-
Microorganisms Jul 2023The recent global emergence of the pandemic has accelerated research in several areas of science whose valuable outputs and findings can help to address future health...
The recent global emergence of the pandemic has accelerated research in several areas of science whose valuable outputs and findings can help to address future health challenges in the event of emerging infectious agents. We conducted a comprehensive shotgun analysis targeting multiple aspects to compare differences in bacterial spectrum and viral presence through culture-independent RNA sequencing. We conducted a comparative analysis of the microbiome between healthy individuals and those with varying degrees of COVID-19 severity, including a total of 151 participants. Our findings revealed a noteworthy increase in microbial species diversity among patients with COVID-19, irrespective of disease severity. Specifically, our analysis revealed a significant difference in the abundance of bacterial phyla between healthy individuals and those infected with COVID-19. We found that , among other bacterial , showed a notably higher abundance in healthy individuals compared to infected individuals. Conversely, Bacteroides showed a lower abundance in the latter group. Infected people, regardless of severity and symptoms, have the same proportional representation of , , , , and . In addition to and numerous phage groups, we identified sequences of clinically significant viruses such as , , and in several samples. Analyses were performed retrospectively, therefore, in the case of various WHO variants such as (B.1.1.7), (B.1.617.2), (B.1.1.529), and strains are represented. Additionally, the presence of specific virus strains has a certain effect on the distribution of individual microbial taxa.
PubMed: 37512976
DOI: 10.3390/microorganisms11071804 -
The Science of the Total Environment Oct 2023The effective detection of viruses in aircraft wastewater is crucial to establish surveillance programs for monitoring virus spread via aircraft passengers. This study...
The effective detection of viruses in aircraft wastewater is crucial to establish surveillance programs for monitoring virus spread via aircraft passengers. This study aimed to compare the performance of two virus concentration workflows, adsorption-extraction (AE) and Nanotrap® Microbiome A Particles (NMAP), in detecting the prevalence and concentrations of 15 endogenous viruses including ssDNA, dsDNA, ssRNA in 24 aircraft lavatory wastewater samples. The viruses tested included two indicator viruses, four enteric viruses, and nine respiratory viruses. The results showed that cross-assembly phage (crAssphage), human polyomavirus (HPyV), rhinovirus A (RhV A), and rhinovirus B (RhV B) were detected in all wastewater samples using both workflows. However, enterovirus (EV), human norovirus GII (HNoV GII), human adenovirus (HAdV), bocavirus (BoV), parechovirus (PeV), epstein-barr virus (EBV). Influenza A virus (IAV), and respiratory syncytial virus B (RsV B) were infrequently detected by both workflows, and hepatitis A virus (HAV), influenza B virus (IBV), and respiratory syncytial virus B (RsV A) were not detected in any samples. The NMAP workflow had greater detection rates of RNA viruses (EV, PeV, and RsV B) than the AE workflow, while the AE workflow had greater detection rates of DNA viruses (HAdV, BoV, and EBV) than the NMAP workflow. The concentration of each virus was also analyzed, and the results showed that crAssphage had the highest mean concentration (6.76 log GC/12.5 mL) followed by HPyV (5.46 log GC/12.5 mL using the AE workflow, while the mean concentrations of enteric and respiratory viruses ranged from 2.48 to 3.63 log GC/12.5 mL. Using the NMAP workflow, the mean concentration of crAssphage was 5.18 log GC/12.5 mL and the mean concentration of HPyV was 4.20 log GC/12.5 mL, while mean concentrations of enteric and respiratory viruses ranged from 2.55 to 3.74 log GC/12.5 mL. Significantly higher (p < 0.05) mean concentrations of crAssphage and HPyV were observed when employing the AE workflow in comparison to the NMAP workflow. Conversely, the NMAP workflow yielded significantly greater (p < 0.05) concentrations of RhV A, and RhV B compared to the AE workflow. The findings of this study can aid in the selection of an appropriate concentration workflow for virus surveillance studies and contribute to the development of efficient virus detection methods.
