Parainfluenza Virus Type Research Articles

Nonparametric bootstrap methods for interval estimation of the area under the ROC curve with correlated diagnostic test data: application to whole-virus ELISA testing in swine.

Developing and evaluating novel diagnostic assays are crucial components of contemporary diagnostic research. The receiver operating characteristic (ROC) curve and the area under the ROC curve (AUC) are frequently used to evaluate diagnostic assays' performance. The variation in AUC estimation can be quantified nonparametrically using resampling methods, such as bootstrapping, and then used to construct interval estimation for the AUC. When multiple observations are observed from the same subject, which is very common in veterinary diagnostic tests evaluation experiments, a traditional bootstrap-based method can fail to provide valid interval estimations of AUC. In particular, the traditional method does not account for the correlation among data observations and could result in interval estimation that fails to cover the true AUC adequately at the desired confidence level. In this paper, we proposed two novel methods to calculate the confidence interval of the AUC for correlated diagnostic test data based on cluster bootstrapping and hierarchical bootstrapping, respectively. Our simulation studies showed that both proposed methods had adequate coverage probabilities which were higher than the existing traditional method when there were intra-subject correlations. We also discussed applying the proposed methods to evaluate a novel whole-virus ELISA (wv-ELISA) diagnostic assay in detecting porcine parainfluenza virus type-1 antibodies in swine serum.

Non-specific effects of Pneumococcal and Haemophilus vaccines in children aged 5 years and under: a systematic review

ObjectiveTo determine the evidence for non-specific effects of the Pneumococcal and Haemophilus influenza vaccine in children aged 5 years and under.Data sourcesA key word literature search of MEDLINE, EMBASE, The...

2655. Phase 1 Safety and Immunogenicity Results of Two Investigational mRNA Vaccines, mRNA-1345, a Respiratory Syncytial Virus Vaccine, and mRNA-1653, a Human Metapneumovirus and Parainfluenza Virus Type 3 Combination Vaccine in Seropositive Young Children

Abstract Background Respiratory syncytial virus (RSV), human metapneumovirus (hMPV), and parainfluenza virus type 3 (PIV3) are common respiratory illnesses in children. Two investigational vaccines, mRNA-1345, encoding the RSV prefusion stabilized F (preF) glycoprotein, and mRNA-1653, encoding the hMPV and PIV3 F glycoproteins, are in clinical trials. Methods Two phase 1, randomized, observer-blind, placebo-controlled trials in children aged 12-59 months assessed safety and immunogenicity of mRNA-1345 (NCT04528719) and mRNA-1653 (NCT04144348). In the mRNA-1345 trial, RSV-seropositive children (N=46) were randomized to receive 3 doses of mRNA-1345 (15 µg or 30 µg) or placebo 2 months apart. In the mRNA-1653 trial, hMPV- and PIV3-seropositive children (N=27) were randomized to receive 2 doses of mRNA-1653 (10 µg or 30 µg) or placebo 2 months apart. Interim data through Month (M) 5 for mRNA-1345 and M3 for mRNA-1653 are reported. Results mRNA-1345 and mRNA-1653 were well-tolerated. The most frequently reported solicited local adverse reaction (AR) was tenderness at injection site (mRNA-1345, 35.7%-71.4%; placebo, 26.7%-42.9% and mRNA-1653, 44.4%-60.0%; placebo, 12.5%-30.0%); solicited systemic ARs (mRNA-1345, 12.5%-53.3%; placebo, 33.3%-50.0% and mRNA-1653, 33.3%-55.6%; placebo, 12.5%-60.0%) were mostly grade 1/2. One mRNA-1345 injection boosted RSV neutralizing antibody (nAb) titers (geometric mean fold rise [GMFR] over baseline: RSV-A=18.9-34.9; RSV-B=7.2-14.3) and RSV preF and postF binding antibody (bAb) concentrations (GMFR: preF=13.9-26.5; postF=9.3-16.0); additional injections did not further elevate antibody levels (Fig 1A and 2A). One mRNA-1653 injection boosted hMPV and PIV3 nAb titers (GMFR over baseline: hMPV-A=2.9-6.1; hMPV-B=6.2-13.2; PIV3=2.8-3.0) and preF and postF bAb concentrations (GMFR: hMPV preF=5.3-6.1; postF=4.6-6.5 and PIV3 preF=13.9-14.2; postF=11.0-12.1); a second injection did not further increase antibody levels (Fig 1B,C and 2B,C). In both trials, bAb responses were generally preF biased. Conclusion In seropositive children aged 12-59 months, mRNA-1345 and mRNA-1653 were well-tolerated and boosted RSV and hMPV plus PIV3 antibodies, respectively, supporting their continued development and that of a combination RSV and hMPV vaccine. Disclosures Matthew D. Snape, MBBS, MD, FRCPCH, FPM, FMedSci, Moderna Biotech UK, Inc.,: Employee|Moderna Biotech UK, Inc.,: Stocks/Bonds Sabine Schnyder Ghamloush, MD, Moderna, Inc.: Employee|Moderna, Inc.: Stocks/Bonds Grace L. Chen, MD, MPH, Moderna, Inc.: Employee|Moderna, Inc.: Stocks/Bonds Rakesh Dhar, MD, Moderna, Inc.: Employee|Moderna, Inc.: Stocks/Bonds Runa Mithani, PharmD, Moderna, Inc: Employee|Moderna, Inc: Stocks/Bonds Vinicius Righi, PharmD, MBA, Moderna, Inc.: Employee|Moderna, Inc.: Stocks/Bonds Louie Morsy, BS, Moderna, Inc.: Employee|Moderna, Inc.: Stocks/Bonds Archana Kapoor, PhD, Moderna, Inc.: Employee|Moderna, Inc.: Stocks/Bonds Bethany Girard, Ph.D., Moderna, Inc.: salary|Moderna, Inc.: Stocks/Bonds Laila El Asmar, PhD, Moderna, Inc.: Employee|Moderna, Inc.: Stocks/Bonds Christine A. Shaw, PhD, Moderna, Inc.: Employee|Moderna, Inc.: Stocks/Bonds

