elderly (p<0.05), but not RSV VL. HRV VL was higher when detected alone than in samples coinfected with RSV-A and with RSV-B. There was a significant increase of RSV-A VL when codetecting with HRV (p=0.001) and when co-detecting with RSV-B+HRV versus RSV-A+ RSV-B (p=0.02). Conclusions Many parameters influence the natural history of respiratory viral infections, and quantifying respiratory viral loads can help disentangle their contributions to viral outcome.
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Affiliation(s)
- Hortense Petat
- University of Rouen Normandy, Dynamicure INSERM UMR 1311, CHU Rouen, Department of Pediatrics and Adolescent Medicine, Rouen, France
- University of Caen Normandy, Dynamicure INSERM UMR 1311, Centre hospitalo-universitaire (CHU) Caen, Department of Virology, Caen, France
| | - Sandrine Corbet
- University of Caen Normandy, Dynamicure INSERM UMR 1311, Centre hospitalo-universitaire (CHU) Caen, Department of Virology, Caen, France
| | - Bryce Leterrier
- University of Caen Normandy, Dynamicure INSERM UMR 1311, Centre hospitalo-universitaire (CHU) Caen, Department of Virology, Caen, France
| | - Astrid Vabret
- University of Caen Normandy, Dynamicure INSERM UMR 1311, Centre hospitalo-universitaire (CHU) Caen, Department of Virology, Caen, France
| | - Meriadeg Ar Gouilh
- University of Caen Normandy, Dynamicure INSERM UMR 1311, Centre hospitalo-universitaire (CHU) Caen, Department of Virology, Caen, France
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Lin GL, Drysdale SB, Snape MD, O'Connor D, Brown A, MacIntyre-Cockett G, Mellado-Gomez E, de Cesare M, Ansari MA, Bonsall D, Bray JE, Jolley KA, Bowden R, Aerssens J, Bont L, Openshaw PJM, Martinon-Torres F, Nair H, Golubchik T, Pollard AJ. Targeted metagenomics reveals association between severity and pathogen co-detection in infants with respiratory syncytial virus. Nat Commun 2024; 15:2379. [PMID: 38493135 PMCID: PMC10944482 DOI: 10.1038/s41467-024-46648-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 02/23/2024] [Indexed: 03/18/2024] Open
Abstract
Respiratory syncytial virus (RSV) is the leading cause of hospitalisation for respiratory infection in young children. RSV disease severity is known to be age-dependent and highest in young infants, but other correlates of severity, particularly the presence of additional respiratory pathogens, are less well understood. In this study, nasopharyngeal swabs were collected from two cohorts of RSV-positive infants <12 months in Spain, the UK, and the Netherlands during 2017-20. We show, using targeted metagenomic sequencing of >100 pathogens, including all common respiratory viruses and bacteria, from samples collected from 433 infants, that burden of additional viruses is common (111/433, 26%) but only modestly correlates with RSV disease severity. In contrast, there is strong evidence in both cohorts and across age groups that presence of Haemophilus bacteria (194/433, 45%) is associated with higher severity, including much higher rates of hospitalisation (odds ratio 4.25, 95% CI 2.03-9.31). There is no evidence for association between higher severity and other detected bacteria, and no difference in severity between RSV genotypes. Our findings reveal the genomic diversity of additional pathogens during RSV infection in infants, and provide an evidence base for future causal investigations of the impact of co-infection on RSV disease severity.
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Affiliation(s)
- Gu-Lung Lin
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK.
- NIHR Oxford Biomedical Research Centre, Oxford, UK.
| | - Simon B Drysdale
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
- Centre for Neonatal and Paediatric Infection, Institute for Infection and Immunity, St George's, University of London, London, UK
| | - Matthew D Snape
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Daniel O'Connor
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Anthony Brown
- Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK
| | | | - Esther Mellado-Gomez
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Wellcome Sanger Institute, Hinxton, UK
| | - Mariateresa de Cesare
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Human Technopole, Milan, Italy
| | - M Azim Ansari
- Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - David Bonsall
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - James E Bray
- Department of Biology, University of Oxford, Oxford, UK
| | | | - Rory Bowden
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Jeroen Aerssens
- Translational Biomarkers, Infectious Diseases Therapeutic Area, Janssen Pharmaceutica NV, Beerse, Belgium
| | - Louis Bont
- Department of Pediatrics, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, Netherlands
- ReSViNET Foundation, Zeist, Netherlands
| | | | - Federico Martinon-Torres
- Translational Pediatrics and Infectious Diseases, Pediatrics Department, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain
- Genetics, Vaccines, Infectious Diseases and Pediatrics Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago, University of Santiago de Compostela, Santiago de Compostela, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
| | - Harish Nair
- Centre for Global Health, Usher Institute, Edinburgh Medical School, University of Edinburgh, Edinburgh, UK
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Tanya Golubchik
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
- Sydney Infectious Diseases Institute, School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, Australia.
| | - Andrew J Pollard
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
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Johnson MG, Strizki JM, Jensen E, Cohen J, Katlama C, Fishchuk R, Ponce-de-León A, Fourie N, Cheng CY, McCoy D, Vesnesky M, Norice CT, Zhang Y, Williams-Diaz A, Brown ML, Carmelitano P, Grobler JA, Paschke A, De Anda C. Respiratory virus coinfections during the COVID-19 pandemic: epidemiologic analysis and clinical outcomes from the Phase 2/3 molnupiravir trial (MOVe-OUT). Microbiol Spectr 2024; 12:e0356323. [PMID: 38299867 PMCID: PMC10913477 DOI: 10.1128/spectrum.03563-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 12/13/2023] [Indexed: 02/02/2024] Open
Abstract
This exploratory post hoc analysis assessed the incidence of respiratory viral coinfections and their impact on clinical outcomes in non-hospitalized adults with mild-to-moderate coronavirus disease-2019 (COVID-19) treated with molnupiravir versus placebo for 5 days in the Phase 2/3 MOVe-OUT trial (NCT04575597), which took place in October 2020 to January 2021 (Phase 2, n = 302) and May 2021 to October 2021 (Phase 3, n = 1,433). Among 1,735 total randomized participants, 1,674 had a baseline respiratory pathogen panel (NxTAG Respiratory Pathogen Panel for the Luminex MAGPIX instrument) performed and 69 (4.1%) were coinfected with at least one additional respiratory viral pathogen. Human rhinovirus/enterovirus (39/69, 56.5%) was the most common coinfection detected at baseline. In the modified intention-to-treat population, two participants with coinfecting respiratory RNA viruses were hospitalized and received respiratory interventions through Day 29, and none died; one participant in the molnupiravir group was coinfected with human rhinovirus/enterovirus, and one participant in the placebo group was coinfected with human metapneumovirus. Hospitalization or death occurred in 6.2% and 9.0% of non-coinfected participants in the molnupiravir versus placebo group, respectively, and over 90% did not require respiratory interventions. Most coinfecting respiratory RNA viruses detected at baseline were not detected at the end of therapy in both the molnupiravir and placebo groups. In summary, participants coinfected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and another respiratory RNA virus were not more likely to be hospitalized or die, or require respiratory interventions, compared to participants who were not coinfected with another respiratory RNA virus at baseline in both groups. IMPORTANCE Respiratory viral coinfections are known to occur with coronavirus disease-2019 (COVID-19). In a cohort of non-hospitalized adults with mild-to-moderate COVID-19 treated with molnupiravir versus placebo in the MOVe-OUT trial during October 2020 to October 2021, 4.1% of participants had a documented viral coinfection; human rhinovirus/enterovirus was the most common pathogen detected with the NxTAG Respiratory Pathogen Panel assay. Participants who had a coinfection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and another respiratory RNA virus were not more likely to have worse clinical outcomes compared to those participants without a viral coinfection, and many coinfecting respiratory RNA viruses were no longer detected at the end of the 5-day treatment period in both groups.
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Affiliation(s)
| | | | | | - Jonathan Cohen
- Jadestone Clinical Research, LLC, Rockville, Maryland, USA
| | - Christine Katlama
- AP-HP. Sorbonne Université, Hôpital—Pitié Salpêtrière, Paris, France
- Université Toulouse III Paul Sabatier, CHU de Toulouse, Toulouse, France
| | - Roman Fishchuk
- CNE Central City Clinical Hospital of Ivano-Frankivsk City Council, Ivano-Frankivsk, Ukraine
| | - Alfredo Ponce-de-León
- Instituto Nacional de Ciencias Medicas y Nutrición Salvador Zubiran, Mexico City, Mexico
| | - Nyda Fourie
- IATROS International, Bloemfontein, South Africa
| | | | | | | | | | - Ying Zhang
- Merck & Co., Inc., Rahway, New Jersey, USA
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Maison N, Omony J, Rinderknecht S, Kolberg L, Meyer-Bühn M, von Mutius E, Hübner J, von Both U. Old foes following news ways?-Pandemic-related changes in the epidemiology of viral respiratory tract infections. Infection 2024; 52:209-218. [PMID: 37644253 PMCID: PMC10811157 DOI: 10.1007/s15010-023-02085-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 08/13/2023] [Indexed: 08/31/2023]
Abstract
INTRODUCTION Following lockdown periods and restricting public health measures in response to the COVID-19 pandemic, respiratory tract infections (RTIs) rose significantly worldwide. This led to an increased burden on children's hospitals compromising medical care of acutely and chronically ill children. We characterized changes in the epidemiological pattern of circulating respiratory viral infections. METHODS We assessed the number of patients with RTIs and the annual distribution of virus detections between 2019 and 2022 based on 4809 clinical samples (4131 patients) from a German pediatric tertiary care-center. We investigated the impact of lockdown periods on spectra of circulating respiratory viruses, pattern of coinfections, age, and seasonality of infections. RESULTS A fourfold increase in the number of respiratory virus detections was observed in 2022 vs 2019 with numbers doubling in 2022 (vs 2021). In 2022, seasonal patterns of circulating virus, particularly Adeno and seasonal Coronavirus were far less pronounced compared to previous years, in fact almost disappeared for Rhinoviruses.". SARS-CoV-2, Parainfluenza- and human Metapneumovirus detections increased significantly in 2022 (2019 vs 2022, p < 0.01). Coinfections with multiple viruses occurred more frequently since 2021 compared to pre-pandemic years, especially in younger children (2019 vs 2022, p < 0.01). CONCLUSION Compared to pre-pandemic years, we observed a dramatic increase in pediatric RTIs with an incrementing spectrum of viruses and a predominance in Rhino/Enterovirus infections - leading to a high rate of hospital admissions, particularly in conjunction with other viruses. This caused an acute shortage in medical care and may also be followed by an increase of virus-triggered secondary chronic respiratory diseases like asthma-rendering a burden on the health system.
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Affiliation(s)
- Nicole Maison
- Department for Asthma and Allergy, Dr Von Hauner Children's Hospital, LMU University Hospital, LMU Munich, Lindwurmstr. 4, 80337, Munich, Germany.
- Institute for Asthma- and Allergy Prevention (IAP), Helmholtz Zentrum Munich, German Research Center for Environmental Health (GmbH), Munich, Germany.
- German Center for Lung Research (DZL), Munich, Germany.
| | - Jimmy Omony
- Institute for Asthma- and Allergy Prevention (IAP), Helmholtz Zentrum Munich, German Research Center for Environmental Health (GmbH), Munich, Germany
| | - Sophia Rinderknecht
- Department for Asthma and Allergy, Dr Von Hauner Children's Hospital, LMU University Hospital, LMU Munich, Lindwurmstr. 4, 80337, Munich, Germany
| | - Laura Kolberg
- Department of Infectious Diseases, Dr Von Hauner Children's Hospital, LMU University Hospital, LMU, Munich, Germany
| | - Melanie Meyer-Bühn
- Department of Infectious Diseases, Dr Von Hauner Children's Hospital, LMU University Hospital, LMU, Munich, Germany
| | - Erika von Mutius
- Department for Asthma and Allergy, Dr Von Hauner Children's Hospital, LMU University Hospital, LMU Munich, Lindwurmstr. 4, 80337, Munich, Germany
- Institute for Asthma- and Allergy Prevention (IAP), Helmholtz Zentrum Munich, German Research Center for Environmental Health (GmbH), Munich, Germany
- German Center for Lung Research (DZL), Munich, Germany
| | - Johannes Hübner
- Department of Infectious Diseases, Dr Von Hauner Children's Hospital, LMU University Hospital, LMU, Munich, Germany
| | - Ulrich von Both
- Department of Infectious Diseases, Dr Von Hauner Children's Hospital, LMU University Hospital, LMU, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany
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5
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Farzi R, Pirbonyeh N, Kadivar MR, Moattari A. Prevalence of Influenza Viruses A and B, Adenovirus, Respiratory Syncytial Virus, and Human Metapneumonia Viruses among Children with Acute Respiratory Tract Infection. Adv Virol 2024; 2024:7613948. [PMID: 38292215 PMCID: PMC10824580 DOI: 10.1155/2024/7613948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 10/04/2023] [Accepted: 12/23/2023] [Indexed: 02/01/2024] Open
Abstract
Background Acute respiratory tract infection (ARTI) is a significant cause of morbidity and mortality among children worldwide. The majority of acute respiratory infections in children are caused by viruses, with respiratory syncytial virus (RSV) being the most frequently encountered. Other important viral pathogens include human metapneumovirus, human coronaviruses, adenovirus, and influenza. These infections can lead to complications such as bronchitis and pneumonia. So, this study aimed to evaluate the prevalence of influenza viruses A and B, adenovirus, respiratory syncytial virus (RSV), and human metapneumovirus (HMPV) in children with ARTI. Methods The molecular diagnostic of polymerase chain reaction approach was used to detect influenza (A and B), metapneumovirus, respiratory syncytial virus (RSV), and adenovirus in respiratory samples of children with acute respiratory infection hospitalization in a teaching hospital of the Shiraz University of Medical Sciences in January 2016-March 2017. Results Of the 340 patients examined, 208 (61.20%) were male and the median age was 3.13 ± 2.38 years. Respiratory viruses were found in 179 (52.64%) patients. The male-to-female ratio was 1.63 : 1 in patients who were viral positive. Detection rates for influenza A, adenovirus, influenza B, RSV, and HMPV were 28.23%, 24.70%, 8.52%, 3.23%, and 2.64%, respectively, and coinfections were detected in 24.02%. The most common combination of two-virus coinfections was IFVA/AdV, followed by IFVB/AdV, AdV, IFVB/IFVA, RSV/IFVA, HMPV/AdV, RSV/AdV, and HMPV/IFVA. Conclusion The high prevalence of respiratory viruses in children hospitalized with ARTI suggests that viral infection may play a role in disease pathogenesis. This should be confirmed through the conduct of case-control studies and may inform the role of vaccination to prevent respiratory viral infections.