Topics: Humans; Wastewater; Workflow; Adsorption; Epstein-Barr Virus Infections; Toilet Facilities; Herpesvirus 4, Human; Microbiota; Bacteriophages; Polyomavirus; Adenoviruses, Human
PubMed: 37348715
DOI: 10.1016/j.scitotenv.2023.165007 -
Risk Analysis : An Official Publication... Mar 2024The risk assessments during the COVID-19 pandemic were primarily based on dose-response models derived from the pooled datasets for infection of animals susceptible to...
The risk assessments during the COVID-19 pandemic were primarily based on dose-response models derived from the pooled datasets for infection of animals susceptible to SARS-CoV. Despite similarities, differences in susceptibility between animals and humans exist for respiratory viruses. The two most commonly used dose-response models for calculating the infection risk of respiratory viruses are the exponential and the Stirling approximated β-Poisson (BP) models. The modified version of the one-parameter exponential model or the Wells-Riley model was almost solely used for infection risk assessments during the pandemic. Still, the two-parameter (α and β) Stirling approximated BP model is often recommended compared to the exponential dose-response model due to its flexibility. However, the Stirling approximation restricts this model to the general rules of β ≫ 1 and α ≪ β, and these conditions are very often violated. To refrain from these requirements, we tested a novel BP model by using the Laplace approximation of the Kummer hypergeometric function instead of the conservative Stirling approximation. The datasets of human respiratory airborne viruses available in the literature for human coronavirus (HCoV-229E) and human rhinovirus (HRV-16 and HRV-39) are used to compare the four dose-response models. Based on goodness-of-fit criteria, the exponential model was the best fitting model for the HCoV-229E (k = 0.054) and for HRV-39 datasets (k = 1.0), whereas the Laplace approximated BP model followed by the exact and Stirling approximated BP models are preferred for both the HRV-16 (α = 0.152 and β = 0.021 for Laplace BP) and the HRV-16 and HRV-39 pooled datasets (α = 0.2247 and β = 0.0215 for Laplace BP).
Topics: Animals; Humans; Rhinovirus; Pandemics; COVID-19; Coronavirus 229E, Human; Risk Assessment
PubMed: 37317640
DOI: 10.1111/risa.14178 -
Viruses Mar 2023A 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... (Review)
Review
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.
Topics: Child; Humans; Infant; Rhinovirus; COVID-19; Common Cold; Respiratory Tract Infections; Asthma; Enterovirus Infections; Risk Factors; Picornaviridae Infections
PubMed: 37112805
DOI: 10.3390/v15040825 -
Viruses Mar 2023Rhinoviruses (RVs) are major instigators of acute exacerbations of asthma, COPD, and other respiratory diseases. RVs are categorized into three species (RV-A, RV-B, and...
Rhinoviruses (RVs) are major instigators of acute exacerbations of asthma, COPD, and other respiratory diseases. RVs are categorized into three species (RV-A, RV-B, and RV-C), which comprise more than 160 serotypes, making it difficult to develop an effective vaccine. Currently, no effective treatment for RV infection is available. Pulmonary surfactant is an extracellular complex of lipids and proteins that plays a central role in regulating innate immunity in the lung. The minor pulmonary surfactant lipids, palmitoyl-oleoyl-phosphatidylglycerol (POPG) and phosphatidylinositol (PI), are potent regulators of inflammatory processes and exert antiviral activity against respiratory syncytial virus (RSV) and influenza A viruses (IAV). In the current study, we examined the potencies of POPG and PI against rhinovirus A16 (RV-A16) in primary human airway epithelial cells (AECs) differentiated at an air-liquid interface (ALI). After AECs were infected with RV-A16, PI reduced the viral RNA copy number by 70% and downregulated (55-75%) the expression of antiviral (MDA5, IRF7, and IFN-lambda) and CXCL11 chemokine genes. In contrast, POPG only slightly decreased MDA5 (24%) and IRF7 (11%) gene expression but did not inhibit IFN-lambda gene expression or RV-A16 replication in AECs. However, both POPG and PI inhibited (50-80%) IL6 gene expression and protein secretion and CXCL11 protein secretion. PI treatment dramatically attenuated global gene expression changes induced by RV-A16 infection alone in AECs. The observed inhibitory effects were indirect and resulted mainly from the inhibition of virus replication. Cell-type enrichment analysis of viral-regulated genes opposed by PI treatment revealed the PI-inhibited viral induction of goblet cell metaplasia and the virus-induced downregulation of ciliated, club, and ionocyte cell types. Notably, the PI treatment also altered the ability of RV-A16 to regulate the expression of some phosphatidylinositol 4-kinase (); acyl-CoA-binding, domain-containing (); and low-density lipoprotein receptor () genes that play critical roles in the formation and functioning of replication organelles (ROs) required for RV replication in host cells. These data suggest PI can be used as a potent, non-toxic, antiviral agent for RV infection prophylaxis and treatment.