Isolation and Identification of a Genotype C Bovine Parainfluenza Virus Type 3 and Its Pathogenicity in Albino Guinea Pigs

Bovine parainfluenza virus type 3 (BPIV3) is a significant pathogen in cattle, causing a range of respiratory symptoms from mild to severe. In this study, we isolated a BPIV3 (BPIV3/SX/2021) strain using Madin-Darby bovine kidney cells from a lung tissue sample obtained in Shaanxi province. The full length of the BPIV3/SX/2021 strain is 15,474 nt, encoding six structural and three accessory proteins. A phylogenetic analysis revealed that SX2021strain belongs to BPIV3 genotype C, and the isolate shares the highest sequence homology with the other genotype C strains isolated in China. A genetic comparison of the BPIV3c strain isolated in China showed that some amino acid residues have mutations in the F and HN genes that affect the protein structure. Animal challenge experiments showed that experimental infection of guinea pigs with the BPIV3c strain SX2021 displayed depression and dyspnea clinical signs. Histopathological analysis of the lung and trachea showed that morphological changes consisted of lesions of bronchial epithelial cell shedding, alveoli septa thickening, focal fiber hyperplasia, and macrophage infiltration. The virus load analysis indicated that the SX2021 strain displayed a higher replication level in the lungs and trachea. These results provide strong evidence that the evolution of BPIV3, and the isolated BPIV3 strain SX2021 provide useful data to determine the pathogenesis of the virus.

Circulation of Parainfluenza Virus in Nashville, Tennessee Before and During the COVID-19 Pandemic

