Clinical findings in 111 cases of influenza A (H7N9) virus infection

Clinical significance of lower respiratory tract culture within 48 h of admission in patients with viral pneumonia: an observational study

BACKGROUND

The aim of this retrospective study was to examine the risk factors of positive lower respiratory tract cultures and to investigate whether nosocomial infections are common in patients with positive lower respiratory tract cultures.

METHODS

We enrolled 86 patients diagnosed with influenza A-related critical illness who were treated at Fuzhou Pulmonary Hospital of Fujian in China between 1st October 2013 and 31st March 2019. The of admission were used to divide the enrolled patients into two groups. Sputum and bronchoalveolar lavage fluid specimens were collected within 48 h after admission for culture. All samples were cultured immediately after sampling. Nosocomial infections are defined as any symptom or sign of pulmonary infiltration, confirmed by X-ray, after 5 days of admission and positive results from one or more cultures.

RESULTS

The average age of this cohort was (54.13 ± 16.52) years. Based on the culture results, Staphylococcus aureus and Candida albicans had the highest positive rates (3.40% (3/86) and 20.90% (18/86), respectively). In patients with positive lower respiratory tract cultures, the incidence of nosocomial infection was 73.30% (22/30) five days after admission. However, the incidence of nosocomial infection was lower (42.80%, 24/56) in patients with negative lower respiratory tract cultures. Hemoptysis, systolic pressure at admission, and blood urea nitrogen level at admission were all independent risk factors for positive lower respiratory tract cultures within 48 h of admission.

CONCLUSION

Our data showed that a significant proportion of patients with pneumonia exhibited co-infections with bacteria or fungi within five days of hospital admission. Hemoptysis, systolic pressure, and blood urea nitrogen levels at admission emerged as the key risk factors. These findings underscore the necessity of closely monitoring patients with influenza infection, particularly for positive bacterial or fungal cultures within the initial 48 h of admission.

Clinical Profile, Intensive Care Needs and Predictors of Outcome Among Children Admitted with Non-COVID Severe Acute Respiratory Illness (SARI) During the Pandemic

OBJECTIVES

To study the epidemiology of non-coronavirus disease-2019 (non-COVID-19) respiratory viral infections with respect to their clinical profile, intensive care needs and predictors of outcome once the non-pharmacological interventions (NPI) during the coronavirus disease-2019 (COVID-19) pandemic were relaxed.

METHODS

Retrospective analysis of children with Severe Acute Respiratory Illness (SARI) who were SARS-CoV-2 negative, admitted to the Pediatric Emergency/Intensive Care Unit (PICU) from July 2021 through October 2021 was conducted.

RESULTS

One hundred and thirty nine children with median age of 11 (4-28.5) mo were included. Besides respiratory symptoms in all, diarrhea was reported in 90 (64.7%) children. Nearly half (n = 66; 47%) presented in hypoxemic respiratory failure (SpO2 <88%). Fifty-two (37.4%) children had co-morbidities, commonest being congenital heart disease in 12 (23.1%). Baseline parameters revealed leukopenia (specifically lymphopenia) 39 (28%), elevated aspartate transaminase [Serum glutamic-oxaloacetic transaminase (SGOT)] in 108 (77.6%), elevated N-acetyl-cysteine-activated creatinine kinase (CK-NAC) 23 (79%) and lactate dehydrogenase (LDH) 15 (88%). Intensive care needs included mechanical ventilation 51 (36.6%), vasoactive support 34 (24.5%), and renal replacement therapy 10 (7.1%). Forty-two (30.2%) children developed multi-organ dysfunction syndrome (MODS). One hundred and three (74.1%) children were discharged, 31 (22.3%) died, and 5 (3.6%) left against medical advice. On multivariate regression analysis, elevated liver enzymes (>5 times normal), hypoxemic respiratory failure at admission, hypotensive shock and MODS predicted mortality.

CONCLUSIONS

A surge in non-COVID SARI was observed once lockdown measures were relaxed. Nearly 1/3rd progressed to multi-organ failure and died. Elevated liver enzymes, hypoxemic respiratory failure at admission, hypotensive shock and MODS predicted death.

