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Journal of Clinical Microbiology Mar 2024Respiratory syncytial virus (RSV) is a leading cause of acute lower respiratory tract infections causing significant morbidity and mortality among children and the...
UNLABELLED
Respiratory syncytial virus (RSV) is a leading cause of acute lower respiratory tract infections causing significant morbidity and mortality among children and the elderly; two RSV vaccines and a monoclonal antibody have recently been approved. Thus, there is an increasing need for a detailed and continuous genomic surveillance of RSV circulating in resource-rich and resource-limited settings worldwide. However, robust, cost-effective methods for whole genome sequencing of RSV from clinical samples that are amenable to high-throughput are still scarce. We developed Next-RSV-SEQ, an experimental and computational pipeline to generate whole genome sequences of historic and current RSV genotypes by in-solution hybridization capture-based next generation sequencing. We optimized this workflow by automating library preparation and pooling libraries prior to enrichment in order to reduce hands-on time and cost, thereby augmenting scalability. Next-RSV-SEQ yielded near-complete to complete genome sequences for 98% of specimens with Cp values ≤31, at median on-target reads >93%, and mean coverage depths between ~1,000 and >5,000, depending on viral load. Whole genomes were successfully recovered from samples with viral loads as low as 230 copies per microliter RNA. We demonstrate that the method can be expanded to other respiratory viruses like parainfluenza virus and human metapneumovirus. Next-RSV-SEQ produces high-quality RSV genomes directly from culture isolates and, more importantly, clinical specimens of all genotypes in circulation. It is cost-efficient, scalable, and can be extended to other respiratory viruses, thereby opening new perspectives for a future effective and broad genomic surveillance of respiratory viruses.
IMPORTANCE
Respiratory syncytial virus (RSV) is a leading cause of severe acute respiratory tract infections in children and the elderly, and its prevention has become an increasing priority. Recently, vaccines and a long-acting monoclonal antibody to protect effectively against severe disease have been approved for the first time. Hence, there is an urgent need for genomic surveillance of RSV at the global scale to monitor virus evolution, especially with an eye toward immune evasion. However, robust, cost-effective methods for RSV whole genome sequencing that are suitable for high-throughput of clinical samples are currently scarce. Therefore, we have developed Next-RSV-SEQ, an experimental and computational pipeline that produces reliably high-quality RSV genomes directly from clinical specimens and isolates.
Topics: Child; Humans; Aged; Respiratory Syncytial Virus, Human; Respiratory Tract Infections; High-Throughput Nucleotide Sequencing; Whole Genome Sequencing; Antibodies, Monoclonal; Respiratory Syncytial Virus Infections
PubMed: 38407068
DOI: 10.1128/jcm.01111-23 -
International Forum of Allergy &... Aug 2023The role of microbes in chronic rhinosinusitis (CRS) is poorly understood. We hypothesize that analyzing prior microbial exposures via assessing microbial protein...
BACKGROUND
The role of microbes in chronic rhinosinusitis (CRS) is poorly understood. We hypothesize that analyzing prior microbial exposures via assessing microbial protein serological reactivity in CRS versus controls may offer insights for CRS etiopathogenesis.
METHODS
We profiled IgG and IgA antibodies to individual microbial proteins in serum samples of CRS patients and controls using a novel high-throughput microarray protein technology, Nucleic Acid Programmable Protein Array (NAPPA). The study was conducted on 118 subjects (39 CRS, 79 controls). A CRS-focused NAPPA array, with 1557 potentially sero-reactive microbial proteins elected from a pre-screening of 6500 genes of interest was constructed. It included membrane-associated proteins from 47 bacterial species and all proteins from 43 viral strains. Differences between CRS and controls were compared across individual antimicrobial antibodies and the species.
RESULTS
Chronic rhinosinusitis patients had significantly elevated antimicrobial antibodies compared with controls. One bacterium (Staphylococcus aureus) and three viral strains (human metapneumovirus, human herpesvirus 5, and human herpesvirus 4) were identified as sources of the proteins that showed significantly elevated sero-reactivity in CRS patients. Within CRS, patients with polyps had elevated antibodies against S. aureus, influenza A virus (H1N1, H3N2), and rhinovirus B14. CRS patients without polyps showed more antibodies against human herpesvirus 1 and vaccinia virus WR.