Abstract Background During the COVID-19 pandemic, nonpharmaceutical interventions (NPIs) were introduced and altered circulation of common respiratory viruses, including the parainfluenza viruses (PIVs). Our aim was to describe the circulation of PIVs in Nashville, Tennessee before and during the pandemic. Methods We retrieved records of all respiratory specimens tested using a clinician-ordered respiratory pathogen panel (RPP) test between 01/01/2018, and 12/01/2022, at Vanderbilt University Medical Center. Using the results of RPP testing, we evaluated the proportion of PIV-positive tests before and during the COVID-19 pandemic, including by age groups (0–4, 5–17, 18–64, ≥65), and by PIV types 1-4. Any individual with a medical encounter >14 days was considered a distinct case. We used 04/01/2020, the day Tennessee’s stay-at-home order took effect, as the start date of the pandemic period. Results Of the 58,001 tests ordered during the 60-month study period, 2,601 (4.5%) tests were positive for PIV. PIV-3 was the most common serotype (1,493, 57.4%), followed by PIV-4 (374,14.4%), PIV-2 (356,13.7%), and PIV-1 (351,13.5%). The median age of those who tested PIV-positive was 2.6 years (IQR, 0.9–7.3 years) and 1,395 (53.6%) were male. PIV-1 and PIV-2 were more common children compared to adults. Before the pandemic, PIV-1 and PIV-2 peaked biennially, with PIV-1 peaking in the fall of odd months and PIV-2 peaking in the fall of even years. (Figure 1). PIV-3 and PIV-4 circulated annually, with PIV-3 peaking in the spring and PIV-4 peaking in the fall. During the pandemic, all PIV serotypes skipped a season, but resurfaced the following season. The distribution of detections across age groups was comparable before and during the pandemic. Figure 1. Monthly proportions of RPP tests positive for parainfluenza virus (PIV) in Nashville, Tennessee before and during the COVID-19 pandemic (January 2018–December 2022). The dashed line represents the first day Tennessee’s stay-at-home order was in effect. Co-detection refers to detection of more than one PIV serotype simultaneously. Conclusion The circulation of PIV in Nashville, Tennessee was disrupted during the COVID-19 pandemic, with PIVs not circulating for an entire season. However, circulation resumed the following season. Further investigation is needed to determine if clinical outcomes differed before and during the pandemic and the influence of NPIs shaped PIV transmission.

Prevalence of respiratory viruses among hospitalized children with lower respiratory tract infections during the COVID-19 pandemic in Wuhan, China

ObjectivesWe aimed to investigate the continuous changes in respiratory virus epidemics in hospitalized children with lower respiratory tract infections (LRTIs) persisting from January 2019 to December 2022 in Wuhan, China. MethodsWe retrospectively enrolled children with LRTIs admitted to the Wuhan Children's Hospital. Specimens were nasopharyngeal aspirates which had been collected and detected the following microorganisms with direct immunofluorescence: influenza virus types A and B, respiratory syncytial virus, parainfluenza virus types 1-3, and adenovirus. We also analyzed demographic data and laboratory test results. ResultsA total of 22,660 patients were enrolled. The total virus detection rate in 2019, 2021, and 2022 significantly declined gradually (36.96% vs 29.47% vs 22.62%, P value < 0.001). All the detected viruses did not follow previously observed seasonal patterns during the COVID-19 pandemic. Children hospitalized for LRTIs were older during the COVID-19 pandemic in contrast to the pre-period, particularly notable in cases attributed to respiratory syncytial virus and parainfluenza virus type 3 infections. ConclusionsThis work adds to our knowledge of the epidemiology characteristics of respiratory viruses spanning the COVID-19 pandemic among children with LRTIs. The circulation of respiratory viruses changed consistently, and active LRTI surveillance in children remains critical for defining the healthcare burden of respiratory viruses.

Persistent paramyxovirus infections: in co-infections the parainfluenza virus type 5 persistent phenotype is dominant over the lytic phenotype.

Parainfluenza virus type 5 (PIV5) can either have a persistent or a lytic phenotype in cultured cells. We have previously shown that the phenotype is determined by the phosphorylation status of the phosphoprotein (P). Single amino acid substitutions at critical residues, including a serine-to-phenylalanine substitution at position 157 on P, result in a switch between persistent and lytic phenotypes. Here, using PIV5 vectors expressing either mCherry or GFP with persistent or lytic phenotypes, we show that in co-infections the persistent phenotype is dominant. Thus, in contrast to the cell death observed with cells infected solely with the lytic variant, in co-infected cells persistence is immediately established and both lytic and persistent genotypes persist. Furthermore, 10-20 % of virus released from dually infected cells contains both genotypes, indicating that PIV5 particles can package more than one genome. Co-infected cells continue to maintain both genotypes/phenotypes during cell passage, as do individual colonies of cells derived from a culture of persistently infected cells. A refinement of our model on how the dynamics of virus selection may occur in vivo is presented.