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Affiliation(s)
- Rana Farzi
- Department of Bacteriology and Virology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Neda Pirbonyeh
- Department of Bacteriology and Virology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
- Burn and Wound Healing Research Center, Microbiology Department, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohammad Rahim Kadivar
- Department of Pediatrics, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
- Professor Alborzi Clinical Microbiology Research Center, Namazi Hospital, Shiraz Medical University, Shiraz, Iran
| | - Afagh Moattari
- Department of Bacteriology and Virology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
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6
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Grech AK, Foo CT, Paul E, Aung AK, Yu C. Epidemiological trends of respiratory tract pathogens detected via mPCR in Australian adult patients before COVID-19. BMC Infect Dis 2024; 24:38. [PMID: 38166699 PMCID: PMC10763466 DOI: 10.1186/s12879-023-08750-7] [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: 03/24/2023] [Accepted: 10/25/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND Respiratory tract infections (RTIs) are a major global health burden due to their high morbidity and mortality. This retrospective study described the epidemiology of respiratory pathogens in adults over a 5-year period at an Australian tertiary healthcare network. METHODS All multiplex reverse transcription polymerase chain reaction respiratory samples taken between the 1st of November 2014 and the 31st of October 2019 were included in this study. Overall prevalence and variations according to seasons, age groups and sex were analysed, as well as factors associated with prolonged hospital and intensive care length of stay. RESULTS There were 12,453 pathogens detected amongst the 12,185 positive samples, with coinfection rates of 3.7%. Picornavirus (Rhinovirus), Influenza A and respiratory syncytial virus were the most commonly detected pathogens. Mycoplasma pneumoniae was the most commonly detected atypical bacteria. Significant differences in the prevalence of Chlamydia pneumoniae and Human metapneumovirus infections were found between sexes. Longest median length of intensive care and hospital stay was for Legionella species. Seasonal variations were evident for certain pathogens. CONCLUSIONS The high rates of pathogen detection and hospitalisation in this real-world study highlights the significant burden of RTIs, and the urgent need for an improved understanding of the pathogenicity as well as preventative and treatment options of RTIs.
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Affiliation(s)
- Audrey K Grech
- Department of Respiratory Medicine, Alfred Health, 55 Commercial Road, Melbourne, VIC, 3004, Australia
| | - Chuan T Foo
- Department of Respiratory Medicine, Eastern Health, Melbourne, Australia
- Monash Lung and Sleep, Monash Health, Melbourne, Australia
| | - Eldho Paul
- ANZIC-RC, School of Public Health and Preventive Medicine, Monash University, Melbourne, Australia
| | - Ar K Aung
- School of Public Health and Preventive Medicine, Monash University, Melbourne, Australia
- Department of General Medicine, Alfred Health, Melbourne, Australia
| | - Christiaan Yu
- Department of Respiratory Medicine, Alfred Health, 55 Commercial Road, Melbourne, VIC, 3004, Australia.
- Monash Lung and Sleep, Monash Health, Melbourne, Australia.
- Central Clinical School, Monash University, Melbourne, Australia.
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Mochan E, Sego TJ. Mathematical Modeling of the Lethal Synergism of Coinfecting Pathogens in Respiratory Viral Infections: A Review. Microorganisms 2023; 11:2974. [PMID: 38138118 PMCID: PMC10745501 DOI: 10.3390/microorganisms11122974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 12/05/2023] [Accepted: 12/08/2023] [Indexed: 12/24/2023] Open
Abstract
Influenza A virus (IAV) infections represent a substantial global health challenge and are often accompanied by coinfections involving secondary viruses or bacteria, resulting in increased morbidity and mortality. The clinical impact of coinfections remains poorly understood, with conflicting findings regarding fatality. Isolating the impact of each pathogen and mechanisms of pathogen synergy during coinfections is challenging and further complicated by host and pathogen variability and experimental conditions. Factors such as cytokine dysregulation, immune cell function alterations, mucociliary dysfunction, and changes to the respiratory tract epithelium have been identified as contributors to increased lethality. The relative significance of these factors depends on variables such as pathogen types, infection timing, sequence, and inoculum size. Mathematical biological modeling can play a pivotal role in shedding light on the mechanisms of coinfections. Mathematical modeling enables the quantification of aspects of the intra-host immune response that are difficult to assess experimentally. In this narrative review, we highlight important mechanisms of IAV coinfection with bacterial and viral pathogens and survey mathematical models of coinfection and the insights gained from them. We discuss current challenges and limitations facing coinfection modeling, as well as current trends and future directions toward a complete understanding of coinfection using mathematical modeling and computer simulation.
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Affiliation(s)
- Ericka Mochan
- Department of Computational and Chemical Sciences, Carlow University, Pittsburgh, PA 15213, USA
| | - T. J. Sego
- Department of Medicine, University of Florida, Gainesville, FL 32611, USA;
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Petat H, Schuers M, Marguet C, Humbert X, Le Bas F, Rabiaza A, Corbet S, Leterrier B, Vabret A, Ar Gouilh M. Positive and negative viral associations in patients with acute respiratory tract infections in primary care: the ECOVIR study. Front Public Health 2023; 11:1269805. [PMID: 38074759 PMCID: PMC10706622 DOI: 10.3389/fpubh.2023.1269805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Accepted: 10/30/2023] [Indexed: 12/18/2023] Open
Abstract
Introduction Acute respiratory infections (ARIs) are the most common viral infections encountered in primary care settings. The identification of causal viruses is still not available in routine practice. Although new strategies of prevention are being identified, knowledge of the relationships between respiratory viruses remains limited. Materials and methods ECOVIR was a multicentric prospective study in primary care, which took place during two pre-pandemic seasons (2018-2019 and 2019-2020). Patients presenting to their General practitioner (GP) with ARIs were included, without selecting for age or clinical conditions. Viruses were detected on nasal swab samples using a multiplex Polymerase Chain Reaction test focused on 17 viruses [Respiratory Syncytial Virus-A (RSV-A), RSV-B, Rhinovirus/Enterovirus (HRV), human Metapneumovirus (hMPV), Adenovirus (ADV), Coronaviruses (CoV) HKU1, NL63, 229E, OC43, Influenza virus (H1 and H3 subtypes), Influenza virus B, Para-Influenza viruses (PIVs) 1-4, and Bocavirus (BoV)]. Results Among the 668 analyzed samples, 66% were positive for at least one virus, of which 7.9% were viral codetections. The viral detection was negatively associated with the age of patients. BoV, ADV, and HRV occurred more significantly in younger patients than the other viruses (p < 0.05). Codetections were significantly associated with RSV, HRV, BoV, hMPV, and ADV and not associated with influenza viruses, CoV, and PIVs. HRV and influenza viruses were negatively associated with all the viruses. Conversely, a positive association was found between ADV and BoV and between PIVs and BoV. Conclusion Our study provides additional information on the relationships between respiratory viruses, which remains limited in primary care.
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Affiliation(s)
- Hortense Petat
- Department of Paediatrics and Adolescent Medicine Rouen, Univ Rouen Normandie, Dynamicure INSERM UMR 1311, CHU Rouen, Rouen, France
| | - Matthieu Schuers
- Department of General Practice, Univ Rouen Normandie, INSERM U1142, CHU Rouen, Rouen, France
| | - Christophe Marguet
- Department of Paediatrics and Adolescent Medicine Rouen, Univ Rouen Normandie, Dynamicure INSERM UMR 1311, CHU Rouen, Rouen, France
| | - Xavier Humbert
- Department of General Practice, Univ Caen Normandie santé, Caen, France
| | - François Le Bas
- Department of General Practice, Univ Caen Normandie santé, Caen, France
| | - Andry Rabiaza
- Department of General Practice, Univ Caen Normandie santé, Caen, France
| | - Sandrine Corbet
- Department of Virology, Univ Caen Normandie, INSERM Dynamicure UMR 1311, CHU Caen, Caen, France
| | - Bryce Leterrier
- Department of Virology, Univ Caen Normandie, INSERM Dynamicure UMR 1311, CHU Caen, Caen, France
| | - Astrid Vabret
- Department of Virology, Univ Caen Normandie, INSERM Dynamicure UMR 1311, CHU Caen, Caen, France
| | - Meriadeg Ar Gouilh
- Department of Virology, Univ Caen Normandie, INSERM Dynamicure UMR 1311, CHU Caen, Caen, France
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Gil E, Roy S, Best T, Hatcher J, Breuer J. Increasing rhinovirus prevalence in paediatric intensive care patients since the SARS-CoV2 pandemic. J Clin Virol 2023; 166:105555. [PMID: 37536014 DOI: 10.1016/j.jcv.2023.105555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 07/27/2023] [Accepted: 07/28/2023] [Indexed: 08/05/2023]
Abstract
BACKGROUND Rhinovirus (HRV) is a significant seasonal pathogen in children. The emergence of SARS-CoV2, and the social restrictions introduced in, disrupted viral epidemiology. Here we describe the experience of Great Ormond Street Hospital (GOSH), where HRV almost entirely disappeared from the paediatric intensive care units (PICU) during the first national lockdown and then rapidly re-emerged with a fast-increasing incidence, leading to concerns about possible nosocomial transmission in a vulnerable population. OBJECTIVES To describe alterations in HRV infection amongst PICU patients at GOSH since the emergence of SARS-COV2 STUDY DESIGN: 10,950 nasopharyngeal aspirate viral PCR samples from GOSH PICU patients from 2019 to 2023 were included. 3083 returned a positive result for a respiratory virus, with 1530 samples positive for HRV. 66 HRV isolates from August 2020 - Jan 2021, the period of rapidly increasing HRV incidence, were sequenced. Electronic health record data was retrospectively collected for the same period. RESULTS Following a reduction in the incidence of HRV infection during the first national lockdown, multiple genotypes of HRV emerged amongst GOSH PICU patients, with the incidence of HRV infection rapidly surging to levels higher than that seen prior to the emergence of SARS-CoV2 and continuing to circulate at increased incidence year-round. CONCLUSIONS The incidence of HRV infection amongst GOSH PICU patients is markedly higher than prior to the emergence of SARS-CoV2, a pattern not seen in other respiratory viruses. The increased burden of HRV-infection in vulnerable PICU patients has both clinical and infection prevention and control Implications.
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Affiliation(s)
- Eliza Gil
- Department of Clinical Research, London School of Hygiene and Tropical Medicine; Department of Microbiology, Virology & Infection Control, Great Ormond Street Hospital for Children, UK; Infection, Immunity and Inflammation Department, GOS Institute of Child Health, University College London, London, UK.
| | - Sunando Roy
- Infection, Immunity and Inflammation Department, GOS Institute of Child Health, University College London, London, UK
| | - Tim Best
- Department of Microbiology, Virology & Infection Control, Great Ormond Street Hospital for Children, UK
| | - James Hatcher
- Department of Microbiology, Virology & Infection Control, Great Ormond Street Hospital for Children, UK
| | - Judith Breuer
- Department of Microbiology, Virology & Infection Control, Great Ormond Street Hospital for Children, UK; Infection, Immunity and Inflammation Department, GOS Institute of Child Health, University College London, London, UK
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10
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Salim S, Celiloglu H, Tayyab F, Malik ZA. Seasonal Prevalence of Respiratory Pathogens Among Children in the United Arab Emirates: A Multicenter Cross-Sectional Study in the Pre-COVID-19 Era. Cureus 2023; 15:e45204. [PMID: 37842349 PMCID: PMC10576196 DOI: 10.7759/cureus.45204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/14/2023] [Indexed: 10/17/2023] Open
Abstract
Background Viral respiratory infections in children pose a significant burden on healthcare facilities globally. In the United Arab Emirates (UAE) these account for 15% of all healthcare encounters among children. However, the seasonal prevalence and molecular epidemiology of respiratory viral infections in the UAE remains unknown. We sought to determine trends in seasonal viral prevalence in order to monitor disease activity and optimize the timing of Respiratory Syncytial Virus (RSV) prophylaxis among high-risk infants in the UAE. Methods This cross-sectional multicenter study included children 0-18 years of age who presented to a large private healthcare group in Dubai, UAE, and had upper respiratory samples collected for multiplex polymerase chain reaction (mPCR) testing between January 1st and December 31st, 2019. Sociodemographic, clinical, and molecular data were examined for children who tested positive for any pathogen on the mPCR panel. Results A total of three thousand and ninety-eight infants and children had mPCR assays performed during the study period, of which 2427 (78.3%) were positive for any respiratory pathogen. The median age of our sample population was 39 months and 56.8% were male. Emergency room was the most common site (34.7%) of sample collection and the vast majority of children presented with fever (85.3%). Rhinovirus/enterovirus was the most prevalent viral infection (45%) throughout the year and peaked in September, followed by Influenza (20.2%), and RSV (17.1%). RSV season, defined as an infection prevalence of >10%, occurred from August to December with a peak in October. Adenovirus (15.6%) infections peaked in June and accounted for 43% of hospitalizations in our study (p<0.05). Viral co-infections with RSV and rhinovirus/enterovirus were most common and observed in 19.9 % of children. Conclusion Rhinovirus/enterovirus is the most prevalent viral pathogen throughout the calendar year among the pediatric population in the UAE. RSV season begins earlier than reported in other countries regionally, hence RSV prophylaxis should be initiated in August to optimize protection among high-risk infants.
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Affiliation(s)
- Sara Salim
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai Healthcare City, Dubai, ARE
| | - Handan Celiloglu
- Department of Microbiology, Mediclinic City Hospital, Dubai Healthcare City, Dubai, ARE
| | - Farah Tayyab
- Department of Microbiology, Mediclinic City Hospital, Dubai Healthcare City, Dubai, ARE
| | - Zainab A Malik
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai Healthcare City, Dubai, ARE
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11
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Pinky L, DeAguero JR, Remien CH, Smith AM. How Interactions during Viral-Viral Coinfection Can Shape Infection Kinetics. Viruses 2023; 15:1303. [PMID: 37376603 DOI: 10.3390/v15061303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 05/29/2023] [Accepted: 05/30/2023] [Indexed: 06/29/2023] Open
Abstract
Respiratory viral infections are a leading global cause of disease with multiple viruses detected in 20-30% of cases, and several viruses simultaneously circulating. Some infections with unique viral copathogens result in reduced pathogenicity, while other viral pairings can worsen disease. The mechanisms driving these dichotomous outcomes are likely variable and have only begun to be examined in the laboratory and clinic. To better understand viral-viral coinfections and predict potential mechanisms that result in distinct disease outcomes, we first systematically fit mathematical models to viral load data from ferrets infected with respiratory syncytial virus (RSV), followed by influenza A virus (IAV) after 3 days. The results suggest that IAV reduced the rate of RSV production, while RSV reduced the rate of IAV infected cell clearance. We then explored the realm of possible dynamics for scenarios that had not been examined experimentally, including a different infection order, coinfection timing, interaction mechanisms, and viral pairings. IAV coinfection with rhinovirus (RV) or SARS-CoV-2 (CoV2) was examined by using human viral load data from single infections together with murine weight-loss data from IAV-RV, RV-IAV, and IAV-CoV2 coinfections to guide the interpretation of the model results. Similar to the results with RSV-IAV coinfection, this analysis shows that the increased disease severity observed during murine IAV-RV or IAV-CoV2 coinfection was likely due to the slower clearance of IAV-infected cells by the other viruses. The improved outcome when IAV followed RV, on the other hand, could be replicated when the rate of RV infected cell clearance was reduced by IAV. Simulating viral-viral coinfections in this way provides new insights about how viral-viral interactions can regulate disease severity during coinfection and yields testable hypotheses ripe for experimental evaluation.
