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Viruses Nov 2022Viral respiratory infections contribute to significant morbidity and mortality in children. Currently, there are limited reports on the composition and abundance of the...
Metagenomic Analysis of Respiratory RNA Virome of Children with and without Severe Acute Respiratory Infection from the Free State, South Africa during COVID-19 Pandemic Reveals Higher Diversity and Abundance in Summer Compared with Winter Period.
Viral respiratory infections contribute to significant morbidity and mortality in children. Currently, there are limited reports on the composition and abundance of the normal commensal respiratory virome in comparison to those in severe acute respiratory infections (SARIs) state. This study characterised the respiratory RNA virome in children ≤ 5 years with (n = 149) and without (n = 139) SARI during the summer and winter of 2020/2021 seasons in South Africa. Nasopharyngeal swabs were, collected, pooled, enriched for viral RNA detection, sequenced using Illumina MiSeq, and analysed using the Genome Detective bioinformatic tool. Overall, , , , , , and families were the most abundant viral population in both groups across both seasons. Human rhinovirus and endogenous retrovirus K113 were detected in most pools, with exclusive detection of in SARI pools. Generally, higher viral diversity/abundance was seen in children with SARI and in the summer pools. Several plant/animal viruses, eukaryotic viruses with unclear pathogenicity including a distinct rhinovirus A type, were detected. This study provides remarkable data on the respiratory RNA virome in children with and without SARI with a degree of heterogeneity of known viruses colonizing their respiratory tract. The implication of the detected viruses in the dynamics/progression of SARI requires further investigations.
Topics: Child; Animals; Humans; Virome; South Africa; COVID-19; Seasons; RNA; Pandemics; Respiratory Tract Infections; Pneumonia; Viruses; Respiratory System
PubMed: 36423125
DOI: 10.3390/v14112516 -
Virus Research Jan 2023Human rhinovirus (HRV), the main etiologic agent of the common cold, is responsible for significant morbidity, medical costs, and the loss of productivity in the...
Human rhinovirus (HRV), the main etiologic agent of the common cold, is responsible for significant morbidity, medical costs, and the loss of productivity in the workplace and school. To prevent the spread of HRV, accurate, low-cost and rapid diagnostics of HRV is crucial for identifying those at-risk for the illness associated with HRV, with the most frequently detected species, including HRV species A (HRV-A) and C (HRV-C). Here, a novel HRV-A and/or HRV-C molecular diagnostic assay that integrates reverse-transcription recombinase polymerase amplification assay (RT-RPA) amplification with CRISPR/Cas12a detection, with the result readout using a fluorescence detector or lateral flow strip (LFS). The established assay could be completed within 50 min without complex instruments and skilled technicians. The limit of detection of the RT-RPA-Cas12a-mediated real-time fluorescence or LFS assay could reach 0.1 copy/μl, and 0.5 copy/μl for the end-point fluorescence assay with a UV light illuminator readout, respectively. Meanwhile, the assay demonstrates excellent specificity without cross-reactivity to non-target viruses. Furthermore, they were appraised using 80 clinical samples, and RT-RPA-Cas12a-mediated fluorescence or LFS assay displayed high-accuracy with positive and negative predictive agreement of 96.7%, 95% and 100%, respectively. Taken together, the RT-RPA-Cas12a-mediated assay is a rapid, sensitive, and specific detection tool for routine and on-site detection method for HRV-A and/or HRV-C infections, and shows great promise for use in resource-poor or constrained settings.
PubMed: 36375713
DOI: 10.1016/j.virusres.2022.199001 -
Cureus Sep 2022Background The copy number of the oligonucleotide 5'-purine-uridine-uridine-purine-uridine-3' (purUUpurU) motif in a viral genome was previously shown to correlate with...
