Cause Of Respiratory Infections Research Articles

Epidemiology of respiratory virus before and during COVID-19 pandemic.

The COVID pandemic has forcefully turned the spotlight on the importance of the diagnosis of respiratory virus infections. Viruses have always been a frequent and common cause of respiratory tract infections. Rapid molecular diagnostics applied to the diagnostics of respiratory virus infections has revolutionized microbiology laboratories only a few years ago. Few studies illustrate the epidemiology of respiratory viruses, and fewer still those that have compared the pre-pandemic to the pandemic period. During the first year of the pandemic (2020-2021) it was clear to everyone to witness a sudden disappearance of the circulation of all the other respiratory viruses, especially those typically isolated during the winter time, such as RSV and Influenza virus. In our study we wanted to verify this phenomenon and to study the epidemiology of our local reality, analyzing three consecutive flu seasons (2018-2019, 2019-2020, 2020-2021). The results lead us to note that the prevalence of positivity to respiratory virus infections went from 49.8% (2018-2019) and 39% (2019-2020) to 13.4% (2020-2021). This decrease is at least partly attributable to the security measures adopted (social distancing and mask), but it certainly opens up new scenarios when the restriction measures will be terminated. We believe such studies can provide real-world evidence of the effectiveness of public health interventions implemented during current and future pandemics.

Ephedrae Herba and Cinnamomi Cortex interactions with G glycoprotein inhibit respiratory syncytial virus infectivity

Although respiratory syncytial virus (RSV) is a major cause of respiratory tract infection in children, no effective therapies are available. Recently, RSV G, the attachment glycoprotein, has become a major focus in the development of therapeutic strategies against RSV infection. Treatment of RSV-infected cultured cells with maoto, a traditional herbal medicine for acute febrile diseases, significantly reduced the viral RNA and titers. RSV attachment to the cell surface was inhibited both in the presence of maoto and when RSV particles were pre-treated with maoto. We demonstrated that maoto components, Ephedrae Herba (EH) and Cinnamomi Cortex (CC), specifically interacted with the central conserved domain (CCD) of G protein, and also found that this interaction blocked viral attachment to the cellular receptor CX3CR1. Genetic mutation of CX3C motif on the CCD, the epitope for CX3CR1, decreased the binding capacity to EH and CC, suggesting that CX3C motif was the target for EH and CC. Finally, oral administration of maoto for five days to RSV-infected mice significantly reduced the lung viral titers. These experiments clearly showed the anti-RSV activity of EH and CC mixed in maoto. Taken together, this study provides insights for the rational design of therapies against RSV infection.

Respiratory Syncytial Virus-Associated Hospital Admissions and Bed Days in Children

Respiratory syncytial virus (RSV) is a leading cause of respiratory tract infections (RTIs) in young children. High-quality country-specific estimates of bed days and length of stay (LOS) show the population burden of RSV-RTI on secondary care services and the burden among patients, and can be used to inform RSV immunization implementation decisions. We estimated the hospital burden of RSV-associated RTI (RSV-RTI) in children under 5 years in 7 European countries (Finland, Denmark, Norway, Scotland, England, the Netherlands, and Italy) using routinely collected hospital databases during 2001-2018. We described RSV-RTI admission rates during the first year of life by birth month and assessed their correlation with RSV seasonality in 5 of the countries (except for England and Italy). We estimated average annual numbers and rates of bed days for RSV-RTI and other-pathogen RTI, as well as the hospital LOS. We found that infants born 2 months before the peak month of RSV epidemics more frequently had the highest RSV-RTI hospital admission rate. RSV-RTI hospital episodes accounted for 9.9-21.2 bed days per 1000 children aged <5 years annually, with the median (interquartile range) LOS ranging from 2 days (0.5-4 days) to 4 days (2-6 days) between countries. Between 70% and 89% of these bed days were in infants aged <1 year, representing 40.3 (95% confidence interval [CI], 40.1-40.4) to 91.2 (95% CI, 90.6-91.8) bed days per 1000 infants annually. The number of bed days for RSV-RTI was higher than that for RTIs associated with other pathogens in infants aged <1 year, especially in those <6 months. RSV disease prevention therapies (monoclonal antibodies and maternal vaccines) for infants could help prevent a substantial number of bed days due to RSV-RTI. "High-risk" birth months should be considered when developing RSV immunization schedules. Variation in LOS between countries might reflect differences in hospital care practices.

