RESUMEN
Although rhinoviruses play a major role in exacerbations of childhood asthma, the presence of rhinovirus (RV) RNA in plasma, referred to as viremia, has been investigated in a few studies. The aim of the study was to investigate the presence of rhinovirus viremia at the time of asthma exacerbation and to describe the molecular characteristics of rhinoviruses associated with viremia. We conducted an observational, prospective, multicenter study in eight pediatric hospitals (VIRASTHMA2). Preschool-aged recurrent wheezers (1-5 years) hospitalized for a severe exacerbation were included. Reverse-transcription polymerase chain reaction (RT-PCR) and molecular typing for RV/enteroviruses (EV) were performed on nasal swabs and plasma. Plasma specimens were available for 105 children with positive RT-PCR for RV/EV in respiratory specimens. Thirty-six (34.3%) had positive viremia. In plasma, 28 (82.4%) of the typable specimens were RV-C, five (14.7%) were EV-D68, and one was RV-A (2.9%). In all cases, the RV/EV type was identical in the plasma and respiratory specimens. In conclusion, RV/EV viremia is frequent in severe exacerbations of preschool recurrent wheezers, particularly in RV-C infections.
Asunto(s)
Asma , Infecciones por Picornaviridae , Rhinovirus , Viremia , Humanos , Viremia/virología , Preescolar , Rhinovirus/genética , Rhinovirus/aislamiento & purificación , Rhinovirus/clasificación , Asma/virología , Masculino , Femenino , Estudios Prospectivos , Infecciones por Picornaviridae/virología , Lactante , ARN Viral/genética , Reacción en Cadena de la Polimerasa de Transcriptasa Inversa , Plasma/virologíaRESUMEN
Throughout the COVID-19 pandemic, rhinovirus (RV) remained notable persistence, maintaining its presence while other seasonal respiratory viruses were largely suppressed by pandemic restrictions during national lockdowns. This research explores the epidemiological dynamics of RV infections among pediatric populations on Hainan Island, China, specifically focusing on the impact before and after the zero-COVID policy was lifted. From January 2021 to December 2023, 19 680 samples were collected from pediatric patients hospitalized with acute lower respiratory tract infections (ARTIs) at the Hainan Maternal and Child Health Hospital. The infection of RV was detected by tNGS. RV species and subtypes were identified in 32 RV-positive samples representing diverse time points by analyzing the VP4/VP2 partial regions. Among the 19 680 pediatric inpatients with ARTIs analyzed, 21.55% were found to be positive for RV infection, with notable peaks observed in April 2021 and November 2022. A gradual annual decline in RV infections was observed, alongside a seasonal pattern of higher prevalence during the colder months. The highest proportion of RV infections was observed in the 0-1-year age group. Phylogenetic analysis on 32 samples indicated a trend from RV-A to RV-C in 2022. This observation suggests potential evolving dynamics within the RV species although further studies are needed due to the limited sample size. The research emphasizes the necessity for ongoing surveillance and targeted management, particularly for populations highly susceptible to severe illnesses caused by RV infections.
Asunto(s)
COVID-19 , Variación Genética , Filogenia , Infecciones por Picornaviridae , Infecciones del Sistema Respiratorio , Rhinovirus , Humanos , Rhinovirus/genética , Rhinovirus/clasificación , Rhinovirus/aislamiento & purificación , China/epidemiología , Lactante , Preescolar , Infecciones por Picornaviridae/epidemiología , Infecciones por Picornaviridae/virología , Niño , Femenino , Masculino , COVID-19/epidemiología , COVID-19/virología , Infecciones del Sistema Respiratorio/virología , Infecciones del Sistema Respiratorio/epidemiología , Recién Nacido , Estaciones del Año , Adolescente , Prevalencia , Niño Hospitalizado/estadística & datos numéricos , SARS-CoV-2/genética , Hospitalización/estadística & datos numéricosRESUMEN
This study aimed to determine the incidence and etiological, seasonal, and genetic characteristics of respiratory viral coinfections involving severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Between October 2020 and January 2024, nasopharyngeal samples were collected from 2277 SARS-CoV-2-positive patients. Two multiplex approaches were used to detect and sequence SARS-CoV-2, influenza A/B viruses, and other seasonal respiratory viruses: multiplex real-time polymerase chain reaction (PCR) and multiplex next-generation sequencing. Coinfections of SARS-CoV-2 with other respiratory viruses were detected in 164 (7.2%) patients. The most common co-infecting virus was respiratory syncytial virus (RSV) (38 cases, 1.7%), followed by bocavirus (BoV) (1.2%) and rhinovirus (RV) (1.1%). Patients ≤ 16 years of age had the highest rate (15%) of mixed infections. Whole-genome sequencing produced 19 complete genomes of seasonal respiratory viral co-pathogens, which were subjected to phylogenetic and amino acid analyses. The detected influenza viruses were classified into the genetic groups 6B.1A.5a.2a and 6B.1A.5a.2a.1 for A(H1N1)pdm09, 3C.2a1b.2a.2a.1 and 3C.2a.2b for A(H3N2), and V1A.3a.2 for the B/Victoria lineage. The RSV-B sequences belonged to the genetic group GB5.0.5a, with HAdV-C belonging to type 1, BoV to genotype VP1, and PIV3 to lineage 1a(i). Multiple amino acid substitutions were identified, including at the antibody-binding sites. This study provides insights into respiratory viral coinfections involving SARS-CoV-2 and reinforces the importance of genetic characterization of co-pathogens in the development of therapeutic and preventive strategies.