Development and evaluation of a monoclonal antibody-based blocking ELISA to detect antibodies against the E2 protein of bovine viral diarrhea virus-1

With the rapid development of cattle industry, bovine viral diarrhea virus (BVDV) is becoming widespread in China, which causes serious economic losses to the industry. Effective vaccination and viral surveillance are critical for the prevent and control of BVDV infection. In the present study, the immunogenic domain of E2 protein of BVDV-1 was expressed by prokaryotic pET-28a vector. Monoclonal antibodies (mAbs) against E2 protein were prepared and systemically examined by western blot, immunofluorescence assay, blocking ELISA (bELISA) and virus neutralization test (VNT). The mAb 1E2B3, which showed good reactivity and neutralizing activity to BVDV-1 strains, was selected for ELISA establishment. After a series of screening and optimization, a novel bELISA for highly sensitive and specific detection of BVDV-1 antibodies was established, using HRP-labeled 1E2B3 and recombinant E2 protein. ROC analysis of 91 positive and 84 negative reference bovine serum samples yielded the area under the curve (AUC) of 0.9903. A diagnostic specificity of 96.43 % and a sensitivity of 95.6 % were achieved when the cutoff value was set at 24.31 %. There was no cross reaction to the positive sera of classical swine fever virus (CSFV), BVDV-2, border disease virus (BDV), bovine parainfluenza virus type 3 (BPIV3), infectious bovine rhinotracheitis virus (IBRV), foot-and-mouth disease virus (FMDV), Mycoplasma bovis (M.bovis) and Brucella. The total agreement rate of bELISA with VNT was 93.96 % (249/265). In addition, the result of bELISA was positively correlated with neutralizing antibody titer, and the bELISA could well distinguish the serum samples before and after BVDV vaccination. These results indicate that the established bELISA in this study is specific, sensitive, simple and convenient, which provides technical support for the vaccine efficacy evaluation, prevention and control of BVD in the future.

Immunogenicity and protective efficacy of a recombinant adenovirus containing the fusion protein of bovine parainfluenza virus type 3 genotype C in mice

Bovine parainfluenza virus type 3 (BPIV3) is a viral respiratory pathogen of cattle that causes substantial economic losses. A replicating-defective recombinant human adenovirus type 5 (HAd5), carrying a fusion protein of BPIV3 genotype C (HAd5-F), was constructed and evaluated for its immunogenicity and protective efficacy in mice. After intramuscular injection with the HAd5-F, the IgG titers against F proteins increased to 1:102,400, and virus-neutralizing titers increased to 1:256, significantly higher than those in the group injected with inactivated BPIV3C in mice (p<0.05). The splenic CD4+/CD8+T lymphocytes and IFN-γ+/IL-4+ cytokine percentages were more significant in the HAd5-F group than those in the control group. A BPIV3C challenge in a mouse model was used to assess protective efficacy of the HAd5-F. The viral loads in the lungs and tracheas of mice immunized with the HAd5-F were significantly lower than those in the control group (p<0.0001). There were no significant histopathological alterations in the lungs of mice vaccinated with the HAd5-F. These findings suggested that the HAd5-F elicited excellent immunity against BPIV3C infection.

Markers of antroponotic viral infections in vervet monkeys arrived from their natural habitat (Tanzania).

Various human viruses have been identified in wild monkeys and in captive primates. Cases of transmission of viruses from wild monkeys to humans and vice versa are known. The aim of this study was to identify markers of anthroponotic viral infections in vervet monkeys (Chlorocebus pygerythrus) arrived from their natural habitat (Tanzania). Fecal samples (n = 56) and blood serum samples (n = 75) obtained from 75 animals, respectively, on days 10 and 23 after admission to the primate center, were tested for the markers of anthroponotic viral infections (Ebola virus, Marburg virus, lymphocytic choriomeningitis, hepatitis C virus, herpes simplex virus (HSV), cytomegalovirus (CMV), Epstein-Barr virus (EBV), parainfluenza types 1 and 3, intestinal adenoviruses, rotaviruses) by enzyme immunoassay (ELISA) and polymerase chain reaction (PCR). Among the examined animals, markers of 6 out of 11 tested viral infections were identified. Detection rates of IgG antibodies to HSV-1,2 (15.9%) and CMV (15.9%) were two times as low as IgG antibodies to EBV (31.8%). Among the markers of respiratory viral infections, IgG antibodies to parainfluenza virus type 1 were found (6.8%). 14.3% of the animals had rotavirus antigen, and 94% had simian adenovirus DNA. Markers of hemorrhagic fevers Ebola, Marburg, LCM, hepatitis C, and type 3 parainfluenza were not detected. When importing monkeys from different regions of the world, an expanded screening for viral infections is needed considering the epidemiological situation both in the country of importation and in the country of destination.