Viral RNA N6-methyladenosine modification modulates both innate and adaptive immune responses of human respiratory syncytial virus.

Human respiratory syncytial virus (RSV) is the leading cause of respiratory tract infections in humans. A well-known challenge in the development of a live attenuated RSV vaccine is that interferon (IFN)-mediated antiviral responses are strongly suppressed by RSV nonstructural proteins which, in turn, dampens the subsequent adaptive immune responses. Here, we discovered a novel strategy to enhance innate and adaptive immunity to RSV infection. Specifically, we found that recombinant RSVs deficient in viral RNA N6-methyladenosine (m6A) and RSV grown in m6A methyltransferase (METTL3)-knockdown cells induce higher expression of RIG-I, bind more efficiently to RIG-I, and enhance RIG-I ubiquitination and IRF3 phosphorylation compared to wild-type virion RNA, leading to enhanced type I IFN production. Importantly, these m6A-deficient RSV mutants also induce a stronger IFN response in vivo, are significantly attenuated, induce higher neutralizing antibody and T cell immune responses in mice and provide complete protection against RSV challenge in cotton rats. Collectively, our results demonstrate that inhibition of RSV RNA m6A methylation enhances innate immune responses which in turn promote adaptive immunity.

Novel and extendable genotyping system for human respiratory syncytial virus based on whole-genome sequence analysis.

BackgroundHuman respiratory syncytial virus (RSV) is one of the leading causes of respiratory infections, especially in infants and young children. Previous RSV sequencing studies have primarily focused on partial sequencing of G gene (200–300 nucleotides) for genotype characterization or diagnostics. However, the genotype assignment with G gene has not recapitulated the phylogenetic signal of other genes, and there is no consensus on RSV genotype definition.MethodsWe conducted maximum likelihood phylogenetic analysis with 10 RSV individual genes and whole‐genome sequence (WGS) that are published in GenBank. RSV genotypes were determined by using phylogenetic analysis and pair‐wise node distances.ResultsIn this study, we first statistically examined the phylogenetic incongruence, rate variation for each RSV gene sequence and WGS. We then proposed a new RSV genotyping system based on a comparative analysis of WGS and the temporal distribution of strains. We also provide an RSV classification tool to perform RSV genotype assignment and a publicly accessible up‐to‐date instance of Nextstrain where the phylogenetic relationship of all genotypes can be explored.ConclusionsThis revised RSV genotyping system will provide important information for disease surveillance, epidemiology, and vaccine development.

Unnecessary antibiotic treatment of children hospitalised with respiratory syncytial virus (RSV) bronchiolitis: risk factors and prescription patterns

Respiratory syncytial virus (RSV) is a leading cause of respiratory tract infections, especially in young children. Antibiotics are often unnecessarily prescribed for the treatment of RSV. Such treatments affect antibiotic resistance in future bacterial infections of treated patients and the general population. This study aimed to understand risk factors for and patterns of unnecessary antibiotic prescription in children with RSV. In a single-centre, retrospective study in Israel, we obtained data for children aged ≤2 years (n=1016) hospitalised for RSV bronchiolitis during 2008-2018 and ascertained not to have bacterial co-infections. Antibiotic misuse was defined as prescription of antibiotics during hospitalisation of the study population. Demographic and clinical variables were assessed as predictors of unnecessary antibiotic treatment in a multivariable logistic regression model. The unnecessary antibiotic treatment rate of children infected with RSV and ascertained not to have a bacterial co-infection was estimated at 33.4% (95% CI 30.5-36.4%). An increased likelihood of antibiotic misuse was associated with drawing bacterial cultures and with variables indicative of a severe patient status such as lower oxygen saturation, higher body temperature, tachypnoea and prior recent emergency room visit. Older age and female sex were also associated with an increased likelihood of unnecessary antibiotic treatment. Unnecessary antibiotic treatment in RSV patients was very common and may be largely attributed to physicians' perception of patients' severity. Improving prescription guidelines, implementing antibiotic stewardship programmes and utilising decision support systems may help achieve a better balance between prescribing and withholding antibiotic treatment.