Asunto(s)
COVID-19 , Coinfección , Filogenia , SARS-CoV-2 , Humanos , Coinfección/virología , Coinfección/epidemiología , SARS-CoV-2/genética , SARS-CoV-2/clasificación , SARS-CoV-2/aislamiento & purificación , COVID-19/virología , COVID-19/epidemiología , Persona de Mediana Edad , Adulto , Femenino , Masculino , Adolescente , Preescolar , Niño , Anciano , Adulto Joven , Lactante , Infecciones del Sistema Respiratorio/virología , Infecciones del Sistema Respiratorio/epidemiología , Rhinovirus/genética , Rhinovirus/clasificación , Rhinovirus/aislamiento & purificación , Virus de la Influenza A/genética , Virus de la Influenza A/clasificación , Virus de la Influenza A/aislamiento & purificación , Virus Sincitial Respiratorio Humano/genética , Virus Sincitial Respiratorio Humano/aislamiento & purificación , Virus Sincitial Respiratorio Humano/clasificación , Nasofaringe/virología , Secuenciación Completa del Genoma , China/epidemiología , Estaciones del Año , Anciano de 80 o más Años , Genoma Viral , Virus de la Influenza B/genética , Virus de la Influenza B/aislamiento & purificación , Virus de la Influenza B/clasificaciónRESUMEN
Allergic rhinitis (AR) is a global health challenge that particularly affects the quality of life of children. Human rhinovirus (HRV) infection usually causes common cold in the upper respiratory tract (URT) and can also affect airway allergy development, such as asthma exacerbation, but its relationship with AR is poorly understood. The study aimed to gain insight into the characteristics of HRV that is prevalent in AR children and its role in AR severity. A total of 362 children with symptomatic AR were enrolled from southwestern China during 2022-2023, and nasal lavage samples were collected for HRV molecular characterization and cytokine measurement. HRV was detected in 40% of the AR children, with peak detection in autumn. The positive rate was not correlated with whether the subjects were under allergen-specific immunotherapy (AIT). Among the detected HRVs, 42% were species A, 36% were species B, and 22% were species C, involving 21 A genotypes, 6 B genotypes, and 7 C genotypes. HRV positivity was significantly associated with symptom severity (visual analog scale [VAS] score) and elevated levels of local nasal IgE, interleukin-25 (IL-25), IL-4, and CXCL13 in AR children who did not receive antiallergic treatment. All three species of HRV strains (A1B, A21, B27, B70, and C17) had been isolated and were able to infect respiratory epithelial tissue in vitro. Complete genome sequencing showed that the antigenic epitopes of the isolated HRVs had certain variations. Our work reveals the etiological characteristics of URT-HRV in AR children and suggests a role of HRV infection in the pathogenesis of childhood AR. IMPORTANCE: Our study revealed high human rhinovirus (HRV) detection rate in children with allergic rhinitis (AR), and HRV infection (A, B, or C species) is positively associated with the symptom severity in AR children. Elevated nasal IgE, interleukin-25 (IL-25), IL-4, and CXCL13 levels suggest a potential pathogenic mechanism by which HRV infection induces nasal type 2 immune/inflammation responses and local IgE production in AR patients. In addition, etiological analysis found that the main prevalent HRV species in AR children are A and B (~80%), which is different from acute respiratory infection and asthma exacerbation, where species A and C are dominant. The data reveal the distinct species prevalence characteristics of HRV infection in AR. Finally, we isolated all three species of HRV strains from nasal cavity of AR children with varying degrees of antigenic epitope mutations and in vitro infectivity, highlighting the importance of strengthening monitoring and intervention for respiratory HRV infection in AR children.
