Virus Infection Research Articles

Identifying microglia-derived NFKBIA as a potential contributor to the pathogenesis of Alzheimer's disease and age-related macular degeneration.

BackgroundAlzheimer's disease (AD) and age-related macular degeneration (AMD) place considerable health burden on affected individuals and significant economic burden on society.ObjectiveThis study aims to explore the shared cellular and molecular mechanisms underlying the pathogenesis of AD and AMD.MethodsThe investigation in this study is conducted via single-cell and bulk tissue transcriptomic analysis. Transcriptomic datasets of AD and AMD were obtained from the GEO database. The shared differentially expressed genes (DEGs) in control and AD- and AMD-affected samples were identified. Functional enrichment analysis for DEGs was subsequently performed. Then, the protein-protein interaction (PPI) network of these DEGs was established via the STRING database and hub genes of this network were identified by Cytoscape software. Single-cell transcriptomic analysis was performed using Seurat R package to explore their expression in different cell types.ResultsDifferential analysis identified 127 shared DEGs of the two diseases, including 71 upregulated and 56 downregulated genes. Upregulated DEGs were enriched in inflammation, gliogenesis, cell apoptosis, and response to bacterial and viral infection and downregulated DEGs were enriched in mitochondrial function and energy production. PPI network and Cytoscape determined 10 hub genes, of which the NFKBIA gene was associated with the severity of both AD and AMD. Moreover, single-cell transcriptomic analysis showed that NFKBIA was highly expressed in microglia from disease-affected tissues.ConclusionsThe findings indicated that microglia with high NFKBIA expression were important contributors to the progression of both AD and AMD. Microglia-derived NFKBIA might serve as a potential therapeutic target for AD and AMD.

Mood symptoms, cognitive function, and changes of brain hemodynamics in patients with COVID-19: A functional near-infrared spectroscopy study

BACKGROUND Many patients with coronavirus disease 2019 (COVID-19) may experience emotional issues and cognitive impairment. However, it remains unclear whether the brain mediates the impact of COVID-19 on the emergence of psychopathological symptoms. It remains unclear whether anxiety and depression are caused by stressors or viral infection. AIM To use functional near-infrared spectroscopy (fNIRS) to detect cortical hemodynamic changes in patients with COVID-19 and their relationship with mental symptoms (mainly depression and anxiety), to investigate whether COVID-19 causes these changes by affecting brain function. METHODS A total of 58 subjects, comprising 29 patients with first acute COVID-19 infection and 29 healthy controls without COVID-19 infection and without anxiety or depression were recruited. Then cortical activation during the performance of the verbal fluency test (VFT) and brain connectivity during the resting state (rs) were evaluated by 53-channel fNIRS. For the COVID-19-infected group, Patient Health Questionnaire-9 (PHQ-9) and General Anxiety Disorder-7 (GAD-7) were used to assess the emotional state before fNIRS measures. RESULTS For the rs, compared to the uninfected group, the infected group exhibited lower rs functional connectivity (FC) in the dorsolateral prefrontal cortex (DLPFC), which was correlated with both the PHQ score and GAD score. During the VFT, the infected group exhibited significantly lower cortical activation than the uninfected group in both Broca-left and Broca-right. Besides, the integral value in the DLPFC-L showed a significant negative correlation with the PHQ-9 score during the VFT in the infected group. CONCLUSION There were significant differences in the bilateral Broca area and DLPFC between the COVID-19-infected and uninfected groups, which may be the reason why COVID-19 infection impairs cognitive function and language function and leads to psychiatric symptoms. In addition, the rsFC in patients with COVID-19 was positively correlated with the severity of depression and anxiety, which may be related to the fact that the mental symptoms of patients with COVID-19 are characterized by depression and anxiety, rather than depression or anxiety alone. Our study provides evidence that the psychological and emotional issues caused by COVID-19 are not only due to external social factors but also involve more direct brain neural mechanisms and abnormal neural circuits, which also provide insights into the future treatment and prognosis of individuals with COVID-19.

Surveillance for Serological Evidence of Bourbon and Heartland Virus Infection in White-Tailed Deer and Feral Swine in Texas.