Total and pathogen-specific serum Immunoglobulin G concentrations in neonatal beef calves, Part 1: Risk factors.

Maternal antibodies, delivered to the calf via colostrum, are crucial to prevent calfhood diseases and death. However, knowledge regarding the factors influencing this transfer of total and specific Immunoglobulin G (IgG) against common enteric and respiratory disease pathogens under current production conditions is sparse. The objectives of this study were to determine risk factors influencing total and pathogen-specific immunoglobulin G (IgG) concentrations against Escherichia coli (E. coli), bovine Rotavirus (BRoV), Cryptosporidium parvum (C. parvum), Bovine Viral Diarrhea Virus type 1 and 2 (BVDV), Parainfluenza Virus Type 3 (PI-3), Bovine Respiratory Syncytial Virus (BRSV), and Bovine Herpesvirus type 1 (BHV-1) in the serum of newborn beef calves. A total of 420 serum samples were collected from 1- to 7-day-old beef calves born on 6 farms in Alberta, Canada. Samples were analyzed by radial immunodiffusion for total IgG concentration and by enzyme-linked immunosorbent assays for pathogen-specific IgG concentrations against E. coli, BRoV, C. parvum, BVDV, PI-3, BRSV, and BHV-1. Multivariable multilevel linear and logistic regression models were built to evaluate dam- and calf-level risk factors associated with total and pathogen-specific IgG concentrations, failed transfer of passive immunity (FTPI; serum IgG < 10g/L), and inadequate transfer of passive immunity (ITPI; serum IgG < 24g/L). Farm was included as a random effect in all models to account for clustering at the herd level. Of the 420 calves included in this study, 5% (n=20) and 18% (n=75) of calves had FTPI and ITPI, respectively. Receiving colostrum intervention (i.e., being fed colostrum or colostrum product by either bottle or tube) was the most consistent risk factor for low total IgG concentration and significantly increased the odds of FTPI (Odds ratio (OR): 6.1, 95% CI: 2.0-18.9) and ITPI (OR: 4.8, 95% CI: 2.1-10.8). Calves born to cows consistently had higher pathogen-specific IgG concentrations (P<0.0001), compared to calves born from heifers, and calves born to vaccinated dams had significantly higher BRoV, BVDV, and BHV-1-specific IgG concentrations. Interestingly, E.coli-specific IgG concentrations were associated with dam vaccination only in cows but not in heifers, which was likely due to differing vaccination strategies used. This study highlights the need to review and refine protocols with respect to dam vaccination and colostrum intervention on cow-calf operations.

Total and pathogen-specific serum Immunoglobulin G concentrations in neonatal beef calves, Part 2: Associations with health and growth.

The association of poor transfer of passive immunity (TPI) with negative health outcomes is extensively researched in dairy calves. However, few field studies have examined the effect of total and particularly pathogen-specific Immunoglobulin G (IgG) concentrations on pre-weaning health and growth of beef calves. Hence, the objective of this study was to determine the association of total and pathogen-specific IgG concentrations against selected pathogens associated with neonatal calf diarrhea (NCD) and bovine respiratory disease (BRD) and the odds of pre-weaning treatments, mortality, and the growth of newborn beef calves. A total of 420 serum samples from 1- to 7-day old beef calves born on 6 farms in Alberta, Canada, were available for this observational study. Serum samples were analyzed by radial immunodiffusion for total IgG concentration and by enzyme-linked immunosorbent assays for pathogen-specific IgG concentrations against Escherichia coli (E. coli), bovine Rotavirus (BRoV), Cryptosporidium parvum (C. parvum), Bovine Viral Diarrhea Virus (BVDV), Parainfluenza Virus Type 3 (PI-3), Bovine Respiratory Syncytial Virus (BRSV), and Bovine Herpesvirus Type 1 (BHV-1). Data about the individual dam- and calf-level risk factors, calf treatments, mortality, and birth and weaning weights were collected. Multivariable multilevel logistic and linear regression models were built to evaluate the association of total and pathogen-specific IgG concentrations with the odds of mortality and average daily gain (ADG), respectively, while their association with the odds of pre-weaning treatment was established by univariable logistic regression analysis. The odds of calves with IgG concentrations <10g/L of getting treated (OR 7.9, 95 % CI 2.7-23.7) and dying (OR: 18.5, 95 % CI: 3.7-93.4) were higher than for their counterparts (P<0.0001). Calves with IgG concentrations <24g/L also had higher odds of dying (OR: 10.1, 95 % CI: 2.6-40.2) and had lower ADG (-0.09kg, SE: 0.03, P<0.002) than calves with IgG concentrations ≥24g/L. Higher BVDV-specific IgG concentration was protective against mortality (OR: 0.97, 95 % CI: 0.96-0.99, P<0.001). This study highlights the negative association of inadequate TPI with health and growth of beef calves and thus, the need to refine protocols for dam vaccination and colostrum intervention in cow-calf operations to meet these higher IgG targets.