Asunto(s)
Infecciones por Picornaviridae , Rinitis Alérgica , Rhinovirus , Humanos , Rhinovirus/genética , Rhinovirus/inmunología , Rhinovirus/aislamiento & purificación , Rhinovirus/clasificación , Niño , Masculino , Femenino , Infecciones por Picornaviridae/virología , Infecciones por Picornaviridae/inmunología , Infecciones por Picornaviridae/epidemiología , Preescolar , China/epidemiología , Rinitis Alérgica/virología , Rinitis Alérgica/inmunología , Inmunoglobulina E/inmunología , Inmunoglobulina E/sangre , Índice de Severidad de la Enfermedad , Citocinas/metabolismo , Citocinas/inmunología , Genotipo , Infecciones del Sistema Respiratorio/virología , Infecciones del Sistema Respiratorio/inmunología , Adolescente , Filogenia , Resfriado Común/virología , Resfriado Común/inmunología , Resfriado Común/epidemiologíaRESUMEN
Acute respiratory infections are a major global burden in resource-limited countries, including countries in Africa. Although COVID-19 has been well studied since the pandemic emerged in Gabon, Central Africa, less attention has been paid to other respiratory viral diseases, and very little data are available. Herein, we provide the first data on the genetic diversity and detection of 18 major respiratory viruses in Gabon during the COVID-19 pandemic. Of 582 nasopharyngeal swab specimens collected from March 2020 to July 2021, which were SARS-CoV-2 negative, 156 were positive (26%) for the following viruses: enterovirus (20.3%), human rhinovirus (HRV) (4.6%), human coronavirus OC43 (1.2%), human adenovirus (0.9%), human metapneumovirus (hMPV) (0.5%), influenza A virus (IAV) (0.3%), and human parainfluenza viruses (0.5%). To determine the genetic diversity and transmission route of the viruses, phylogenetic analyses were performed using genome sequences of the detected viruses. The IAV strain detected in this study was genetically similar to strains isolated in the USA, whereas the hMPV strain belonging to the A2b subtype formed a cluster with Kenyan strains. This study provides the first complete genomic sequences of HRV, IAV, and hMPV detected in Gabon, and provides insight into the circulation of respiratory viruses in the country.
Asunto(s)
COVID-19 , Variación Genética , Filogenia , Infecciones del Sistema Respiratorio , Humanos , Gabón/epidemiología , COVID-19/epidemiología , COVID-19/virología , Infecciones del Sistema Respiratorio/virología , Infecciones del Sistema Respiratorio/epidemiología , SARS-CoV-2/genética , SARS-CoV-2/clasificación , SARS-CoV-2/aislamiento & purificación , Masculino , Adulto , Femenino , Niño , Persona de Mediana Edad , Adolescente , Preescolar , Adulto Joven , Rhinovirus/genética , Rhinovirus/aislamiento & purificación , Rhinovirus/clasificación , Virus/genética , Virus/clasificación , Virus/aislamiento & purificación , Metapneumovirus/genética , Metapneumovirus/aislamiento & purificación , Metapneumovirus/clasificación , Genoma Viral , Nasofaringe/virología , Lactante , Anciano , Pandemias , Virus de la Influenza A/genética , Virus de la Influenza A/aislamiento & purificación , Virus de la Influenza A/clasificaciónRESUMEN
This study aims to analyze the epidemiological and pathogenic characteristics of an outbreak primarily caused by respiratory syncytial virus (RSV), human rhinovirus (HRV), and human metapneumovirus (HMPV) in a kindergarten and primary school. The outbreak was investigated by field epidemiological investigation, and the common respiratory pathogens were screened by RT-PCR detection technology. The attack rate of this outbreak was 63.95% (110/172). Main symptoms included cough (85.45%), sore throat (60.91%), and sneezing (60.00%). Multifactorial logistic regression analysis revealed that continuous handwashing and mouth and nose covering when sneezing were protective factors. All 15 collected throat swab specimens tested positive for viruses, with HMPV as the predominant pathogen (80.00%), followed by HRV (53.33%), and two cases of positive respiratory syncytial virus (13.33%). Among them, six samples showed coinfections of HMPV and HRV, and one had coinfections of HMPV and RSV, resulting in a coinfection rate of 46.67%. Genetic sequencing indicated that the HMPV genotype in this outbreak was A2c, and the HRV genotype was type A, resulting in a coinfection outbreak of HMPV, HRV, and RSV in schools and kindergartens, suggesting that multi-pathogen surveillance of respiratory tract infections should be strengthened.