CT findings of 144 in-hospital patients with influenza pneumonia: A retrospective analysis

BACKGROUND/PURPOSE

Patients with influenza infection during their period of admission may have worse computed tomography (CT) manifestation according to the clinical status. This study aimed to evaluate the CT findings of in-hospital patients due to clinically significant influenza pneumonia with correlation of clinical presentations.

METHODS

In this retrospective, single center case series, 144 patients were included. All in-hospital patients were confirmed influenza infection and underwent CT scan. These patients were divided into three groups according to the clinical status of the most significant management: (1) without endotracheal tube and mechanical ventilator (ETTMV) or extracorporeal membrane oxygenation (ECMO); (2) with ETTMV; (3) with ETTMV and ECMO. Pulmonary opacities were scored according to extent. Spearman rank correlation analysis was used to evaluate the correlation between clinical parameters and CT scores.

RESULTS

The predominant CT manifestation of influenza infection was mixed ground-glass opacity (GGO) and consolidation with both lung involvement. The CT scores were all reach significant difference among all three groups (8.73 ± 6.29 vs 12.49 ± 6.69 vs 18.94 ± 4.57, p < 0.05). The chest CT score was correlated with age, mortality, and intensive care unit (ICU) days (all p values were less than 0.05). In addition, the CT score was correlated with peak lactate dehydrogenase (LDH) level and peak C-reactive protein (CRP) level (all p values were less than 0.05). Concomitant bacterial infection had higher CT score than primary influenza pneumonia (13.02 ± 7.27 vs 8.95 ± 5.99, p < 0.05).

CONCLUSION

Thin-section chest CT scores correlated with clinical and laboratory parameters in in-hospital patients with influenza pneumonia.

Effects of canine influenza infection and DA2PP vaccination on the development of platelet-associated immunoglobulins and platelet counts in dogs

BACKGROUND

Immune thrombocytopenia (ITP) is commonly associated with platelet-associated immunoglobulins (PAIg). Demonstration of PAIg can help determine etiologies for thrombocytopenia. In humans, ITP and thrombocytopenia have been associated with various vaccinations and influenza infections, respectively.

OBJECTIVES

We aimed to evaluate platelet counts and PAIg in research dogs with H3N2 and in research and client-owned dogs routinely vaccinated for distemper, adenovirus-2, parainfluenza, and parvovirus (DA2PP). The hypotheses were that H3N2 infection but not DA2PP vaccination would decrease platelet counts, and neither would result in the detection of PAIg.

METHODS

Three pilot studies. Platelet counts and PAIg, measured by direct flow cytometry as %IgG, were evaluated in eight research Beagles following experimental infection with H3N2 (experiment 1), nine research Beagles vaccinated for DA2PP (experiment 2), and thirty client-owned dogs vaccinated for DA2PP (experiment 3). All animals were considered healthy at the start of the experiments.

RESULTS

Transient, self-resolving decreases in platelet counts and increases in %IgG occurred following H3N2 infection, and one dog became thrombocytopenic and positive for PAIg. Following DA2PP vaccination, %IgG increased in research and client-owned dogs, but only one dog was considered positive for PAIg with a concurrent increase in platelet count. Mean PAIg increased from baseline in client-owned dogs following vaccination.

CONCLUSIONS

Transient PAIg and thrombocytopenia can occur following H3N2 infection, while routine vaccination for DA2PP in this group of dogs was not associated with the development of thrombocytopenia or clinically relevant formation of PAIg.

Mesenchymal stem cells prevent H7N9 virus infection via rejuvenating immune environment to inhibit immune-overactivity

BACKGROUND

Influenza is a clinically important infectious disease with a high fatality rate, which always results in severe pneumonia. Mesenchymal stem cells (MSCs) exhibit promising therapeutic effects on severe viral pneumonia, but whether MSCs prevent virus infection and contribute to the prevention of influenza remains unknown.

