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Makhsous N, Goya S, Avendaño CC, Rupp J, Kuypers J, Jerome KR, Boeckh M, Waghmare A, Greninger AL. Within-Host Rhinovirus Evolution in Upper and Lower Respiratory Tract Highlights Capsid Variability and Mutation-Independent Compartmentalization. J Infect Dis 2024; 229:403-412. [PMID: 37486790 PMCID: PMC10873175 DOI: 10.1093/infdis/jiad284] [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: 05/02/2023] [Revised: 07/13/2023] [Accepted: 07/17/2023] [Indexed: 07/26/2023] Open
Abstract
BACKGROUND Rhinovirus (RV) infections can progress from the upper (URT) to lower (LRT) respiratory tract in immunocompromised individuals, causing high rates of fatal pneumonia. Little is known about how RV evolves within hosts during infection. METHODS We sequenced RV complete genomes from 12 hematopoietic cell transplant patients with infection for up to 190 days from both URT (nasal wash, NW) and LRT (bronchoalveolar lavage, BAL). Metagenomic and amplicon next-generation sequencing were used to track the emergence and evolution of intrahost single nucleotide variants (iSNVs). RESULTS Identical RV intrahost populations in matched NW and BAL specimens indicated no genetic adaptation is required for RV to progress from URT to LRT. Coding iSNVs were 2.3-fold more prevalent in capsid over nonstructural genes. iSNVs modeled were significantly more likely to be found in capsid surface residues, but were not preferentially located in known RV-neutralizing antibody epitopes. Newly emergent, genotype-matched iSNV haplotypes from immunocompromised individuals in 2008-2010 could be detected in Seattle-area community RV sequences in 2020-2021. CONCLUSIONS RV infections in immunocompromised hosts can progress from URT to LRT with no specific evolutionary requirement. Capsid proteins carry the highest variability and emergent mutations can be detected in other, including future, RV sequences.
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Affiliation(s)
- Negar Makhsous
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, USA
| | - Stephanie Goya
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, USA
| | - Carlos C Avendaño
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, USA
| | - Jason Rupp
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, USA
| | - Jane Kuypers
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, USA
| | - Keith R Jerome
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, USA
| | - Michael Boeckh
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, USA
- Department of Medicine, University of Washington, Seattle, USA
| | - Alpana Waghmare
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, USA
- Department of Pediatrics, University of Washington, Seattle, USA
| | - Alexander L Greninger
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, USA
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Berginc N, Sočan M, Prosenc Trilar K, Petrovec M. Seasonality and Genotype Diversity of Human Rhinoviruses during an Eight-Year Period in Slovenia. Microorganisms 2024; 12:341. [PMID: 38399745 PMCID: PMC10893136 DOI: 10.3390/microorganisms12020341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 01/31/2024] [Accepted: 02/02/2024] [Indexed: 02/25/2024] Open
Abstract
Due to the high socioeconomic burden of rhinoviruses, the development of prevention and treatment strategies is of high importance. Understanding the epidemiological and clinical features of rhinoviruses is essential in order to address these issues. Our study aimed to define the seasonality and molecular epidemiology of rhinoviruses in Slovenia. Over a period of eight years, a total of 20,425 patients from sentinel primary healthcare settings and sentinel hospitals were examined for a panel of respiratory viruses in the national programme for the surveillance of influenza-like illnesses and acute respiratory infections. The patients were from all age groups and had respiratory infections of various severity. Infection with a rhinovirus was confirmed using an RT-rPCR in 1834 patients, and 1480 rhinoviruses were genotyped. The molecular analysis was linked to demographical and meteorological data. We confirmed the year-round circulation of rhinoviruses with clear seasonal cycles, resulting in two seasonal waves with peaks in spring and autumn. High levels of genotype variability and co-circulation were confirmed between and within seasons and were analysed in terms of patient age, the patient source reflecting disease severity, and meteorological factors. Our study provides missing scientific information on the genotype diversity of rhinoviruses in Slovenia. As most previous investigations focused on exclusive segments of the population, such as children or hospitalised patients, and for shorter study periods, our study, with its design, size and length, contributes complementary aspects and new evidence-based knowledge to the regional and global understanding of rhinovirus seasonality and molecular epidemiology.
