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Journal of Virological Methods Mar 2009Acute viral respiratory infections are among the most common causes of human disease. Rapid and accurate diagnosis of viral respiratory infections is important for... (Comparative Study)
Comparative Study
Acute viral respiratory infections are among the most common causes of human disease. Rapid and accurate diagnosis of viral respiratory infections is important for providing timely therapeutic interventions. This study evaluated a new multiplex PCR assay (Seegene Inc., Seoul, Korea) for simultaneous detection and identification of 12 respiratory viruses using two primer mixes. The viruses included parainfluenza viruses 1, 2, and 3, human metapneumovirus, human coronavirus 229E/NL63 and OC43, adenovirus, influenza viruses A and B, human respiratory syncytial viruses A and B, and human rhinovirus A. The analytical sensitivity of the assay was 10-100 copies per reaction for each type of virus. There was no cross-reactivity with common bacterial or viral pathogens. A comparison with conventional viral culture and immunofluorescence was carried out using 101 respiratory specimens from 92 patients. Using viral culture, 57 specimens (56.4%) were positive without co-infection. The same viruses were identified in all 57 specimens using the multiplex PCR. Seven of the 57 specimens (12.3%) were found to be co-infected with other respiratory viruses, and 19 of 44 (43.2%) specimens which were negative by culture were positive by the multiplex PCR. The Seeplex Respiratory Virus Detection assay represents a significant improvement over the conventional methods for the detection of a broad spectrum of respiratory viruses.
Topics: Adolescent; Adult; Aged; Animals; Cell Line; Child; Child, Preschool; DNA, Viral; Humans; Infant; Middle Aged; Polymerase Chain Reaction; RNA, Viral; Respiratory Tract Infections; Sensitivity and Specificity; Species Specificity; Viruses; Young Adult
PubMed: 19063921
DOI: 10.1016/j.jviromet.2008.11.007 -
Detection of central nervous system viral infections in adults in Manado, North Sulawesi, Indonesia.PloS One 2018Central nervous system (CNS) viral infections are important causes of morbidity and mortality worldwide but the systematic survey of patients admitted to hospitals with... (Clinical Trial)
Clinical Trial
Central nervous system (CNS) viral infections are important causes of morbidity and mortality worldwide but the systematic survey of patients admitted to hospitals with CNS infections in many countries, including Indonesia, is limited. To obtain more information regarding the causes of CNS infections in Indonesia, this study was performed to detect and identify viral agents associated with CNS infections amongst in-patients at a referral hospital in Manado, North Sulawesi, Indonesia. Adult patients admitted to R.D. Kandou General Hospital with presumed CNS infection were enrolled. Cerebrospinal fluid, serum, and throat swab samples were collected and tested using molecular, serological, and virus isolation assays. A confirmed viral etiology was established in three and a probable/possible in 11 out of 74 patients. The most common was herpes simplex virus 1 (7/74, 9.5%), followed by Epstein-Barr virus (2/74, 2.7%), cytomegalovirus (1/74, 1.4%), enterovirus D68 (1/74, 1.4%), rhinovirus A (1/74, 1.4%), dengue virus (1/64, 1.6%), and Japanese encephalitis virus (1/64, 1.6%). There were 20 fatal cases (27.0%) during hospitalization in which eight were associated with viral causes. We identified herpes simplex virus 1 as the most common cause of CNS infection among adults in North Sulawesi with most of the cases remaining undiagnosed. Our study highlights the challenges in establishing the etiology of viral CNS infections and the importance of using a wide range of molecular and serological detection methods to identify CNS viruses.
Topics: Adolescent; Adult; Aged; Central Nervous System Viral Diseases; Female; Humans; Indonesia; Male; Middle Aged
PubMed: 30444898
DOI: 10.1371/journal.pone.0207440 -
The American Journal of Tropical... Nov 2010A cross-sectional study was performed in children 5 through 10 years of age presenting to outpatient clinics in Nyanza Province, Kenya, in which nasal swab and blood...
A cross-sectional study was performed in children 5 through 10 years of age presenting to outpatient clinics in Nyanza Province, Kenya, in which nasal swab and blood specimens were collected during the high malaria transmission season. Patients presenting with malaria-like symptoms within 4 days of fever onset were enrolled in the study. Plasmodium parasitemia was determined by blood smear microscopy. Nasal swabs were screened for a panel of respiratory viruses by polymerase chain reaction. Influenza A, rhinoviruses, and other respiratory viruses were detected in 18%, 26%, and 12% of 197 specimens, respectively. Four of 36 patients with influenza A had a positive malaria blood slide, compared with 20 of 52 patients with rhinovirus. A significant burden of disease caused by influenza A in febrile children during the study period was observed, highlighting the need for further research into the burden of influenza disease in regions where malaria is holoendemic.