CONCLUSIONS
Compared with healthy controls, CRS patients' serum samples showed significantly increased sero-reactivity to both bacterial and viral proteins, reflecting recent or current infection or active colonization. Significantly higher antibodies against S. aureus, human metapneumovirus, human herpesvirus 5, and human herpesvirus 4 in CRS need further study.
Topics: Humans; Staphylococcus aureus; Antibody Formation; Influenza A Virus, H1N1 Subtype; Influenza A Virus, H3N2 Subtype; Sinusitis; Microbiota; Anti-Infective Agents; Chronic Disease; Rhinitis
PubMed: 36504343
DOI: 10.1002/alr.23107 -
Chest Dec 2023In immunocompromised patients with acute respiratory failure (ARF), the clinical significance of respiratory virus detection in the nasopharynx remains uncertain.
BACKGROUND
In immunocompromised patients with acute respiratory failure (ARF), the clinical significance of respiratory virus detection in the nasopharynx remains uncertain.
RESEARCH QUESTION
Is viral detection in nasopharyngeal swabs associated with causes and outcomes of ARF in immunocompromised patients?
STUDY DESIGN AND METHODS
This preplanned post hoc analysis of a randomized controlled trial enrolled immunocompromised patients admitted to 32 ICUs for ARF between May 2016 and December 2017. Nasopharyngeal swabs sampled at inclusion were assessed for 23 respiratory pathogens using multiplex polymerase chain reaction (PCR) assay. Causes of ARF were established by managing physicians and were reviewed by three expert investigators masked to the multiplex PCR assay results. Associations between virus detection in nasopharyngeal swabs, causes of ARF, and composite outcome of day 28 mortality, invasive mechanical ventilation (IMV), or both were assessed.
RESULTS
Among the 510 sampled patients, the multiplex PCR assay results were positive in 103 patients (20.2%), and a virus was detected in 102 samples: rhinoviruses or enteroviruses in 35.5%, coronaviruses in 10.9%, and flu-like viruses (influenza virus, parainfluenza virus, respiratory syncytial virus, human metapneumovirus) in 52.7%. The cause of ARF varied significantly according to the results of the multiplex PCR assay, especially the proportion of viral pneumonia: 50.0% with flu-like viruses, 14.0% with other viruses, and 3.6% when no virus was detected (P < .001). No difference was found in the composite outcome of day 28 mortality, IMV, or both according to positive assay findings (54.9% vs 54.7%; P = .965). In a pre-established subgroup analysis, flu-like virus detection was associated with a higher rate of day 28 mortality, IMV, or both among recipients of allogeneic hematopoietic stem cell transplantation compared with those without detected virus.
INTERPRETATION
In immunocompromised patients with ARF, the results of nasopharyngeal multiplex PCR assays are not associated with IMV or mortality. A final diagnosis of viral pneumonia is retained in one-third of patients with positive assay results and in one-half of the patients with a flu-like virus.
Topics: Humans; Immunocompromised Host; Multiplex Polymerase Chain Reaction; Nasopharynx; Pneumonia, Viral; Respiratory Insufficiency; Respiratory Tract Infections; Viruses; Randomized Controlled Trials as Topic
PubMed: 37567412
DOI: 10.1016/j.chest.2023.07.4222 -
Medicine Oct 2023Respiratory syncytial virus (RSV) and human metapneumovirus (hMPV) infections are common in children worldwide. However, the clinical factors related to extended...
Clinical factors associated with extended hospitalization in pediatric patients ≥3 years of age with respiratory syncytial virus or human metapneumovirus infection: A Japanese single-center, retrospective study.
Respiratory syncytial virus (RSV) and human metapneumovirus (hMPV) infections are common in children worldwide. However, the clinical factors related to extended hospitalization in Japanese patients aged ≥3 years remain elusive. We aimed to elucidate the clinical risk factors contributing to hospital stays ≥7 days in patients with RSV and hMPV infections. Patients ≥3 years of age who were hospitalized due to RSV or hMPV infection between 2014 to 2020 were included. Twenty-one RSV- and 27 hMPV-infected patients were enrolled. Patients were divided into 2 groups: hospitalization for ≥ and <7 days. Univariate and multivariate analyses determined the clinical risk factors contributing to hospital stay ≥7 days. The RSV- and hMPV-infected patients had similar clinical characteristics. The clinical risk factors contributing to extended hospitalization were analyzed in the 48 infected patients of the 2 groups. The presence of prophylactic antibiotics usage, co-bacterial colonization, and underlying diseases were extracted by univariate analysis (P < .05). In multivariate analysis, underlying diseases were determined as an independent clinical risk factor (odds ratio 8.09, P = .005). Underlying diseases contributed to extended hospitalization in RSV- or hMPV-infected patients ≥3 years of age.