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Affiliation(s)
- Lubna Pinky
- Department of Pediatrics, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Joseph R DeAguero
- Bioinformatics and Computational Biology Program, University of Idaho, Moscow, ID 83844, USA
| | - Christopher H Remien
- Department of Mathematics and Statistical Science, University of Idaho, Moscow, ID 83844, USA
| | - Amber M Smith
- Department of Pediatrics, University of Tennessee Health Science Center, Memphis, TN 38163, USA
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12
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Pinky L, DeAguero JR, Remien CH, Smith AM. How Interactions During Viral-Viral Coinfection Can Shape Infection Kinetics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.05.535744. [PMID: 37066297 PMCID: PMC10104040 DOI: 10.1101/2023.04.05.535744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Respiratory virus infections are a leading cause of disease worldwide with multiple viruses detected in 20-30% of cases and several viruses simultaneously circulating. Some infections with viral copathogens have been shown to result in reduced pathogenicity while other virus pairings can worsen disease. The mechanisms driving these dichotomous outcomes are likely variable and have only begun to be examined in the laboratory and clinic. To better understand viral-viral coinfections and predict potential mechanisms that result in distinct disease outcomes, we first systematically fit mathematical models to viral load data from ferrets infected with respiratory syncytial virus (RSV) followed by influenza A virus (IAV) after 3 days. The results suggested that IAV reduced the rate of RSV production while RSV reduced the rate of IAV infected cell clearance. We then explored the realm of possible dynamics for scenarios not examined experimentally, including different infection order, coinfection timing, interaction mechanisms, and viral pairings. IAV coinfection with rhinovirus (RV) or SARS-CoV-2 (CoV2) was examined by using human viral load data from single infections together with murine weight loss data from IAV-RV, RV-IAV, and IAV-CoV2 coinfections to guide the interpretation of the model results. Similar to the results with RSV-IAV coinfection, this analysis showed that the increased disease severity observed during murine IAV-RV or IAV-CoV2 coinfection was likely due to slower clearance of IAV infected cells by the other viruses. On the contrary, the improved outcome when IAV followed RV could be replicated when the rate of RV infected cell clearance was reduced by IAV. Simulating viral-viral coinfections in this way provides new insights about how viral-viral interactions can regulate disease severity during coinfection and yields testable hypotheses ripe for experimental evaluation.
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13
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Nguyen E, Saw C, Morkos M, Abass F, Foley D, Bulsara M. Unusual local epidemic of paediatric respiratory syncytial virus during a time of global pandemic. J Paediatr Child Health 2023; 59:464-469. [PMID: 36625316 DOI: 10.1111/jpc.16326] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 12/19/2022] [Accepted: 12/23/2022] [Indexed: 01/11/2023]
Abstract
BACKGROUND Western Australia (WA) public health measures to eradicate SARS-CoV-2 resulted in a secondary reduction in paediatric respiratory syncytial virus (RSV) admissions. Following an absent expected 2020 winter peak, RSV-positive admissions surged during the summer of 2020. AIM This report examines the number of RSV-positive admissions and severities across 36 months to better understand this out-of-season epidemic. METHODS A retrospective observational study was performed assessing the number and severity of RSV-related respiratory hospitalisations at a peripheral paediatric centre from March 2018 to February 2021. Data were extracted from the hospital clinical database. RESULTS The total number of included participants was n = 294. The total number of RSV hospitalisations in SY (study year) 2018 (March 2018 to February 2019), SY 2019 (March 2019 to February 2020) and SY 2020 (March 2020 to February 2021) was 67, 98 and 129, respectively. Prior to SARS-CoV-2, RSV hospitalisations were highest during the winter months. In SY 2020, there were 0 RSV hospitalisations during winter, while 101 admissions in the following summer season. The proportion of admissions requiring respiratory support was significantly reduced in SY 2020 (34.1%) compared to SY 2018 (46.9%, P = 0.050) and SY 2019 (55.2%, P = 0.004). The median length of stay (LOS) in 2020 was 2.0 which was significantly reduced from 2018 and 2019 which was 3.0, P = 0.001; and 3.0, P < 0.001, respectively. CONCLUSION Following a period of RSV absence, there was an unprecedented surge in admission, however, with lower severity and shorter LOS.
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Affiliation(s)
- Edward Nguyen
- Paediatric Department, SJOG Midland Public Hospital, Perth, Western Australia, Australia
| | - Chia Saw
- Paediatric Department, SJOG Midland Public Hospital, Perth, Western Australia, Australia
| | - Michael Morkos
- Paediatric Department, SJOG Midland Public Hospital, Perth, Western Australia, Australia
| | - Fuad Abass
- Paediatric Department, SJOG Midland Public Hospital, Perth, Western Australia, Australia
| | - David Foley
- Microbiology, PathWest Reference Laboratory, Perth, Western Australia, Australia
| | - Max Bulsara
- UWA School of Population Health, Perth, Western Australia, Australia
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14
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Cui A, Xie Z, Xu J, Hu K, Zhu R, Li Z, Li Y, Sun L, Xiang X, Xu B, Zhang R, Gao Z, Zhang Y, Xu W. Comparative analysis of the clinical and epidemiological characteristics of human influenza virus versus human respiratory syncytial virus versus human metapneumovirus infection in nine provinces of China during 2009-2021. J Med Virol 2022; 94:5894-5903. [PMID: 35981880 DOI: 10.1002/jmv.28073] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 07/29/2022] [Accepted: 08/16/2022] [Indexed: 01/06/2023]
Abstract
A comparative analysis of confirmed cases of human influenza virus (HIFV), human respiratory syncytial virus (HRSV), and human metapneumovirus (HMPV) was conducted to describe their clinical and epidemiological characteristics. During 2009-2021, active surveillance of acute respiratory infections (ARIs) was performed in nine provinces of China. Clinical and epidemiological information and laboratory testing results of HIFV, HRSV, and HMPV were analyzed. Among 11591 ARI patients, the single-infection rates of HIFV, HRSV, and HMPV were 15.00%, 9.59%, and 2.24%, respectively; the coinfection rate of these three viruses was 0.64%. HIFV infection was mainly in adults aged 15-59 years, accounting for 39.10%. HRSV and HMPV infections were mainly in children under 5 years old, accounting for 87.13% and 83.46%, respectively. Patients with HRSV infection were younger than HMPV. HRSV and HMPV had high similarities in clinical manifestations, presenting with lower respiratory symptoms. HIFV mainly presented with an upper respiratory infection. The epidemic peak of HRSV was earlier than that of HIFV, and that of HMPV was later than those of HRSV and HFIV. A total of 85.14% of coinfection cases were children under 5 years old. Coinfection might increase the risk of pneumonia in HIFV cases. During 2020-2021, the positive rates and seasonal patterns of these three viruses changed due to the impact of the COVID-19 pandemic. Certain clinical and epidemiological features were observed in HIFV, HRSV, and HMPV infections, which could be beneficial for guiding clinical diagnosis, treatment, and prevention of these three viruses in China.
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Affiliation(s)
- Aili Cui
- NHC Key Laboratory of Medical Virology and Viral Diseases, Chinese Centers for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention, Beijing, China
| | - Zhibo Xie
- NHC Key Laboratory of Medical Virology and Viral Diseases, Chinese Centers for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention, Beijing, China
| | - Jing Xu
- Viral Disease Department, Shaanxi Center for Disease Control and Prevention, Xi'an, China
| | - Kongxin Hu
- Institute of Health Inspection and Quarantine, Chinese Academy of Inspection and Quarantine, Beijing, China
| | - Runan Zhu
- Department of Virology, Beijing Key Laboratory of Pediatric Virology, Capital Institute of Pediatrics, Beijing, China
| | - Zhong Li
- Department of Viral Diseases, Shandong Center for Disease Control and Prevention, Institute for Communicable Disease Control and Prevention, Jinan, China
| | - Yan Li
- Hebei Center for Disease Control and Prevention, Institute for Prevention and Control of Viral Diseases, Shijiazhuang, China
| | - Liwei Sun
- Precision Medicine Research Center, Children's Hospital of Changchun, Changchun, China
| | - Xingyu Xiang
- Microbiological Examination Department, Hunan Center for Disease Control and Prevention, Changsha, China
| | - Baoping Xu
- Respiratory Department, Research Unit of Critical Infection in Children, China National Clinical Research Center of Respiratory Diseases, National Center for Children's Health, Beijing Children's Hospital, Chinese Academy of Medical Sciences, Capital Medical University, Beijing, China
| | - Rongbo Zhang
- Department of Immunology, School of Medicine, Anhui University of Science and Technology, Huainan, China
| | - Zhenguo Gao
- Xinjiang Uyghur Autonomous Region Center for Disease Control and Prevention, Institute for Infectious Disease Prevention and Treatment, Wulumuqi, China
| | - Yan Zhang
- NHC Key Laboratory of Medical Virology and Viral Diseases, Chinese Centers for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention, Beijing, China
| | - Wenbo Xu
- NHC Key Laboratory of Medical Virology and Viral Diseases, Chinese Centers for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention, Beijing, China
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15
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Respiratory Syncytial Virus Protects Bystander Cells against Influenza A Virus Infection by Triggering Secretion of Type I and Type III Interferons. J Virol 2022; 96:e0134122. [DOI: 10.1128/jvi.01341-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Influenza A virus (IAV) and respiratory syncytial virus (RSV) are common recurrent respiratory infectants that show a relatively high coincidence. We demonstrated that preinfection with RSV partitions the cell population into a subpopulation susceptible to subsequent infection with IAV and an IAV-proof subpopulation.
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16
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Takashima MD, Grimwood K, Sly PD, Lambert SB, Ware RS. Interference between rhinovirus and other RNA respiratory viruses in the first 2-years of life: A longitudinal community-based birth cohort study. J Clin Virol 2022; 155:105249. [PMID: 35939878 DOI: 10.1016/j.jcv.2022.105249] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 07/27/2022] [Accepted: 07/30/2022] [Indexed: 10/16/2022]
Abstract
BACKGROUND Cross-sectional studies report negative associations between rhinovirus and other RNA respiratory viruses. However, longitudinal studies with frequent, serial sampling are needed to identify the directionality of this relationship and its nature. OBJECTIVE To investigate the association between rhinovirus and other RNA respiratory viruses detected 1-week apart. METHODS The Observational Research in Childhood Infectious Diseases cohort study was conducted in Brisbane, Australia (2010-2014). Parents collected nasal swabs weekly from birth until age 2-years. Swabs were analysed by real-time polymerase chain reaction. The association between new rhinovirus detections and five other RNA viruses (influenza, respiratory syncytial virus, parainfluenza viruses, seasonal human coronaviruses, and human metapneumovirus) in paired swabs 1-week apart were investigated. RESULTS Overall, 157 children provided 8,101 swabs, from which 4,672 paired swabs 1-week apart were analysed. New rhinovirus detections were negatively associated with new pooled RNA respiratory virus detections 1-week later (adjusted odds ratio (aOR) 0.48; 95% confidence interval (CI): 0.13-0.83), as were pooled RNA virus detections with new rhinovirus detections the following week (aOR 0.34; 95%CI: 0.09-0.60). At the individual species level, rhinovirus had the strongest negative association with new seasonal human coronavirus detections in the subsequent week (aOR 0.34; 95%CI: 0.120.95) and respiratory syncytial virus had the strongest negative association with rhinovirus 1-week later (aOR 0.21; 95%CI: 0.050.88). CONCLUSION A strong, negative bidirectional association was observed between rhinovirus and other RNA viruses in a longitudinal study of a community-based cohort of young Australian children. This suggests within-host interference between RNA respiratory viruses.
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Affiliation(s)
- Mari D Takashima
- Menzies Health Institute Queensland and School of Medicine and Dentistry, Griffith University, Gold Coast 4222, Queensland, Australia.
| | - Keith Grimwood
- Menzies Health Institute Queensland and School of Medicine and Dentistry, Griffith University, Gold Coast 4222, Queensland, Australia; Departments of Infectious Diseases and Paediatrics, Gold Coast Health, Gold Coast 4215, Queensland, Australia
| | - Peter D Sly
- Children's Health and Environment Program, Child Health Research Centre, The University of Queensland, South Brisbane 4101, Queensland, Australia; Australian Infectious Diseases Research Centre, The University of Queensland, St Lucia 4072, Queensland, Australia
| | - Stephen B Lambert
- UQ Centre for Clinical Research, The University of Queensland, Herston 4006, Queensland, Australia; National Centre for Immunisation Research and Surveillance, Westmead 2145, New South Wales, Australia
| | - Robert S Ware
- Menzies Health Institute Queensland and School of Medicine and Dentistry, Griffith University, Gold Coast 4222, Queensland, Australia
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17
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Halabi KC, Stockwell MS, Alba L, Vargas C, Reed C, Saiman L. Clinical and socioeconomic burden of rhinoviruses/enteroviruses in the community. Influenza Other Respir Viruses 2022; 16:891-896. [PMID: 35485187 PMCID: PMC9343330 DOI: 10.1111/irv.12989] [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: 03/04/2022] [Accepted: 03/13/2022] [Indexed: 11/26/2022] Open
Abstract
Background The epidemiology, clinical features, and socioeconomic burden associated with detection of rhinoviruses (RV)/enteroviruses (EV) from individuals in the community with acute respiratory infections (ARIs) are not fully understood. Methods To assess the clinical and socioeconomic burden associated with RV/EV, a secondary analysis of data collected during a prospective, community‐based ARI surveillance study was performed. From December 2012 to September 2017, adult and pediatric participants with ARIs had nasopharyngeal specimens obtained and tested by multiplex polymerase chain reaction assay. Characteristics and socioeconomic burden including missed school or work and/or antibiotic use among participants who did and did not seek medical care and among participants with and without co‐detection of another respiratory pathogen with RV/EV were compared. Results Throughout the study period, RV/EV was detected in 54.7% (885/1617) of ARIs with a respiratory pathogen detected. Most ARI episodes associated with RV/EV occurred in females (59.1%) and children ≤17 years old (64.2%). Those ≤17 years were more likely to seek medical care. Compared to those not seeking medical care (n = 686), those seeking medical care (n = 199) had a longer duration of illness (5 vs. 7 days) and were more likely to miss work/school (16.4% vs. 47.7%) and/or use antibiotics (3.6% vs. 34.2%). Co‐detection occurred in 8% of ARIs of which 81% occurred in children. Co‐detection was not associated with longer illness, more missed work/or school, or antibiotic use. Conclusion Non‐medically attended and medically attended ARIs associated with RV/EV resulted in clinical and socioeconomic burden, regardless of co‐detection of other respiratory pathogens.
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Affiliation(s)
| | - Melissa S Stockwell
- Columbia University Irving Medical Center, New York, New York, USA.,Mailman School of Public Health, Columbia University, New York, New York, USA.,New York-Presbyterian Hospital, New York, New York, USA
| | - Luis Alba
- Columbia University Irving Medical Center, New York, New York, USA
| | - Celibell Vargas
- Columbia University Irving Medical Center, New York, New York, USA
| | - Carrie Reed
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Lisa Saiman
- Columbia University Irving Medical Center, New York, New York, USA.,New York-Presbyterian Hospital, New York, New York, USA
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18
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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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19
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Abstract
Multiple respiratory viruses can concurrently or sequentially infect the respiratory tract and lead to virus‒virus interactions. Infection by a first virus could enhance or reduce infection and replication of a second virus, resulting in positive (additive or synergistic) or negative (antagonistic) interaction. The concept of viral interference has been demonstrated at the cellular, host, and population levels. The mechanisms involved in viral interference have been evaluated in differentiated airway epithelial cells and in animal models susceptible to the respiratory viruses of interest. A likely mechanism is the interferon response that could confer a temporary nonspecific immunity to the host. During the coronavirus disease pandemic, nonpharmacologic interventions have prevented the circulation of most respiratory viruses. Once the sanitary restrictions are lifted, circulation of seasonal respiratory viruses is expected to resume and will offer the opportunity to study their interactions, notably with severe acute respiratory syndrome coronavirus 2.