Topics: Child; Child, Preschool; Cohort Studies; Cross-Sectional Studies; Female; Humans; Kenya; Malaria; Male; Outpatients; Respiratory Tract Infections; Virus Diseases; Virus Shedding
PubMed: 21036828
DOI: 10.4269/ajtmh.2010.10-0174 -
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 -
Clinical Chemistry Jul 2020More than 2 months separated the initial description of SARS-CoV-2 and discovery of its widespread dissemination in the United States. Despite this lengthy interval,...
BACKGROUND
More than 2 months separated the initial description of SARS-CoV-2 and discovery of its widespread dissemination in the United States. Despite this lengthy interval, implementation of specific quantitative reverse transcription (qRT)-PCR-based SARS-CoV-2 tests in the US has been slow, and testing is still not widely available. Metagenomic sequencing offers the promise of unbiased detection of emerging pathogens, without requiring prior knowledge of the identity of the responsible agent or its genomic sequence.
METHODS
To evaluate metagenomic approaches in the context of the current SARS-CoV-2 epidemic, laboratory-confirmed positive and negative samples from Seattle, WA were evaluated by metagenomic sequencing, with comparison to a 2019 reference genomic database created before the emergence of SARS-CoV-2.
RESULTS
Within 36 h our results showed clear identification of a novel human Betacoronavirus, closely related to known Betacoronaviruses of bats, in laboratory-proven cases of SARS-CoV-2. A subset of samples also showed superinfection or colonization with human parainfluenza virus 3 or Moraxella species, highlighting the need to test directly for SARS-CoV-2 as opposed to ruling out an infection using a viral respiratory panel. Samples negative for SARS-CoV-2 by RT-PCR were also negative by metagenomic analysis, and positive for Rhinovirus A and C. Unlike targeted SARS-CoV-2 qRT-PCR testing, metagenomic analysis of these SARS-CoV-2 negative samples identified candidate etiological agents for the patients' respiratory symptoms.
CONCLUSION
Taken together, these results demonstrate the value of metagenomic analysis in the monitoring and response to this and future viral pandemics.
Topics: Betacoronavirus; COVID-19; Coronavirus Infections; Enterovirus; Humans; Metagenomics; Nasopharynx; Pandemics; Phylogeny; Pneumonia, Viral; RNA, Viral; Real-Time Polymerase Chain Reaction; SARS-CoV-2; Sequence Analysis, RNA; Superinfection
PubMed: 32379863
DOI: 10.1093/clinchem/hvaa106 -
Journal of Virology Sep 2019The influence of living in small remote villages on the diversity of viruses in the nasal mucosa was investigated in three Colombian villages with very different levels...
The influence of living in small remote villages on the diversity of viruses in the nasal mucosa was investigated in three Colombian villages with very different levels of geographic isolation. Metagenomic analysis was used to characterize viral nucleic acids in nasal swabs from 63 apparently healthy young children. Sequences from human virus members of the families , , , , , , and were detected in decreasing proportions of children. The number of papillomavirus infections detected was greater among Hispanic children most exposed to outside contacts, while anellovirus infections were more common in the isolated indigenous villages. The diversity of the other human viruses detected did not differ among the villages. Closely related variants of rhinovirus A or B were identified in 2 to 4 children from each village, reflecting ongoing transmission clusters. Genomes of viruses not currently known to infect humans, including members of the families , , , and and circular Rep-encoding single-stranded DNA (CRESS-DNA) virus, were also detected in nasal swabs, possibly reflecting environmental contamination from insect, fungal, or unknown sources. Despite the high levels of geographic and cultural isolation, the overall diversity of human viruses in the nasal passages of children was not reduced in highly isolated indigenous villages, indicating ongoing exposure to globally circulating viruses. Extreme geographic and cultural isolation can still be found in some indigenous South American villages. Such isolation may be expected to limit the introduction of otherwise common and widely distributed viruses. Very small population sizes may also result in rapid local viral extinction due to a lack of seronegative subjects to maintain transmission chains for rapidly cleared viruses. We compared the viruses in the nasal passages of young children in three villages with increasing levels of geographic isolation. We found that isolation did not reduce the overall diversity of viral infections. Multiple infections with nearly identical rhinoviruses could be detected within each village, likely reflecting recent viral introductions and transmission clusters among epidemiologically linked members of these very small communities. We conclude that, despite their geographic isolation, remote indigenous villages show evidence of ongoing exposure to globally circulating viruses.