Topics: Child; Child, Preschool; Humans; Infant; Comorbidity; East Asian People; Hospitalization; Length of Stay; Metapneumovirus; Paramyxoviridae Infections; Respiratory Syncytial Virus Infections; Respiratory Syncytial Virus, Human; Respiratory Tract Infections; Retrospective Studies; Japan
PubMed: 37861549
DOI: 10.1097/MD.0000000000035565 -
Advances in Virology 2024Acute respiratory tract infection (ARTI) is a significant cause of morbidity and mortality among children worldwide. The majority of acute respiratory infections in...
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.
PubMed: 38292215
DOI: 10.1155/2024/7613948 -
Scientific Reports Sep 2023Human metapneumovirus (hMPV) can cause severe acute respiratory infection (ARI). We aimed to clarify the clinical and molecular epidemiological features of hMPV. We...
Human metapneumovirus (hMPV) can cause severe acute respiratory infection (ARI). We aimed to clarify the clinical and molecular epidemiological features of hMPV. We conducted an ARI surveillance targeting hospitalized children aged 1 month to 14 years in Nha Trang, Vietnam. Nasopharyngeal swabs were tested for respiratory viruses with PCR. We described the clinical characteristics of hMPV patients in comparison with those with respiratory syncytial virus (RSV) and those with neither RSV nor hMPV, and among different hMPV genotypes. Among 8822 patients, 278 (3.2%) were hMPV positive, with a median age of 21.0 months (interquartile range: 12.7-32.5). Among single virus-positive patients, hMPV cases were older than patients with RSV (p < 0.001) and without RSV (p = 0.003). The proportions of clinical pneumonia and wheezing in hMPV patients resembled those in RSV patients but were higher than in non-RSV non-hMPV patients. Seventy percent (n = 195) were genotyped (A2b: n = 40, 20.5%; A2c: n = 99, 50.8%; B1: n = 37, 19%; and B2: n = 19, 9.7%). The wheezing frequency was higher in A2b patients (76.7%) than in those with other genotypes (p = 0.033). In conclusion, we found a moderate variation in clinical features among hMPV patients with various genotypes. No seasonality was observed, and the multiple genotype co-circulation was evident.
Topics: Child; Humans; Infant; Metapneumovirus; Child, Hospitalized; Molecular Epidemiology; Respiratory Sounds; Vietnam; Respiratory Tract Infections; Respiratory Syncytial Virus, Human
PubMed: 37735242
DOI: 10.1038/s41598-023-42692-z -
Frontiers in Pediatrics 2023The management of respiratory viruses prior to hematopoietic cell transplant (HCT) can be controversial and requires special consideration of host factors, transplant... (Review)
Review
The management of respiratory viruses prior to hematopoietic cell transplant (HCT) can be controversial and requires special consideration of host factors, transplant parameters, and the specific respiratory virus (RV). In the setting of adenovirus (ADV), human metapneumovirus (HMPV), influenza, parainfluenza virus (PIV), and respiratory syncytial virus (RSV) detection prior to hematopoietic cell transplant (HCT), clinical practice guidelines recommend transplant delay when possible; however, there is much more ambiguity when other respiratory viruses, such as seasonal coronaviruses (CoVs), human rhinovirus (HRV), and SARS-CoV-2, are detected. Our aims for this review include detailing clinical practical guidelines and reviewing current literature on pre-transplant respiratory viral infections (RVIs), including antiviral therapies and prevention strategies, when available. We will center our discussion on three representative clinical scenarios, with the goal of providing practical guidance to clinicians.
PubMed: 38304442
DOI: 10.3389/fped.2023.1339239 -
Cardiology in the Young Sep 2023This study investigates the hygiene standards in the context of the COVID-19 pandemic and their impact on the perioperative incidence of human metapneumovirus as well as...
INTRODUCTION
This study investigates the hygiene standards in the context of the COVID-19 pandemic and their impact on the perioperative incidence of human metapneumovirus as well as the typical symptom burden of human metapneumovirus-infected children with CHDs.