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Affiliation(s)
- Nataša Berginc
- Department of Public Health Microbiology, National Laboratory of Health, Environment and Food, 1000 Ljubljana, Slovenia;
| | - Maja Sočan
- Centre for Infectious Diseases, National Institute of Public Health, 1000 Ljubljana, Slovenia
| | - Katarina Prosenc Trilar
- Department of Public Health Microbiology, National Laboratory of Health, Environment and Food, 1000 Ljubljana, Slovenia;
| | - Miroslav Petrovec
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
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Kocoglu Barlas U, Akcay N, Menentoglu ME, Sevketoglu E, Duyu M, Telhan L, Kangin M, Tugrul HC, Erdogan S, Durak C, Guney Sahin E, Umur O, Sik SG, Citak A, Yaman A. Assessment of the Clinical Course of Human Rhinovirus/Enterovirus Infections in Pediatric Intensive Care. Pediatr Infect Dis J 2023; 42:e454-e460. [PMID: 37820286 DOI: 10.1097/inf.0000000000004127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
BACKGROUND This study aims to evaluate the clinical course of human rhinovirus/enterovirus (HRV/EV) infections in the pediatric intensive care unit. METHODS The study was conducted as a multicenter, prospective observational study from September 2022 to December 2022. Cases with positive polymerase chain reaction testing for HRV/EV of nasopharyngeal swab samples within the first 24 hours of pediatric intensive care unit admission were recorded. There were 2 groups: 1-24 months and >24 months. RESULTS A total of 75 cases (39 male) were included in the study. The median age for all cases was 21 months. The highest polymerase chain reaction positivity rates were observed in October (37.33%). Among the cases, 32 (42.67%) presented with bronchopneumonia/pneumonia, 24 (32%) presented with acute bronchiolitis/bronchitis and 7 (9.33%) presented with sepsis/septic shock. The frequency of pediatric acute respiratory distress syndrome was found to be 6.67%. In the age group of 1-24 months, mean lymphocyte and liver enzyme levels were higher, while in the age group of >24 months, mean hemoglobin and mean kidney function test levels were higher ( P ≤ 0.05). Continuous oxygen therapy was provided to 65.3% of the cases, noninvasive ventilation to 33.3%, high-flow nasal cannula-oxygen therapy to 32% and invasive mechanical ventilation to 16%. CONCLUSIONS HRV/EV infections primarily affect the respiratory system and generally exhibit a clinical course with low mortality rates (1, 1.3%). In cases with underlying chronic diseases, more severe clinical conditions such as pediatric acute respiratory distress syndrome and septic shock may occur.
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Affiliation(s)
- Ulkem Kocoglu Barlas
- From the Pediatric Intensive Care Unit, Department of Pediatrics, Istanbul Medeniyet University, Goztepe Prof Dr Süleyman Yalcin City Hospital, Istanbul, Turkey
| | - Nihal Akcay
- Pediatric Intensive Care Unit, Department of Pediatrics, University of Health Sciences Turkey, Kanuni Sultan Suleyman Training and Research Hospital, Istanbul, Turkey
| | - Mehmet Emin Menentoglu
- Pediatric Intensive Care Unit, Department of Pediatrics, University of Health Sciences Turkey, Bakirkoy Dr Sadi Konuk Training and Research Hospital, Istanbul, Turkey
| | - Esra Sevketoglu
- Pediatric Intensive Care Unit, Department of Pediatrics, University of Health Sciences Turkey, Bakirkoy Dr Sadi Konuk Training and Research Hospital, Istanbul, Turkey
| | - Muhterem Duyu
- From the Pediatric Intensive Care Unit, Department of Pediatrics, Istanbul Medeniyet University, Goztepe Prof Dr Süleyman Yalcin City Hospital, Istanbul, Turkey
| | - Leyla Telhan
- Pediatric Intensive Care Unit, Department of Pediatrics, Istanbul Medipol University, Bagcilar Mega Hospital, Istanbul, Turkey