Background: The tick-borne pathogens, Bourbon virus (BRBV) and Heartland virus (HRTV) are the cause of febrile illnesses that may progress to severe and fatal diseases. Materials and Methods: As a preliminary effort to determine if these viruses were enzootic in Texas, ticks and blood samples were collected from feral swine (Sus scrofa) and white-tailed deer (Odocoileus virginianus) (WTD) killed by gunning as part of an abatement program during 2019-2021 in Travis County, Texas. Ticks were collected from these animals by hand and blood samples were obtained by cardiac puncture using 22-gauge needles and 5 mL syringes. Information was recorded for each animal, including date, sex, and location. The species of ticks were identified morphologically using a taxonomic key, and serum samples were tested for neutralizing antibodies to BRBV and HRTV. Results: A total of 83 Ixodes scapularis and 58 Amblyomma americanum ticks were collected from feral swine, and 196 I. scapularis and 11 Dermacentor albipictus from WTD. Although A. americanum, the implicated vector of both viruses was collected from feral swine, neutralizing antibody was not detected to BRBV, but 12% (9/75) had antibody to HRTV as evidence of a previous infection. Of the serum samples obtained from WTD, all were negative for BRBV neutralizing antibody, but 6.6%% (5/75) were positive for HRTV antibody. Conclusion: These preliminary results indicated that HRTV was enzootic in Travis, County, Texas and further studies are warranted to determine the specific tick vectors and the possible role of WTD and feral swine in the maintenance and transmission cycle of this virus.

Comparative pathology of ducks experimentally inoculated with three different recombinant Newcastle disease viruses.

Although velogenic Newcastle disease viruses (NDVs) generally show low pathogenicity in waterfowl such as ducks, lethal infection by NDVs has been reported sporadically. A previous study revealed that a serially-passaged NDV isolate showed increased virulence in ducks, and that the viral proteins harbored a total of 11 amino acid substitutions. Among them, the fusion protein (F), matrix protein (M), and hemagglutinin-neuraminidase (HN) were suspected to be involved in enhanced virulence. The present study aimed to clarify the association between genetic mutations in NDVs and pathogenicity in ducks by comparing histopathological findings in ducks inoculated with three recombinant (r)NDVs: rM44 (Q44R substitution in M), rF142 (I142M substitution in F), and rM+F+HN (Q44R, N123D, and D342N substitutions in M; I142M and E304K substitutions in F; and G538R substitution in HN; three viral proteins compatible with amino acid sequences from passaged NDV). Seven-day-old ducks were intranasally inoculated with rM44, rF142, or rM+F+HN. Gross and histopathological lesions in the heart, thymus, brain, and pancreas were more severe in ducks inoculated with rM+F+HN than in ducks inoculated with rM44 or rF142. In particular, myocarditis associated with NDV antigens and mixed inflammatory cells was prominent in rM+F+HN-inoculated ducks. Therefore, the increased virulence of NDV in ducks is not due to a single amino acid substitution in one protein, but rather to the synergistic effects of multiple mutations in three viral proteins.

Identification and validation of TFs and lncRNAs in response to Tomato Leaf Curl Bangalore Virus (ToLCBaV) infection in tomato (Solanum spp.)

Tomato leaf curl Bangalore virus (ToLCBaV), often a woeful reason for complete failure of tomato crop in southern India. The plant response to virus infection is a complicated network involving several defence routes. Every defence route involves transcription factors (TFs) and other regulatory transcripts including lncRNA as important regulators of gene expression. These regulators act as both pro-viral and anti-viral factors involved in modulating disease symptoms. This study has reported and validated several TFs and lncRNAs from transcriptome study of tomato lines, IIHR2611 (R) and IIHR 2843 (S) in response to virus infection. Validation was done based on expression analysis of selected TFs and lncRNAs using qPCR at different intervals of ToLCBaV infection. TFs, DREB protein 1A (3.53 folds) and Protein RADIALIS-like 3 (5.27 folds) were induced in R plants upon ToLCBaV infection. Whereas, WRKY TF-53 was upregulated in S (3.36 folds) and down regulated in R (− 3.80 folds) plants upon virus infection. Four lncRNAs were found differentially expressed among R and S lines when analysed using qPCR. The differential temporal gene expression of TFs among S and R plants in response to ToLCBaV infection regulate the resistance or susceptibility. Further studies on the mechanism of resistance of TFs and lncRNAs will aid in unravelling novel antiviral defence pathways in tomato. These findings provide a basis for developing molecular markers for marker-assisted selection and targets for genome editing, paving the way for breeding durable ToLCBaV-resistant tomato cultivars. Understanding the role of TFs and lncRNAs in host-virus interactions could also help address viral infections in other crop species.

Strong association with remote EBV infection in children with MS as opposed to other acquired demyelinating disorders

BackgroundThe link between multiple sclerosis (MS) and Epstein-Barr virus (EBV) is well established in adults but less clear in paediatric cases. In addition, the role of EBV and other viral...