Topics: Biodiversity; Child; Child, Preschool; Colombia; Female; Humans; Indigenous Peoples; Male; Metagenomics; Nose; Phylogeny; Phylogeography; Viruses
PubMed: 31189707
DOI: 10.1128/JVI.00681-19 -
JCI Insight Aug 2018Enterovirus D68 (EV-D68) shares biologic features with rhinovirus (RV). In 2014, a nationwide outbreak of EV-D68 was associated with severe asthma-like symptoms. We...
Enterovirus D68 (EV-D68) shares biologic features with rhinovirus (RV). In 2014, a nationwide outbreak of EV-D68 was associated with severe asthma-like symptoms. We sought to develop a mouse model of EV-D68 infection and determine the mechanisms underlying airway disease. BALB/c mice were inoculated intranasally with EV-D68 (2014 isolate), RV-A1B, or sham, alone or in combination with anti-IL-17A or house dust mite (HDM) treatment. Like RV-A1B, lung EV-D68 viral RNA peaked 12 hours after infection. EV-D68 induced airway inflammation, expression of cytokines (TNF-α, IL-6, IL-12b, IL-17A, CXCL1, CXCL2, CXCL10, and CCL2), and airway hyperresponsiveness, which were suppressed by anti-IL-17A antibody. Neutrophilic inflammation and airway responsiveness were significantly higher after EV-D68 compared with RV-A1B infection. Flow cytometry showed increased lineage-, NKp46-, RORγt+ IL-17+ILC3s and γδ T cells in the lungs of EV-D68-treated mice compared with those in RV-treated mice. EV-D68 infection of HDM-exposed mice induced additive or synergistic increases in BAL neutrophils and eosinophils and expression of IL-17, CCL11, IL-5, and Muc5AC. Finally, patients from the 2014 epidemic period with EV-D68 showed significantly higher nasopharyngeal IL-17 mRNA levels compared with patients with RV-A infection. EV-D68 infection induces IL-17-dependent airway inflammation and hyperresponsiveness, which is greater than that generated by RV-A1B, consistent with the clinical picture of severe asthma-like symptoms.
Topics: Allergens; Animals; Asthma; Bronchoalveolar Lavage Fluid; Cell Line, Tumor; Child; Child, Preschool; Disease Models, Animal; Enterovirus; Enterovirus D, Human; Enterovirus Infections; Female; Humans; Infant; Infant, Newborn; Interleukin-17; Lung; Male; Mice; Nasopharynx; Neutrophils; Pyroglyphidae; RNA, Messenger
PubMed: 30135310
DOI: 10.1172/jci.insight.121882 -
Bioorganic & Medicinal Chemistry Aug 2008Human enterovirus (EV) belongs to the picornavirus family, which consists of over 200 medically relevant viruses. A peptidomimetic inhibitor AG7088 was developed to...
Human enterovirus (EV) belongs to the picornavirus family, which consists of over 200 medically relevant viruses. A peptidomimetic inhibitor AG7088 was developed to inhibit the 3C protease of rhinovirus (a member of the family), a chymotrypsin-like protease required for viral replication, by forming a covalent bond with the active site Cys residue. In this study, we have prepared the recombinant 3C protease from EV71 (TW/2231/98), a particular strain which causes severe outbreaks in Asia, and developed inhibitors against the protease and the viral replication. For inhibitor design, the P3 group of AG7088, which is not interacting with the rhinovirus protease, was replaced with a series of cinnamoyl derivatives directly linked to P2 group through an amide bond to simplify the synthesis. While the replacement caused decreased potency, the activity can be largely improved by substituting the alpha,beta-unsaturated ester with an aldehyde at the P1' position. The best inhibitor 10b showed EC(50) of 18 nM without apparent toxicity (CC(50)>25 microM). Our study provides potent inhibitors of the EV71 3C protease as anti-EV71 agents and facilitates the combinatorial synthesis of derivatives for further improving the inhibitory activity.
