Respiratory Virus Research Articles

Abstract IA007: Respiratory viral infection promotes the awakening and outgrowth of dormant metastatic breast cancer cells in lungs

Abstract Breast cancer is the second most common cancer globally. Most deaths from breast cancer are due to metastatic disease which often follows long periods of clinical dormancy. Understanding the mechanisms that disrupt the quiescence of dormant disseminated cancer cells (DCC) is crucial for addressing metastatic progression. Infection with respiratory viruses (e.g. influenza or SARS-CoV-2) is common and triggers an inflammatory response locally and systemically. Here we show that influenza virus infection leads to loss of the pro-dormancy mesenchymal phenotype in breast DCC in the lung, causing DCC proliferation within days of infection, and a greater than 100-fold expansion of carcinoma cells into metastatic lesions within two weeks. Such DCC phenotypic change and expansion is interleukin-6 (IL-6)-dependent. We further show that CD4 T cells are required for the maintenance of pulmonary metastatic burden post-influenza virus infection, in part through attenuation of CD8 cell responses in the lungs. Single-cell RNA-seq analyses reveal DCC-dependent impairment of T-cell activation in the lungs of infected mice. SARS-CoV-2 infected mice also showed increased breast DCC expansion in lungs post-infection. Expanding our findings to human observational data, we observed that cancer survivors contracting a SARS-CoV-2 infection have substantially increased risks of lung metastatic progression and cancer-related death compared to cancer survivors who did not. These discoveries underscore the significant impact of respiratory viral infections on the resurgence of metastatic cancer, offering novel insights into the interconnection between infectious diseases and cancer metastasis. Citation Format: Shi B. Chia, Bryan J. Johnson, Junxiao Hu, Roel Vermeulen, Marc Chadeau-Hyam, Fernando Guntoro, Hugh Montgomery, Meher Boorgula, Varsha Sreekanth, Andrew Goodspeed, Bennett Davenport, Felipe Valenca-Pereira, Vadym Zaberezhnyy, Wolfgang E Schleicher, Dexiang Gao, Andreia N. Cadar, Michael Papanicolaou, Afshin Beheshti, Stephen B. Baylin, James Costello, Jenna M. Bartley, Thomas E. Morrison, Julio A. Aguirre-Ghiso, Mercedes Rincon, James DeGregori. Respiratory viral infection promotes the awakening and outgrowth of dormant metastatic breast cancer cells in lungs [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Tumor-body Interactions: The Roles of Micro- and Macroenvironment in Cancer; 2024 Nov 17-20; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2024;84(22_Suppl):Abstract nr IA007.

Microfluidic qPCR for detection of 21 common respiratory viruses in children with influenza-like illness.

Multiple respiratory viruses lead to high morbidity and mortality, yet global surveillance platforms focus primarily on seasonal influenza viruses. The COVID-19 pandemic and new RSV vaccines highlight the importance of a broader approach. Upper respiratory tract swabs from children aged 24-59months presenting with influenza-like illness in The Gambia were collected during follow-up of a live-attenuated influenza vaccine randomised controlled trial in 2017-18. A microfluidic quantitative polymerase chain reaction (qPCR) assay was established and used to detect 21 respiratory viruses. 76.6% of samples had one or more viruses detected (n = 121/158). The viruses detected most frequently were rhinovirus (n = 37/158, 23.4%) and adenovirus (n = 34/158, 21.5%), followed by parainfluenza virus 3, influenza B and human metapneumovirus B. A third of positive samples had multiple viruses detected (two n = 31/121, 25.6%; three n = 9/121, 7.4%). Our data demonstrates how microfluidic qPCR is a useful tool for high-throughput, comprehensive detection of multiple respiratory viruses in surveillance platforms. Rapidly changing epidemiology exemplifies the need for new, broader approaches to virus surveillance in low-resource settings to respond to future epidemics and to guide the need for and use of new prevention and therapeutic measures.

A Gaussian Process Regression and Wavelet Transform Time Series approaches to modeling Influenza A.