Viral and Atypical Bacterial Detection in Young Nepalese Children Hospitalized with Severe Pneumonia.

ABSTRACTRespiratory viruses cause a substantial proportion of respiratory tract infections in children but are underrecognized as a cause of severe pneumonia hospitalization in low-income settings. We employed 22 real-time PCR assays and retrospectively reanalyzed 610 nasopharyngeal aspirate specimens from children aged 2 to 35 months with severe pneumonia (WHO definition) admitted to Kanti Childrens’ Hospital in Kathmandu, Nepal, from January 2006 through June 2008. Previously, ≥1 of 7 viruses had been detected by multiplex reverse transcription-PCR in 30% (188/627) of cases. Reanalyzing the stored specimens, we detected ≥1 pathogens, including 18 respiratory viruses and 3 atypical bacteria, in 98.7% (602/610) of cases. Rhinovirus (RV) and respiratory syncytial virus (RSV) were the most common, detected in 318 (52.1%) and 299 (49%) cases, respectively, followed by adenovirus (AdV) (10.6%), human metapneumovirus (hMPV) (9.7%), parainfluenza virus type 3 (8.4%), and enterovirus (7.7%). The remaining pathogens were each detected in less than 5%. Mycoplasma pneumoniae was most common among the atypical bacteria (3.7%). Codetections were observed in 53.3% of cases. Single-virus detection was more common for hMPV (46%) and RSV (41%) than for RV (22%) and AdV (6%). The mean cycle threshold value for detection of each pathogen tended to be lower in single-pathogen detections than in codetections. This finding was significant for RSV, RV, and AdV. RSV outbreaks occurred at the end of the monsoon or during winter. An expanded diagnostic PCR panel substantially increased the detection of respiratory viruses in young Nepalese children hospitalized with severe pneumonia.IMPORTANCE Respiratory viruses are an important cause of respiratory tract infections in children but are underrecognized as a cause of pneumonia hospitalization in low-income settings. Previously, we detected at least one of seven respiratory viruses by PCR in 30% of young Nepalese children hospitalized with severe pneumonia over a period of 36 months. Using updated PCR assays detecting 21 different viruses and atypical bacteria, we reanalyzed 610 stored upper-respiratory specimens from these children. Respiratory viruses were detected in nearly all children hospitalized for pneumonia. RSV and rhinovirus were the predominant pathogens detected. Detection of two or more pathogens was observed in more than 50% of the pneumonia cases. Single-virus detection was more common for human metapneumovirus and RSV than for rhinovirus and adenovirus. The concentration of virus was higher (low cycle threshold [CT] value) for single detected pathogens, hinting at a high viral load as a marker of clinical significance.