| | - Murat Kangin
- Pediatric Intensive Care Unit, Department of Pediatrics, Istanbul Medipol University, Bagcilar Mega Hospital, Istanbul, Turkey
| | - Hazal Ceren Tugrul
- Pediatric Intensive Care Unit, Department of Pediatrics, University of Health Sciences Turkey, Umraniye Training and Research Hospital, Istanbul, Turkey
| | - Seher Erdogan
- Pediatric Intensive Care Unit, Department of Pediatrics, University of Health Sciences Turkey, Umraniye Training and Research Hospital, Istanbul, Turkey
| | - Cansu Durak
- Pediatric Intensive Care Unit, Department of Pediatrics, University of Health Sciences Turkey, Sancaktepe Sehit Prof Dr Ilhan Varank Training and Research Hospital, Istanbul, Turkey
| | - Ebru Guney Sahin
- Pediatric Intensive Care Unit, Department of Pediatrics, University of Health Sciences Turkey, Sancaktepe Sehit Prof Dr Ilhan Varank Training and Research Hospital, Istanbul, Turkey
| | - Ozge Umur
- Pediatric Intensive Care Unit, Department of Pediatrics, Acibadem Mehmet Ali Aydinlar University, Atakent Hospital, Istanbul, Turkey
| | - Sare Guntulu Sik
- Pediatric Intensive Care Unit, Department of Pediatrics, Acibadem Mehmet Ali Aydinlar University, Atakent Hospital, Istanbul, Turkey
| | - Agop Citak
- Pediatric Intensive Care Unit, Department of Pediatrics, Acibadem Mehmet Ali Aydinlar University, Atakent Hospital, Istanbul, Turkey
| | - Ayhan Yaman
- Pediatric Intensive Care Unit, Department of Pediatrics, Istinye University, Bahcesehir Liv Hospital, Istanbul, Turkey
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Posada MJG, Dajil HJC, Díaz APN, Castillo Vidal JDD, Barreto DDJS, Sanchez MC, Coll HS, Mattar S. Not all respiratory infections were SARS-CoV-2 during the pandemic, analysis in a clinic on the Colombian Caribbean coast. J Infect Public Health 2023; 16:1403-1409. [PMID: 37480671 PMCID: PMC10270728 DOI: 10.1016/j.jiph.2023.06.008] [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: 02/15/2023] [Revised: 05/30/2023] [Accepted: 06/08/2023] [Indexed: 07/24/2023] Open
Abstract
INTRODUCTION Acute Respiratory Infections (ARIs) are considered one of the leading causes of morbidity and mortality worldwide. Children under five and older adults are most likely to die from this cause. OBJECTIVE To describe the behavior of infection by respiratory viruses other than SARS-CoV-2 during the pandemic in a clinic in the Colombian Caribbean. METHODS This descriptive and retrospective study evaluates the characteristics, associated comorbidities, and requirements of hospitalization or Intensive Care Unit in patients diagnosed with respiratory viral infections treated at IMAT Oncomedica clinic from July 2020 to August 2022. RESULTS This study evaluated 351 patients with respiratory symptoms, observing an exponential increase in cases of respiratory infection as of April 2022, with a high proportion of syncytial virus infections mainly in children under 18 years of age (22.1%) and Human Rhinovirus/Enterovirus in patients with solid tumors and hematological disorders (48.8%), the latter was associated with a higher rate of hospitalization and ICU requirement in the individuals evaluated. CONCLUSIONS Respiratory viruses other than SARS-CoV-2, such as Rhino/Enterovirus, RSV, and adenovirus, are circulating in the population at a clinic on the Colombian Caribbean coast. The findings should motivate public health authorities to conduct more thorough surveillance in the rest of the state.
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Affiliation(s)
| | | | | | | | | | | | - Hector Serrano Coll
- Tropic Biological Research Institute, Universidad de Córdoba, Montería, Colombia
| | - Salim Mattar
- Colombian Medicine Tropical Institute-CES University, Medellín, Colombia.