The global spread of Influenza A viruses is worsening economic and social challenges. Various mechanistic models have been developed to understand the virus's spread and evaluate intervention effectiveness. This study aimed to model the temporal dynamics of Influenza A using Gaussian Process Regression (GPR) and wavelet transform approaches. The study employed Continuous Wavelet Transform (CWT), Discrete Wavelet Transform (DWT) and Wavelet Power Spectrum to analyze time-series data from 2009 to 2023. The GPR model, known for its non-parametric Bayesian nature, effectively captured non-linear trends in the Influenza A data, while wavelet transforms provided insights into frequency and time-localized characteristics. The integration of GPR with DWT denoising techniques demonstrated superior performance in forecasting Influenza A cases compared to traditional models like Auto Regressive Integrated Moving Averages (ARIMA) and Exponential Smoothing (ETS) using Holt-Winter method. The study identified significant anomalies in Influenza A cases, corresponding to known pandemic events and seasonal variations. These findings highlight the effectiveness of combining wavelet transform analysis with GPR in understanding and predicting infectious disease patterns, offering valuable insights for public health planning and intervention strategies. The research recommends extending this approach to other respiratory viruses to assess its broader applicability.

Porcine reproductive and respiratory syndrome virus degrades TANK-binding kinase 1 via chaperon-mediated autophagy to suppress type I interferon production and facilitate viral proliferation.

Porcine reproductive and respiratory syndrome virus (PRRSV) has led to significant economic losses in the global swine industry. Type I interferon (IFN-I) plays a crucial role in the host's resistance to PRRSV infection. Despite extensive research showing that PRRSV employs multiple strategies to antagonise IFN-I induction, the underlying mechanisms remain to be fully elucidated. In this study, we have discovered that PRRSV inhibits the production of IFN-I by degrading TANK-binding kinase 1 (TBK1) through chaperon-mediated autophagy (CMA). From a mechanistic standpoint, PRRSV nonstructural protein 2 (Nsp2) increases the interaction between the heat shock protein member 8 (HSPA8) and TBK1. This interaction leads to the translocation of TBK1 into lysosomes for degradation, mediated by lysosomal-associated membrane protein 2A (LAMP2A). As a result, the downstream activation of IFN regulatory factor 3 (IRF3) and the production of IFN-I are hindered. Together, these results reveal a new mechanism by which PRRSV suppresses host innate immunity and contribute to the development of new antiviral strategies against the virus.

Construction of engineered probiotic that adhere and display nanobody to neutralize porcine reproductive and respiratory syndrome virus.

Pathogenic blue ear disease caused by porcine reproductive and respiratory syndrome virus (PRRSV) bring severe loss to breeding industry due to high infectivity and mortality. L. plantarum serves as the probiotic host strain, known for its beneficial properties in the gut microbiota. E. coli is used as a cloning host for the initial genetic engineering steps, facilitating the construction and amplification of the desired genetic constructs. In this study, using synthetic biology technology, we constructed engineered probiotics which could adhere and display nanobody on the surface to neutralize virus. Firstly, we screen an optimal nanobody to effectively bind with PRRSV by building library, expression and purification. Then, the integration of adhesion protein and nanobody into the genome of probiotics significantly improved its adhesion to IPEC-J2 cells. In addition, this engineered probiotic is almost non-toxic to cells with good safety, which can be used as a daily probiotics to prevent virus fecal transmission. Our study proposed this novel construction strategy of engineering probiotics with both adhesion and neutralization effects, which provided a new therapeutic view for intestinal virus clearance.

Design and Evaluation of Peptide Inhibitors Targeting the Dimerization of SARS-CoV-2 Main Protease.

The severe acute respiratory syndrome virus 2 (SARS-CoV-2) seriously impacted public health. The evolutionarily conserved viral chymotrypsin-like main protease (Mpro) is an important target for anti-SARS-CoV-2 drug development. Previous studies have shown that the eight N-terminal amino acids (N8) of SARS-CoV Mpro are essential for its dimerization, and are used to design inhibitors against SARS-CoV Mpro dimerization. Here, we established a simple readout assay using SDS-PAGE and Coomassie blue staining to measure inhibitory activity of N8 peptide derived from SARS-CoV-2 Mpro. To optimize its inhibitory effect, we then modified the side-chain length, charge, and hydrophilicity of the N8 peptide, and introduced a mutated Mpro recognition sequence. As a result, we obtained a series of potent peptide inhibitors against SARS-CoV-2 Mpro, with N8-A24 being the most efficient with an IC50 value of 1.44 mM. We observed that N8-A24 reduced Mpro dimerization with an IC50 value of 0.86 mM. Molecular docking revealed that N8-A24 formed hydrogen bond interactions with critical dimeric interface residues, thus inhibiting its dimerization and activity. In conclusion, our study not only discovers a series of peptide inhibitors targeting the SARS-CoV-2 Mpro dimerization, but also provides a promising strategy for the rational design of new inhibitors against COVID-19.