TAKOTSUBO CARDIOMYOPATHY TRIGGERED BY CORONAVIRUS NL63 IN A COVID-19 PANDEMIC

TOPIC: Critical Care TYPE: Global Case Reports INTRODUCTION: Stress-induced cardiomyopathy cases have increased with COVID-19 pandemic, whether as a direct cardiac cause of SARS CoV2 infection or as a consequence of prolonged social isolation and multiple factors disrupting mental health. Among the different types of Coronaviruses, NL63 usually tends to present with mild respiratory and systemic symptoms. This case uniquely demonstrates how other members of the Coronavirus family may also afflict patients with Takotsubo cardiomyopathy. CASE PRESENTATION: 61-year-old male with history significant for multiple respiratory and urinary infections, CHF, CAD, CABG and recent hospitalization for bacterial pneumonia. Chest CT showed ground glass opacities on that admission though improved from 2 months prior. PCR was positive for HCoV-NL63 and was negative for SARS CoV2. He was admitted to the hospital with a fever, productive cough, shortness of breath and 10 lbs weight loss for two weeks. WBC 5,400 with subtle lymphocytopenia, Hgb 15.3 g/dL, platelets 218,000, normal renal function, PCT normal, Hgb A1C 6.0, and CXR negative for acute lung disease. Due to respiratory symptoms and the ongoing pandemic, he was retested for SARS CoV2, which was negative. EKG was negative for ischemia. CRP was elevated at 2.28 that trended down on Meropenem as prior sputum cultures grew Pseudomonas, Serratia and E. Coli. He had a normal initial Troponin that peaked to 2.94, Echocardiogram showed an EF of 20%, with apical ballooning consistent with Takotsubo cardiomyopathy as well as a mobile hyperechoic right atrial structure felt to be a thrombus extending from the SVC and no evidence of endocarditis. An echocardiogram 10 days prior showed an EF of 50-55% with mild diastolic dysfunction without any hyperechoic lesions or valvular abnormalities. On Day 4 he required pressor support while cultures grew fungi for which he was started on fluconazole. Subsequently, Cryptococcus Neoformans was isolated in the CSF and Amphotericin B was added to an increased dose of fluconazole.As he showed signs of volume overload and increased oxygen demands he was treated with loop diuretics, ACE inhibitors, and beta blockers.He was transferred for a TEE to a tertiary care facility and was treated for 42 days with Amphotericin B, Diflucan and Lactulose for hyperammonemia. He completed 6 month therapy with fluconazole.On return to his PCP he was mentating appropriately, is walker dependent and is undergoing B Cell Phenotype testing given his immunocompromised state and recurrent infections. DISCUSSION: This complicated case higlights the possibility of a Takotsubo due to Coronavirus NL63 in a immunosuppressive state. CONCLUSIONS: The presence of a viral respiratory infection due to Coronavirus NL63 presumptively triggered stress induced cardiomyopathy which responded with supportive care during a Covid-19 pandemic in a immunosuppressed patient without evidence of SARS CoV2. REFERENCE #1: Corman VM, Lienau J, Witzenrath M. Coronaviren als Ursache respiratorischer Infektionen [Coronaviruses as the cause of respiratory infections]. Internist (Berl). 2019;60(11):1136-1145. doi:10.1007/s00108-019-00671-5 REFERENCE #2: Jabri A, Kalra A, Kumar A, et al. Incidence of Stress Cardiomyopathy During the Coronavirus Disease 2019 Pandemic. JAMA Netw Open. 2020;3(7):e2014780. Published 2020 Jul 1. doi:10.1001/jamanetworkopen.2020.14780 DISCLOSURES: No relevant relationships by Pablo Echeverria, source=Web Response No relevant relationships by Andrew Mahtani, source=Web Response No relevant relationships by Anum Niazi, source=Web Response No relevant relationships by Luis Paz y Mino, source=Web Response No relevant relationships by Julia Saa, source=Web Response

Clinical manifestation, diagnosis, treatment and prevention of Coronavirus disease-2019 (COVID-19)

COVID-19 is a recently emerged infectious disease that has gripped the entire world resulting into high morbidity as well as mortality. SARS-CoV-2, a novel coronavirus, is one of the causes of respiratory infections that can transmit to other individuals through the respiratory particles and cause symptoms like fever, dry cough, and shortness of breath, anorexia, lethargy, and sore throat in infected patients. COVID-19 is difficult to distinguish during the early stages since it has a variety of clinical signs that are often comparable to other respiratory disorder. Presently, molecular tools are employed to confirm the infection due to COVID- 19. Antibiotics should not be used to prevent or treat COVID-19; however treatments, such as colchicines, monoclonal antibodies, and anticoagulants are currently being studied. Home isolation of suspected cases and those with mild illnesses, as well as those with mild infection and contact and droplet precautions, are all part of the prevention strategy.