Background The copy number of the oligonucleotide 5'-purine-uridine-uridine-purine-uridine-3' (purUUpurU) motif in a viral genome was previously shown to correlate with the severity of acute illness. This study aimed to determine whether purUUpurU content correlates with virulence in other single-strand RNA (ssRNA) viruses that vary in clinical severity. Methodology We determined the copy number of purUUpurU in the genomes of two subtypes of human respiratory syncytial virus (RSV), respiratory syncytial virus A (RSV-A), and respiratory syncytial virus B (RSV-B), which vary in clinical severity. In addition, we determined the purUUpurU content of the four ebolaviruses that cause human disease, dengue virus, rabies virus, human rhinovirus-A, poliovirus type 1, astrovirus, rubella, yellow fever virus, and measles virus. Viral nucleotide sequence files were downloaded from the National Center for Biotechnology Information (NCBI)/National Institutes of Health website. In addition, we determined the cumulative case fatality rate of 20 epidemics of the Ebola virus and compared it with that of the other human ebolaviruses. Results The genomic purUUpurU content correlated with the severity of acute illness caused by both subtypes of RSV and human ebolaviruses. The lowest purUUpurU content was in the genome of the rubella virus, which causes mild disease. Conclusions The quantity of genomic purUUpurU is a virulence factor in ssRNA viruses. Blood hyperviscosity is one mechanism by which purUUpurU causes pathology. Comparative quantitative genomic analysis for purUUpurU will be helpful in estimating the risk posed by emergent ssRNA viruses.
PubMed: 36284814
DOI: 10.7759/cureus.29340 -
Open Forum Infectious Diseases Oct 2022Rhinoviruses (RVs) are among the most frequently detected viruses from hospitalized children with severe acute respiratory infections, being classified into RV-A, RV-B,...
BACKGROUND
Rhinoviruses (RVs) are among the most frequently detected viruses from hospitalized children with severe acute respiratory infections, being classified into RV-A, RV-B, and RV-C (4 clades: C, GAC1, GAC2, and A2). This study aimed to compare the clinical characteristics and respiratory tract illness severity between the RV species and RV-C clades in children in primary care and hospital settings in rural communities in the Philippines.
METHODS
Clinical samples and information of children <5 years old in the Philippines were collected from 2014 to 2016. The samples were tested by reverse-transcription polymerase chain reaction (RT-PCR) targeting the 5'-untranslated region. PCR-positive samples were sequenced, and RV species were identified by phylogenetic analysis.
RESULTS
Overall, 3680 respiratory tract illness episodes in 1688 cohort children were documented; 713 of those were RV positive and identified as RV-A (n = 271), RV-B (n = 47), and RV-C (n = 395: C [n = 76], GAG1 [n = 172], GAG2 [n = 8], A2 [n = 138], and unidentified [n = 1]). Severe illnesses, low oxygen saturation, cough, and wheezing were more common in patients with RV-C, especially with GAC1, than in those with RV-A or RV-B. Furthermore, severe illness was significantly more common in RV-C (GAC1)-positive cases than in RV-A-positive cases (odds ratio, 2.61 [95% CI, 1.17-4.13]).
CONCLUSIONS
Children infected with RV-C had more severe illnesses than children infected with RV-A and RV-B. Moreover, emerging clades of RV-C were associated with increased severity.
PubMed: 36267245
DOI: 10.1093/ofid/ofac387 -
Influenza and Other Respiratory Viruses Jan 2023We determine the presence and diversity of rhinoviruses in nasopharyngeal swab samples from 248 individuals who presented with influenza-like illness (ILI) at a...
We determine the presence and diversity of rhinoviruses in nasopharyngeal swab samples from 248 individuals who presented with influenza-like illness (ILI) at a university clinic in the Southwest United States between October 1, 2020 and March 31, 2021. We identify at least 13 rhinovirus genotypes (A11, A22, A23, A25, A67, A101, B6, B79, C1, C17, C36, and C56, as well a new genotype [AZ88**]) and 16 variants that contributed to the burden of ILI in the community. We also describe the complete capsid protein gene of a member (AZ88**) of an unassigned rhinovirus A genotype.
Topics: Humans; Rhinovirus; Respiratory Tract Infections; Universities; Picornaviridae Infections; Enterovirus Infections; Virus Diseases; Genotype
PubMed: 36168937
DOI: 10.1111/irv.13057 -
Viruses Aug 2022Rhinoviruses (RV) account for a significant number of asthma exacerbations, and RV species C may be associated with a severe course in vulnerable patient groups. Despite...