Burden and Risk Factors for Coinfections in Patients with a Viral Respiratory Tract Infection

Which patients should be monitored for coinfections or should receive empirical antibiotic treatment, in patients with an acute viral respiratory infection, is largely unknown. We evaluated the prevalence, characteristics, outcomes of coinfected patients, and risk factors associated with a coinfection among patients with an acute viral infection. A retrospective, single-center study recruited consecutive patients from October 2022 to March 2023 presenting to the emergency department with signs of a respiratory tract infection. Patients were screened for respiratory viruses and bacterial/fungal secondary infections according to local standard procedures. Outcomes included severe disease, in-hospital complications, all-cause in-hospital and ICU-related mortality, time to death, time to discharge, and time to coinfection. The analysis included 652 patients. A viral infection and a secondary bacterial/fungal infection were detected in 39.1% and 40% of cases. Compared with the rest of the cohort, coinfected patients had more frequently severe disease (88.3%, p < 0.001; 51% in patients with SARS-CoV-2) and higher in-hospital mortality (16.5%, p = 0.010). Nephropathy (OR 3.649, p = 0.007), absence of COVID-19 vaccination (OR 0.160, p < 0.001), SARS-CoV-2 infection (OR 2.390, p = 0.017), and lower blood pressure at admission (OR 0.980, p = 0.007) were independent risk factors for coinfection. Multidrug-resistant pathogens were detected in 30.8% of all coinfections. Patients with a viral infection are at high risk of bacterial coinfections, which carry a significant morbidity and mortality burden.

Recent Vaccination Against SARS-CoV-2 Is Associated with Less Severe Disease in Working-Age Adults

Background: Essential workers, including those working in healthcare and education, are at higher risk of exposure to communicable diseases, including SARS-CoV-2. Reducing the rates of infection is important for their personal health and for the ongoing safe operation of essential services. Methods: Data from participants in two prospective cohort studies who tested positive for SARS-CoV-2 in 2020 through 2023 were used to determine whether vaccination against SARS-CoV-2 is associated with the severity of symptoms in working-age adults. Results: SARS-CoV-2-positive tests (N = 3757) were reported by 3093 participants (mean: 1.2 per person); 1229 (33%) illnesses did not interfere with regular activities, 1926 (51%) made participants too unwell for regular activities, and 602 (16%) required participant bed rest. Compared with vaccine receipt more than 12 months earlier, receipt within six months of an infection was associated with lower risk ratios for more severe illness (too unwell: 0.69 and bed rest: 0.67) compared with being able to conduct regular activities. More recent vaccination was also associated with lower odds reporting of systemic symptoms (fever, myalgia, arthralgia) and fewer solicited symptoms. Conclusion: Staying current with COVID-19 vaccinations should continue to be recommended since receiving a recent immunization lessened the severity of illness. Also, as symptoms of COVID-19 are now largely similar to other respiratory viruses, practitioners need to use this evidence to inform diagnostic testing and return-to-work policies.