Topics: Humans; Pulmonary Surfactants; Rhinovirus; Epithelial Cells; Epithelium; Antiviral Agents; Enterovirus Infections; Lung; Lipids; Picornaviridae Infections
PubMed: 36992456
DOI: 10.3390/v15030747 -
Global Pediatric Health 2023Acute otitis media (AOM) is one of the most common infectious diseases in pediatric clinical facilities and has a significant impact on health care. It is a...
Acute otitis media (AOM) is one of the most common infectious diseases in pediatric clinical facilities and has a significant impact on health care. It is a polymicrobial disease and is usually preceded by a viral upper respiratory tract infection. Data on the spectrum of viruses that cause AOM in Indonesia are still limited. This study analyzed nasopharynx (NP) samples collected from 119 school children with AOM in Banyumas Regency, Central Java, Indonesia. Viral RNA was extracted for cDNA synthesis, followed by PCR and sequencing tools for detection of a panel of respiratory viruses using family-level primers for Coronaviridae, Enterovirus, Bocavirus, and Pneumovirinae for bocavirus. In total, 37 out of 119 NP samples (31.1%) tested positive for viruses. Human rhinovirus B was the predominant virus identified (32.4%) followed by rhinovirus C (29.7%), human rhinovirus A (27%), and human bocavirus (5.4%). Rhinovirus are predominant viral pathogens within school children with AOM in Central Java, Indonesia.
PubMed: 36762370
DOI: 10.1177/2333794X221149899 -
Frontiers in Cellular and Infection... 2022Rhinovirus causes many types of respiratory illnesses, ranging from minor colds to exacerbations of asthma. is an opportunistic pathogen that is increased in abundance...
Rhinovirus causes many types of respiratory illnesses, ranging from minor colds to exacerbations of asthma. is an opportunistic pathogen that is increased in abundance during rhinovirus illnesses and asthma exacerbations and is associated with increased severity of illness through mechanisms that are ill-defined. We used a co-infection model of human airway epithelium differentiated at the air-liquid interface to test the hypothesis that rhinovirus infection promotes adhesion and survival on the respiratory epithelium. Initial experiments showed that infection with alone did not damage the epithelium or induce cytokine production, but increased trans-epithelial electrical resistance, indicative of increased barrier function. In a co-infection model, infection with the more virulent rhinovirus-A and rhinovirus-C, but not the less virulent rhinovirus-B types, increased cell-associated . Immunofluorescent staining demonstrated that adhered to rhinovirus-infected ciliated epithelial cells and infected cells being extruded from the epithelium. Rhinovirus induced pronounced changes in gene expression and secretion of inflammatory cytokines. In contrast, caused minimal effects and did not enhance RV-induced responses. Our results indicate that rhinovirus-A or C infection increases survival and cell association while infection alone does not cause cytopathology or epithelial inflammation. Our findings suggest that rhinovirus and co-infection could promote epithelial damage and more severe illness by amplifying leukocyte inflammatory responses at the epithelial surface.
Topics: Humans; Moraxella catarrhalis; Rhinovirus; Coinfection; Respiratory Mucosa; Asthma; Epithelial Cells; Enterovirus Infections
PubMed: 36733852
DOI: 10.3389/fcimb.2022.1060748 -
The Science of the Total Environment Mar 2023The early warning and tracking of COVID-19 prevalence in the community provided by wastewater surveillance has highlighted its potential for much broader viral disease...