METHODS

ICR mice were pretreated with human umbilical cord (hUC) MSCs and then infected with the influenza H7N9 virus. Weight, survival days, and lung index of mice were recorded. Serum antibody against influenza H7N9 virus was detected according to the hemagglutination inhibition method. Before and after virus infection, T cell and B cell subtypes in the peripheral blood of mice were evaluated by flow cytometry. Cytokines in the supernatants of MSCs, innate immune cells, and mouse broncho alveolar lavage fluid (BALF) were determined by enzyme-linked immunosorbent assay (ELISA) or Luminex Assay.

RESULTS

Pretreatment with MSCs protected mice against influenza H7N9 virus infection. Weight loss, survival rate, and structural and functional damage to the lungs of infected mice were significantly improved. Mechanistically, MSCs modulated T lymphocyte response in virus-infected mice and inhibited the cGAS/STING pathway. Importantly, the protective effect of MSCs was mediated by cell-to-cell communications and attenuation of cytokine storm caused by immune overactivation.

The pathogenesis of influenza in intact alveoli: virion endocytosis and its effects on the lung's air-blood barrier

Lung infection by influenza A virus (IAV) is a major cause of global mortality from lung injury, a disease defined by widespread dysfunction of the lung's air-blood barrier. Endocytosis of IAV virions by the alveolar epithelium - the cells that determine barrier function - is central to barrier loss mechanisms. Here, we address the current understanding of the mechanistic steps that lead to endocytosis in the alveolar epithelium, with an eye to how the unique structure of lung alveoli shapes endocytic mechanisms. We highlight where future studies of alveolar interactions with IAV virions may lead to new therapeutic approaches for IAV-induced lung injury.

Establishment of sex-specific predictive models for critical illness in Chinese people with the Omicron variant

Introduction

The Omicron variant has rapidly spread throughout the world compared to the Delta variant and poses a great threat to global healthcare systems due to its immune evasion and rapid spread. Sex has been identified as a factor significantly associated with COVID-19 mortality, but it remains unclear which clinical indicators could be identified as risk factors in each sex group and which sex-specific risk factors might shape the worse clinical outcome, especially for Omicrons. This study aimed to confirm the relationship between sex and the progression of the Omicron variant and to explore its sex-biased risk factors.

Methods

We conducted a retrospective study including 1,132 hospitalized patients with the COVID-19 Omicron variant from 5 December 2022 to 25 January 2023 at Shanghai General Hospital, and the medical history data and clinical index data of the inpatients for possible sex differences were compared and analyzed. Then, a sex-specific Lasso regression was performed to select the variables significantly associated with critical illness, including intensive care unit admission, invasive mechanical ventilation, or death. A logistic regression was used to construct a sex-specific predictive model distinctively for the critical illness outcome using selected covariates.

Results

Among the collected 115 clinical indicators, up to 72 showed significant sex differences, including the difference in merit and the proportion of people with abnormalities. More importantly, males had greater critical illness (28.4% vs. 19.9%) and a significantly higher intensive care unit occupancy (20.96% vs. 14.49%) and mortality (13.2% vs. 4.9%), and males over 80 showed worse outcomes than females. Predictive models (AUC: 0.861 for males and 0.898 for females) showed 12 risk factors for males and 10 for females. Through a comprehensive sex-stratified analysis of a large cohort of hospitalized Omicron-infected patients, we identified the specific risk factors for critical illness by developing prediction models.

Discussion

Sex disparities and the identified risk factors should be considered, especially in the personalized prevention and treatment of the COVID-19 Omicron variant.

Probenecid Inhibits Influenza A(H5N1) and A(H7N9) Viruses In Vitro and in Mice

Avian influenza (AI) viruses cause infection in birds and humans. Several H5N1 and H7N9 variants are highly pathogenic avian influenza (HPAI) viruses. H5N1 is a highly infectious bird virus infecting primarily poultry, but unlike other AIs, H5N1 also infects mammals and transmits to humans with a case fatality rate above 40%. Similarly, H7N9 can infect humans, with a case fatality rate of over 40%. Since 1996, there have been several HPAI outbreaks affecting humans, emphasizing the need for safe and effective antivirals. We show that probenecid potently inhibits H5N1 and H7N9 replication in prophylactically or therapeutically treated A549 cells and normal human broncho-epithelial (NHBE) cells, and H5N1 replication in VeroE6 cells and mice.