The evaluation of the effectiveness of bacterial lysate in preoperative preparation of children with adenotonsillar pathology

In childhood, the occurrence and steady growth of diseases of the nasopharyngeal tonsils, often acquiring a chronic course and occurring with exacerbations and complications, is facilitated by a number of factors. Etiological factors of adenotonsillar diseases in children are both bacterial and viral pathogens, among which respiratory viruses are among the most significant. Herpes virus infections (HVI) play an important role in the development of chronic upper respiratory tract pathology, especially in the cohort of frequently ill children. Representatives of the herpes virus family are characterized by lymphotropic action, long-term persistence in the body, and a tendency to reproduce in cells, leading to a violation of the immune status. The incidence of relapses in the postoperative period during surgical interventions in the ENT organs in children remains high. Herpesvirus etiology of recurrent infectious and inflammatory diseases of the URT (upper respiratory tract) is the leading factor in the ineffectiveness of tonsillotomy, adenotomy, and repeated proliferation of lymphoid tissue in the postoperative period in preschool children. The use of a drug from the group of bacterial lysates before surgery is justified in the treatment of frequently and long-term ill children with adenotonsillar hypertrophy.

SRCAP is involved in porcine reproductive and respiratory syndrome virus activated Notch signaling pathway.

In the present study, the interactome of the NSP4 originating from PRRSV was studied and SRCAP was confirmed as one of the interactors. Mechanism study showed the interaction of Nsp4 and SRCAP was found to facilitate PRRSV infection by activating non-canonical Notch signaling. ATPase Ⅰ-Ⅳ domain in SRCAP and the 122VITEA126 in Nsp4 were identified as the interacting sites that demined the activating of Notch signaling. Block Notch signaling pathway could inhibit PRRSV infection in vitro and in vivo which may be a new target for antiviral drug development.

Laboratory validation of a clinical metagenomic next-generation sequencing assay for respiratory virus detection and discovery.

Tools for rapid identification of novel and/or emerging viruses are urgently needed for clinical diagnosis of unexplained infections and pandemic preparedness. Here we developed and clinically validated a largely automated metagenomic next-generation sequencing (mNGS) assay for agnostic detection of respiratory viral pathogens from upper respiratory swab and bronchoalveolar lavage samples in <24 h. The mNGS assay achieved mean limits of detection of 543 copies/mL, viral load quantification with 100% linearity, and 93.6% sensitivity, 93.8% specificity, and 93.7% accuracy compared to gold-standard clinical multiplex RT-PCR testing. Performance increased to 97.9% overall predictive agreement after discrepancy testing and clinical adjudication, which was superior to that of RT-PCR (95.0% agreement). To enable discovery of novel, sequence-divergent human viruses with pandemic potential, de novo assembly and translated nucleotide algorithms were incorporated into the automated SURPI+ computational pipeline used by the mNGS assay for pathogen detection. Using in silico analysis, we showed that after removal of all human viral sequences from the reference database, 70 (100%) of 70 representative human viral pathogens could still be identified based on homology to related animal or plant viruses. Our assay, which was granted breakthrough device designation from the US Food and Drug Administration (FDA) in August of 2023, demonstrates the feasibility of routine mNGS testing in clinical and public health laboratories, thus facilitating a robust and rapid response to the next viral pandemic.

Abstract 4132249: Preoperative identification of respiratory viral genomes in the trachea but not in the nasopharynx is a risk factor for postoperative pulmonary hypertension in patients with congenital cardiac communications

Introduction: Pulmonary vascular remodeling is a key determinant of outcomes in patients undergoing surgery for congenital cardiac communications (CCCs). Respiratory epithelial cells infected by viruses express cytokines and growth factors with potential impact on airway and vascular remodeling. Hypothesis: Preoperative exposure to respiratory viruses renders CCC patients susceptible to postoperative pulmonary hypertension. Aims: To investigate if asymptomatic patients carrying respiratory viral genomes (RVGs) in the airways are at risk for pulmonary hypertension following cardiac surgery. To analyze the role of postoperative inflammatory reaction. Methods: The study comprised patients with unrestrictive CCCs undergoing surgery under cardiopulmonary bypass (CPB). In the absence of any signs of recent infection, RVGs were searched for in nasopharyngeal aspirates 2-3 days before surgery, and in tracheal aspirates collected in the operating room (RT-PCR, panel for 19 viruses). Serum levels of 36 inflammatory proteins were measured by chemiluminescence preoperatively and 4 hours post CPB. Pulmonary/systemic mean arterial pressure ratio (PAP/SAP) computed during the first 12 hours postoperatively (invasive assessment) was defined as the study outcome. A cutoff level was set at 0.40. Results: Sixty patients were enrolled (age 11 [7-16] months, median with interquartile range). Preoperative PAP/SAP was 0.78 (0.63-0.88). RVGs were present in nasopharyngeal and tracheal aspirates in 64% and 38% of patients, respectively. The presence of RVGs in tracheal aspirates was associated with an upward shift of postoperative PAP/SAP curve (p=0.006). The same was not observed for positive tests in nasopharyngeal aspirates (p=0.343). Of all factors analyzed as possible predictors of postoperative PAP/SAP &gt;0.40, only preoperative peripheral oxygen saturation and the presence of RVGs in the trachea were selected at multivariate analysis (respective OR with 95% CI, 0.40 [0.23-0.72] and 4.42 [1.17-16.78]. Heightened post-CPB levels of interleukin-1 receptor antagonist and chemokines MIF and MCP-1 were found to increase the risk of having a PAP/SAP &gt;0.40 in RVG carriers (respective OR with 95% CI, 2.04 [1.09-3.81], 2.34 [1.15-4.74] and 2.18 [1.07-4.43]. Conclusion: The observed relation of postoperative hemodynamics to respiratory viruses and post-CPB inflammatory reaction may have pathophysiological and therapeutic implications in pulmonary hypertension associated with congenital heart disease.