Asunto(s)
Coinfección , Brotes de Enfermedades , Metapneumovirus , Epidemiología Molecular , Infecciones por Virus Sincitial Respiratorio , Infecciones del Sistema Respiratorio , Humanos , China/epidemiología , Coinfección/epidemiología , Coinfección/virología , Masculino , Preescolar , Femenino , Niño , Infecciones del Sistema Respiratorio/virología , Infecciones del Sistema Respiratorio/epidemiología , Infecciones por Virus Sincitial Respiratorio/epidemiología , Infecciones por Virus Sincitial Respiratorio/virología , Metapneumovirus/genética , Metapneumovirus/aislamiento & purificación , Genotipo , Rhinovirus/genética , Rhinovirus/aislamiento & purificación , Rhinovirus/clasificación , Filogenia , Infecciones por Paramyxoviridae/epidemiología , Infecciones por Paramyxoviridae/virología , Virus Sincitial Respiratorio Humano/genética , Virus Sincitial Respiratorio Humano/aislamiento & purificación , Instituciones AcadémicasRESUMEN
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has circulated worldwide and causes coronavirus disease 2019 (COVID-19). At the onset of the COVID-19 pandemic, infection control measures were taken, such as hand washing, mask wearing, and behavioral restrictions. However, it is not fully clear how the effects of these non-pharmaceutical interventions changed the prevalence of other pathogens associated with respiratory infections. In this study, we collected 3,508 nasopharyngeal swab samples from 3,249 patients who visited the Yamanashi Central Hospital in Japan from March 1, 2020 to February 28, 2021. We performed multiplex polymerase chain reaction (PCR) using the FilmArray Respiratory Panel and singleplex quantitative reverse transcription PCR targeting SARS-CoV-2 to detect respiratory disease-associated pathogens. At least one pathogen was detected in 246 (7.0%) of the 3,508 samples. Eleven types of pathogens were detected in the samples collected from March-May 2020, during which non-pharmaceutical interventions were not well implemented. In contrast, after non-pharmaceutical interventions were thoroughly implemented, only five types of pathogens were detected, and the majority were SARS-CoV-2, adenoviruses, or human rhinoviruses / enteroviruses. The 0-9 year age group had a higher prevalence of infection with adenoviruses and human rhinoviruses / enteroviruses compared with those 10 years and older, while those 10 years and older had a higher prevalence of infection with SARS-CoV-2 and other pathogens. These results indicated that non-pharmaceutical interventions likely reduced the diversity of circulating pathogens. Moreover, differences in the prevalence of pathogens were observed among the different age groups.
Asunto(s)
Adenovirus Humanos/genética , COVID-19/epidemiología , Enterovirus/genética , Infecciones del Sistema Respiratorio/epidemiología , Rhinovirus/genética , SARS-CoV-2/genética , Adenovirus Humanos/clasificación , Adolescente , Adulto , Anciano , Anciano de 80 o más Años , COVID-19/diagnóstico , COVID-19/prevención & control , COVID-19/virología , Niño , Preescolar , Enterovirus/clasificación , Femenino , Desinfección de las Manos/métodos , Humanos , Lactante , Recién Nacido , Japón/epidemiología , Masculino , Máscaras/provisión & distribución , Persona de Mediana Edad , Reacción en Cadena de la Polimerasa Multiplex , Nasofaringe/virología , Prevalencia , Cuarentena/organización & administración , Infecciones del Sistema Respiratorio/diagnóstico , Infecciones del Sistema Respiratorio/prevención & control , Infecciones del Sistema Respiratorio/virología , Rhinovirus/clasificación , SARS-CoV-2/patogenicidadRESUMEN
Rhinoviruses (RVs) have been reported as one of the main viral causes for severe respiratory illnesses that may require hospitalization, competing with the burden of other respiratory viruses such as influenza and RSV in terms of severity, economic cost, and resource utilization. With three species and 169 subtypes, RV presents the greatest diversity within the Enterovirus genus, and despite the efforts of the research community to identify clinically relevant subtypes to target therapeutic strategies, the role of species and subtype in the clinical outcomes of RV infection remains unclear. This review aims to collect and organize data relevant to RV illness in order to find patterns and links with species and/or subtype, with a specific focus on species and subtype diversity in clinical studies typing of respiratory samples.
Asunto(s)
Infecciones por Picornaviridae/virología , Rhinovirus/clasificación , Rhinovirus/genética , Asma/etiología , Coinfección/virología , Enterovirus , Infecciones por Enterovirus/virología , Técnicas de Genotipaje , Hospitalización , Humanos , Infecciones del Sistema Respiratorio/virología , SerotipificaciónRESUMEN
Rhinoviruses (RV) are a major cause of Severe Acute Respiratory Infection (SARI) in children, with high genotypic diversity in different regions. However, RV type diversity remains unknown in several regions of the world. In this study, the genetic variability of the frequently circulating RV types in Northern Tunisia was investigated, using phylogenetic and phylogeographic analyses with a specific focus on the most frequent RV types: RV-A101 and RV-C45. This study concerned 13 RV types frequently circulating in Northern Tunisia. They were obtained from respiratory samples collected in 271 pediatric SARI cases, between September 2015 and November 2017. A total of 37 RV VP4-VP2 sequences, selected among a total of 49 generated sequences, was compared to 359 sequences from different regions of the world. Evolutionary analysis of RV-A101 and RV-C45 showed high genetic relationship between different Tunisian strains and Malaysian strains. RV-A101 and C45 progenitor viruses' dates were estimated in 1981 and 1995, respectively. Since the early 2000s, the two types had a wide spread throughout the world. Phylogenetic analyses of other frequently circulating strains showed significant homology of Tunisian strains from the same epidemic period, in contrast with earlier strains. The genetic relatedness of RV-A101 and RV-C45 might result from an introduction of viruses from different clades followed by local dissemination rather than a local persistence of an endemic clades along seasons. International traffic may play a key role in the spread of RV-A101, RV-C45, and other RVs.