Cathelicidin-related antimicrobial peptide (CRAMP) is toxic during neonatal murine influenza virus infection.

Respiratory viral infections are a major contributor to mortality in children under 5 years of age, and disproportionately affect preterm neonates. Previously, using our established 3-day-old neonatal murine model of influenza virus infection, we demonstrated that treatment of neonatal mice with intranasal Lactobacillus rhamnosus GG (LGG) prior to influenza viral infection improved survival. Transcriptional analysis revealed expression of the mouse cathelicidin-related antimicrobial peptide (CRAMP, encoded by CRAMP) was downregulated in LGG-treated neonates. Mouse CRAMP is a key effector protein secreted by infected epithelial cells and resident and infiltrating immune cells, but the role of CRAMP in neonatal defense to respiratory viruses is unknown. Neonatal mice with a deleted CRAMP gene (CRAMP-/-) were intranasally infected with influenza virus. CRAMP-/- neonates had improved survival over C57BL/6 neonates after influenza viral infection (75% vs. 14%, p < 0.05). Next, immune cell recruitment to the lung of infected neonates was determined. Surprisingly, at 3-days postinfection, there was increased recruitment of neutrophils, inflammatory monocytes, and alveolar macrophages, coupled with increased proinflammatory cytokine and chemokine production in CRAMP-/- compared to C57BL/6 neonates. However, this changed over the first week of infection. C57BL/6 neonatal mice increased CRAMP production significantly, in direct contrast to their adult counterparts. Inflammatory cytokine production increased that indicated CRAMP amplified the innate immune response later in the infection. Furthermore, we identified pulmonary nonimmune cells as an important source of increased CRAMP levels as the infection progressed and CRAMP production drove mortality. These insights emphasize the age-specific role of CRAMP in influenza viral pathogenesis.

Investigating the dynamics of cytomegalovirus movement in viscoelastic Casson fluid: effects of electric and magnetic fields.

Cytomegalovirus (CMV) is a significant clinical pathogen posing risks, especially for immunocompromised individuals. This study investigates the transport dynamics of CMV within viscoelastic saliva, focusing on factors influencing viral mobility. We employed mathematical models, including the Basset-Boussinesq-Oseen (BBO) equation, to analyze how viral density, particle diameter, saliva viscosity, and external electric and magnetic fields affect CMV movement in the oesophagus. Novel insights include the discovery that smaller CMV particles move significantly faster compared to larger ones, highlighting a critical aspect of viral infectivity. Additionally, we found that increased peristaltic wave amplitudes in the oesophagus greatly enhance viral velocity. More notably, our investigation reveals that the application of external magnetic fields can manipulate CMV transport by exerting forces that reduce viral mobility, thus potentially lowering infection rates through electromagnetic interactions. These findings underscore the complex interplay between fluid rheology, particle shape, and external fields in viral dynamics, suggesting novel therapeutic interventions aimed at controlling CMV spread based on saliva viscosity and electromagnetic manipulation. Our research paves the way for innovative strategies in viral infection management and therapeutic development.

Correlation between hepatitis B surface antibody (anti-HBs) in maternal blood and cord blood in newborn: a study on transplacental acquired maternal antibody

BackgroundHepatitis B Virus infection is a global health problem. Transplacental maternal antibodies can protect the infant early in life from infection. Objectives: This study investigates the correlation between maternal and infant Hepatitis B surface antibodies (anti-HBs) in pairs.MethodsThis cross-sectional study measured anti-HBs in paired mother-infant samples. Blood samples were taken from the mother 3 h before delivery and from the newborn immediately after birth by cord blood, and they were then examined for anti-HBs using the Chemiluminescent Microparticle Immunoassay.ResultsTransplacental transfer of maternal anti-HBs was analyzed in 79 mother-infant pairs. Seventeen mothers (21.5%) had positive anti-HBs and all cord blood of newborns from these mothers had anti-HBs detected. Overall, there were 44 (55.7%) newborn blood cords that were positive for anti-HBs. The geometric mean of anti-HBs cord blood titers in newborns with maternal anti-HBs titers < 10, ≥10, ≥ 100, and ≥ 1,000 mIU/mL were 52.42, 193.83, 437.12, and ≥ 1,000 mIU /mL respectively. This study showed a significant correlation in anti-HBs between mother and infant cord blood (r = 0.863; p < 0,001).ConclusionsAnti-HB antibodies measured in mother and infant cord blood were strongly correlated, demonstrating efficient transplacental antibody transfer to protect infants against Hepatitis B infection. Hepatitis B vaccination is required for mothers to obtain immunogenicity and babies to receive hepatitis B vaccination on time.