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20
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Spantideas N, Bougea AM, Drosou EG, Khanderia N, Rai S. COVID-19 and Seasonal Influenza: No Room for Two. Cureus 2021; 13:e18007. [PMID: 34667682 PMCID: PMC8516323 DOI: 10.7759/cureus.18007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/15/2021] [Indexed: 11/05/2022] Open
Abstract
Objective With the outbreak of COVID-19 in December 2019 fears were expressed for a possible twindemic in the coming flu seasons. Fortunately, this was not the case for the 2019-2020 and 2020-2021 flu seasons as flu showed very low historical rates during these periods. The objective of our study was to look at the existing flu data for the 2019-2021 period and analyze possible reasons for the near absence of seasonal flu. Methods We performed retrospective surveillance regarding seasonal influenza rates for the years 2019-2021, the years that the COVID-19 was present. Epidemiological data concerning seasonal influenza for the years 2019-2021 were collected and analyzed Results Extremely low numbers of flu cases were reported in FluNet, FluView, and TESSy influenza surveillance systems during the years 2019, 2020, and 2021 compared to previous years prior to COVID-19. Conclusions A twindemic outbreak during the 2019-2021 flu seasons did not occur despite expressed concerns. The worldwide implementation of mitigation measures for individuals and communities to control severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission, the increased flu vaccination rate, the virus interference and the lower rate of testing for flu are the main reasons for the marked decrease in reported flu cases during 2019-2021 flu seasons.
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Affiliation(s)
| | - Anastasia M Bougea
- Neurology, Aeginition Hospital, National and Kapodistrian University of Athens, Athens, GRC
| | - Eirini G Drosou
- Speech Therapy, Athens Speech Language and Swallowing Institute, Athens, GRC
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21
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El-Heneidy A, Ware RS, Robson JM, Cherian SG, Lambert SB, Grimwood K. Respiratory virus detection during the COVID-19 pandemic in Queensland, Australia. Aust N Z J Public Health 2021; 46:10-15. [PMID: 34648214 PMCID: PMC8652525 DOI: 10.1111/1753-6405.13168] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 08/01/2021] [Accepted: 08/01/2021] [Indexed: 11/28/2022] Open
Abstract
Objective: To determine if non‐pharmaceutical interventions (NPIs) impacted on respiratory virus detections in Queensland, Australia, during the COVID‐19 pandemic year of 2020. Methods: We analysed weekly counts of influenza, human metapneumovirus, parainfluenza, respiratory syncytial virus, rhinovirus, and adenovirus available from a Queensland laboratory network for the year 2020. These were compared with averaged counts from 2015 to 2019. Results: Overall, 686,199 tests were performed. The timing of NPI implementation was associated with a sharp and sustained decline in influenza, where during the typical annual influenza season (weeks 23–40) no cases were detected from 163,296 tests compared with an average of 26.1% (11,844/45,396) of tests positive in 2015–2019. Similar results were observed for human metapneumovirus and parainfluenza. Respiratory syncytial virus detections also declined but increased in weeks 48–52 (5.6%; 562/10,078) to exceed the 2015–2019 average (2.9%; 150/5,018). Rhinovirus detections increased after schools reopened, peaking in weeks 23–27 (57.4%; 36,228/63,115), exceeding the 2017–2019 detections during that period (21.9%; 8,365/38,072). Conclusions: NPIs implemented to control COVID‐19 were associated with altered frequency and proportions of respiratory virus detections. Implications for public health: NPIs derived from influenza pandemic plans were associated with profound decreases in influenza detections during 2020.
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Affiliation(s)
- Asmaa El-Heneidy
- School of Medicine and Dentistry and Menzies Health Institute Queensland, Griffith University Gold Coast Campus, Queensland
| | - Robert S Ware
- School of Medicine and Dentistry and Menzies Health Institute Queensland, Griffith University Gold Coast Campus, Queensland
| | - Jennifer M Robson
- Department of Microbiology, Sullivan Nicolaides Pathology, Queensland
| | - Sarah G Cherian
- Department of Microbiology, Sullivan Nicolaides Pathology, Queensland
| | | | - Keith Grimwood
- School of Medicine and Dentistry and Menzies Health Institute Queensland, Griffith University Gold Coast Campus, Queensland.,Departments of Paediatrics and Infectious Diseases, Gold Coast Health, Queensland
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22
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Lee YM, Kim T, Park KH, Choi SH, Kwak YG, Choo EJ, Chung JW, Lee MS. Dual respiratory virus detection in adult patients with acute respiratory illness. BMC Infect Dis 2021; 21:997. [PMID: 34556046 PMCID: PMC8460188 DOI: 10.1186/s12879-021-06699-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 09/15/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Nonrandom multiple respiratory virus (RV) detection provides evidence for viral interference among respiratory viruses. However, little is known as to whether it occurs randomly. METHODS The prevalence of dual RV detection (DRVD) in patients with acute respiratory illnesses (ARIs) at 4 academic medical centers was investigated; data about the prevalence of 8 RVs were collected from the Korean national RV surveillance dataset. Linear regression analysis was performed to assess the correlation between observed and estimated prevalence of each type of DRVD. RESULTS In total, 108 patients with ARIs showing DRVD were included in this study between 2011 and 2017. In several types of regression analysis, a strong correlation was observed between the observed and estimated prevalence of each type of DRVD. Excluding three DRVD types (influenza/picornavirus, influenza/human metapneumovirus, and adenovirus/respiratory syncytial virus), the slope of the regression line was higher than that of the line of random occurrence (1.231 > 1.000) and the 95% confidence interval of the regression line was located above the line of random occurrence. CONCLUSIONS Contrary to the results of previous epidemiologic studies, most types of DRVD occur more frequently than expected from the prevalence rates of individual RV, except for three underrepresented pairs above.
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Affiliation(s)
- Yu-Mi Lee
- Division of Infectious Diseases, Department of Internal Medicine, Kyung Hee University Hospital, Kyung Hee University School of Medicine, Seoul, Republic of Korea
| | - Tark Kim
- Division of Infectious Diseases, Department of Internal Medicine, Soonchunhyang University Bucheon Hospital, Bucheon, Republic of Korea
| | - Ki-Ho Park
- Division of Infectious Diseases, Department of Internal Medicine, Kyung Hee University Hospital, Kyung Hee University School of Medicine, Seoul, Republic of Korea
| | - Seong-Ho Choi
- Division of Infectious Diseases, Department of Internal Medicine, Chung-Ang University Hospital, Chung-Ang University College of Medicine, 102 Heukseok-ro, Dongjak-gu, Seoul, 06973, Republic of Korea.
| | - Yee Gyung Kwak
- Division of Infectious Diseases, Department of Internal Medicine, Inje University Ilsan Paik Hospital, Goyang, Republic of Korea
| | - Eun Ju Choo
- Division of Infectious Diseases, Department of Internal Medicine, Soonchunhyang University Bucheon Hospital, Bucheon, Republic of Korea
| | - Jin-Won Chung
- Division of Infectious Diseases, Department of Internal Medicine, Chung-Ang University Hospital, Chung-Ang University College of Medicine, 102 Heukseok-ro, Dongjak-gu, Seoul, 06973, Republic of Korea
| | - Mi Suk Lee
- Division of Infectious Diseases, Department of Internal Medicine, Kyung Hee University Hospital, Kyung Hee University School of Medicine, Seoul, Republic of Korea
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23
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Chekuri S, Szymczak WA, Goldstein DY, Nori P, Marrero Rolon R, Spund B, Singh-Tan S, Mohrmann L, Assa A, Southern WN, Baron SW. SARS-CoV-2 coinfection with additional respiratory virus does not predict severe disease: a retrospective cohort study. J Antimicrob Chemother 2021; 76:iii12-iii19. [PMID: 34555160 PMCID: PMC8460099 DOI: 10.1093/jac/dkab244] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Background The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) claimed over 4 million lives by July 2021 and continues to pose a serious public health threat. Objectives Our retrospective study utilized respiratory pathogen panel (RPP) results in patients with SARS-CoV-2 to determine if coinfection (i.e. SARS-CoV-2 positivity with an additional respiratory virus) was associated with more severe presentation and outcomes. Methods All patients with negative influenza/respiratory syncytial virus testing who underwent RPP testing within 7 days of a positive SARS-CoV-2 test at a large, academic medical centre in New York were examined. Patients positive for SARS-CoV-2 with a negative RPP were compared with patients positive for SARS-CoV-2 and positive for a virus by RPP in terms of biomarkers, oxygen requirements and severe COVID-19 outcome, as defined by mechanical ventilation or death within 30 days. Results Of the 306 SARS-CoV-2-positive patients with RPP testing, 14 (4.6%) were positive for a non-influenza virus (coinfected). Compared with the coinfected group, patients positive for SARS-CoV-2 with a negative RPP had higher inflammatory markers and were significantly more likely to be admitted (P = 0.01). Severe COVID-19 outcome occurred in 111 (36.3%) patients in the SARS-CoV-2-only group and 3 (21.4%) patients in the coinfected group (P = 0.24). Conclusions Patients infected with SARS-CoV-2 along with a non-influenza respiratory virus had less severe disease on presentation and were more likely to be admitted—but did not have more severe outcomes—than those infected with SARS-CoV-2 alone.
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Affiliation(s)
- Sweta Chekuri
- Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, NY, USA.,Department of Medicine, Montefiore Medical Center, Bronx, NY, USA.,Division of Hospital Medicine, Montefiore Medical Center, Bronx, NY, USA
| | - Wendy A Szymczak
- Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, NY, USA.,Department of Pathology, Montefiore Medical Center, Bronx, NY, USA
| | - D Yitzchak Goldstein
- Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, NY, USA.,Department of Pathology, Montefiore Medical Center, Bronx, NY, USA
| | - Priya Nori
- Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, NY, USA.,Department of Medicine, Montefiore Medical Center, Bronx, NY, USA.,Division of Infectious Disease, Montefiore Medical Center, Bronx, NY, USA
| | - Rebecca Marrero Rolon
- Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, NY, USA.,Department of Pathology, Montefiore Medical Center, Bronx, NY, USA
| | - Brian Spund
- Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, NY, USA.,Department of Medicine, Montefiore Medical Center, Bronx, NY, USA.,Division of Hospital Medicine, Montefiore Medical Center, Bronx, NY, USA
| | - Sumeet Singh-Tan
- Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, NY, USA.,Department of Medicine, Montefiore Medical Center, Bronx, NY, USA.,Division of Hospital Medicine, Montefiore Medical Center, Bronx, NY, USA
| | - Laurel Mohrmann
- Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, NY, USA.,Department of Medicine, Montefiore Medical Center, Bronx, NY, USA.,Division of Hospital Medicine, Montefiore Medical Center, Bronx, NY, USA
| | - Andrei Assa
- Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, NY, USA.,Department of Medicine, Montefiore Medical Center, Bronx, NY, USA.,Division of Hospital Medicine, Montefiore Medical Center, Bronx, NY, USA
| | - William N Southern
- Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, NY, USA.,Department of Medicine, Montefiore Medical Center, Bronx, NY, USA.,Division of Hospital Medicine, Montefiore Medical Center, Bronx, NY, USA
| | - Sarah W Baron
- Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, NY, USA.,Department of Medicine, Montefiore Medical Center, Bronx, NY, USA.,Division of Hospital Medicine, Montefiore Medical Center, Bronx, NY, USA
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24
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Kong D, Zheng Y, Hu L, Chen J, Wu H, Teng Z, Zhou Y, Qiu Q, Lu Y, Pan H. Epidemiological and co-infection characteristics of common human coronaviruses in Shanghai, 2015-2020: a retrospective observational study. Emerg Microbes Infect 2021; 10:1660-1668. [PMID: 34350810 PMCID: PMC8381891 DOI: 10.1080/22221751.2021.1965498] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The coronavirus disease (COVID-19) pandemic is a major challenge worldwide. However, the epidemic potential of common human coronaviruses (HCoVs) remains unclear. This study aimed to determine the epidemiological and co-infection characteristics of common HCoVs in individuals with influenza-like illness (ILI) and severe acute respiratory infection (SARI). This retrospective, observational, multicentre study used data collected from patients admitted to nine sentinel hospitals with ILI and SARI from January 2015 through December 2020 in Shanghai, China. We prospectively tested patients for a total of 22 respiratory pathogens using multi-real-time polymerase chain reaction. Of the 4541 patients tested, 40.37% (1833/4541) tested positive for respiratory pathogens and 3.59% (163/4541) tested positive for common HCoVs. HCoV infection was more common in the non-endemic season for respiratory pathogens (odds ratio: 2.33, 95% confidence interval: 1.64–3.31). HCoV-OC43 (41.72%, 68/163) was the most common type of HCoV detected. The co-infection rate was 31.29% (51/163) among 163 HCoV-positive cases, with HCoV-229E (53.13%, 17/32), the HCoV type that was most frequently associated with co-infection. Respiratory pathogens responsible for co-infections with HCoVs included parainfluenza virus, rhinovirus/enterovirus, influenza A virus, and adenovirus. Furthermore, we identified one patient co-infected with HCoV-OC43 and HCoV-NL63/HKU1. The prevalence of common HCoVs remains low in ILI/SARI cases, in Shanghai. However, the seasonal pattern of HCoVs may be opposite to that of other respiratory pathogens. Moreover, HCoVs are likely to co-exist with specific respiratory pathogens. The potential role of co-infections with HCoVs and other pathogenic microorganisms in infection and pathogenesis of ILI and SARI warrants further study.
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Affiliation(s)
- Dechuan Kong
- Department of Acute Communicable Diseases Control and Prevention, Shanghai Municipal Centre for Disease Control and Prevention, Shanghai, People's Republic of China
| | - Yaxu Zheng
- Department of Acute Communicable Diseases Control and Prevention, Shanghai Municipal Centre for Disease Control and Prevention, Shanghai, People's Republic of China.,Department of Epidemiology, Ministry of Education Key Laboratory of Public Health Safety, Fudan School of Public Health, Shanghai, People's Republic of China
| | - Linjie Hu
- Department of Epidemiology, Ministry of Education Key Laboratory of Public Health Safety, Fudan School of Public Health, Shanghai, People's Republic of China
| | - Jian Chen
- Department of Logistics Support, Shanghai Municipal Centre for Disease Control and Prevention, Shanghai, People's Republic of China
| | - Huanyu Wu
- Shanghai Municipal Centre for Disease Control and Prevention, Shanghai, People's Republic of China
| | - Zheng Teng
- Institute of Pathogen Examination, Shanghai Municipal Centre for Disease Control and Prevention, Shanghai, People's Republic of China
| | - Yanqiu Zhou
- Institute of Pathogen Examination, Shanghai Municipal Centre for Disease Control and Prevention, Shanghai, People's Republic of China
| | - Qi Qiu
- Department of Acute Communicable Diseases Control and Prevention, Shanghai Municipal Centre for Disease Control and Prevention, Shanghai, People's Republic of China
| | - Yihan Lu
- Department of Epidemiology, Ministry of Education Key Laboratory of Public Health Safety, Fudan School of Public Health, Shanghai, People's Republic of China
| | - Hao Pan
- Institute of Communicable Diseases Control and Prevention, Shanghai Municipal Centre for Disease Control and Prevention, Shanghai, People's Republic of China
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25
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Jones JP, Norton K. 222-nm ultraviolet light inactivates dried inocula of human rhinovirus and human coronavirus on a glass carrier. J Hosp Infect 2021; 117:190-191. [PMID: 34403769 PMCID: PMC8364420 DOI: 10.1016/j.jhin.2021.08.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 08/06/2021] [Indexed: 11/28/2022]
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26
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Devi P, Khan A, Chattopadhyay P, Mehta P, Sahni S, Sharma S, Pandey R. Co-infections as Modulators of Disease Outcome: Minor Players or Major Players? Front Microbiol 2021; 12:664386. [PMID: 34295314 PMCID: PMC8290219 DOI: 10.3389/fmicb.2021.664386] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 06/16/2021] [Indexed: 12/12/2022] Open
Abstract
Human host and pathogen interaction is dynamic in nature and often modulated by co-pathogens with a functional role in delineating the physiological outcome of infection. Co-infection may present either as a pre-existing pathogen which is accentuated by the introduction of a new pathogen or may appear in the form of new infection acquired secondarily due to a compromised immune system. Using diverse examples of co-infecting pathogens such as Human Immunodeficiency Virus, Mycobacterium tuberculosis and Hepatitis C Virus, we have highlighted the role of co-infections in modulating disease severity and clinical outcome. This interaction happens at multiple hierarchies, which are inclusive of stress and immunological responses and together modulate the disease severity. Already published literature provides much evidence in favor of the occurrence of co-infections during SARS-CoV-2 infection, which eventually impacts the Coronavirus disease-19 outcome. The availability of biological models like 3D organoids, mice, cell lines and mathematical models provide us with an opportunity to understand the role and mechanism of specific co-infections. Exploration of multi-omics-based interactions across co-infecting pathogens may provide deeper insights into their role in disease modulation.