On the issue of the etiology of community-acquired pneumonia in children

According to global statistics, the number of cases of community-acquired pneumonia in children exceeds 150 million per year, and despite the introduction of vaccinations, this figure has not significantly decreased. Respiratory viruses, particularly respiratory syncytial virus, are recognized as the main cause of community-acquired pneumonia among preschool children during non-epidemic periods. Pneumococci also continue to play a significant role among bacterial pathogens. There is a significant increase in the prevalence of M. pneumoniae in the etiological structure of community-acquired pneumonia in recent years. Modern clinical guidelines for the use of antibiotics recommend taking into account patient age, vaccination status, and data on circulating pneumococcal strains when prescribing treatment. The COVID-19 pandemic and its subsequent relaxation of strict restrictions in the last two years have led to changes in the structure of infectious diseases, including the causes of lower respiratory tract infections.

The Effects of Different Respiratory Viruses on the Oxidative Stress Marker Levels in an In Vitro Model: A Pilot Study

Respiratory viruses are among the most common causes of human infections. Examining pathological processes linked to respiratory viral infections is essential for diagnosis, treatment strategies, and developing novel therapeutics. Alterations in oxidative stress levels and homeostasis are significant processes associated with respiratory viral infections. The study aimed to compare selected oxidative stress markers: total oxidative status (TOS), total antioxidant capacity (TAC), and the oxidative stress index (OSI) levels and glutathione peroxidase (GPx) and glutathione reductase (GR) activities in normal (MRC5 cell line) and tumor (A549 cell line) lung cells infected with human coronaviruses (HCoV) OC43 and 229E, human adenovirus type 5 (HAdV5), or human rhinovirus A (HRV A). We observed that a respiratory viral infection more significantly affected non-enzymatic oxidative stress markers in a lung adenocarcinoma model (A549 cells), while human lung fibroblasts (MRC-5 cell line) presented changes in enzymatic and non-enzymatic oxidative stress markers. We suggest that further detailed research is required to analyze this phenomenon.

An Outbreak of Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) in a German Boar Stud: A Retrospective Analysis of PRRSV Shedding in Boar Semen

The porcine reproductive and respiratory syndrome virus (PRRSV) causes high economical costs due to reduced productivity and losses in pig production. The virus can infect sow herds through various routes. One possible risk factor is the transmission of PRRSV through artificial insemination with infected boar semen. For these reasons, conventional boar studs should be closely monitored to detect an outbreak of PRRSV at an early stage. In the presented retrospective study, 2184 fresh semen samples from 336 boars were investigated (RT-qPCR) after an accidental PRRSV introduction to the herd. Hence, the different shedding profiles of PRRSV via semen resulted in 42.2% where no virus was detected, 2.0% intermittent shedding, and 8.4% permanent shedding. The duration of viral shedding varies from 2 days to 83 days post outbreak (on average 33 days). A significant impact of breed on PRRSV shedding duration could not be shown. Also, the distribution of the shedding profile does not follow a consistent mode, indicating that not every boar is shedding the virus via semen.