Molecular epidemiology of respiratory syncytial virus among children and adults in India 2016 to 2018

Respiratory syncytial virus (RSV) is a common cause of respiratory tract infections among children less than 5 years of age and the elderly. This study intended to determine the circulating genotypes of RSV among severe acute respiratory illness (SARI) cases during the period 2016–2018 in India, among hospitalized acute febrile illness cases of age ranging from 1 to 65 years. Throat/nasopharyngeal swab samples were subjected for testing RSV and subgroups by real-time reverse transcriptase polymerase chain reaction (RT-PCR), further sequencing and phylogenetic analysis were performed for the second hypervariable region of the G gene. RSV-A and B subtypes co-circulated during the years 2016, 2017, and 2018, with RSV-A as the dominant subtype in 2016, and RSV-B as the dominant subgroup in 2017 and 2018. Phylogenetic analysis revealed that the circulating genotypes of RSV were GA2 (16/16), of RSV-A, and GB5 (23/23) of RSV-B in the South, North, and Northeast region of India during the period between 2016 and 2018. Here we report the first study comprising the distribution of RSV-A and B genotypes in the different geographic regions of India among children and adults during the year 2016 to 2018. We also report GA2.3.7 lineage of GA2 genotype for the first time in India to the best of our knowledge.

Exploring the epidemiological changes of common respiratory viruses since the COVID-19 pandemic: a hospital study in Hangzhou, China.

Adenovirus, respiratory syncytial virus, and influenza virus are common causes of respiratory infections. The COVID-19 pandemic had a significant impact on their prevalence. The aim of this study was to analyze the epidemic changes of common respiratory viruses in the Affiliated Hospital of Hangzhou Normal University in Hangzhou, China, from October of 2017 to February of 2021. We collected statistics from 121,529 patients in the outpatient and inpatient departments of the hospital who had throat or nose swabs collected for testing for four virus antigens by the colloidal gold method. Of these, 13,200 (10.86%) were positive for influenza A virus, 8,402 (6.91%) were positive for influenza B virus, 6,056 (4.98%) were positive for adenovirus, and 4,739 (3.90%) were positive for respiratory syncytial virus. The positivity rates of the influenza A virus (0-14 years old, P = 0.376; over 14 years old, P = 0.197) and respiratory syncytial virus (0-14 years old, P = 0.763; over 14 years old, P = 0.465) did not differ significantly by gender. After January of 2020, influenza virus infection decreased significantly. The positivity rate of respiratory syncytial virus remained high, and its epidemic season was similar to before. Strict respiratory protection and regulation of crowd activities have a great impact on the epidemic characteristics of viruses. After major changes in the public health environment, virus epidemics and their mutations should be monitored closely, extensively, and continuously.

Impact of mandatory vaccination of healthcare personnel on rates of influenza and other viral respiratory pathogens.

The implementation of mandatory influenza vaccination policies among healthcare personnel (HCP) is controversial. Thus, we examined the affect of mandatory influenza vaccination policies among HCP working in outpatient settings. Four Veterans' Affairs (VA) health systems and three non-VA medical centers. We analyzed rates of influenza and other viral causes of respiratory infections among HCP working in outpatient sites at 4 VA health systems without mandatory influenza vaccination policies and 3 non-VA health systems with mandatory influenza vaccination policies. Influenza vaccination was associated with a decreased risk of influenza (odds ratio, 0.17; 95% confidence interval [CI], 0.13-0.22) but an increased risk of other respiratory viral infections (incidence rate ratio, 1.26; 95% CI, 1.02-1.57). Our fitted regression models suggest that if influenza vaccination rates in clinics where vaccination was not mandated had equalled those where vaccine was mandated, HCP influenza infections would have been reduced by 52.1% (95% CI, 51.3%-53.0%). These observations, their possible causes, and additional strategies to reduce influenza and other viral respiratory illnesses among HCP working in ambulatory clinics warrant further investigation.