Coinfection of SARS-CoV-2 with other respiratory pathogens in outpatients from Ecuador.

Worldwide, the COVID-19 pandemic caused by SARS-CoV-2 has enormously impacted healthcare systems, especially in low and middle-income countries. Coinfections with respiratory pathogens in COVID-19 patients may contribute to worse outcomes. This study identified the presence of 12 viral coinfections and pneumococcal carriers among individuals with SARS-CoV-2 infection in outpatient and community settings in Ecuador. From January 2020 to November 2021, 215 nasopharyngeal and nasal swabs were taken from individuals who reported symptoms of COVID-19 or had known exposure to someone with confirmed or suspected COVID-19. One hundred fifty-eight tested positive for SARS-CoV-2 by RT-qPCR and coinfections were detected in 12% (19/158) of SARS-CoV-2-positive patients; the most frequent coinfection was with influenza A virus at 4.4% (7/158; 95% CI: 1.2-7.6), followed by respiratory syncytial virus with 3.1% (5/158; 95% CI: 0.4-5.8), and finally rhinovirus and human coronavirus NL63 with 1.2% (2/158). Pneumococcal carriage was detected in 3.7% (6/158; 95% CI: 0.76-6.64) of SARS-CoV-2 cases. Influenza B, adenovirus, human metapneumovirus (HMPV), parainfluenza virus types 1, 2, and 3, and human coronavirus HKU1 were undetected. To our knowledge, this is the first study of coinfection of SARS-CoV-2 and respiratory pathogens performed on outpatients in Latin America. The high proportion of outpatients with viral coinfections reported in our cohort allows us to suggest that testing for SARS-CoV-2 and other common respiratory pathogens should be carried out to ensure accurate diagnoses, prompt patient treatment, and appropriate isolation.

A fatal case of neonatal viral sepsis caused by human parainfluenza virus type 3

BackgroundSepsis is a systemic inflammatory response syndrome caused by severe infection in children, but cases of sepsis associated with human parainfluenza virus (HPIV) have been rarely reported in newborns.Case presentationWe report a case of HPIV-3 positive full-term newborn admitted to the Neonatal Intensive Care Unit of Beijing Children’s Hospital due to hematuria, gloomy spirit, inactivity and loss of appetite for 6 h. He had septic shock when he arrived the Accident & Emergency Department requiring immediate intubation and mechanical ventilation. Intravenous antibiotics were started. He had completely negative response to all anti-shock treatments including fluid resuscitation and vasopressor supports, and died 14 h later. Viral nucleic acid detection and metagenomic next-generation sequencing (mNGS) analyses of nasopharyngeal aspirate and blood specimens verified an HPIV-3 infection, with negative bacterial culture results. The HPIV-3 strain detected in this patient was subtyped as HPIV C3a, and two unreported amino acid mutations were found in the HN protein region.ConclusionThe patient had a severe infection associated with HPIV-3, which was the cause of sepsis and septic shock. This study showed the diagnostic value of mNGS in etiological diagnosis, especially in severe neonatal case.