Asunto(s)
Rhinovirus/clasificación , Rhinovirus/genética , Síndrome Respiratorio Agudo Grave/epidemiología , Evolución Biológica , Proteínas de la Cápside/genética , Niño , Preescolar , Epidemias , Evolución Molecular , Femenino , Variación Genética/genética , Genotipo , Humanos , Lactante , Filogenia , Filogeografía/métodos , Neumonía , Rhinovirus/patogenicidad , Síndrome Respiratorio Agudo Grave/virología , Túnez/epidemiologíaRESUMEN
Rhinoviruses (RVs) constitute a substantial public health burden. To evaluate their abundance and genetic diversity in adult patients, RV RNA in respiratory samples was assessed using real-time RT-PCR and the partial nucleic acid sequencing of viral genomes. Additionally, clinical data were retrieved from patient charts to determine the clinical significance of adult RV infections. In total, the respiratory specimens of 284 adult patients (18-90 years), collected from 2013 to 2017, were analyzed. Infections occurred throughout the entire year, with peaks occurring in fall and winter, and showed a remarkably high intra- and interseasonal diversity of RV genotypes. RV species were detected in the following ratios: 60.9% RV-A 173, 12.7% RV-B, and 26.4% RV-C. No correlations between RV species and underlying comorbidities such as asthma (p = 0.167), COPD (p = 0.312) or immunosuppression (p = 0.824) were found. However, 21.1% of the patients had co-infections with other pathogens, which were associated with a longer hospital stay (p = 0.024), LRTI (p < 0.001), and pneumonia (p = 0.01). Taken together, this study shows a pronounced genetic diversity of RV in adults and underlines the important role of co-infections. No correlation of specific RV species with a particular clinical presentation could be deduced.
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Epidemiología Molecular , Infecciones por Picornaviridae/epidemiología , Infecciones por Picornaviridae/virología , Rhinovirus/genética , Centros de Atención Terciaria , Adolescente , Adulto , Anciano , Anciano de 80 o más Años , Coinfección/epidemiología , Coinfección/virología , Femenino , Genoma Viral , Genotipo , Alemania/epidemiología , Humanos , Masculino , Persona de Mediana Edad , Filogenia , Infecciones por Picornaviridae/diagnóstico , Salud Pública , Reacción en Cadena en Tiempo Real de la Polimerasa , Sistema Respiratorio/virología , Infecciones del Sistema Respiratorio/virología , Rhinovirus/clasificación , Rhinovirus/aislamiento & purificación , Estaciones del Año , Adulto JovenRESUMEN
INTRODUCTION: Rhinoviruses (HRV) are among the leading causes of Severe Acute Respiratory Infection (SARI). Their burden and genetic diversity vary from one region to another and little is known in Northern African regions. This study describes epidemiological patterns and genotypic diversity of HRV in SARI cases during a two and half year's study, in Northern Tunisia. METHODOLOGY: A total of 271 SARI cases, admitted into the Pediatric Intensive Care Unit of Bechir Hamza Children's Hospital in Tunis, were collected between September 2015 and December 2017. The investigation concerned 104 samples positive for HRV and/or HEV (Human Enterovirus) obtained among these cases. Specific HRV and HEV detections were assessed by real-time PCRs. The HRV molecular typing was based on the VP4-VP2 genomic region analyses. RESULTS: Among the viral SARI cases, 33.5% and 12.3% were positive for HRV and HEV respectively. Molecular investigations showed high prevalence of HRV-A (63.3%) followed by HRV-C (30.6%) and HRV-B (6.1%) and high genotypic diversity with 27 types. HRV cases were mostly detected in toddlers younger than 6 months. A total of 16 cases (28%) were found with bacterial and/or viral co-infection. HRV-C infection and HRV-A with bacterial co-infection were associated with complicated infection. Some of the detected types showed a continuous circulation or turnover during an extended period. HRV-A101 and HRV-C45 were the most frequently detected types. CONCLUSIONS: This study revealed, for the first time, the high HRV diversity in Tunisia, a North-African region. Specific phylogenetic investigations may help to evaluate their diversity and to trace their spread and epidemiological origin.
Asunto(s)
Infecciones por Picornaviridae/epidemiología , Rhinovirus/aislamiento & purificación , Síndrome Respiratorio Agudo Grave/epidemiología , Preescolar , Femenino , Humanos , Incidencia , Lactante , Recién Nacido , Masculino , Tipificación Molecular , Infecciones por Picornaviridae/virología , Rhinovirus/clasificación , Rhinovirus/genética , Síndrome Respiratorio Agudo Grave/virología , Túnez/epidemiologíaRESUMEN
Viral co-infections occur in COVID-19 patients, potentially impacting disease progression and severity. However, there is currently no dedicated method to identify viral co-infections in patient RNA-seq data. We developed PACIFIC, a deep-learning algorithm that accurately detects SARS-CoV-2 and other common RNA respiratory viruses from RNA-seq data. Using in silico data, PACIFIC recovers the presence and relative concentrations of viruses with > 99% precision and recall. PACIFIC accurately detects SARS-CoV-2 and other viral infections in 63 independent in vitro cell culture and patient datasets. PACIFIC is an end-to-end tool that enables the systematic monitoring of viral infections in the current global pandemic.