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Affiliation(s)
- Priti Devi
- INtegrative GENomics of HOst-PathogEn Laboratory, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Azka Khan
- INtegrative GENomics of HOst-PathogEn Laboratory, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Partha Chattopadhyay
- INtegrative GENomics of HOst-PathogEn Laboratory, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Priyanka Mehta
- INtegrative GENomics of HOst-PathogEn Laboratory, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Shweta Sahni
- INtegrative GENomics of HOst-PathogEn Laboratory, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Sachin Sharma
- INtegrative GENomics of HOst-PathogEn Laboratory, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Rajesh Pandey
- INtegrative GENomics of HOst-PathogEn Laboratory, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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27
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Ljubin-Sternak S, Meštrović T, Lukšić I, Mijač M, Vraneš J. Seasonal Coronaviruses and Other Neglected Respiratory Viruses: A Global Perspective and a Local Snapshot. Front Public Health 2021; 9:691163. [PMID: 34291031 PMCID: PMC8287126 DOI: 10.3389/fpubh.2021.691163] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 06/04/2021] [Indexed: 02/02/2023] Open
Abstract
Respiratory viral infections are the leading cause of morbidity and mortality in the world; however, there are several groups of viruses that are insufficiently routinely sought for, and can thus be considered neglected from a diagnostic and clinical standpoint. Timely detection of seasonality of certain respiratory viruses (e.g., enveloped viruses such as seasonal coronaviruses) in the local context can aid substantially in targeted and cost-effective utilization of viral diagnostic approaches. For the other, non-enveloped and year-round viruses (i.e., rhinovirus, adenovirus, and bocavirus), a continuous virological diagnosis needs to be implemented in clinical laboratories to more effectively address the aetiology of respiratory infections, and assess the overall impact of these viruses on disease burden. While the coronavirus disease 2019 (COVID-19) pandemic is still actively unfolding, we aimed to emphasize the persistent role of seasonal coronaviruses, rhinoviruses, adenoviruses and bocaviruses in the aetiology of respiratory infections. Consequently, this paper concentrates on the burden and epidemiological trends of aforementioned viral groups on a global level, but also provides a snapshot of their prevalence patterns in Croatia in order to underscore the potential implications of viral seasonality. An overall global prevalence in respiratory tract infections was found to be between 0.5 and 18.4% for seasonal coronaviruses, between 13 and 59% for rhinoviruses, between 1 and 36% for human adenoviruses, and between 1 and 56.8% for human bocaviruses. A Croatian dataset on patients with respiratory tract infection and younger than 18 years of age has revealed a fairly high prevalence of rhinoviruses (33.4%), with much lower prevalence of adenoviruses (15.6%), seasonal coronaviruses (7.1%), and bocaviruses (5.3%). These insights represent a relevant discussion point in the context of the COVID-19 pandemic where the testing of non-SARS-CoV-2 viruses has been limited in many settings, making the monitoring of disease burden associated with other respiratory viruses rather difficult.
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Affiliation(s)
- Sunčanica Ljubin-Sternak
- Clinical Microbiology Department, Andrija Štampar Teaching Institute of Public Health, Zagreb, Croatia.,Medical Microbiology Department, University of Zagreb School of Medicine, Zagreb, Croatia
| | - Tomislav Meštrović
- Clinical Microbiology and Parasitology Unit, Zora Profozić Polyclinic, Zagreb, Croatia.,University Centre Varaždin, University North, Varaždin, Croatia
| | - Ivana Lukšić
- Clinical Microbiology Department, Andrija Štampar Teaching Institute of Public Health, Zagreb, Croatia
| | - Maja Mijač
- Clinical Microbiology Department, Andrija Štampar Teaching Institute of Public Health, Zagreb, Croatia.,Medical Microbiology Department, University of Zagreb School of Medicine, Zagreb, Croatia
| | - Jasmina Vraneš
- Clinical Microbiology Department, Andrija Štampar Teaching Institute of Public Health, Zagreb, Croatia.,Medical Microbiology Department, University of Zagreb School of Medicine, Zagreb, Croatia
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28
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Sarkar S, Ratho RK, Singh M, Singh MP, Singh A, Sharma M. Comparative analysis of epidemiology, clinical features and cytokine response of Respiratory Syncytial and Human Metapneumovirus infected children with acute lower respiratory infections. Jpn J Infect Dis 2021; 75:56-62. [PMID: 34193665 DOI: 10.7883/yoken.jjid.2021.151] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Both Human Respiratory Syncytial virus (RSV) and Human Metapneumovirus (hMPV) cause immune-mediated under-five acute respiratory infections (ARI), but differences in their disease pathogenesis, if any, are not well-known. This study was undertaken to analyze the epidemio-clinico-immunological features of RSV and hMPV infections. Naso-pharyngeal aspirates from children (aged two months to five years) with ARI presenting to our tertiary care center between December 2013 to March 2016 were subjected to real-time polymerase chain reaction for detection of RSV and hMPV. Positive samples were analyzed for co-infections and levels of cytokines. Of 349 naso-pharyngeal aspirates, RSV was detected in 40.68% (142/349), hMPV in 6.59% (23/349) and both in 1.4% (5/349). Co-infections were common, rhinovirus being the commonest co-offender. The demographical and clinical parameters of RSV- and hMPV-infected children were comparable. MMP-9/TIMP-1 ratio was significantly higher in RSV-mediated ARI and IFN-γ in hMPV-mediated ARI. Both RSV and hMPV are common among north Indian children with ARI and coinfections are not uncommon. Their clinical features being non-discriminatory, molecular diagnosis should be utilized to ascertain their individual epidemiology. The differences in their immune-pathogenesis (MMP-9/TIMP-1 ratio in RSV and IFN-γ in hMPV) could serve as useful tools for developing newer drugs.
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Affiliation(s)
- Subhabrata Sarkar
- Department of Virology, Postgraduate Institute of Medical Education and Research, India
| | - Radha Kanta Ratho
- Department of Virology, Postgraduate Institute of Medical Education and Research, India
| | - Meenu Singh
- Department of Pediatric Pulmonology, Advanced Pediatrics Centre, Postgraduate Institute of Medical Education and Research, India
| | - Mini Pritam Singh
- Department of Virology, Postgraduate Institute of Medical Education and Research, India
| | - Amarjeet Singh
- School and Public Health, Postgraduate Institute of Medical Education and Research, India
| | - Megha Sharma
- Department of Virology, Postgraduate Institute of Medical Education and Research, India
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29
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Rhinovirus Reduces the Severity of Subsequent Respiratory Viral Infections by Interferon-Dependent and -Independent Mechanisms. mSphere 2021; 6:e0047921. [PMID: 34160242 PMCID: PMC8265665 DOI: 10.1128/msphere.00479-21] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Coinfection by heterologous viruses in the respiratory tract is common and can alter disease severity compared to infection by individual virus strains. We previously found that inoculation of mice with rhinovirus (RV) 2 days before inoculation with a lethal dose of influenza A virus [A/Puerto Rico/8/34 (H1N1) (PR8)] provides complete protection against mortality. Here, we extended that finding to a second lethal respiratory virus, pneumonia virus of mice (PVM), and analyzed potential mechanisms of RV-induced protection. RV completely prevented mortality and weight loss associated with PVM infection. Major changes in host gene expression upon PVM infection were delayed compared to PR8. RV induced earlier recruitment of inflammatory cells, which were reduced at later times in RV-inoculated mice. Findings common to both virus pairs included the upregulated expression of mucin-associated genes and dampening of inflammation-related genes in mice that were inoculated with RV before lethal virus infection. However, type I interferon (IFN) signaling was required for RV-mediated protection against PR8 but not PVM. IFN signaling had minor effects on PR8 replication and contributed to controlling neutrophilic inflammation and hemorrhagic lung pathology in RV/PR8-infected mice. These findings, combined with differences in virus replication levels and disease severity, suggest that the suppression of inflammation in RV/PVM-infected mice may be due to early, IFN-independent suppression of viral replication, while that in RV/PR8-infected mice may be due to IFN-dependent modulation of immune responses. Thus, a mild upper respiratory viral infection can reduce the severity of a subsequent severe viral infection in the lungs through virus-dependent mechanisms. IMPORTANCE Respiratory viruses from diverse families cocirculate in human populations and are frequently detected within the same host. Although clinical studies suggest that infection by multiple different respiratory viruses may alter disease severity, animal models in which we can control the doses, timing, and strains of coinfecting viruses are critical to understanding how coinfection affects disease severity. Here, we compared gene expression and immune cell recruitment between two pairs of viruses (RV/PR8 and RV/PVM) inoculated sequentially in mice, both of which result in reduced severity compared to lethal infection by PR8 or PVM alone. Reduced disease severity was associated with suppression of inflammatory responses in the lungs. However, differences in disease kinetics and host and viral gene expression suggest that protection by coinfection with RV may be due to distinct molecular mechanisms. Indeed, we found that antiviral cytokine signaling was required for RV-mediated protection against lethal infection by PR8 but not PVM.
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30
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Cheemarla NR, Watkins TA, Mihaylova VT, Wang B, Zhao D, Wang G, Landry ML, Foxman EF. Dynamic innate immune response determines susceptibility to SARS-CoV-2 infection and early replication kinetics. J Exp Med 2021; 218:212380. [PMID: 34128960 PMCID: PMC8210587 DOI: 10.1084/jem.20210583] [Citation(s) in RCA: 112] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 05/21/2021] [Accepted: 06/01/2021] [Indexed: 12/25/2022] Open
Abstract
Initial replication of SARS-CoV-2 in the upper respiratory tract is required to establish infection, and the replication level correlates with the likelihood of viral transmission. Here, we examined the role of host innate immune defenses in restricting early SARS-CoV-2 infection using transcriptomics and biomarker-based tracking in serial patient nasopharyngeal samples and experiments with airway epithelial organoids. SARS-CoV-2 initially replicated exponentially, with a doubling time of ∼6 h, and induced interferon-stimulated genes (ISGs) in the upper respiratory tract, which rose with viral replication and peaked just as viral load began to decline. Rhinovirus infection before SARS-CoV-2 exposure accelerated ISG responses and prevented SARS-CoV-2 replication. Conversely, blocking ISG induction during SARS-CoV-2 infection enhanced viral replication from a low infectious dose. These results show that the activity of ISG-mediated defenses at the time of SARS-CoV-2 exposure impacts infection progression and that the heterologous antiviral response induced by a different virus can protect against SARS-CoV-2.
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Affiliation(s)
- Nagarjuna R Cheemarla
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT.,Department of Immunobiology, Yale School of Medicine, New Haven, CT
| | - Timothy A Watkins
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT.,Department of Immunobiology, Yale School of Medicine, New Haven, CT
| | - Valia T Mihaylova
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT
| | - Bao Wang
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT.,Department of Immunobiology, Yale School of Medicine, New Haven, CT
| | - Dejian Zhao
- Department of Genetics, Yale School of Medicine, New Haven, CT.,Yale Center for Genomic Analysis, Yale School of Medicine, New Haven, CT
| | - Guilin Wang
- Department of Genetics, Yale School of Medicine, New Haven, CT.,Yale Center for Genomic Analysis, Yale School of Medicine, New Haven, CT
| | - Marie L Landry
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT.,Department of Internal Medicine, Yale School of Medicine, New Haven, CT
| | - Ellen F Foxman
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT.,Department of Immunobiology, Yale School of Medicine, New Haven, CT
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Pacheco GA, Gálvez NMS, Soto JA, Andrade CA, Kalergis AM. Bacterial and Viral Coinfections with the Human Respiratory Syncytial Virus. Microorganisms 2021; 9:microorganisms9061293. [PMID: 34199284 PMCID: PMC8231868 DOI: 10.3390/microorganisms9061293] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 06/05/2021] [Accepted: 06/08/2021] [Indexed: 02/07/2023] Open
Abstract
The human respiratory syncytial virus (hRSV) is one of the leading causes of acute lower respiratory tract infections in children under five years old. Notably, hRSV infections can give way to pneumonia and predispose to other respiratory complications later in life, such as asthma. Even though the social and economic burden associated with hRSV infections is tremendous, there are no approved vaccines to date to prevent the disease caused by this pathogen. Recently, coinfections and superinfections have turned into an active field of study, and interactions between many viral and bacterial pathogens have been studied. hRSV is not an exception since polymicrobial infections involving this virus are common, especially when illness has evolved into pneumonia. Here, we review the epidemiology and recent findings regarding the main polymicrobial infections involving hRSV and several prevalent bacterial and viral respiratory pathogens, such as Staphylococcus aureus, Pseudomonas aeruginosa, Streptococcus pneumoniae, Haemophilus influenzae, Moraxella catarrhalis, Klebsiella pneumoniae, human rhinoviruses, influenza A virus, human metapneumovirus, and human parainfluenza viruses. As reports of most polymicrobial infections involving hRSV lack a molecular basis explaining the interaction between hRSV and these pathogens, we believe this review article can serve as a starting point to interesting and very much needed research in this area.
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Affiliation(s)
- Gaspar A. Pacheco
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Millennium Institute of Immunology and Immunotherapy, Pontificia Universidad Católica de Chile, Santiago 8320000, Chile; (G.A.P.); (N.M.S.G.); (J.A.S.); (C.A.A.)
| | - Nicolás M. S. Gálvez
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Millennium Institute of Immunology and Immunotherapy, Pontificia Universidad Católica de Chile, Santiago 8320000, Chile; (G.A.P.); (N.M.S.G.); (J.A.S.); (C.A.A.)
| | - Jorge A. Soto
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Millennium Institute of Immunology and Immunotherapy, Pontificia Universidad Católica de Chile, Santiago 8320000, Chile; (G.A.P.); (N.M.S.G.); (J.A.S.); (C.A.A.)
| | - Catalina A. Andrade
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Millennium Institute of Immunology and Immunotherapy, Pontificia Universidad Católica de Chile, Santiago 8320000, Chile; (G.A.P.); (N.M.S.G.); (J.A.S.); (C.A.A.)
| | - Alexis M. Kalergis
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Millennium Institute of Immunology and Immunotherapy, Pontificia Universidad Católica de Chile, Santiago 8320000, Chile; (G.A.P.); (N.M.S.G.); (J.A.S.); (C.A.A.)