Topics: 3C Viral Proteases; Amino Acid Sequence; Antiviral Agents; Binding Sites; Cell Line, Tumor; Computer Simulation; Cysteine Endopeptidases; Drug Design; Enterovirus A, Human; Humans; Models, Molecular; Molecular Structure; Structure-Activity Relationship; Substrate Specificity; Viral Proteins
PubMed: 18583140
DOI: 10.1016/j.bmc.2008.06.015 -
PloS One 2017Non-bacterial acute gastroenteritis (AGE) associated with virus infection affects individuals living in developing countries, especially children. To investigate whether...
Non-bacterial acute gastroenteritis (AGE) associated with virus infection affects individuals living in developing countries, especially children. To investigate whether shedding of certain human enterovirus (EV) is more frequently detected in the stool of individuals with AGE of unknown etiology than individuals without AGE symptoms, we tested fecal samples collected from 2,692 individuals with diarrhea between January 2010 and December 2016. Samples were tested for rotavirus, norovirus, and EV by reverse-transcription polymerase chain reaction (RT-PCR) and adenovirus by PCR. EV-positive samples were subjected to sequencing and phylogenetic analysis to identify EV species and types. Findings were compared to EV found in 1,310 fecal samples from individuals without AGE who were diagnosed with hand, foot, and mouth disease (HFMD). While the majority of viruses identified in AGE consisted of human rotavirus (22.7%), norovirus (11.4%) and adenovirus (9.3%), we identified EV (6.2%) belonging mainly to species B, C, and rhinovirus. In contrast, >92% of EV found without AGE symptoms belonged to species A. Although AGE symptoms are not often attributed to EV infection, EV was associated with diarrhea of unknown etiology at least in 3.4% of AGE cases. While CV-A6 was most likely to be found in stools of HFMD patients, rhinovirus A and C were the two most common EV species associated with AGE. Elucidating group-specific EV infection in diseases with and without AGE will be useful in assisting identification, clinical management, and the surveillance of EV infection in the community.
Topics: Acute Disease; Adolescent; Base Sequence; Child; Child, Preschool; Cohort Studies; Diarrhea; Enterovirus; Enterovirus Infections; Female; Gastroenteritis; Genotype; Hand, Foot and Mouth Disease; Humans; Male; Phylogeny; Thailand
PubMed: 28750058
DOI: 10.1371/journal.pone.0182078 -
Journal of Infection in Developing... Aug 2016Influenza-like illness (ILI) and acute respiratory infection (ARI) are common presentations during winter and indiscriminate antibiotic use contributes significantly to...
INTRODUCTION
Influenza-like illness (ILI) and acute respiratory infection (ARI) are common presentations during winter and indiscriminate antibiotic use contributes significantly to the emerging post-antibiotic era.
METHODOLOGY
Otherwise healthy 152 patients, presenting to outpatient clinics with ILI/ARI, were included. Patients had history & physical, CRP, hemogram and nasopharyngeal swabs for rhinovirus A/B, influenza A/B, adenovirus A/B/C/D/E, coronavirus 229E/NL63 and OC43, parainfluenza virus 1/2/3, respiratory syncytial virusA/B, metapneumovirus and Mycoplasma pneumoniae, Chlamydia pneumoniae, Legionella pneumophila and Bordetella pertussis by PCR and for ABHS culture.
RESULTS
Median (IR) age was 26.5 (16.5). Time to presentation was shorter in men (p = 0.027). Patients with rhinovirus had lower rates (20%) of myalgia (p = 0.043). Patients with influenza virus had higher rates (97%) of elevated CRP (p = 0.016). Logistic regression revealed that patients with ILI/ARI and CRP ≥ 5 mg/L were 60 times more likely to have influenza virus infection than other viral agents (OR = 60.0, 95% CI = 2.65 to 1,358.2, p = 0.010). Rhinovirus predominated in December (54%), March (36%), and April (33%). Influenza virus predominated in January (51%). Fever was most common with adenovirus (p = 0.198). All GABHS cultures were negative. Atypical organisms and Bordetella pertussis were negative in all but one patient.
CONCLUSIONS
Influenza virus is the most likely pathogen in ILI/ARI when CRP ≥ 5 mg/L. This might be explained by tissue destruction. Myalgia is rare with rhinovirus probably due to absence of viremia. Negative bacteria by PCR and culture suggest unnecessary antibiotic use in ILI/ARI.
Topics: Adolescent; Adult; Bacteria; C-Reactive Protein; Diagnosis, Differential; Female; Humans; Male; Middle Aged; Respiratory Tract Infections; Virus Diseases; Viruses; Young Adult
PubMed: 27482806
DOI: 10.3855/jidc.6939