Identification of Etiological Agents of Pertussis-Like Syndrome in Children Younger Than 5 Years Old Hospitalized in Southwestern Iran

Background: Despite the global vaccination program, there are many new cases of pertussis in different societies annually. Objectives: This study aimed to investigate the prevalence of some microorganisms associated with pertussis-like syndrome and compare the clinical presentations between Bordetella pertussis and pertussis-like syndrome in children. Methods: Children younger than 5 years old suspected of pertussis-like syndrome were admitted to a hospital in Ahvaz, Iran, and examined from July 2018 to July 2019. Nasopharyngeal samples were evaluated using molecular methods. The studied microorganisms were the following: Bordetella pertussis, B. parapertussis, Mycoplasma pneumoniae, Chlamydophila pneumoniae, adenovirus, respiratory syncytial virus, and parainfluenza virus type III. Results: Forty-five children were enrolled. Bordetella pertussis was detected in 15 cases (33.3%), respiratory syncytial virus in 14 (31.1%), C. pneumoniae in 3 (6.7%), and parainfluenza virus type III in 3 (6.7%). The collected samples were negative in terms of M. pneumoniae, adenovirus, and B. parapertussis. In the case of paroxysmal cough, the clinical symptoms were significantly different between pertussis and pertussis-like groups. Conclusions: The results indicated that children with pertussis-like syndrome are commonly infected with B. pertussis and respiratory syncytial virus, so more attention should be paid to this issue. The study also demonstrated the importance of molecular diagnosis methods, along with diagnosis based on clinical symptoms, in children suspected of pertussis-like syndrome.

Prediction and Analysis of Transcription Factor Binding Sites: Practical Examples and Case Studies Using R Programming.

Transcription factors (TFs) bind to specific regions of DNA known as transcription factor binding sites (TFBSs) and modulate gene expression by interacting with the transcriptional machinery. TFBSs are typically located upstream of target genes, within a few thousand base pairs of the transcription start site. The binding of TFs to TFBSs influences the recruitment of the transcriptional machinery, thereby regulating gene transcription in a precise and specific manner. This chapter provides practical examples and case studies demonstrating the extraction of upstream gene regions from the genome, identification of TFBSs using PWMEnrich R/Bioconductor package, interpretation of results, and preparation of publication-ready figures and tables. The EOMES promoter is used as a case study for single DNA sequence analysis, revealing potential regulation by the LHX9-FOXP1 complex during embryonic development. Additionally, an example is presented on how to investigate TFBSs in the upstream regions of a group of genes, using a case study of differentially expressed genes in response to human parainfluenza virus type 1 (HPIV1) infection and interferon-beta. Key regulators identified in this context include the STAT1:STAT2 heterodimer and interferon regulatory factor family proteins. The presented protocol is designed to be accessible to individuals with basic computer literacy. Understanding the interactions between TFs and TFBSs provides insights into the complex transcriptional regulatory networks that govern gene expression, with broad implications for several fields such as developmental biology, immunology, and disease research.

Development and validation of a pentaplex assay for the identification of antibodies against common viral diseases in cattle.

Animal welfare and economic implications of infectious diseases in cattle demand an efficient surveillance as the foundation for control and eradication programmes. Bovine respiratory syncytial virus (BRSV), Parainfluenza virus type 3 (PI3V), Bovine herpes virus-1 (BoHV-1), Bovine viral diarrhoea virus (BVDV), and Enzootic bovine leukosis virus (EBLV) cause common and often underdiagnosed diseases in cattle that are endemic in most countries [1]. A hallmark of individual exposure to a viral pathogen is the presence of antibodies directed towards that virus. The aim of this study was to develop and validate a pentaplex assay to simultaneously detect and quantify antibodies against BRSV, PI3V, BoHV-1, BVDV and EBLV in serum, as an efficient tool to yield epidemiological data. Monoplex assays were initially developed using either complete BRSV or BoHV-1 viral lysates, or recombinant proteins for BVDV, EBLV or PI3V as capture antigens. In addition, 125 serum samples from unvaccinated cattle, which were classified as positive or negative for each of the viruses by commercial ELISA kits, were used for validation. Conditions established for the Luminex monoplex assays were adopted for the pentaplex assay. The accuracy, determined by the area under the ROC curve, was greater than 0.97, and assay diagnostic sensitivities and specificities were over 95 and 90%, respectively, for all antigens. Intra (r) and interassay (R) coefficients of variation were under 10 and 20 %, respectively. Selectivity towards target viruses was shown by binding inhibition assays where unbound viruses reduced fluorescence intensities. Diagnostic agreement for samples analysed simultaneously in the monoplex and multiplex assays was almost perfect. In conclusion, a highly sensitive pentaplex assay was validated for the simultaneous identification of antibodies directed against BVDV, BoHV-1, PI3V, BRSV and EBLV in serum. The developed pentaplex assay complies with performance characteristics established by international guidelines for diagnostic tests and may be used as a tool for the implementation of epidemiological surveillance.