Avian influenza virus cross-infections as test case for pandemic preparedness: From epidemiological hazard models to sequence-based early viral warning systems

Pandemic preparedness starts with an early warning system of viruses with a pandemic potential. Based on information collected in a multitude of surveys, hazard models were developed identifying influenza viruses presenting a pandemic threat. Scores are attributed for 10 viral traits by expert panels which identified avian influenza viruses (AIV) belonging to subtypes H7N9 and H5N1 as representing the greatest pandemic risk. In 2013, more than 100 human cases infected with AIV H7N9 were observed in China. Case fatality rate (CFR) was high (27%), but the human-to-human transmission rate was low and by serological evidence H7N9 did not spread widely. Nevertheless, until 2019 more than 1500 H7N9 patients were identified characterized by a high CFR of 39%. Serology demonstrated that mild infections with H7N9 were widespread. In 2003, more than 400 people experienced AIV H7N7 cross-infection causing mainly conjunctivitis during a large poultry epidemic in The Netherlands. Between 1996 and 2019, a total of 881 human infections with avian H5N1 viruses were documented showing a CFR of 52%. Outbreaks were centred on South East Asia and showed close associations with epizootics in poultry. Mutations predisposing to human cross-infections were identified in the haemagglutinin (HA) and the RNA polymerase subunit PB2 of human H7N9 isolates. Human H5N1 isolates showed mutations in the receptor binding domain of HA and transmission in mammals could be obtained by as few as four additional aa changes introduced experimentally. Researchers have defined viral point mutations in HA, PB2 and the nucleoprotein NP that allowed AIV to cross the species barrier to mammals with respect to receptor recognition, RNA replication and escape from innate immunity respectively. Based on this insight a sequence-based early warning system for AIV preadapted to human transmission could be envisioned. Mink farms and live poultry markets are prime targets for such sequencing efforts.

Mathematical modeling of the infectious spread and outbreak dynamics of avian influenza with seasonality transmission for chicken farms

A compartmental model with a time-varying contact rate, the seasonality effect, and its corresponding nonautonomous model are investigated. The model is developed based on the six compartments: susceptible, latent, infected, asymptomatic, treated, and recovered individuals. We determine the effective reproduction number for this nonautonomous system, and analytic discussion shows that at least one positive periodic solution exists for R0>1. The model is simulated using the RK-45 numerical method, and the parameter values for the model are taken from the available literature. From the numerical results, we observe that the degree of seasonality and vaccine efficacy significantly impact the amplitude of the epidemic curve. The latent-infected phase plane shows that periodic solutions exhibit a period-doubling bifurcation as the amplitude of seasonality increases. Finally, the model outcome was compared with the actual field data and found to be consistent.

Comparative Pathology of Animal Models for Influenza A Virus Infection

Animal models are essential for studying disease pathogenesis and to test the efficacy and safety of new vaccines and therapeutics. For most diseases, there is no single model that can recapitulate all features of the human condition, so it is vital to understand the advantages and disadvantages of each. The purpose of this review is to describe popular comparative animal models, including mice, ferrets, hamsters, and non-human primates (NHPs), that are being used to study clinical and pathological changes caused by influenza A virus infection with the aim to aid in appropriate model selection for disease modeling.

Associations of telomere length with risk of mortality from influenza and pneumonia in US adults: a prospective cohort study of NHANES 1999-2002

BACKGROUND

Due to the ongoing Coronavirus disease 2019 (COVID-19) pandemic, interest has arisen to realize the relationship between telomere length (TL) and influenza and pneumonia mortality.

AIM

Our study attempted to investigate this correlation by analyzing information gathered from the National Health and Nutrition Examination Survey (NHANES) 1999-2002.

METHODS

A total of 7229 participants were involved in the conducted research. We utilized Cox proportional risk model analysis to determine the hazard ratio (HR) and 95% confidence interval (CI) for TL and influenza and pneumonia mortality.