- Departamento de Endocrinología, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago 8320000, Chile
- Correspondence: ; Tel.: +56-2-686-2842; Fax: +56-2-222-5515
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32
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Kovesdi I, Bakacs T. Therapeutic Exploitation of Viral Interference. Infect Disord Drug Targets 2021; 20:423-432. [PMID: 30950360 DOI: 10.2174/1871526519666190405140858] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Revised: 03/18/2019] [Accepted: 03/19/2019] [Indexed: 02/06/2023]
Abstract
Viral interference, originally, referred to a state of temporary immunity, is a state whereby infection with a virus limits replication or production of a second infecting virus. However, replication of a second virus could also be dominant over the first virus. In fact, dominance can alternate between the two viruses. Expression of type I interferon genes is many times upregulated in infected epithelial cells. Since the interferon system can control most, if not all, virus infections in the absence of adaptive immunity, it was proposed that viral induction of a nonspecific localized temporary state of immunity may provide a strategy to control viral infections. Clinical observations also support such a theory, which gave credence to the development of superinfection therapy (SIT). SIT is an innovative therapeutic approach where a non-pathogenic virus is used to infect patients harboring a pathogenic virus. For the functional cure of persistent viral infections and for the development of broad- spectrum antivirals against emerging viruses a paradigm shift was recently proposed. Instead of the virus, the therapy should be directed at the host. Such a host-directed-therapy (HDT) strategy could be the activation of endogenous innate immune response via toll-like receptors (TLRs). Superinfection therapy is such a host-directed-therapy, which has been validated in patients infected with two completely different viruses, the hepatitis B (DNA), and hepatitis C (RNA) viruses. SIT exerts post-infection interference via the constant presence of an attenuated non-pathogenic avian double- stranded (ds) RNA viral vector which boosts the endogenous innate (IFN) response. SIT could, therefore, be developed into a biological platform for a new "one drug, multiple bugs" broad-spectrum antiviral treatment approach.
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Affiliation(s)
- Imre Kovesdi
- ImiGene, Inc., Rockville, MD, USA,HepC, Inc., Budapest, Hungary
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Hendaus MA, Jomha FA. Can virus-virus interactions impact the dynamics of the covid-19 pandemic? J Biomol Struct Dyn 2021; 40:9571-9575. [PMID: 33998968 DOI: 10.1080/07391102.2021.1926327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Viral respiratory infections can occur in pandemics and can spread rapidly within communities resulting in health concerns globally. Several respiratory viruses co-circulate at one specific time. However, interface between different viruses has not been clearly established. This interaction is crucial to delineate, especially during pandemics, including the one relate to covid-19. This commentary will provide a brief description of how respiratory viruses interact and the outcome of this interaction on a pandemic.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mohamed A Hendaus
- Department of Pediatrics, Sidra Medicine, Doha, Qatar.,Weill Cornell Medicine, Ar-Rayyan, Qatar
| | - Fatima A Jomha
- School of Pharmacy, Lebanese International University, Beirut, Lebanon
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34
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Nawrocki J, Olin K, Holdrege MC, Hartsell J, Meyers L, Cox C, Powell M, Cook CV, Jones J, Robbins T, Hemmert A, Ginocchio CC. The Effects of Social Distancing Policies on Non-SARS-CoV-2 Respiratory Pathogens. Open Forum Infect Dis 2021; 8:ofab133. [PMID: 34322558 PMCID: PMC7989184 DOI: 10.1093/ofid/ofab133] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 03/15/2021] [Indexed: 11/12/2022] Open
Abstract
Background The initial focus of the US public health response to coronavirus disease 2019 (COVID-19) was the implementation of numerous social distancing policies. While COVID-19 was the impetus for imposing these policies, it is not the only respiratory disease affected by their implementation. This study aimed to assess the impact of social distancing policies on non-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) respiratory pathogens typically circulating across multiple US states. Methods Linear mixed-effect models were implemented to explore the effects of 5 social distancing policies on non-SARS-CoV-2 respiratory pathogens across 9 states from January 1 through May 1, 2020. The observed 2020 pathogen detection rates were compared week by week with historical rates to determine when the detection rates were different. Results Model results indicate that several social distancing policies were associated with a reduction in total detection rate, by nearly 15%. Policies were associated with decreases in pathogen circulation of human rhinovirus/enterovirus and human metapneumovirus, as well as influenza A, which typically decrease after winter. Parainfluenza viruses failed to circulate at historical levels during the spring. The total detection rate in April 2020 was 35% less than the historical average. Many of the pathogens driving this difference fell below the historical detection rate ranges within 2 weeks of initial policy implementation. Conclusions This analysis investigated the effect of multiple social distancing policies implemented to reduce transmission of SARS-CoV-2 on non-SARS-CoV-2 respiratory pathogens. These findings suggest that social distancing policies may be used as an impactful public health tool to reduce communicable respiratory illness.
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Affiliation(s)
| | | | | | | | | | - Charles Cox
- BioFire Diagnostics, LLC, Salt Lake City, Utah, USA
| | | | | | - Jay Jones
- BioFire Diagnostics, LLC, Salt Lake City, Utah, USA
| | - Tom Robbins
- BioFire Diagnostics, LLC, Salt Lake City, Utah, USA
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Cheemarla NR, Watkins TA, Mihaylova VT, Wang B, Zhao D, Wang G, Landry ML, Foxman EF. Magnitude and timing of the antiviral response determine SARS-CoV-2 replication early in infection. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.01.22.21249812. [PMID: 33532783 PMCID: PMC7852233 DOI: 10.1101/2021.01.22.21249812] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The interferon response is a potent antiviral defense mechanism, but its effectiveness depends on its timing relative to viral replication. Here, we report viral replication and host response kinetics in patients at the start of SARS-CoV-2 infection and explore the impact of these kinetics experimentally. In both longitudinal patient nasopharyngeal samples and airway epithelial organoids, we found that SARS-CoV-2 initially replicated exponentially with a doubling time of ~6hr, and induced interferon stimulated genes (ISGs) with delayed timing relative to viral replication. Prior exposure to rhinovirus increased ISG levels and blocked SARS-CoV-2 replication. Conversely, inhibiting ISG induction abrogated interference by rhinovirus and enhanced SARS-CoV-2 replication rate. These results demonstrate the importance of initial interferon-mediated defenses in determining the extent to which SARS-CoV-2 can replicate at the start of infection and indicate that biological variables that alter the airway interferon response, including heterologous induction of innate immunity by other viruses, could profoundly impact SARS-CoV-2 susceptibility and transmission.
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Affiliation(s)
| | - Timothy A. Watkins
- Department of Laboratory Medicine, Yale School of Medicine, New Haven CT, U.S.A. 06520
- Department of Immunobiology, Yale School of Medicine, New Haven CT, U.S.A. 06520
| | - Valia T. Mihaylova
- Department of Laboratory Medicine, Yale School of Medicine, New Haven CT, U.S.A. 06520
| | - Bao Wang
- Department of Laboratory Medicine, Yale School of Medicine, New Haven CT, U.S.A. 06520
- Department of Immunobiology, Yale School of Medicine, New Haven CT, U.S.A. 06520
| | - Dejian Zhao
- Department of Genetics, Yale School of Medicine, New Haven CT, U.S.A. 06520
- Yale Center for Genomic Analysis, Yale School of Medicine, New Haven CT, U.S.A. 06520
| | - Guilin Wang
- Department of Genetics, Yale School of Medicine, New Haven CT, U.S.A. 06520
- Yale Center for Genomic Analysis, Yale School of Medicine, New Haven CT, U.S.A. 06520
| | - Marie L. Landry
- Department of Laboratory Medicine, Yale School of Medicine, New Haven CT, U.S.A. 06520
- Department of Internal Medicine, Yale School of Medicine, New Haven CT, U.S.A. 06520
| | - Ellen F. Foxman
- Department of Laboratory Medicine, Yale School of Medicine, New Haven CT, U.S.A. 06520
- Department of Immunobiology, Yale School of Medicine, New Haven CT, U.S.A. 06520
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Bizot E, Bousquet A, Charpié M, Coquelin F, Lefevre S, Le Lorier J, Patin M, Sée P, Sarfati E, Walle S, Visseaux B, Basmaci R. Rhinovirus: A Narrative Review on Its Genetic Characteristics, Pediatric Clinical Presentations, and Pathogenesis. Front Pediatr 2021; 9:643219. [PMID: 33829004 PMCID: PMC8019700 DOI: 10.3389/fped.2021.643219] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 02/03/2021] [Indexed: 12/11/2022] Open
Abstract
Human rhinoviruses (HRVs) are the leading cause of common colds. With the development of new molecular methods since the 2000s, HRVs have been increasingly involved among severe clinical infections. Recent knowledge of the HRV genetic characteristics has also improved the understanding of their pathogenesis. This narrative review aims to provide a current comprehensive knowledge about this virus in the pediatric community. HRVs represent a main cause of upper and lower respiratory tract infections in children. HRV is the second virus involved in bronchiolitis and pneumonia in children, and HRV bronchiolitis has a higher risk of recurrent wheezing episode or asthma. Some recent findings described HRVs in stools, blood, or cerebrospinal fluid, thanks to new molecular techniques such as polymerase chain reaction (PCR) by detecting HRVs with high sensibility. However, the high rate of asymptomatic carriage and the prolonged excretion in postsymptomatic patients complicate interpretation. No sufficient data exist to avoid antibiotic therapy in pediatric high-risk population with HRV detection. Severe clinical presentations due to HRVs can be more frequent in specific population with chronic pathology or genetic particularity. Inflammatory response is mediated by the nuclear factor (NF)-kappa B pathway and production of interferon (IFN)-beta and IFN-gamma, interleukin 8 (IL8), and IL1b. No specific treatment or antiviral therapy exists, although research is still ongoing. Nowadays, in addition to benign diseases, HRVs are recognized to be involved in some severe clinical presentations. Recent advances in genetic knowledge or specific inflammatory response may lead to specific treatment.
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Affiliation(s)
- Etienne Bizot
- Department of Microbiology, Robert Debré Hospital, APHP, Paris, France.,Departement of Emergency and Pediatrics, Louis-Mourier Hospital, APHP, Colombes, France
| | - Anais Bousquet
- Departement of Emergency and Pediatrics, Louis-Mourier Hospital, APHP, Colombes, France
| | - Maelle Charpié
- Departement of Emergency and Pediatrics, Louis-Mourier Hospital, APHP, Colombes, France
| | - Florence Coquelin
- Departement of Emergency and Pediatrics, Louis-Mourier Hospital, APHP, Colombes, France
| | - Servane Lefevre
- Departement of Emergency and Pediatrics, Louis-Mourier Hospital, APHP, Colombes, France
| | - Justin Le Lorier
- Departement of Emergency and Pediatrics, Louis-Mourier Hospital, APHP, Colombes, France
| | - Margaux Patin
- Departement of Emergency and Pediatrics, Louis-Mourier Hospital, APHP, Colombes, France
| | - Perrine Sée
- Departement of Emergency and Pediatrics, Louis-Mourier Hospital, APHP, Colombes, France
| | - Eytan Sarfati
- Departement of Emergency and Pediatrics, Louis-Mourier Hospital, APHP, Colombes, France
| | - Servane Walle
- Departement of Emergency and Pediatrics, Louis-Mourier Hospital, APHP, Colombes, France
| | - Benoit Visseaux
- Department of Virology, Bichat Hospital, APHP, Paris, France.,University of Paris, Inserm, IAME, UMR1137, Paris, France
| | - Romain Basmaci
- Departement of Emergency and Pediatrics, Louis-Mourier Hospital, APHP, Colombes, France.,University of Paris, Inserm, IAME, UMR1137, Paris, France
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Wu A, Mihaylova VT, Landry ML, Foxman EF. Interference between rhinovirus and influenza A virus: a clinical data analysis and experimental infection study. LANCET MICROBE 2020; 1:e254-e262. [PMID: 33103132 PMCID: PMC7580833 DOI: 10.1016/s2666-5247(20)30114-2] [Citation(s) in RCA: 126] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Background During the 2009 pandemic of an emerging influenza A virus (IAV; H1N1pdm09), data from several European countries indicated that the spread of the virus might have been interrupted by the annual autumn rhinovirus epidemic. We aimed to investigate viral interference between rhinovirus and IAV with use of clinical data and an experimental model. Methods We did a clinical data analysis and experimental infection study to investigate the co-occurrence of rhinovirus and IAV in respiratory specimens from adults (≥21 years) tested with a multiplex PCR panel at Yale-New Haven Hospital (CT, USA) over three consecutive winter seasons (Nov 1 to March 1, 2016–17, 2017–18, and 2018–19). We compared observed versus expected co-detections using data extracted from the Epic Systems electronic medical record system. To assess how rhinovirus infection affects subsequent IAV infection, we inoculated differentiated primary human airway epithelial cultures with rhinovirus (HRV-01A; multiplicity of infection [MOI] 0·1) or did mock infection. On day 3 post-infection, we inoculated the same cultures with IAV (H1N1 green fluorescent protein [GFP] reporter virus or H1N1pdm09; MOI 0·1). We used reverse transcription quantitative PCR or microscopy to quantify host cell mRNAs for interferon-stimulated genes (ISGs) on day 3 after rhinovirus or mock infection and IAV RNA on days 4, 5, or 6 after rhinovirus or mock infection. We also did sequential infection studies in the presence of BX795 (6 μM), to inhibit the interferon response. We compared ISG expression and IAV RNA and expression of GFP by IAV reporter virus. Findings Between July 1, 2016, and June 30, 2019, examination of 8284 respiratory samples positive for either rhinovirus (n=3821) or IAV (n=4463) by any test method was used to establish Nov 1 to March 1 as the period of peak virus co-circulation. After filtering for samples within this time frame meeting the inclusion criteria (n=13 707), there were 989 (7·2%) rhinovirus and 922 (6·7%) IAV detections, with a significantly lower than expected odds of co-detection (odds ratio 0·16, 95% CI 0·09–0·28). Rhinovirus infection of cell cultures induced ISG expression and protected against IAV infection 3 days later, resulting in an approximate 50 000-fold decrease in IAV H1N1pdm09 viral RNA on day 5 post-rhinovirus inoculation. Blocking the interferon response restored IAV replication following rhinovirus infection. Interpretation These findings show that one respiratory virus can block infection with another through stimulation of antiviral defences in the airway mucosa, supporting the idea that interference from rhinovirus disrupted the 2009 IAV pandemic in Europe. These results indicate that viral interference can potentially affect the course of an epidemic, and this possibility should be considered when designing interventions for seasonal influenza epidemics and the ongoing COVID-19 pandemic. Funding National Institutes of Health, National Institute of General Medical Sciences, and the Yale Department of Laboratory Medicine.