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COVID-19/diagnóstico , Coinfección/diagnóstico , Aprendizaje Profundo , Infecciones por Virus ARN/diagnóstico , Virus ARN/aislamiento & purificación , SARS-CoV-2/aislamiento & purificación , Prueba de COVID-19 , Coinfección/virología , Coronaviridae/aislamiento & purificación , Humanos , Metapneumovirus/clasificación , Metapneumovirus/aislamiento & purificación , Redes Neurales de la Computación , Orthomyxoviridae/clasificación , Orthomyxoviridae/aislamiento & purificación , Infecciones por Virus ARN/virología , Virus ARN/clasificación , RNA-Seq , Rhinovirus/clasificación , Rhinovirus/aislamiento & purificación , SARS-CoV-2/clasificación , Sensibilidad y EspecificidadRESUMEN
INTRODUCTION: Human rhinovirus (HRV) is one of the most common human viral pathogens related to infections of the upper and lower respiratory tract, which can result in bronchiolitis and pneumonia. However, the relevance of HRV in human health was under-estimated for long time due to the absence of molecular targets for influenza and influenza-like syndrome surveillance in Brasília, Brazil. OBJECTIVES: The main objective of this study was analyze the clinical characteristics and outcomes of HRV infections in comparison with patients without HRV and other common respiratory viruses. MATERIALS AND METHODS: For this purpose, new specific primer sets were designed based on the high throughput sequencing analysis in previous study. These primers were used for HRV detection by RT-qPCR and Sanger sequencing of amplified cDNA of 5' genomic region. The phylogenetic tree with representative HRV isolates was constructed using the Mega X software. Statistical analysis considering the patient profiles were performed using IBM SPSS program with non-parametric tests. RESULTS: The most prevalent virus in negative samples was rhinovirus (n = 40), including three rhinovirus species (rhinovirus A, B, and C). The odds ratio associated with HRV infection was 2.160 for patients younger than 2 years and 4.367 for people living in rural areas. The multiple analysis showed lower chance of patients with HRV presenting respiratory distress. CONCLUSION: In this study, it was reported the predominance of rhinoviruses in cases of respiratory illness for negative patients for the influenza and influenza-like syndrome surveillance, being rhinorrhea, the most significant symptom associated with the disease.
Asunto(s)
Infecciones por Picornaviridae/epidemiología , Infecciones por Picornaviridae/virología , Infecciones del Sistema Respiratorio/epidemiología , Infecciones del Sistema Respiratorio/virología , Rhinovirus/genética , Brasil/epidemiología , Niño , Preescolar , Femenino , Humanos , Masculino , Persona de Mediana Edad , Filogenia , Infecciones por Picornaviridae/diagnóstico , Rhinovirus/clasificación , Rhinovirus/patogenicidad , Virus/clasificación , Virus/genética , Virus/aislamiento & purificaciónRESUMEN
BACKGROUND: In severe bronchiolitis, it is unclear if delayed clearance or sequential infection of respiratory syncytial virus (RSV) or rhinovirus (RV) is associated with recurrent wheezing. METHODS: In a 17-center severe bronchiolitis cohort, we tested nasopharyngeal aspirates (NPA) upon hospitalization and 3 weeks later (clearance swab) for respiratory viruses using PCR. The same RSV subtype or RV genotype in NPA and clearance swab defined delayed clearance (DC); a new RSV subtype or RV genotype at clearance defined sequential infection (SI). Recurrent wheezing by age 3 years was defined per national asthma guidelines. RESULTS: Among 673 infants, RSV DC and RV DC were not associated with recurrent wheezing, and RSV SI was rare. The 128 infants with RV SI (19%) had nonsignificantly higher risk of recurrent wheezing (hazard ratio [HR], 1.31; 95% confidence interval [CI], .95-1.80; P = .10) versus infants without RV SI. Among infants with RV at hospitalization, those with RV SI had a higher risk of recurrent wheezing compared to children without RV SI (HR, 2.49; 95% CI, 1.22-5.06; P = .01). CONCLUSIONS: Among infants with severe bronchiolitis, those with RV at hospitalization followed by a new RV infection had the highest risk of recurrent wheezing.