Rhinoviruses (RV) account for a significant number of asthma exacerbations, and RV species C may be associated with a severe course in vulnerable patient groups. Despite important evidence on the role of RV reported by clinicians and life scientists, there are still unanswered questions regarding their influence on asthma exacerbation in young patients. Thus, we measured the RVspecies-specific IgG titers in our German pediatric exacerbation cohort using a microarray-based technology. For this approach, human sera of patients with exacerbated asthma and wheeze, as well as healthy control subjects ( = 136) were included, and correlation analyses were performed. Concordantly with previously published results, we observed significantly higher cumulative levels of RV species A-specific IgG ( = 0.011) and RV-C-specific IgG ( = 0.051) in exacerbated asthma group compared to age-matched controls. Moreover, atopic wheezers had increased RV-specific IgG levels for species A ( = 0.0011) and species C ( = 0.0009) compared to non-atopic wheezers. Hypothesizing that bacterial infection positively correlates with immune memory against RV, we included nasopharyngeal swab results in our analyses and detected limited correlations. Interestingly, the eosinophil blood titer positively correlated with RV-specific IgG levels. With these observations, we add important observations to the existing data regarding exacerbation in pediatric and adolescent medicine. We propose that scientists and clinicians should pay more attention to the relevance of RV species in susceptible pediatric patients.
Topics: Adolescent; Antibody Formation; Asthma; Child; Enterovirus Infections; Humans; Immunoglobulin G; Picornaviridae Infections; Rhinovirus
PubMed: 36146664
DOI: 10.3390/v14091857 -
Omics : a Journal of Integrative Biology Jul 2022Viral genomics has become crucial in clinical diagnostics and ecology, not to mention to stem the COVID-19 pandemic. Whole-genome sequencing (WGS) is pivotal in gaining...
Viral genomics has become crucial in clinical diagnostics and ecology, not to mention to stem the COVID-19 pandemic. Whole-genome sequencing (WGS) is pivotal in gaining an improved understanding of viral evolution, genomic epidemiology, infectious outbreaks, pathobiology, clinical management, and vaccine development. Genome assembly is one of the crucial steps in WGS data analyses. A series of different assemblers has been developed with the advent of high-throughput next-generation sequencing (NGS). Various studies have reported the evaluation of these assembly tools on distinct datasets; however, these lack data from viral origin. In this study, we performed a comparative evaluation and benchmarking of eight assemblers: SOAPdenovo, Velvet, assembly by short sequences (ABySS), iterative graph assembler (IDBA), SPAdes, Edena, iterative virus assembler, and VICUNA on the viral NGS data from distinct Illumina (GAIIx, Hiseq, Miseq, and Nextseq) platforms. WGS data of diverse viruses, that is, severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), dengue virus 3, human immunodeficiency virus 1, hepatitis B virus, human herpesvirus 8, human papillomavirus 16, rhinovirus A, and West Nile virus, were utilized to assess these assemblers. Performance metrics such as genome fraction recovery, assembly lengths, NG50, N50, contig length, contig numbers, mismatches, and misassemblies were analyzed. Overall, three assemblers, that is, SPAdes, IDBA, and ABySS, performed consistently well, including for genome assembly of SARS-CoV-2. These assembly methods should be considered and recommended for future studies of viruses. The study also suggests that implementing two or more assembly approaches should be considered in viral NGS studies, especially in clinical settings. Taken together, the benchmarking of eight genome assemblers reported in this study can inform future public health and ecology research concerning the viruses, the COVID-19 pandemic, and viral outbreaks.
Topics: Benchmarking; COVID-19; Genome, Viral; High-Throughput Nucleotide Sequencing; Humans; Pandemics; SARS-CoV-2; Sequence Analysis, DNA; Software
PubMed: 35759429
DOI: 10.1089/omi.2022.0042 -
Cureus Mar 2022The occurrence of rhabdomyolysis in pediatric patients is considered a rare complication that can follow certain viral infections in a syndrome better defined as...
The occurrence of rhabdomyolysis in pediatric patients is considered a rare complication that can follow certain viral infections in a syndrome better defined as virus-associated rhabdomyolysis. In this research, we will present the case of a ten-year-old male patient who presented to the emergency department with chief complaints of severe bilateral leg pain and inability to walk. Furthermore, the patient complained of dysphagia for both solid and liquid along with dark-colored urine. Initial investigations showed an increase in creatine kinase (CK), C-reactive protein (CRP), and liver enzymes. Additionally, urine analysis was obtained with positive traces of blood, protein, and white blood cell. X-ray was ordered with no significant finding. Finally, the diagnosis was reached in accordance to the results of the respiratory panel multiplex (PCR) as the third case of rhinovirus-induced rhabdomyolysis. He was treated with isotonic intravenous fluids, and he was discharged on hospital day 20 with a CK of 2062 IU/L. The patient was discharged fully recovered, was able to stand and walk alone, and with no complications. In this third to be reported case of rhinovirus-induced rhabdomyolysis, we aim to increase the knowledge among the general pediatric field regarding the possible presentation and treatment of any similar case.