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Affiliation(s)
- Anchi Wu
- Department of Laboratory Medicine (A Wu BSE, V T Mihaylova PhD, Prof M L Landry MD, Prof E F Foxman MD), Department of Internal Medicine (Prof M L Landry), and Department of Immunobiology (A Wu, Prof E F Foxman), Yale University School of Medicine, New Haven, CT, USA
| | - Valia T Mihaylova
- Department of Laboratory Medicine (A Wu BSE, V T Mihaylova PhD, Prof M L Landry MD, Prof E F Foxman MD), Department of Internal Medicine (Prof M L Landry), and Department of Immunobiology (A Wu, Prof E F Foxman), Yale University School of Medicine, New Haven, CT, USA
| | - Marie L Landry
- Department of Laboratory Medicine (A Wu BSE, V T Mihaylova PhD, Prof M L Landry MD, Prof E F Foxman MD), Department of Internal Medicine (Prof M L Landry), and Department of Immunobiology (A Wu, Prof E F Foxman), Yale University School of Medicine, New Haven, CT, USA
| | - Ellen F Foxman
- Department of Laboratory Medicine (A Wu BSE, V T Mihaylova PhD, Prof M L Landry MD, Prof E F Foxman MD), Department of Internal Medicine (Prof M L Landry), and Department of Immunobiology (A Wu, Prof E F Foxman), Yale University School of Medicine, New Haven, CT, USA
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Nickbakhsh S, Ho A, Marques DFP, McMenamin J, Gunson RN, Murcia PR. Epidemiology of Seasonal Coronaviruses: Establishing the Context for the Emergence of Coronavirus Disease 2019. J Infect Dis 2020; 222:17-25. [PMID: 32296837 PMCID: PMC7184404 DOI: 10.1093/infdis/jiaa185] [Citation(s) in RCA: 134] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 04/14/2020] [Indexed: 12/23/2022] Open
Abstract
Public health preparedness for coronavirus (CoV) disease 2019 (COVID-19) is challenging in the absence of setting-specific epidemiological data. Here we describe the epidemiology of seasonal CoVs (sCoVs) and other cocirculating viruses in the West of Scotland, United Kingdom. We analyzed routine diagnostic data for >70 000 episodes of respiratory illness tested molecularly for multiple respiratory viruses between 2005 and 2017. Statistical associations with patient age and sex differed between CoV-229E, CoV-OC43, and CoV-NL63. Furthermore, the timing and magnitude of sCoV outbreaks did not occur concurrently, and coinfections were not reported. With respect to other cocirculating respiratory viruses, we found evidence of positive, rather than negative, interactions with sCoVs. These findings highlight the importance of considering cocirculating viruses in the differential diagnosis of COVID-19. Further work is needed to establish the occurrence/degree of cross-protective immunity conferred across sCoVs and with COVID-19, as well as the role of viral coinfection in COVID-19 disease severity.
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Affiliation(s)
- Sema Nickbakhsh
- MRC-University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Antonia Ho
- MRC-University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Diogo F P Marques
- Public Health Scotland, NHS National Services Scotland, Glasgow, United Kingdom
| | - Jim McMenamin
- Public Health Scotland, NHS National Services Scotland, Glasgow, United Kingdom
| | - Rory N Gunson
- West of Scotland Specialist Virology Centre, NHS Greater Glasgow and Clyde, Glasgow, United Kingdom
| | - Pablo R Murcia
- MRC-University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
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Dynamics and predisposition of respiratory viral co-infections in children and adults. Clin Microbiol Infect 2020; 27:631.e1-631.e6. [PMID: 32540470 DOI: 10.1016/j.cmi.2020.05.042] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 05/26/2020] [Accepted: 05/30/2020] [Indexed: 01/06/2023]
Abstract
OBJECTIVES The epidemiology of respiratory co-infection pairings is poorly understood. Here we assess the dynamics of respiratory viral co-infections in children and adults and determine predisposition for or against specific viral pairings. METHODS Over five respiratory seasons from 30 November 2013 through 6 June 2018, the mono-infection and co-infection prevalence of 13 viral pathogens was tabulated at The Cleveland Clinic. Employing a model to proportionally distribute viral pairs using individual virus co-infection rate with prevalence patterns of concurrent co-circulating viruses, we compared predicted occurrence with observed occurrence of 132 viral pairing permutations using binomial analysis. RESULTS Of 30 535 respiratory samples, 9843 (32.2%) were positive for at least one virus and 1018 (10.8%) of these were co-infected. Co-infected samples predominantly originated from children. Co-infection rate in paediatric population was 35.0% (2068/5906), compared with only 5.8% (270/4591) in adults. Adenovirus C (ADVC) had the highest co-infection rate (426/623, 68.3%) while influenza virus B had the lowest (55/546, 10.0%). ADVC-rhinovirus (HRV), respiratory syncytial virus A (RSVA)-HRV and RSVB-HRV pairings occurred at significantly higher frequencies than predicted by the proportional distribution model (p < 0.05). Additionally, several viral pairings had fewer co-infections than predicted by our model: notably metapneumovirus (hMPV)-parainfluenza virus 3, hMPV-RSVA and RSVA-RSVB. CONCLUSIONS This is one of the largest studies on respiratory viral co-infections in children and adults. Co-infections are substantially more common in children, especially under 5 years of age, and the most frequent pairings occurred at a higher frequency than would be expected by random. Specific pairings occur at altered rates compared with those predicted by proportional distribution, suggesting either direct or indirect interactions result between specific viral pathogens.
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40
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Bruyndonckx R, Coenen S, Butler C, Verheij T, Little P, Hens N, Beutels P, Ieven M, Goossens H. Respiratory syncytial virus and influenza virus infection in adult primary care patients: Association of age with prevalence, diagnostic features and illness course. Int J Infect Dis 2020; 95:384-390. [PMID: 32320810 PMCID: PMC7167228 DOI: 10.1016/j.ijid.2020.04.020] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Revised: 04/06/2020] [Accepted: 04/07/2020] [Indexed: 02/05/2023] Open
Abstract
RSV prevalence in patients age 75+ was twice the prevalence in those under 60. Influenza prevalence is not associated with age. Diagnostics are not associated with age for RSV and influenza. Illness course is associated with age for both RSV and influenza.
Objectives To better target new vaccines and treatments being developed for respiratory syncytial virus (RSV) and influenza virus (influenza), we studied the association of age with prevalence, diagnostic features and course of illness of these infections in primary care patients. Methods Secondary analysis of observational data on the aetiology, diagnosis and prognosis in adults presenting to primary care with acute cough in 12 European countries (2007–2010) using regression analyses corrected for clustering of patients within countries. Age groups were 18–59 years, 60–74 years, and 75 years and older (75+). Results Nasopharyngeal swabs for 144 (4.6%), 169 (5.4%) and 104 (3.4%) out of 3104 patients were polymerase chain reaction (PCR) positive for RSV, influenza A and influenza B, respectively. RSV prevalence in patients 75+ (8.5%) was twice the prevalence in those under 60 years (4.2%). Influenza prevalence was not associated with age. Diagnostic features for these viruses were not associated with age. Symptom duration was associated with age for RSV and influenza B, but not for influenza A. The odds of unresolved symptoms after 28 days were associated with age for RSV only. Illness deterioration was associated with age for RSV, with patients 75+ at increased risk, but not for influenza. Conclusion In adults presenting to primary care with acute cough, the diagnostic features of RSV or influenza infection are not associated with age. For RSV both the prevalence and illness course are significantly worse at higher age, for influenza only the illness course is.
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Affiliation(s)
- Robin Bruyndonckx
- Data Science Institute (DSI), Hasselt University, Hasselt, Belgium; Laboratory of Medical Microbiology, Vaccine & Infectious Diseases Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium.
| | - Samuel Coenen
- Laboratory of Medical Microbiology, Vaccine & Infectious Diseases Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium; Department of Epidemiology and Social Medicine (ESOC), University of Antwerp, Antwerp, Belgium; Department of Primary and Interdisciplinary Care (ELIZA), University of Antwerp, Antwerp, Belgium
| | - Chris Butler
- Institute for Primary Care and Public Health, Cardiff University, Cardiff, UK
| | - Theo Verheij
- Julius Centre for Health Sciences and Primary Care, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Paul Little
- Aldermoor Health Centre, University of Southampton, Southampton, UK
| | - Niel Hens
- Data Science Institute (DSI), Hasselt University, Hasselt, Belgium; Centre for Health Economic Research and Modelling Infectious Diseases (CHERMID), Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
| | - Philippe Beutels
- Centre for Health Economic Research and Modelling Infectious Diseases (CHERMID), Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
| | - Margareta Ieven
- Laboratory of Medical Microbiology, Vaccine & Infectious Diseases Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
| | - Herman Goossens
- Laboratory of Medical Microbiology, Vaccine & Infectious Diseases Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
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Reply to Kloepfer and Gern: Independent studies suggest an arms race between influenza and rhinovirus: What next? Proc Natl Acad Sci U S A 2020; 117:6988-6989. [PMID: 32127475 PMCID: PMC7132304 DOI: 10.1073/pnas.2000903117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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42
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Chen ICM, Loh JP, Chuah CXP, Gao QHC, Sun Y, Ng SH, Koh WHV, Goh EH, Zhao X, Tambyah PA, Cook AR, Chng J, Pang J, Tan BH, Lee VJ. Evidence for Cross-Protection Against Subsequent Febrile Respiratory Illness Episodes From Prior Infections by Different Viruses Among Singapore Military Recruits 2009-2014. J Infect Dis 2020; 219:1913-1923. [PMID: 30722024 PMCID: PMC6534195 DOI: 10.1093/infdis/jiz046] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 01/27/2019] [Indexed: 12/22/2022] Open
Abstract
Background Few studies have evaluated the relative cross-protection conferred by infection with different groups of viruses through studies of sequential infections in humans. We investigated the presence of short-lived relative cross-protection conferred by specific prior viral infections against subsequent febrile respiratory illness (FRI). Methods Men enlisted in basic military training between December 2009 and December 2014 were recruited, with the first FRI as the study entry point. ResPlex II assays and real-time polymerase chain reaction assays were used to detect viral pathogens in nasal wash samples, and survival analyses were performed to determine whether infection with particular viruses conferred short-lived relative cross-protection against FRI. Results Prior infection with adenovirus (hazard ratio [HR], 0.24; 95% confidence interval [CI], .14–.44) or influenza virus (HR, 0.52; 95% CI, .38–.73) conferred relative protection against subsequent FRI episode. Results were statistically significant even after adjustment for the interval between enlistment and FRI (P < .001). Adenovirus-positive participants with FRI episodes tended to be protected against subsequent infection with adenovirus, coronavirus, enterovirus/rhinovirus, and influenza virus (P = .062–.093), while men with influenza virus–positive FRI episodes tended be protected against subsequent infection with adenovirus (P = .044) and influenza virus (P = .081). Conclusion Prior adenovirus or influenza virus infection conferred cross-protection against subsequent FRI episodes relative to prior infection due to other circulating viruses.
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Affiliation(s)
- I-Cheng Mark Chen
- Saw Swee Hock School of Public Health, National University of Singapore and National University Hospital System, Singapore.,Infectious Disease Research and Training Office, National Centre for Infectious Diseases, Singapore
| | | | - Cheryl X P Chuah
- Saw Swee Hock School of Public Health, National University of Singapore and National University Hospital System, Singapore
| | | | - Yinxiaohe Sun
- Saw Swee Hock School of Public Health, National University of Singapore and National University Hospital System, Singapore.,Centre for Infectious Disease Epidemiology and Research, Saw Swee Hock School of Public Health, National University of Singapore and National University Hospital System, Singapore
| | | | | | - Ee Hui Goh
- Saw Swee Hock School of Public Health, National University of Singapore and National University Hospital System, Singapore
| | - Xiahong Zhao
- Saw Swee Hock School of Public Health, National University of Singapore and National University Hospital System, Singapore
| | - Paul Anantharajah Tambyah
- Yong Loo Lin School of Medicine, National University of Singapore and National University Hospital System, Singapore
| | - Alex R Cook
- Saw Swee Hock School of Public Health, National University of Singapore and National University Hospital System, Singapore
| | - Jeremiah Chng
- Biodefence Centre, Headquarters Medical Corps, Singapore Armed Forces, Singapore
| | - Junxiong Pang
- Saw Swee Hock School of Public Health, National University of Singapore and National University Hospital System, Singapore.,Centre for Infectious Disease Epidemiology and Research, Saw Swee Hock School of Public Health, National University of Singapore and National University Hospital System, Singapore
| | - Boon-Huan Tan
- DSO National Laboratories, Singapore.,Infection and Immunity, Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Vernon J Lee
- Saw Swee Hock School of Public Health, National University of Singapore and National University Hospital System, Singapore.,Biodefence Centre, Headquarters Medical Corps, Singapore Armed Forces, Singapore
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43
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Virus-virus interactions impact the population dynamics of influenza and the common cold. Proc Natl Acad Sci U S A 2019; 116:27142-27150. [PMID: 31843887 PMCID: PMC6936719 DOI: 10.1073/pnas.1911083116] [Citation(s) in RCA: 267] [Impact Index Per Article: 53.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
When multiple pathogens cocirculate this can lead to competitive or cooperative forms of pathogen–pathogen interactions. It is believed that such interactions occur among cold and flu viruses, perhaps through broad-acting immunity, resulting in interlinked epidemiological patterns of infection. However, to date, quantitative evidence has been limited. We analyzed a large collection of diagnostic reports collected over multiple years for 11 respiratory viruses. Our analyses provide strong statistical support for the existence of interactions among respiratory viruses. Using computer simulations, we found that very short-lived interferences may explain why common cold infections are less frequent during flu seasons. Improved understanding of how the epidemiology of viral infections is interlinked can help improve disease forecasting and evaluation of disease control interventions. The human respiratory tract hosts a diverse community of cocirculating viruses that are responsible for acute respiratory infections. This shared niche provides the opportunity for virus–virus interactions which have the potential to affect individual infection risks and in turn influence dynamics of infection at population scales. However, quantitative evidence for interactions has lacked suitable data and appropriate analytical tools. Here, we expose and quantify interactions among respiratory viruses using bespoke analyses of infection time series at the population scale and coinfections at the individual host scale. We analyzed diagnostic data from 44,230 cases of respiratory illness that were tested for 11 taxonomically broad groups of respiratory viruses over 9 y. Key to our analyses was accounting for alternative drivers of correlated infection frequency, such as age and seasonal dependencies in infection risk, allowing us to obtain strong support for the existence of negative interactions between influenza and noninfluenza viruses and positive interactions among noninfluenza viruses. In mathematical simulations that mimic 2-pathogen dynamics, we show that transient immune-mediated interference can cause a relatively ubiquitous common cold-like virus to diminish during peak activity of a seasonal virus, supporting the potential role of innate immunity in driving the asynchronous circulation of influenza A and rhinovirus. These findings have important implications for understanding the linked epidemiological dynamics of viral respiratory infections, an important step towards improved accuracy of disease forecasting models and evaluation of disease control interventions.