Asunto(s)
Bronquiolitis/epidemiología , Coinfección/epidemiología , Infección Hospitalaria/epidemiología , Hospitalización , Infecciones por Picornaviridae/epidemiología , Ruidos Respiratorios , Infecciones por Virus Sincitial Respiratorio/epidemiología , Bronquiolitis/diagnóstico , Bronquiolitis/virología , Coinfección/virología , Infección Hospitalaria/virología , Humanos , Incidencia , Tipificación Molecular , Infecciones por Picornaviridae/virología , Modelos de Riesgos Proporcionales , Recurrencia , Infecciones por Virus Sincitial Respiratorio/virología , Virus Sincitial Respiratorio Humano/clasificación , Virus Sincitial Respiratorio Humano/genética , Rhinovirus/clasificación , Rhinovirus/genética , Carga ViralRESUMEN
BACKGROUND: Young children with rhinovirus (RV) infection-particularly bronchiolitis-are at high risk for developing childhood asthma. Emerging evidence suggests clinical heterogeneity within RV bronchiolitis. However, little is known about these biologically distinct subgroups (endotypes) and their relations with asthma risk. OBJECTIVE: We aimed to identify RV bronchiolitis endotypes and examine their longitudinal relations with asthma risk. METHODS: As part of a multicenter prospective cohort study of infants (age <12 months) hospitalized for bronchiolitis, we integrated clinical, RV species (RV-A, RV-B, and RV-C), nasopharyngeal microbiome (16S rRNA gene sequencing), cytokine, and metabolome (liquid chromatography tandem mass spectrometry) data collected at hospitalization. We then applied network and clustering approaches to identify bronchiolitis endotypes. We also examined their longitudinal association with risks of developing recurrent wheeze by age 3 years and asthma by age 5 years. RESULTS: Of 122 infants hospitalized for RV bronchiolitis (median age, 4 months), we identified 4 distinct endotypes-mainly characterized by RV species, microbiome, and type 2 cytokine (T2) response: endotype A, virusRV-CmicrobiomemixedT2low; endotype B, virusRV-AmicrobiomeHaemophilusT2low; endotype C, virusRSV/RVmicrobiomeStreptococcusT2low; and endotype D, virusRV-CmicrobiomeMoraxellaT2high. Compared with endotype A infants, endotype D infants had a significantly higher rate of recurrent wheeze (33% vs 64%; hazard ratio, 2.23; 95% CI, 1.00-4.96; P = .049) and a higher risk for developing asthma (28% vs 59%; odds ratio, 3.74: 95% CI, 1.21-12.6; P = .03). CONCLUSIONS: Integrated-omics analysis identified biologically meaningful RV bronchiolitis endotypes in infants, such as one characterized by RV-C infection, Moraxella-dominant microbiota, and high T2 cytokine response, at higher risk for developing recurrent wheeze and asthma. This study should facilitate further research toward validating our inferences.
Asunto(s)
Asma/etiología , Asma/metabolismo , Bronquiolitis/complicaciones , Bronquiolitis/virología , Resfriado Común/complicaciones , Resfriado Común/virología , Rhinovirus , Factores de Edad , Susceptibilidad a Enfermedades , Humanos , Lactante , Recién Nacido , Metaboloma , Proteoma , Rhinovirus/clasificación , Rhinovirus/genética , Rhinovirus/inmunología , Medición de Riesgo , TranscriptomaAsunto(s)
COVID-19/epidemiología , COVID-19/prevención & control , Resfriado Común/epidemiología , Gripe Humana/epidemiología , Gripe Humana/prevención & control , Distanciamiento Físico , Estaciones del Año , Adenoviridae/aislamiento & purificación , Anticuerpos Neutralizantes/inmunología , Linfocitos B/inmunología , COVID-19/transmisión , COVID-19/virología , Coinfección/inmunología , Coinfección/virología , Resfriado Común/prevención & control , Resfriado Común/transmisión , Resfriado Común/virología , Desinfección de las Manos , Humanos , Gripe Humana/transmisión , Gripe Humana/virología , Máscaras/estadística & datos numéricos , Orthomyxoviridae/clasificación , Orthomyxoviridae/aislamiento & purificación , Rhinovirus/clasificación , Rhinovirus/aislamiento & purificación , SARS-CoV-2/inmunología , Linfocitos T/inmunología , Viaje/estadística & datos numéricos , IncertidumbreRESUMEN
Human rhinovirus (hRV) is a predominant respiratory viral pathogen. The determinants that lead to adverse clinical outcomes in hospitalized patients are unclear. Our objective was to analyze the epidemiological and clinical characteristics of hRV infections in a hospitalized population and to compare non-severe and severe infections. The study was based on data from all patients with a respiratory episode admitted to Hospital from October 2015 to September 2016. During the study period, out of 2465 respiratory episodes, 434 were detected positive for hRV. Most of the coinfections involved the respiratory syncytial virus (RSV) and very few influenza viruses. A possible interference between rhinovirus and influenza virus is suggested. Airway involvement was present in a large part of hRV infections with 28.4 % (nâ¯=â¯48/169) of bronchiolitis and 3.6 % (nâ¯=â¯6/169) of bronchitis. One third of patients had at least one of the following severity criteria: need for oxygen therapy, hospitalization ≥ 5 days, and admission to the ICU. On multivariate analysis, a respiratory co-infection with RSV and the presence of a chronic respiratory disease (including a history of asthma) were shown to be independent risk factors for the onset of a severe infection in patients ≤ 2 years old. In a case control study based on 70 patients, hRV-A was the predominant lineage, followed closely by hRV-C. High viral load or viral genotypes were not associated with severe infection.