Discovery of AIC263282, a Hepatitis B Virus Capsid Assembly Modulator Ready for Candidate Profiling.

Hepatitis B Virus (HBV) infections remain a threat to the global public health. Nucleoside analogues remain the mainstay of therapy despite their discouraging cure rates achieved. Capsid assembly modulators (CAMs) have been at the center of HBV research, but despite having shown clinical efficacy on viral load in clinical studies, market entry has been elusive. Herein, we present the optimization program of our lead series. Setting our focus on potency, solubility, and hERG liability, these studies resulted in AIC263282, a new, potent capsid assembly modulator with improved physicochemical properties, which is ready for profiling as a preclinical candidate.

Early Experience on Universal Prophylaxis in Infants against Respiratory Syncytial Virus: Facts and Expectations.

During the 2023/24 season, nirsevimab significantly reduced the risk of bronchiolitis and confirmed respiratory syncytial virus (RSV) infections in primary care, hospital, and pediatric intensive care unit admissions among infants aged 0 to 11 months, even in a season with a high community RSV burden, particularly for older infants. These findings are very useful for public health authorities to continue to implement immunization campaigns against RSV in the coming seasons. Moreover, universal immunization against RSV represents a transformative step toward reducing the burden of RSV in infants. With promising evidence from recently published studies, the expectations for a reduction of RSV-associated hospitalizations, alongside the improvement of public health outcomes and equitable access to these measures, are high. However, achieving these goals will require addressing challenges related to vaccine uptake, funding, and RSV surveillance to prompt detect resistances due to mutations of the virus. These interventions need to be integrated into public health strategies because they hold the potential to make a significant impact on infant's health worldwide.

Deficiency in platelet 12-lipoxygenase exacerbates inflammation and disease severity during SARS-CoV-2 infection

Platelets, known for maintaining blood balance, also participate in antimicrobial defense. Upon severeacute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, platelets become hyperactivated, releasing molecules such as cytokines, granule contents, and bioactive lipids. The key effector biolipids produced by platelets include 12-hydroxyeicosatetraenoic acid (12-HETE) and 12-hydroxyeicosatrienoic acid (12-HETrE), produced by 12-lipoxygenase (12-LOX), and prostaglandins and thromboxane, produced by cyclooxygenase-1. While prostaglandin E2 and thromboxane B2 were previously associated with lung inflammation in severe COVID-19, the role of platelet 12-LOX in SARS-CoV-2 infection remains unclear. Using mice deficient for platelets' 12-LOX, we report that SARS-CoV-2 infection resulted in higher lung inflammation characterized by histopathological tissue analysis, increased leukocyte infiltrates, and cytokine production relative to wild-type mice. In addition, distinct platelet and lung transcriptomic changes, including alterations in NOD-like receptor (NLR) family pyrin domain-containing 1 (NLRP1) inflammasome-related gene expression, were observed. Mass spectrometry lipidomic analysis in 12-LOX-deficient-infected mice revealed significant changes in bioactive lipid content, including reduced levels of 12-HETrE that inversely correlated with disease severity. Finally, platelet 12-LOX deficiency was associated with increased morbidity and lower survival rates relative to wild type (WT) mice. Overall, this study highlights the complex interplay between 12-LOX-related lipid metabolism and inflammatory responses during SARS-CoV-2 infection. The findings provide valuable insights into potential therapeutic targets aimed at mitigating severe outcomes, emphasizing the pivotal role of platelet enzymes in the host response to viral infections.

Approach to Short Duration Fever in Children in Office Practice.

Fever is the second most common symptom after respiratory complaints in pediatric practice, often causing parental anxiety despite usually resulting from self-limiting viral infections. Without localized symptoms, diagnosing hidden bacterial infections is challenging. Tropical regions like India present additional diagnostic challenges due to endemic diseases like malaria, dengue, and typhoid. This review provides an algorithmic approach to evaluate and manage short-duration fever in children, tailored to the Indian epidemiological context. The approach requires careful clinical assessment and consideration of bacterial and tropical etiologies. While most cases are self-limited viral infections, early identification of serious bacterial infections (SBI) is crucial in reducing morbidity and mortality. A structured approach is outlined, based on clinical symptoms, signs, age, and vaccination status. Children are divided into three groups: neonates (0-28 d), young infants (29-90 d), and older infants/toddlers (3-36 mo). Neonates and sick/toxic-appearing children with fever warrant immediate hospital admission for empirical antibiotics and diagnostic work-up. Management of young infants is stratified according to risk factors for SBI such as bacteremia, urinary tract infections (UTI), and pneumonia. Well-appearing older infants/toddlers are often managed as outpatients, with investigations tailored to specific clinical and epidemiological contexts.