Harnessing Bacillus subtilis Spore Surface Display (BSSD) Technology for Mucosal Vaccines and Drug Delivery: Innovations in Respiratory Virus Immunization

Respiratory viruses present significant global health challenges due to their rapid evolution, efficient transmission, and zoonotic potential. These viruses primarily spread through aerosols and droplets, infecting respiratory epithelial cells and causing diseases of varying severity. While traditional intramuscular vaccines are effective in reducing severe illness and mortality, they often fail to induce sufficient mucosal immunity, thereby limiting their capacity to prevent viral transmission. Mucosal vaccines, which specifically target the respiratory tract’s mucosal surfaces, enhance the production of secretory IgA (sIgA) antibodies, neutralize pathogens, and promote the activation of tissue-resident memory B cells (BrMs) and local T cell responses, leading to more effective pathogen clearance and reduced disease severity. Bacillus subtilis spore surface display (BSSD) technology is emerging as a promising platform for the development of mucosal vaccines. By harnessing the stability and robustness of Bacillus subtilis spores to present antigens on their surface, BSSD technology offers several advantages, including enhanced stability, cost-effectiveness, and the ability to induce strong local immune responses. Furthermore, the application of BSSD technology in drug delivery systems opens new avenues for improving patient compliance and therapeutic efficacy in treating respiratory infections by directly targeting mucosal sites. This review examines the potential of BSSD technology in advancing mucosal vaccine development and explores its applications as a versatile drug delivery platform for combating respiratory viral infections.

EpiFusion: Joint inference of the effective reproduction number by integrating phylodynamic and epidemiological modelling with particle filtering.

Accurately estimating the effective reproduction number (Rt) of a circulating pathogen is a fundamental challenge in the study of infectious disease. The fields of epidemiology and pathogen phylodynamics both share this goal, but to date, methodologies and data employed by each remain largely distinct. Here we present EpiFusion: a joint approach that can be used to harness the complementary strengths of each field to improve estimation of outbreak dynamics for large and poorly sampled epidemics, such as arboviral or respiratory virus outbreaks, and validate it for retrospective analysis. We propose a model of Rt that estimates outbreak trajectories conditional upon both phylodynamic (time-scaled trees estimated from genetic sequences) and epidemiological (case incidence) data. We simulate stochastic outbreak trajectories that are weighted according to epidemiological and phylodynamic observation models and fit using particle Markov Chain Monte Carlo. To assess performance, we test EpiFusion on simulated outbreaks in which transmission and/or surveillance rapidly changes and find that using EpiFusion to combine epidemiological and phylodynamic data maintains accuracy and increases certainty in trajectory and Rt estimates, compared to when each data type is used alone. We benchmark EpiFusion's performance against existing methods to estimate Rt and demonstrate advances in speed and accuracy. Importantly, our approach scales efficiently with dataset size. Finally, we apply our model to estimate Rt during the 2014 Ebola outbreak in Sierra Leone. EpiFusion is designed to accommodate future extensions that will improve its utility, such as explicitly modelling population structure, accommodations for phylogenetic uncertainty, and the ability to weight the contributions of genomic or case incidence to the inference.

Observational Study on the Clinical Reality of Community-Acquired Respiratory Virus Infections in Adults and Older Individuals

The impact of common respiratory virus infections on adults and older individuals in the community is unclear, excluding seasonal influenza viruses. We examined FilmArray® tests performed on 1828 children aged &lt;10 years and 10,803 adults, including cases with few respiratory symptoms, between January 2021 and June 2024. Approximately 80% of the children tested positive for ≥1 viruses, while 9.5% of the adults tested positive mostly for severe acute respiratory syndrome corona virus-2 (SARS-CoV-2). Besides SARS-CoV-2 infection, 66 out of 97 patients (68.0%) aged &gt;60 years with rhinovirus/enterovirus (RV/EV), respiratory syncytial virus (RSV), parainfluenza virus-3 (PIV-3), or human metapneumovirus (hMPV) infection required hospitalization, of whom seven died; 26 out of 160 patients (16.3%) aged &lt;60 years required hospitalization mostly because of deterioration of bronchial asthma, with no reported deaths. In older patients with RV/EV infection, three with few respiratory symptoms died due to worsened heart failure. Although the frequency of common respiratory virus infections in older adults is low, it may be overlooked because of subclinical respiratory symptoms, and its clinical significance in worsening comorbidities in older adults should not be underestimated.