Asunto(s)
Coinfección/virología , Hospitalización/estadística & datos numéricos , Infecciones por Picornaviridae/epidemiología , Infecciones por Virus Sincitial Respiratorio/epidemiología , Rhinovirus/genética , Índice de Severidad de la Enfermedad , Adolescente , Adulto , Anciano , Estudios de Casos y Controles , Niño , Preescolar , Coinfección/epidemiología , Comorbilidad , Femenino , Genotipo , Humanos , Lactante , Masculino , Persona de Mediana Edad , Virus Sincitial Respiratorio Humano/genética , Rhinovirus/clasificación , Rhinovirus/patogenicidad , Factores de Riesgo , Carga Viral , Adulto JovenRESUMEN
Enteroviruses (EVs) and rhinoviruses (RVs) are significant pathogens of humans and are the subject of intensive clinical and epidemiological research and public health measures, notably in the eradication of poliovirus and in the investigation and control of emerging pathogenic EV types worldwide. EVs and RVs are highly diverse in their antigenic properties, tissue tropism, disease associations and evolutionary relationships, but the latter often conflict with previously developed biologically defined terms, such as "coxsackieviruses", "polioviruses" and "echoviruses", which were used before their genetic interrelationships were understood. This has created widespread formatting problems and inconsistencies in the nomenclature for EV and RV types and species in the literature and public databases. As members of the International Committee for Taxonomy of Viruses (ICTV) Picornaviridae Study Group, we describe the correct use of taxon names for these viruses and have produced a series of recommendations for the nomenclature of EV and RV types and their abbreviations. We believe their adoption will promote greater clarity and consistency in the terminology used in the scientific and medical literature. The recommendations will additionally provide a useful reference guide for journals, other publications and public databases seeking to use standardised terms for the growing multitude of enteroviruses and rhinoviruses described worldwide.
Asunto(s)
Enterovirus/clasificación , Rhinovirus/clasificación , Terminología como Asunto , HumanosRESUMEN
BACKGROUND: Rhinovirus is the most common virus causing respiratory tract illnesses in children. Rhinoviruses are classified into species A, B and C. We examined the associations between different rhinovirus species and respiratory illness severity. METHODS: This is a retrospective observational cohort study on confirmed rhinovirus infections in 134 children 3-23 months of age, who were enrolled in 2 prospective studies on bronchiolitis and acute otitis media, respectively, conducted simultaneously in Turku University Hospital, Turku, Finland, between September 2007 and December 2008. RESULTS: Rhinovirus C is the most prevalent species in our study, and it was associated with severe wheezing and febrile illness. We also noted that history of atopic eczema was associated with wheezing. CONCLUSIONS: Our understanding of rhinovirus C as the most pathogenic rhinovirus species was fortified. Existing research supports the idea that atopic characteristics are associated with the severity of the rhinovirus C-induced illness.
Asunto(s)
Enterovirus/patogenicidad , Fiebre/virología , Infecciones por Picornaviridae/complicaciones , Ruidos Respiratorios/etiología , Infecciones del Sistema Respiratorio/complicaciones , Preescolar , Femenino , Finlandia , Humanos , Lactante , Masculino , Estudios Prospectivos , Ruidos Respiratorios/fisiopatología , Infecciones del Sistema Respiratorio/virología , Estudios Retrospectivos , Rhinovirus/clasificación , Rhinovirus/patogenicidadRESUMEN
BACKGROUND: Respiratory syncytial virus (RSV)- and rhinovirus (RV)-induced bronchiolitis are associated with an increased risk of asthma, but more detailed information is needed on virus types. OBJECTIVE: To study whether RSV or RV types are differentially associated with the future use of asthma control medication. METHODS: Over 2 consecutive winter seasons (2008-2010), we enrolled 408 children hospitalized for bronchiolitis at age less than 24 months into a prospective, 3-center, 4-year follow-up study in Finland. Virus detection was performed by real-time reverse transcription PCR from nasal wash samples. Four years later, we examined current use of asthma control medication. RESULTS: A total of 349 (86%) children completed the 4-year follow-up. At study entry, the median age was 7.5 months, and 42% had RSV, 29% RV, 2% both RSV and RV, and 27% non-RSV/-RV etiology. The children with RV-A (adjusted hazard ratio, 2.3; P = .01), RV-C (adjusted hazard ratio, 3.5; P < .001), and non-RSV/-RV (adjusted hazard ratio, 2.0; P = .004) bronchiolitis started the asthma control medication earlier than did children with RSV bronchiolitis. Four years later, 27% of patients used asthma control medication; both RV-A (adjusted odds ratio, 3.0; P = .03) and RV-C (adjusted odds ratio, 3.7; P < .001) etiology were associated with the current use of asthma medication. The highest risk was found among patients with RV-C, atopic dermatitis, and fever (adjusted odds ratio, 5.0; P = .03). CONCLUSIONS: Severe bronchiolitis caused by RV-A and RV-C was associated with earlier initiation and prolonged use of asthma control medication. The risk was especially high when bronchiolitis was associated with RV-C, atopic dermatitis, and fever.