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Makhsous N, Goya S, Avendaño C, Rupp J, Kuypers J, Jerome KR, Boeckh M, Waghmare A, Greninger AL. Within-host rhinovirus evolution in upper and lower respiratory tract highlights capsid variability and mutation-independent compartmentalization. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.11.540440. [PMID: 37214809 PMCID: PMC10197658 DOI: 10.1101/2023.05.11.540440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Background Human rhinovirus (HRV) infections can progress from the upper (URT) to lower (LRT) respiratory tract in immunocompromised individuals, causing high rates of fatal pneumonia. Little is known about how HRV evolves within hosts during infection. Methods We sequenced HRV complete genomes from 12 hematopoietic cell transplant patients with prolonged infection for up to 190 days from both URT (nasal wash, NW) and LRT (bronchoalveolar lavage, BAL) specimens. Metagenomic (mNGS) and amplicon-based NGS were used to study the emergence and evolution of intra-host single nucleotide variants (iSNVs). Results Identical HRV intra-host populations in matched NW and BAL specimens indicated no genetic adaptation is required for HRV to progress from URT to LRT. Microbial composition between matched NW and BAL confirmed no cross-contamination during sampling procedure. Coding iSNVs were 2.3-fold more prevalent in capsid over non-structural genes, adjusted for length. iSNVs modeled onto HRV capsid structures were significantly more likely to be found in surface residues, but were not preferentially located in known HRV neutralizing antibody epitopes. Newly emergent, serotype-matched iSNV haplotypes from immunocompromised individuals from 2008-2010 could be detected in Seattle-area community HRV sequences from 2020-2021. Conclusion HRV infections in immunocompromised hosts can progress from URT to LRT with no specific evolutionary requirement. Capsid proteins carry the highest variability and emergent mutations can be detected in other, including future, HRV sequences.
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Affiliation(s)
- Negar Makhsous
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, 98102, USA
| | - Stephanie Goya
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, 98102, USA
| | - Carlos Avendaño
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, 98102, USA
| | - Jason Rupp
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, 98102, USA
| | - Jane Kuypers
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, 98102, USA
| | - Keith R. Jerome
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, 98102, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, 98109, USA
| | - Michael Boeckh
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, 98109, USA
- Department of Medicine, University of Washington, Seattle, 98102, USA
| | - Alpana Waghmare
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, 98109, USA
- Department of Pediatrics, University of Washington, Seattle, 98105, USA
| | - Alexander L Greninger
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, 98102, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, 98109, USA
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Ljubin-Sternak S, Meštrović T. Rhinovirus—A True Respiratory Threat or a Common Inconvenience of Childhood? Viruses 2023; 15:v15040825. [PMID: 37112805 PMCID: PMC10144685 DOI: 10.3390/v15040825] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/22/2023] [Accepted: 03/22/2023] [Indexed: 03/29/2023] Open
Abstract
A decade-long neglect of rhinovirus as an important agent of disease in humans was primarily due to the fact that they were seen as less virulent and capable of causing only mild respiratory infections such as common cold. However, with an advent of molecular diagnostic methods, an increasing number of reports placed them among the pathogens found in the lower respiratory tract and recognized them as important risk factors for asthma-related pathology in childhood. As the spread of rhinovirus was not severely affected by the implementation of social distancing and other measures during the coronavirus disease 2019 (COVID-19) pandemic, its putative pathogenic role has become even more evident in recent years. By concentrating on children as the most vulnerable group, in this narrative review we first present classification and main traits of rhinovirus, followed by epidemiology and clinical presentation, risk factors for severe forms of the disease, long-term complications and the pathogenesis of asthma, as well as a snapshot of treatment trials and studies. Recent evidence suggests that the rhinovirus is a significant contributor to respiratory illness in both high-risk and low-risk populations of children.
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Piralla A, Pariani E. Editorial for the Special Issue "Epidemiology of Enterovirus Disease". Microorganisms 2022; 10:microorganisms10061221. [PMID: 35744739 PMCID: PMC9228421 DOI: 10.3390/microorganisms10061221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 06/11/2022] [Indexed: 11/16/2022] Open
Abstract
Enteroviruses (Enterovirus genus, Picornaviridae family) are distributed worldwide and are among the most common causes of human disease globally [...].
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Affiliation(s)
- Antonio Piralla
- Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
- Correspondence: ; Tel.: +39-038-250-2420
| | - Elena Pariani
- Department of Biomedical Sciences for Health, University of Milan, 20133 Milano, Italy;
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