Small quantities of respiratory syncytial virus RNA only in large droplets around infants hospitalized with acute respiratory infections

BackgroundRespiratory syncytial virus (RSV) is a major cause of respiratory tract infections in young children. The predominant transmission routes for RSV are still a matter of debate. Specifically, it remains unclear if RSV can be transmitted through the air and what the correlation is between the amount of RSV in nasopharynx samples and in the air.MethodsThe amount of RSV in the air around hospitalized RSV infected infants in single-patient rooms was quantified using a six-stage Andersen cascade impactor that collects and fractionates aerosols and droplets according to size. RSV shedding in the nasopharynx of patients was followed longitudinally by quantifying RSV RNA levels and infectious virus in nasopharyngeal aspirates. Nose and throat swabs of parents and swabs of the patient’s bedrail and a datalogger were also collected.ResultsPatients remained RSV positive during the air sampling period and infectious virus was isolated up to 9 days post onset of symptoms. In three out of six patients, low levels of RSV RNA, but no infectious virus, were recovered from impactor collection plates that capture large droplets > 7 μm. For four of these patients, one or both parents were also positive for RSV. All surface swabs were RSV-negative.ConclusionsDespite the prolonged detection of infectious RSV in the nasopharynx of patients, only small amounts of RSV RNA were collected from the air around three out of six patients, which were primarily contained in large droplets which do not remain suspended in the air for long periods of time.

Predominance of Human Bocavirus Genotypes 1 and 2 in Oysters in Thailand.

Human bocavirus (HBoV) has been recognized as an important pathogen that causes respiratory infection and acute gastroenteritis in young children worldwide. HBoV is most likely transmitted by the respiratory route and by fecal-oral transmission. Recently, HBoV has been detected in several types of environmental water and in bivalve shellfish. However, study of the existence of HBoV in oysters is still undocumented in Thailand. In this study, 144 oyster samples collected from different markets in Chiang Mai, Thailand, in 2017 and 2018 were investigated for the presence of HBoV by nested PCR and sequencing. HBoV was detected in 11 out of 144 samples (7.6%). Nine HBoV-positive samples (81.8%) were identified as genotype 1 (HBoV1) and two (18.2%) as HBoV2. A monthly investigation of HBoV in oyster samples from July 2017 to June 2018 showed that HBoV was sporadically detected in particular months spanning the rainy and colder season, with a peak in January. This study demonstrates the presence and genotype diversity of HBoV in oyster samples in Thailand. The findings contribute to evaluating the risk of foodborne transmission of HBoV and to monitoring outbreaks of HBoV in Thailand and in other countries. IMPORTANCE Human bocavirus is recognized as an important cause of respiratory infection and of acute gastroenteritis in children worldwide. Human bocavirus has been widely detected in many clinical specimens, as well as in several types of environmental samples. Most previous studies describe the incidence of bocavirus infection in humans, whereas few data are available for the occurrence of human bocavirus in food materials, particularly that in bivalve shellfish. Our findings provide evidence for the existence and prevalence of human bocavirus in oysters, suggesting that further monitoring of the potential risk of food- and waterborne transmission of this virus to humans should be undertaken.

Prevalence and Risk Factors of Respiratory Syncytial Virus in Children under 5 Years of Age in the WHO European Region: A Systematic Review and Meta-Analysis.