PubMed: 35371843
DOI: 10.7759/cureus.22784 -
Archives of Virology Apr 2022Human rhinoviruses (HRVs) cause acute upper and lower respiratory tract infections and aggravation of asthma and chronic obstructive pulmonary disease. The 5'...
Human rhinoviruses (HRVs) cause acute upper and lower respiratory tract infections and aggravation of asthma and chronic obstructive pulmonary disease. The 5' untranslated region (5' UTR) and the VP4/VP2 region are widely used for genotyping of HRVs. Members of the species Rhinovirus A and Rhinovirus C have been reported to be more frequently associated with severe disease than members of the species Rhinovirus B. We report the clinical and molecular epidemiological characteristics of HRVs circulating from 2012 to 2020 in Shanghai. A total of 5832 nasopharyngeal swabs from patients with acute respiratory infections were collected. A real-time reverse transcription polymerase chain reaction assay was used for virus detection. The 5' untranslated region and VP4/VP2 region were amplified and sequenced for genotyping and phylogenetic analysis. The overall rate of rhinovirus detection was 2.74% (160/5832), with members of species A, B, and C accounting for 68.13% (109/160), 20.00% (32/160), and 11.88% (19/160) of the total, respectively. A peak of HRV infection was observed in autumn (5.34%, 58/1087). Patients in the 3- to 14-year-old age group were the most susceptible to HRV infection (χ = 23.88, P = 0.017). Influenza virus and Streptococcus pneumoniae were detected more frequently than other pathogens in cases of coinfection. Recombination events were identified in 10 strains, which were successfully genotyped by phylogenetic analysis based on the 5' UTR-VP4/VP2 region but not the 5' UTR region alone. We observed a high degree of variability in the relative distribution of HRV genotypes and the prevalence of HRV infection in Shanghai and found evidence of recombination events in the portion of the genome containing the 5' UTR and the VP4/VP2 region between HRV-C strains and HRV-A-like strains. This study is important for surveillance of the spread of HRVs and the emergence of new variants.
Topics: Adolescent; Child; Child, Preschool; China; Humans; Molecular Epidemiology; Phylogeny; Picornaviridae Infections; Rhinovirus
PubMed: 35303167
DOI: 10.1007/s00705-022-05405-x -
International Journal of Infectious... May 2022Rhinoviruses are commonly considered simple "common cold" agents. The link between their molecular epidemiology and patient clinical presentation and outcomes remains...
BACKGROUND
Rhinoviruses are commonly considered simple "common cold" agents. The link between their molecular epidemiology and patient clinical presentation and outcomes remains unclear in adult populations.
MATERIALS/METHODS
All nasopharyngeal or bronchoalveolar lavages were screened using multiplex PCR in 3 Parisian hospitals from January 2018 to September 2018. For all detected rhinoviruses, the VP2/VP4 region was subtyped by sequencing.
RESULTS
The study included 178 unique patients who were positive for human rhinovirus (HRV). They were primarily men (56%), with a median age of 62.2 years (IQR: 46.8-71.4), frequently presenting chronic respiratory diseases (56%) and/or immunosuppression (46%). Of these, 63% were admitted for respiratory distress, including 25% for pneumonia; 95 (53%), 27 (15%), and 56 (32%) were positive for HRV-A, -B, and -C, respectively. HRV-B appeared to be more associated with immunosuppressive treatments (58% vs 30% and 36% of patients for HRV-A and -C, respectively, p = 0.038), higher coinfection rates (54% vs 34% and 23%, p = 0.03), and higher intensive care unit (ICU) admission rates (35% vs 17% and 13%, p = 0.048). Conversely, HRV-A was more frequently associated with pneumonia (54% vs 31% and 11% for HRV-B and -C, respectively, p = 0.01).
CONCLUSIONS
This study highlights the high proportion of chronic respiratory diseases or immunosuppression among hospitalized patients infected with a rhinovirus.
IMPORTANT
Human rhinoviruses (HRVs) are frequently detected in patients hospitalized for respiratory distress. Understanding their molecular differences is crucial to finding target treatments and improving patient outcomes.
Topics: Adult; Aged; Enterovirus; Humans; Male; Middle Aged; Phylogeny; Picornaviridae Infections; Respiratory Distress Syndrome; Respiratory Tract Infections; Rhinovirus
PubMed: 35248716
DOI: 10.1016/j.ijid.2022.02.055