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Mair C, Nickbakhsh S, Reeve R, McMenamin J, Reynolds A, Gunson RN, Murcia PR, Matthews L. Estimation of temporal covariances in pathogen dynamics using Bayesian multivariate autoregressive models. PLoS Comput Biol 2019; 15:e1007492. [PMID: 31834896 PMCID: PMC6934324 DOI: 10.1371/journal.pcbi.1007492] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 12/27/2019] [Accepted: 10/16/2019] [Indexed: 11/22/2022] Open
Abstract
It is well recognised that animal and plant pathogens form complex ecological communities of interacting organisms within their hosts, and there is growing interest in the health implications of such pathogen interactions. Although community ecology approaches have been used to identify pathogen interactions at the within-host scale, methodologies enabling robust identification of interactions from population-scale data such as that available from health authorities are lacking. To address this gap, we developed a statistical framework that jointly identifies interactions between multiple viruses from contemporaneous non-stationary infection time series. Our conceptual approach is derived from a Bayesian multivariate disease mapping framework. Importantly, our approach captures within- and between-year dependencies in infection risk while controlling for confounding factors such as seasonality, demographics and infection frequencies, allowing genuine pathogen interactions to be distinguished from simple correlations. We validated our framework using a broad range of synthetic data. We then applied it to diagnostic data available for five respiratory viruses co-circulating in a major urban population between 2005 and 2013: adenovirus, human coronavirus, human metapneumovirus, influenza B virus and respiratory syncytial virus. We found positive and negative covariances indicative of epidemiological interactions among specific virus pairs. This statistical framework enables a community ecology perspective to be applied to infectious disease epidemiology with important utility for public health planning and preparedness. Disease-causing microorganisms, including viruses, bacteria, protozoa and fungi, form complex communities within animals and plants. These microorganisms can coexist harmoniously or even beneficially, or they may competitively interact for host resources. Well-studied examples include interactions between viruses and bacteria in the respiratory tract. Whilst ecological studies have revealed that some pathogens do interact within their hosts, identifying interactions from available population scale data from health authorities is challenging. This is exacerbated by a lack of large-scale data describing the infection patterns of multiple pathogens within single populations over long time frames. Furthermore, methods for evaluating whether infection frequencies of different pathogens fluctuate together or not over time cannot readily account for alternative explanations. For example, human pathogens may have related seasonal patterns depending on the age groups they infect and the weather conditions they survive in, and not because they are interacting. We developed a robust statistical framework to identify pathogen-pathogen interactions from population scale diagnostic data. This framework serves as a crucial step in identifying such important interactions and will guide new studies to elucidate their underpinning mechanisms. This will have important consequences for public health preparedness and the design of effective disease control interventions.
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Affiliation(s)
- Colette Mair
- MRC-University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
- School of Mathematics and Statistics, College of Science and Engineering, University of Glasgow, Glasgow, United Kingdom
- * E-mail:
| | - Sema Nickbakhsh
- MRC-University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Richard Reeve
- Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Jim McMenamin
- Health Protection Scotland, NHS National Services Scotland, Glasgow, United Kingdom
| | - Arlene Reynolds
- Health Protection Scotland, NHS National Services Scotland, Glasgow, United Kingdom
| | - Rory N. Gunson
- West of Scotland Specialist Virology Centre, NHS Greater Glasgow and Clyde, Glasgow, United Kingdom
| | - Pablo R. Murcia
- MRC-University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Louise Matthews
- Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
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Arden KE, Greer RM, Wang CYT, Mackay IM. Genotypic diversity, circulation patterns and co-detections among rhinoviruses in Queensland, 2001. Access Microbiol 2019; 2:acmi000075. [PMID: 33062934 PMCID: PMC7525053 DOI: 10.1099/acmi.0.000075] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 10/07/2019] [Indexed: 12/13/2022] Open
Abstract
Purpose Rhinoviruses (RVs) occur more frequently than other viruses and more often in people displaying symptoms than in those without. We sought to estimate the spectrum of RV diversity, RV species seasonality and to analyse RV involvement in respiratory virus co-detections. Methodology A convenience collection of 1179 airway sample extracts from patients with suspected respiratory infections, collected during 2001, was subjected to comprehensive molecular testing. Results RVs were the most common virus detected. We were able to genotype ~90 % of RV detections, identifying 70 distinct RVs, spanning all three species. RV-Bs were under-represented. We found RV species co-circulated at times, although one species usually dominated. Each species displayed a bimodal distribution. Conclusion Notably, RVs and influenza A viruses (IFAV) seldom co-occurred, supporting their roles as primary pathogens of the airway among acutely ill infants. Whether RV circulation has a moderating or controlling effect on the IFAV season or is controlled by it cannot be determined from these data. Despite the frequent perception that RVs commonly co-occur with another virus, our findings indicated this was not always the case. Nearly 80 % of RV detections occurred alone. Understanding more about population-level interference between viruses may allow us to harness aspects of it to generate a non-specific antiviral intervention that mimics a putative protective effect. For routine respiratory virus screening to best serve the patient, RV testing should be a principal component of any acute respiratory illness testing algorithm throughout the year.
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Affiliation(s)
- Katherine E Arden
- Child Health Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - Ristan M Greer
- Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia
| | - Claire Y T Wang
- Child Health Research Centre, The University of Queensland, Brisbane, Queensland, Australia.,Centre for Children's Health Research, Children's Health Queensland South Brisbane, Queensland, 4101, Australia
| | - Ian M Mackay
- Child Health Research Centre, The University of Queensland, Brisbane, Queensland, Australia
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Uddin SMI, Englund JA, Kuypers JY, Chu HY, Steinhoff MC, Khatry SK, LeClerq SC, Tielsch JM, Mullany LC, Shrestha L, Katz J. Burden and Risk Factors for Coronavirus Infections in Infants in Rural Nepal. Clin Infect Dis 2019; 67:1507-1514. [PMID: 29668900 PMCID: PMC6206108 DOI: 10.1093/cid/ciy317] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 04/12/2018] [Indexed: 12/12/2022] Open
Abstract
Background Knowledge of risk factors for symptomatic human coronavirus (HCoV) infections in children in community settings is limited. We estimated the disease burden and impact of birth-related, maternal, household, and seasonal factors on HCoV infections among children from birth to 6 months old in rural Nepal. Methods Prospective, active, weekly surveillance for acute respiratory infections (ARIs) was conducted in infants over a period of 3 years during 2 consecutive, population-based randomized trials of maternal influenza immunization. Midnasal swabs were collected for acute respiratory symptoms and tested for HCoV and other viruses by reverse-transcription polymerase chain reaction. Association between HCoV incidence and potential risk factors was modeled using Poisson regression. Results Overall, 282 of 3505 (8%) infants experienced an HCoV ARI within the first 6 months of life. HCoV incidence overall was 255.6 (95% confidence interval [CI], 227.3–286.5) per 1000 person-years, and was more than twice as high among nonneonates than among neonates (incidence rate ratio [IRR], 2.53; 95% CI, 1.52–4.21). HCoV ARI incidence was also positively associated with the number of children <5 years of age per room in a household (IRR, 1.13; 95% CI, 1.01–1.28). Of the 296 HCoV infections detected, 46% were coinfections with other respiratory viruses. While HCoVs were detected throughout the study period, seasonal variation was also observed, with incidence peaking in 2 winters (December–February) and 1 autumn (September–November). Conclusions HCoV is associated with a substantial proportion of illnesses among young infants in rural Nepal. There is an increased risk of HCoV infection beyond the first month of life.
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Affiliation(s)
- S M Iftekhar Uddin
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | | | - Jane Y Kuypers
- Molecular Virology Laboratory, School of Medicine, Seattle
| | - Helen Y Chu
- Harborview Medical Center, University of Washington, Seattle
| | - Mark C Steinhoff
- Global Health Center, Cincinnati Children's Hospital Medical Center, Ohio
| | | | - Steve C LeClerq
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland.,Nepal Nutrition Intervention Project-Sarlahi, Kathmandu
| | - James M Tielsch
- Department of Global Health, Milken Institute School of Public Health, George Washington University, D.C
| | - Luke C Mullany
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Laxman Shrestha
- Department of Pediatrics and Child Health, Institute of Medicine, Tribhuvan University, Kathmandu, Nepal
| | - Joanne Katz
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
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Nolan VG, Arnold SR, Bramley AM, Ampofo K, Williams DJ, Grijalva CG, Self WH, Anderson EJ, Wunderink RG, Edwards KM, Pavia AT, Jain S, McCullers JA. Etiology and Impact of Coinfections in Children Hospitalized With Community-Acquired Pneumonia. J Infect Dis 2019; 218:179-188. [PMID: 29228381 PMCID: PMC7108488 DOI: 10.1093/infdis/jix641] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 12/05/2017] [Indexed: 12/22/2022] Open
Abstract
Background Recognition that coinfections are common in children with community-acquired pneumonia (CAP) is increasing, but gaps remain in our understanding of their frequency and importance. Methods We analyzed data from 2219 children hospitalized with CAP and compared demographic and clinical characteristics and outcomes between groups with viruses alone, bacteria alone, or coinfections. We also assessed the frequency of selected pairings of codetected pathogens and their clinical characteristics. Results A total of 576 children (26%) had a coinfection. Children with only virus detected were younger, more likely to be black, and more likely to have comorbidities such as asthma, compared with children infected with typical bacteria alone. Children with virus-bacterium coinfections had a higher frequency of leukocytosis, consolidation on chest radiography, parapneumonic effusions, intensive care unit admission, and need for mechanical ventilation and an increased length of stay, compared with children infected with viruses alone. Virus-virus coinfections were generally comparable to single-virus infections, with the exception of the need for oxygen supplementation, which was higher during the first 24 hours of hospitalization in some virus-virus pairings. Conclusions Coinfections occurred in 26% of children hospitalized for CAP. Children with typical bacterial infections, alone or complicated by a viral infection, have worse outcomes than children infected with a virus alone.
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Affiliation(s)
- Vikki G Nolan
- Division of Epidemiology, School of Public Health, University of Memphis
| | - Sandra R Arnold
- Department of Pediatrics, University of Tennessee Health Science Center, Memphis
| | - Anna M Bramley
- Centers for Disease Control and Prevention, Emory University School of Medicine, Atlanta, Georgia
| | - Krow Ampofo
- Department of Pediatrics, University of Utah Health Sciences Center, Salt Lake City
| | - Derek J Williams
- Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Carlos G Grijalva
- Department of Health Policy, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Wesley H Self
- Department of Emergency Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Evan J Anderson
- Departments of Pediatrics and Medicine, Emory University School of Medicine, Atlanta, Georgia
| | - Richard G Wunderink
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Kathryn M Edwards
- Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Andrew T Pavia
- Department of Pediatrics, University of Utah Health Sciences Center, Salt Lake City
| | - Seema Jain
- Centers for Disease Control and Prevention, Emory University School of Medicine, Atlanta, Georgia
| | - Jonathan A McCullers
- Department of Pediatrics, University of Tennessee Health Science Center, Memphis
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Douros K, Kotzia D, Kottaridi C, Giotas A, Boutopoulou B, Bozas E, Matziou V, Priftis K, Papaevangelou V. Evidence for respiratory viruses interactions in asymptomatic preschool-aged children. Allergol Immunopathol (Madr) 2019; 47:260-264. [PMID: 30454860 PMCID: PMC7126143 DOI: 10.1016/j.aller.2018.07.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 07/22/2018] [Accepted: 07/24/2018] [Indexed: 11/16/2022]
Abstract
Aim To prospectively evaluate interferences between viruses of the upper respiratory tract in asymptomatic preschool children. Methods Nasal-pharyngeal swabs from 233 preschool aged children were prospectively collected over four consecutive time periods, during one school year. The samples were tested using a RT-PCR DNA/RNA microarray system for nine respiratory viruses. Results Respiratory syncytial virus (RSV) was a predictor of the presence of influenza virus (INFL) (OR: 9.12, CI: 1.52–54.75, p = 0.016), and similarly, INFL predicted the presence of RSV (OR: 4.01, CI: 1.14–14.16, p = 0.030). Also, rhinovirus (RV) was a predictor of adenovirus (ADV) presence (OR: 3.66, CI: 1.10–12.14, p = 0.034), and similarly, ADV predicted the presence of RV (OR: 4.05, CI: 1.02–16.05, p = 0.046). No other significant associations between viruses were observed. Conclusion Our results indicate that respiratory viruses found in carrier stage in asymptomatic children may interact with other viruses and even facilitate their settling in the upper respiratory tract. The pathophysiological role of these interactions is not yet clear.
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Olawoyin O, Kribs C. Invasion reproductive numbers for discrete-time models. Infect Dis Model 2019; 4:44-72. [PMID: 31016273 PMCID: PMC6468161 DOI: 10.1016/j.idm.2019.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 03/16/2019] [Accepted: 03/29/2019] [Indexed: 12/02/2022] Open
Abstract
Although invasion reproductive numbers (IRNs) are utilized frequently in continuous-time models with multiple interacting pathogens, they are yet to be explored in discrete-time systems. Here, we extend the concept of IRNs to discrete-time models by showing how to calculate them for a set of two-pathogen SIS models with coinfection. In our exploration, we address how sequencing events impacts the basic reproductive number (BRN) and IRN. As an illustrative example, our models are applied to rhinovirus and respiratory syncytial virus co-circulation. Results show that while the BRN is unaffected by variations in the order of events, the IRN differs. Furthermore, our models predict copersistence of multiple pathogen strains under cross-immunity, which is atypical of analogous continuous-time models. This investigation shows that sequencing events has important consequences for the IRN and can drastically alter competition dynamics.
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Price OH, Sullivan SG, Sutterby C, Druce J, Carville KS. Using routine testing data to understand circulation patterns of influenza A, respiratory syncytial virus and other respiratory viruses in Victoria, Australia. Epidemiol Infect 2019; 147:e221. [PMID: 31364539 PMCID: PMC6625191 DOI: 10.1017/s0950268819001055] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 02/18/2019] [Accepted: 03/27/2019] [Indexed: 12/29/2022] Open
Abstract
Several studies have reported evidence of interference between respiratory viruses: respiratory viruses rarely reach their epidemic peak concurrently and there appears to be a negative association between infection with one respiratory virus and co-infection with another. We used results spanning 16 years (2002-2017) of a routine diagnostic multiplex panel that tests for nine respiratory viruses to further investigate these interactions in Victoria, Australia. Time series analyses were used to plot the proportion positive for each virus. The seasonality of all viruses included was compared with respiratory syncytial virus (RSV) and influenza A virus using cross-correlations. Logistic regression was used to explore the likelihood of co-infection with one virus given infection with another. Seasonal peaks were observed each year for influenza A and RSV and less frequently for influenza B, coronavirus and parainfluenza virus. RSV circulated an average of 6 weeks before influenza A. Co-infection with another respiratory virus was less common with picornavirus, RSV or influenza A infection. Our findings provide further evidence of a temporal relationship in the circulation of respiratory viruses. A greater understanding of the interaction between respiratory viruses may enable better prediction of the timing and magnitude of respiratory virus epidemics.
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Affiliation(s)
- O. H. Price
- WHO Collaborating Centre for Reference and Research on Influenza, at the Peter Doherty Institute for Infection and Immunity, Victoria 3000, Australia
| | - S. G. Sullivan
- WHO Collaborating Centre for Reference and Research on Influenza, at the Peter Doherty Institute for Infection and Immunity, Victoria 3000, Australia
- School of Population and Global Health, University of Melbourne, Melbourne, Australia
| | - C. Sutterby
- School of Population and Global Health, University of Melbourne, Melbourne, Australia
| | - J. Druce
- Victorian Infectious Diseases Reference Laboratory, at the Peter Doherty Institute for Infection and Immunity, Victoria 3000, Australia
| | - K. S. Carville
- Victorian Infectious Diseases Reference Laboratory, at the Peter Doherty Institute for Infection and Immunity, Victoria 3000, Australia
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