A respiratory syncytial virus (RSV) is the major cause of respiratory tract infection in children under 5 years. However, RSV infection in the European Region of the World Health Organization has not been systematically reviewed. The aim was to determine the prevalence and factors associated with RSV in children under 5 years of age in European regions. A systematic review and meta-analysis was performed. CINAHL, Medline, LILACS, ProQuest, SciELO, and Scopus databases were consulted for studies published in the last 5 years, following Preferred Reporting Items for Systematic Reviews and Meta-analysis guidelines. The search equation was “respiratory syncytial virus AND (newborn OR infant OR child) AND (prevalence OR risk factors)”. Studies reporting the prevalence of RSV were eligible for inclusion in the meta-analysis. A total of 20 articles were included. The meta-analytic prevalence estimation of RSV, with a sample of n = 16,115 children, was 46% (95% CI 34–59%). The main risk factors were age, male gender, winter season, and environmental factors such as cold temperatures, higher relative humidity, high concentrations of benzene, exposure to tobacco, and living in urban areas. Robust age-specific estimates of RSV infection in healthy children should be promoted in order to determine the optimal age for immunization. In addition, it is necessary to analyse in greater depth the potentially predictive factors of RSV infection, to be included in prevention strategies.

Acute Respiratory Tract Infections among Hospitalized Palestinian Patients (2011–2016): A Retrospective Study

Respiratory tract infections (RTIs) are a major public health concern. This study aims to investigate the profiles and epidemiological characteristics of acute RTIs and respiratory pathogens in Palestinian hospitalized patients. Clinical samples from hospitalized patients with symptoms of acute RTIs admitted between January 2011 and December 2016 were referred to the Palestinian Central Public Health Laboratory (PHCL) to identify the causative pathogen. Patients' demographic information and the results of the molecular identification were retrieved from the electronic database at the PHCL. A total of 15413 patients with acute RTIs were hospitalized during the study period. The causal agent was identified only in 28.7% of the patients. Overall, influenza viruses were the most common cause of RTIs among hospitalized Palestinian patients in the West Bank. Children and elderlies were the most affected with RTIs. The elderly population (≥60 years old) had the highest rates. After influenza A virus, respiratory syncytial virus (RSV), and Bordetella pertussis (B. pertussis) were the most common causes of acute RTIs among hospitalized Palestinian patients. Children showed the highest hospitalization rates for RSV, B. pertussis, adenovirus, enterovirus, and Streptococcus pneumoniae. On the other hand, elderlies had the highest rates of influenza. Outbreaks of RTIs occurred mainly during winter (between December and March). The resurgence of B. pertussis in spite of vaccination is alarming and requires further investigation.

Assessment of exposure to influenza A viruses in pigs between weaning and market age

Influenza A viruses (IAVs) are common causes of respiratory infection in pigs. The objective of this study was to characterize the circulation of IAVs between weaning and market age on the basis of development of antibody response and molecular epidemiology of detected viruses. Two batches of weaned pigs were followed in the nursery and finisher barns with a sample of 81 and 75 pigs. Nasal swabs and blood samples were collected from individual pigs for virological and serological analyses. A H3N2 subtype virus, of cluster IV, was detected in Study 1, with a maximum of 97.9% identity to HA gene of viruses previously isolated in Ontario. In Study 2, a H1N1 subtype virus, of 2009 H1N1 pandemic lineage, was detected, with a maximum of 97.8% identity to HA gene of viruses previously isolated in Ontario. On the basis of HA gene, it was observed that pigs were being detected with the same virus over time. The existence of antibody titers for IAV other than the isolated one confirmed that more than one subtype can circulate in the same population. In Study 1, pigs with higher numbers of IAV detection had lower serological titers for the same virus that was confirmed to circulate in the nursery (P < 0.01). Thorough knowledge of all endemic viral strains is fundamental for development of infection and disease control, particularly in complex production systems. This may include consideration of sampling and testing strategies which could detect circulation of all IAV variants, even if they have low prevalence.