Drug repositioning as a promising approach for the eradication of emerging and re-emerging viral agents.

The global impact of emerging and re-emerging viral agents during epidemics and pandemics leads to serious health and economic burdens. Among the major emerging or re-emerging viruses include SARS-CoV-2, Ebola virus (EBOV), Monkeypox virus (Mpox), Hepatitis viruses, Zika virus, Avian flu, Influenza virus, Chikungunya virus (CHIKV), Dengue fever virus (DENV), West Nile virus, Rhabdovirus, Sandfly fever virus, Crimean-Congo hemorrhagic fever (CCHF) virus, and Rift Valley fever virus (RVFV). A comprehensive literature search was performed to identify existing studies, clinical trials, and reviews that discuss drug repositioning strategies for the treatment of emerging and re-emerging viral infections using databases, such as PubMed, Scholar Google, Scopus, and Web of Science. By utilizing drug repositioning, pharmaceutical companies can take advantage of a cost-effective, accelerated, and effective strategy, which in turn leads to the discovery of innovative treatment options for patients. In light of antiviral drug resistance and the high costs of developing novel antivirals, drug repositioning holds great promise for more rapid substitution of approved drugs. Main repositioned drugs have included chloroquine, ivermectin, dexamethasone, Baricitinib, tocilizumab, Mab114 (Ebanga™), ZMapp (pharming), Artesunate, imiquimod, saquinavir, capmatinib, naldemedine, Trametinib, statins, celecoxib, naproxen, metformin, ruxolitinib, nitazoxanide, gemcitabine, Dorzolamide, Midodrine, Diltiazem, zinc acetate, suramin, 5-fluorouracil, quinine, minocycline, trifluoperazine, paracetamol, berbamine, Nifedipine, and chlorpromazine. This succinct review will delve into the topic of repositioned drugs that have been utilized to combat emerging and re-emerging viral pathogens.

Recovery of Antibody Immunity After a Resurgence of Respiratory Syncytial Virus Infections.

Longitudinal measurements of respiratory syncytial virus (RSV) immunity over 4 winter seasons reveal that viral neutralization titers, RSV prefusion F protein (pre-F)-specific immunoglobulin M and immunoglobulin G (IgG) levels, and RSV antibody-dependent cellular phagocytosis function gradually returned to prepandemic levels in female healthcare and school workers of childbearing age after 2 winter seasons, following the resurgence of RSV cases in the Vancouver metropolitan region (British Columbia, Canada). In contrast, pre-F IgG avidity profiles remained unchanged. These findings support the notion that repeated viral infections are necessary to maintain high RSV antibody levels in the population.

King's College criteria and the Clichy-Villejuif criteria require adjustments for assessing acute liver failure due to yellow fever.

Acute liver failure (ALF) is a severe condition characterized by rapid deterioration of liver function in individuals without preexisting liver disease. Liver transplantation (LT) is the most impactful treatment. Yellow fever (YF) is an infectious disease that primarily affects the liver and has a high mortality rate. However, LT can be a viable option for treating rare cases with extensive liver involvement. However, the criteria for assessing the severity of ALF and determining the indications for transplantation have not been specifically validated for cases caused by YF. To present necessary adjustments to established scoring systems for ALF secondary to YF. This was an observational, retrospective, single-center study. Fourteen consecutive patients with confirmed ALF due to YF were monitored in the intensive care unit by a specialized liver transplant team during a three-month epidemic outbreak in Brazil. During hospitalization, general supportive therapeutic measures were implemented, and the patients were regularly assessed using the King's College criteria and the Clichy-Villejuif criteria to determine the severity of liver failure. LT is considered a viable measure for patients with signs of end-stage liver failure. Eight of 14 (57%) patients developed severe neurological alterations within the first 96 hours after hospital admission. Four patients underwent emergency LT, and despite a moderate viral infection of the graft after transplantation, the 5-year survival rate was 50%. Although the King's College criteria and the Clichy-Villejuif criteria are the main scoring systems for ALF, they are insufficient for predicting the risk of mortality in this context, primarily because of low serum bilirubin levels in the final stage of the disease and significant disparities between coagulation abnormalities and patient severity. To ensure good applicability in cases of YF-induced ALF, the authors suggest adaptations to the King's College and Clichy-Villejuif criteria.