The early warning and tracking of COVID-19 prevalence in the community provided by wastewater surveillance has highlighted its potential for much broader viral disease surveillance. In this proof-of-concept study, 46 wastewater samples from four wastewater treatment plants (WWTPs) in Queensland, Australia, were analyzed for the presence and abundance of 13 respiratory viruses, and the results were compared with reported clinical cases. The viruses were concentrated using the adsorption-extraction (AE) method, and extracted nucleic acids were analyzed using qPCR and RT-qPCR. Among the viruses tested, bocavirus (BoV), parechovirus (PeV), rhinovirus A (RhV A) and rhinovirus B (RhV B) were detected in all wastewater samples. All the tested viruses except influenza B virus (IBV) were detected in wastewater sample from at least one WWTP. BoV was detected with the greatest concentration (4.96-7.22 log GC/L), followed by Epstein-Barr virus (EBV) (4.08-6.46 log GC/L), RhV A (3.95-5.63 log GC/L), RhV B (3.74-5.61 log GC/L), and PeV (3.17-5.32 log GC/L). Influenza viruses and respiratory syncytial virus (RSV) are notifiable conditions in Queensland, allowing the gene copy (GC) concentrations to be compared with reported clinical cases. Significant correlations (ρ = 0.60, p < 0.01 for IAV and ρ = 0.53, p < 0.01 for RSV) were observed when pooled wastewater influenza A virus (IAV) and RSV log GC/L concentrations were compared to log clinical cases among the four WWTP catchments. The positive predictive value for the presence of IAV and RSV in wastewater was 97 % for both IAV and RSV clinical cases within the four WWTP catchments. The overall accuracy of wastewater analysis for predicting clinical cases of IAV and RSV was 97 and 90 %, respectively. This paper lends credibility to the application of wastewater surveillance to monitor respiratory viruses of various genomic characteristics, with potential uses for increased surveillance capabilities and as a tool in understanding the dynamics of disease circulation in the communities.
Topics: Humans; Wastewater; Queensland; Epstein-Barr Virus Infections; Herpesvirus 4, Human; COVID-19; Wastewater-Based Epidemiological Monitoring; Respiratory Syncytial Viruses; Influenza B virus; Australia; Influenza, Human
PubMed: 36539100
DOI: 10.1016/j.scitotenv.2022.161023 -
Canadian Respiratory Journal 2022Human rhinovirus (HRV) can lead to a variety of respiratory illnesses; it is also an uncommon cause of community-acquired pneumonia (CAP). We described the...
INTRODUCTION
Human rhinovirus (HRV) can lead to a variety of respiratory illnesses; it is also an uncommon cause of community-acquired pneumonia (CAP). We described the characteristics and outcomes of patients hospitalized for CAP due to HRV.
METHODS
We retrospectively studied consecutive adult patients admitted to King Abdulaziz Medical City-Riyadh with CAP due to HRV between 2016 and 2019. The diagnosis was made by respiratory multiplex PCR within 48 hours of hospitalization. We compared patients requiring ICU admission to those who did not.
RESULTS
One-hundred-and-six patients were studied (peak hospitalization between November and January, median age 71.5 years, hypertension 59%, diabetes 50%, and chronic respiratory disease 44.3%); 16 (15.1%) patients required ICU admission. The median pneumonia severity index score (PSI) was 107, with no significant difference between ICU and nonICU patients. ICU patients had a higher prevalence of tachypnea (62.5% vs. 26.7%, =0.005), hemoptysis (12.5% vs 0%, =0.001), and lymphopenia (71.4% vs 26.3%, =0.01). Chest X-ray on presentation showed bilateral infiltrates in 47/101 (46.5%) patients and unilateral infiltrates in 26/101 (25.7%) patients. Systemic corticosteroids were used in 54.7% of patients (the median initial dose was 120 mg of prednisone equivalent and was higher in nonICU patients). Most (69.2%) ICU patients received mechanical ventilation (median duration of 8 days). Bacterial coinfection (6.6%) and superinfection (3.8%) were rare. The overall hospital mortality was 9.4% (higher for ICU patients: 37.5% vs. 4.4%, < 0.001).
CONCLUSIONS
Most patients with CAP due to HRV were elderly and had significant comorbidities. ICU admission was required in almost one in six patients and was associated with higher mortality.
Topics: Adult; Humans; Aged; Retrospective Studies; Rhinovirus; Intensive Care Units; Severity of Illness Index; Community-Acquired Infections; Pneumonia; Hospitalization
PubMed: 36531535
DOI: 10.1155/2022/1349994