Elastase Activity From Pseudomonas aeruginosa Respiratory Isolates and ICU Mortality

Pseudomonas aeruginosa (PA) is a common cause of respiratory infection and morbidity. Pseudomonas elastase is an important virulence factor regulated by the lasR gene. Whether PA elastase activity is associated with worse clinical outcomes in ICU patients is unknown. Is there an association between PA elastase activity and worse host outcomes in a cohort of ICU patients? PA respiratory isolates from 238 unique ICU patients from two tertiary-care centers within the University of Pittsburgh Medical Center health system were prospectively collected and screened for total protease and elastase activity, biofilm production, antimicrobial resistance, and polymicrobial status. The association between pathogen characteristics and 30-day and 90-day mortality was calculated using logistic regression. For subgroup analysis, two patterns of early (≤72 h) and late sample (>72 h) collection from the index ICU admission were distinguished using a finite mixture model. Lung inflammation and injury was evaluated in a mouse model using a PA high elastase vslow elastase producer. PA elastase activity was common in ICU respiratory isolates representing 75%of samples and was associated with increased 30-day mortality (adjusted OR [95% CI]: 1.39 [1.05-1.83]). Subgroup analysis demonstrated that elastase activity was a risk factor for 30- and 90-day mortality in the early sample group, whereas antimicrobial resistance was a risk factor for 90-day mortality in the late sample group. Whole genome sequencing of high and low elastase producers showed that predicted loss-of-function lasR genotypes were less common among high elastase producers. Mice infected with a high elastase producer showed increased lung bacterial burden and inflammatory profile compared with mice infected with a low elastase producer. Elastase activity is associated with 30-day ICU mortality. A high elastase producing clinical isolate confers increased lung tissue inflammation compared with a low elastase producer invivo.

Computer-Aided Prediction and Identification of Phytochemicals as Potential Drug Candidates against MERS-CoV

The Middle East respiratory syndrome coronavirus (MERS-CoV) is the major leading cause of respiratory infections listed as blueprint of diseases by the World Health Organization. It needs immediate research in the developing countries including Saudi Arabia, South Korea, and China. Still no vaccine has been developed against MERS-CoV; therefore, an effective strategy is required to overcome the devastating outcomes of MERS. Computer-aided drug design is the effective method to find out potency of natural phytochemicals as inhibitors of MERS-CoV. In the current study, the molecular docking approach was employed to target receptor binding of CoV. A total of 150 phytochemicals were docked as ligands in this study and found that some of the phytochemicals successfully inhibited the catalytic triad of MERS-CoV. The docking results brought novel scaffolds which showed strong ligand interactions with Arg178, Arg339, His311, His230, Lys146, and Arg139 residues of the viral domains. From the top ten ligands found in this study (i.e., rosavin, betaxanthin, quercetin, citromitin, pluviatilol, digitogenin, ichangin, methyl deacetylnomilinate, kobusinol A, and cyclocalamin) based on best S -score values, two phytochemicals (i.e., pluviatilol and kobusinol A) exhibited all drug-likeness properties following the pharmacokinetic parameters which are important for bioavailability of drug-like compounds, and hence, they can serve as potential drug candidates to stop the viral load. The study revealed that these phytochemicals would serve as strong potential inhibitors and a starting point for the development of vaccines and proteases against MERS-CoV. Further, in vivo studies are needed to confirm the efficacy of these potential drug candidates.

Surveillance for Severe Acute Respiratory Infections among Hospitalized Subjects from 2015/2016 to 2019/2020 Seasons in Tuscany, Italy.

In Italy, the influenza season lasts from October until April of the following year. Influenza A and B viruses are the two viral types that cocirculate during seasonal epidemics and are the main causes of respiratory infections. We analyzed influenza A and B viruses in samples from hospitalized patients at Le Scotte University Hospital in Siena (Central Italy). From 2015 to 2020, 182 patients with Severe Acute Respiratory Infections were enrolled. Oropharyngeal swabs were collected from patients and tested by means of reverse transcriptase-polymerase chain reaction to identify influenza A(H3N2), A(H1N1)pdm09 and B. Epidemiological and virological surveillance remain an essential tool for monitoring circulating viruses and possible mismatches with seasonal vaccine strains, and provide information that can be used to improve the composition of influenza vaccines.