Genetic analyses and functional validation of ruminant SLAMs reveal potential hosts for PPRV

Peste des petits ruminants (PPR), caused by the peste des petits ruminants virus (PPRV), is a highly contagious disease affecting ruminants. While goats and sheep are well-known hosts, PPRV has also spread to wild ruminants, and it remains unclear which ruminant species can be infected. SLAM (Signaling lymphocytic activation molecule) acts as the primary receptor for PPRV, playing a crucial role in the viral infection process. Identifying which ruminant SLAMs can mediate PPRV infection is essential for understanding the potential hosts of PPRV, which is vital for effective eradication efforts. In this study, we first extracted 77 ruminant species’ SLAM sequences from ruminant genome database. Based on these sequences, we predicted the structures of ruminant SLAMs. The analysis revealed that SLAM conformation is similar across ruminant species, and the potential PPRV H protein binding domain residues were conserved among SLAMs of these 77 species. Phylogenetic analysis of SLAM grouped ruminants into six families. We then selected representative SLAMs from each ruminant family to assess their role in PPRV infection. Our findings demonstrated that ruminant SLAMs efficiently mediated PPRV infection, with enhanced viral amplification observed in cells expressing SLAM from java mouse deer (Tragulidae) and goat (Bovidae), compared to cells expressing SLAM from white tailed deer (Cervidae) and giraffe (Giraffidae). These results underscore the need to consider a broader range of potential host populations beyond goat and sheep in efforts to prevent and eradicate PPRV.

Chebulinic acid suppresses porcine epidemic diarrhea virus infection by inhibiting viral entry and viral main protease

Chebulinic acid suppresses porcine epidemic diarrhea virus infection by inhibiting viral entry and viral main protease

Impact of hepatitis C virus infection control on preventing the postoperative recurrence of intrahepatic cholangiocarcinoma

Impact of hepatitis C virus infection control on preventing the postoperative recurrence of intrahepatic cholangiocarcinoma

Metatranscriptomic profiling reveals pathogen and host response signatures of pediatric acute sinusitis and upper respiratory infection

BackgroundAcute sinusitis (AS) is a frequent cause of antibiotic prescriptions in children. Distinguishing bacterial AS from common viral upper respiratory infections (URIs) is crucial to prevent unnecessary antibiotic use but is challenging with current diagnostic methods. Despite its speed and cost, untargeted RNA sequencing of clinical samples from children with suspected AS has the potential to overcome several limitations of other methods. In addition, RNA-seq may reveal novel host-response biomarkers for development of future diagnostic assays that distinguish bacterial from viral infections. There are however no available RNA-seq datasets of pediatric AS that provide a comprehensive view of both pathogen etiology and host immune response.MethodsHere, we performed untargeted RNA-seq (metatranscriptomics) of nasopharyngeal samples from 221 children with AS and performed a comprehensive analysis of pathogen etiology and the impact of bacterial and viral infections on host immune responses. Accuracy of RNA-seq-based pathogen detection was evaluated by comparison with culture tests for three common bacterial pathogens and qRT-PCR tests for 12 respiratory viruses. Host gene expression patterns were explored to identify potential host responses that distinguish bacterial from viral infections.ResultsRNA-seq-based pathogen detection showed high concordance with culture or qRT-PCR, showing 87%/81% sensitivity (sens) / specificity (spec) for detecting three AS-associated bacterial pathogens, and 86%/92% (sens/spec) for detecting 12 URI-associated viruses, respectively. RNA-seq also detected an additional 22 pathogens not tested for clinically and identified plausible pathogens in 11/19 (58%) of cases where no organism was detected by culture or qRT-PCR. We reconstructed genomes of 196 viruses across the samples including novel strains of coronaviruses, respiratory syncytial virus, and enterovirus D68, which provide useful genomic data for ongoing pathogen surveillance programs.By analyzing host gene expression, we identified host-response signatures that differentiate bacterial and viral infections, revealing hundreds of candidate gene biomarkers for future diagnostic assays.ConclusionsOur study provides a one-of-kind dataset that profiles the interplay between pathogen infection and host responses in pediatric AS and URI. It reveals bacterial and viral-specific host responses that could enable new diagnostic approaches and demonstrates the potential of untargeted RNA-seq in diagnostic analysis of AS and URI.