Interplay of Modified Sialic Acid Inhibitors and the Human Parainfluenza Virus 1 Hemagglutinin-Neuraminidase Active Site.

In the search for effective antivirals against Paramyxoviridae, the dynamics of human parainfluenza virus type 1 hemagglutinin-neuraminidase (hPIV1-HN) inhibition offers a promising perspective. This study focuses on the potential of C5- and C4-modified 2,3-unsaturated sialic acid (DANA) inhibitors and highlights their interaction with the hPIV1-HN enzyme. We show that a strategic substitution, replacing the C5 isopropyl group in BCX 2798 with a trifluoroacetyl function, increases inhibitory potency 3- to 4-fold. At the same time, we explore the special properties of the catalytic site of hPIV1-HN, which harbors only small substituents and favors a C4 sulfonylamido function over a carbonyl function, in contrast to the C4 pocket of Newcastle disease virus hemagglutinin-neuraminidase (NDV-HN). Based on these findings, we present a newly identified potent inhibitor that has the preferred C5 trifluoroacetamido and C4 trifluorosulfonylamide groups. The results of this study pave the way for a deeper understanding of the C4 and C5 binding pockets of hPIV1-HN and promote the development of new, more selective inhibitors.

Hylin-a1: A Pan-Inhibitor against Emerging and Re-Emerging Respiratory Viruses.

Pandemic and epidemic outbreaks of respiratory viruses are a challenge for public health and social care system worldwide, leading to high mortality and morbidity among the human populations. In light of the limited efficacy of current vaccines and antiviral drugs against respiratory viral infections and the emergence and re-emergence of new viruses, novel broad-spectrum antiviral drugs are needed for the prevention and treatment of these infections. Antimicrobial peptides with an antiviral effect, also known as AVPs, have already been reported as potent inhibitors of viral infections by affecting different stages of the virus lifecycle. In the present study, we analyzed the activity of the AVP Hylin-a1, secreted by the frog Hypsiboas albopunctatus, against a wide range of respiratory viruses, including the coronaviruses HCoV-229E and SARS-CoV-2, measles virus, human parainfluenza virus type 3, and influenza virus H1N1. We report a significant inhibitory effect on infectivity in all the enveloped viruses, whereas there was a lack of activity against the naked coxsackievirus B3. Considering the enormous therapeutic potential of Hylin-a1, further experiments are required to elucidate its mechanism of action and to increase its stability by modifying the native sequence.

A Single-Dose Intranasal Combination Panebolavirus Vaccine.

Ebolaviruses Ebola (EBOV), Sudan (SUDV), and Bundibugyo (BDBV) cause severe human disease, which may be accompanied by hemorrhagic syndrome, with high case fatality rates. Monovalent vaccines do not offer cross-protection against these viruses whose endemic areas overlap. Therefore, development of a panebolavirus vaccine is a priority. As a vaccine vector, human parainfluenza virus type 3 (HPIV3) has the advantages of needle-free administration and induction of both systemic and local mucosal antibody responses in the respiratory tract. To minimize the antivector immunity, genes encoding the HPIV3 envelope proteins F and HN were removed from the vaccine constructs, resulting in expression of only the ebolavirus envelope protein-glycoprotein. These second-generation vaccine constructs were used to develop a combination vaccine against EBOV, SUDV, and BDBV. A single intranasal vaccination of guinea pigs or ferrets with the trivalent combination vaccine elicited humoral responses to each of the targeted ebolaviruses, including binding and neutralizing antibodies, as well as Fc-mediated effector functions. This vaccine protected animals from death and disease caused by lethal challenges with EBOV, SUDV, or BDBV. The combination vaccine elicited protection that was comparable to that induced by the monovalent vaccines, thus demonstrating the value of this combination trivalent vaccine.