MATERIALS AND METHODS
Between March 2018 and July 2021, all patients of a cardiac paediatric ICU of a German university hospital were included in this retrospective cohort analysis.
RESULTS
A total of 589 patients with CHD were included in the analysis. Three hundred and fifty-two patients (148 females and 204 males) were admitted before the introduction of social distancing and face masks between March 2018 and 15 April 2020 (cohort A). Two hundred and thirty-seven patients (118 females and 119 males) were admitted after the introduction between April 16 and July 2021 (cohort B). In cohort A, human metapneumovirus was detected in 11 out of 352 patients (3.1%) during their stay at cardiac paediatric ICU. In cohort B, one patient out of 237 (0.4%) tested positive for human metapneumovirus. Patients who tested positive for human metapneumovirus stayed in cardiac paediatric ICU for a median of 17.5 days (range, 2-45 days). Patients without a detected human metapneumovirus infection stayed in the cardiac paediatric ICU for a median of 4 days (range, 0.5-114 days). Nine out of 12 (75%) human metapneumovirus-positive patients showed atelectasis.
CONCLUSION
Perioperative human metapneumovirus infections prolong cardiac paediatric ICU stay in children with CHD. In affected patients, pulmonary impairment with typical symptoms appears. Under certain circumstances, a complication-rich perioperative infection with human metapneumovirus could be prevented in paediatric cardiac high-risk patients by prophylactic hygiene intervention.
Topics: Male; Female; Humans; Child; COVID-19; Metapneumovirus; Retrospective Studies; Pandemics; Cohort Studies; Paramyxoviridae Infections; Intensive Care Units, Pediatric
PubMed: 35920053
DOI: 10.1017/S1047951122002645 -
Digestive Diseases and Sciences Aug 2023Gastrointestinal (GI) symptoms are recognized sequelae of acute respiratory illness (ARI), but their prevalence is not well documented. Our study aim was to assess the...
BACKGROUND
Gastrointestinal (GI) symptoms are recognized sequelae of acute respiratory illness (ARI), but their prevalence is not well documented. Our study aim was to assess the incidence of GI symptoms in community ARI cases for persons of all ages and their association with clinical outcomes.
METHODS
We collected mid-nasal swabs, clinical, and symptom data from Seattle-area individuals during the 2018-2019 winter season as part of a large-scale prospective community surveillance study. Swabs were tested by polymerase chain reaction (PCR) for 26 respiratory pathogens. Likelihood of GI symptoms given demographic, clinical, and microbiological covariates were analyzed with Fisher's exact, Wilcoxon-rank-sum, and t-tests and multivariable logistic regression.
RESULTS
In 3183 ARI episodes, 29.4% had GI symptoms (n = 937). GI symptoms were significantly associated with pathogen detection, illness interfering with daily life, seeking care for the illness, and greater symptom burden (all p < 0.05). Controlling for age, > 3 symptoms, and month, influenza (p < 0.001), human metapneumovirus (p = 0.004), and enterovirus D68 (p = 0.05) were significantly more likely to be associated with GI symptoms than episodes with no pathogen detected. Seasonal coronaviruses (p = 0.005) and rhinovirus (p = 0.04) were significantly less likely to be associated with GI symptoms.
CONCLUSION
In this community-surveillance study of ARI, GI symptoms were common and associated with illness severity and respiratory pathogen detection. GI symptoms did not track with known GI tropism, suggesting GI symptoms may be nonspecific rather than pathogen-mediated. Patients presenting with GI and respiratory symptoms should have respiratory virus testing, even if the respiratory symptom is not the primary concern.
Topics: Humans; Infant; Respiratory Tract Infections; Prospective Studies; Virus Diseases; Nausea; Gastrointestinal Diseases; Diarrhea; Vomiting
PubMed: 37269371
DOI: 10.1007/s10620-023-07976-4 -
Frontiers in Public Health 2023Acute respiratory infections (ARIs) are the most common viral infections encountered in primary care settings. The identification of causal viruses is still not...
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 ( < 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.
Topics: Humans; Prospective Studies; Respiratory Tract Infections; Viruses; Virus Diseases; Primary Health Care
PubMed: 38074759
DOI: 10.3389/fpubh.2023.1269805