The introduction of a highly virulent PRRSV strain in pig farms is associated with a change in the pattern of influenza A virus infection in nurseries

The present study aimed to determine the dynamics of influenza A virus (IAV) infection in two endemically infected farms (F1 and F2), where a longitudinal follow-up of piglets was performed from birth to 8–12 weeks of age. During the study, a highly virulent isolate of porcine reproductive and respiratory syndrome virus (PRRSV) was introduced on both farms. This allowed us to examine the impact of such introduction on the patterns of infection, disease, and the antibody response of pigs to IAV infection. The introduction of the new PRRSV strain coincided with a change in the dynamics of IAV infection on both farms. In F1, the cumulative incidence of IAV increased from 20% before the outbreak to 67.5%, together with the existence of animals that tested positive for IAV (RT‒qPCR) in nasal swabs for two or more consecutive samples. In F2, the cumulative incidence of IAV increased from 50% before the PRRSV outbreak to 70%, and the proportion of prolonged IAV shedders increased sharply. Additionally, some animals were infected with the same IAV twice during the observation period. In contrast to previous reports, our study revealed that prolonged shedding was not related to the titres of maternally derived antibodies at the time of infection but was significantly (p < 0.05) related to PRRSV infection status. Notably, both before and after the PRRSV outbreak, a high proportion of IAV-infected piglets did not seroconvert, which was significantly (p < 0.05) related to the hemagglutination inhibition titres against IAV when infected.

Respiratory viruses associated with severe acute respiratory infection in children aged

With the increased availability of licensed vaccines for respiratory viruses such as severe acute respiratory syndrome coronavirus 2, respiratory syncytial virus (RSV), and influenza virus, a better understanding of the viral aetiology of severe acute respiratory infections (SARI) among children could help in optimising the use of these vaccines. We conducted a study among children aged <5 years hospitalised with SARI at a tertiary care children's hospital in north India and tested for common respiratory pathogens. We randomly enrolled eligible SARI cases aged <5 years from August 2013 to July 2015. SARI cases were defined as either <7-day history of fever with cough or in children aged eight days to three months, a physician diagnosis of acute lower respiratory infection requiring hospitalisation. We also enrolled an age-group matched control without any acute illness in a 2:1 ratio from the outpatient clinic within 24 hours of case enrolment. Nasopharyngeal and/or oropharyngeal swabs were collected and tested using TaqMan Array Cards, a real-time reverse transcription polymerase chain reaction-based multi-pathogen testing platform for selected respiratory viruses among the enrolled cases and controls. We compared the prevalence of each pathogen among cases and controls using the χ2 (χ2) or Fisher exact test (P < 0.05). We used logistic regression to estimate adjusted odds ratios (aORs) which were then used to calculate aetiologic fractions (EFs). We enrolled 840 cases and 419 outpatient controls. Almost half of the individuals in the whole sample were aged <6 months (n = 521, 41.4%). Females made up 33.7% of cases and 37.2% of controls. Viral detections were more common among cases (69%, 95% confidence interval (CI) = 66, 73) compared to controls (33%; 95% CI = 29, 38) (P < 0.01). RSV (n = 257, 31%; 95% CI = 28, 34%) was the most common virus detected among cases. Influenza A was detected among 24 (3%; 95% CI = 2, 4%), and influenza B among 5 (1%; 95% CI = 0, 1%) cases. The association between the virus and SARI was strongest for RSV (aOR = 23; 95% CI = 12, 47; EF = 96%). Antivirals were administered to 1% of SARI cases while 78% received antibiotics. Using a multi-pathogen molecular detection method, we detected respiratory viruses among more than two-thirds of children aged <5 years admitted with SARI in the Delhi tertiary care children's hospital. The guidelines for preventing and managing SARI cases among children could be optimised further with the improved availability of antivirals and vaccines.