RESULTS

During the average follow-up time of 204.10 ± 51.26 months, 33 (0.45%) participants died from influenza and pneumonia. After adjusting for multiple variables, shorter TL was associated with higher influenza-pneumonia mortality. In subgroup analyses stratified by sex, men exhibited stronger associations with influenza-pneumonia mortality than women (Model 1: HRmale: 0.014 vs HRfemale: 0.054; Model 2: HRmale: 0.082 vs HRfemale: 0.890; Model 3: HRmale: 0.072 vs HRfemale: 0.776). For subgroup analyses by visceral adiposity index (VAI), all statistically significant (P < 0.05) models displayed an inverse relationship between TL and influenza and pneumonia mortality.

CONCLUSIONS

Our research provides further proof for the connection between shorter telomeres and higher influenza-pneumonia mortality. Larger prospective researches are essential to support our results and explain the underlying mechanisms.

Emerging Infectious Diseases Are Virulent Viruses-Are We Prepared? An Overview

The recent pandemic caused by SARS-CoV-2 affected the global population, resulting in a significant loss of lives and global economic deterioration. COVID-19 highlighted the importance of public awareness and science-based decision making, and exposed global vulnerabilities in preparedness and response systems. Emerging and re-emerging viral outbreaks are becoming more frequent due to increased international travel and global warming. These viral outbreaks impose serious public health threats and have transformed national strategies for pandemic preparedness with global economic consequences. At the molecular level, viral mutations and variations are constantly thwarting vaccine efficacy, as well as diagnostic, therapeutic, and prevention strategies. Here, we discuss viral infectious diseases that were epidemic and pandemic, currently available treatments, and surveillance measures, along with their limitations.

A five-day treatment course of zanamivir for the flu with a single, self-administered, painless microneedle array patch: Revolutionizing delivery of poorly membrane-permeable therapeutics

Seasonal influenza virus infections cause a substantial number of deaths each year. While zanamivir (ZAN) is efficacious against oseltamivir-resistant influenza strains, the efficacy of the drug is limited by its route of administration, oral inhalation. Herein, we present the development of a hydrogel-forming microneedle array (MA) in combination with ZAN reservoirs for treating seasonal influenza. The MA was fabricated from Gantrez® S-97 crosslinked with PEG 10,000. Various reservoir formulations included ZAN hydrate, ZAN hydrochloric acid (HCl), CarraDres™, gelatin, trehalose, and/or alginate. In vitro permeation studies with a lyophilized reservoir consisting of ZAN HCl, gelatin, and trehalose resulted in rapid and high delivery of up to 33 mg of ZAN across the skin with delivery efficiency of up to ≈75% by 24 h. Pharmacokinetics studies in rats and pigs demonstrated that a single administration of a MA in combination with a CarraDres™ ZAN HCl reservoir offered a simple and minimally invasive delivery of ZAN into the systemic circulation. In pigs, efficacious plasma and lung steady-state levels of ∼120 ng/mL were reached within 2 h and sustained between 50 and 250 ng/mL over 5 days. MA-enabled delivery of ZAN could enable a larger number of patients to be reached during an influenza outbreak.

The use of the nutritional supplements during the covid-19 outbreak in Saudi Arabia: A cross-sectional study

BACKGROUND

COVID-19 causes moderate to severe illness and is spreading globally. During a pandemic, vitamins and minerals are vital to health. Therefore, the prevalence and epidemiology of supplement use in Saudi Arabia during the COVID-19 pandemic must be known.

METHODS

This cross-sectional study was conducted in Saudi Arabia using an online survey. The study was conducted from June to March 2022 on both adults and children. The link to the survey was shared on social media platforms. The survey included questions on participants' demographics, vaccination status, supplements they used, and side effects of supplements. Participation in this study was optional, and there was no obligation to participate. There was a declaration about the aim of the study and different objectives before starting the survey.

RESULTS

The present study reported that most of the participants reported that they used vitamin C (64.6 %), zinc (51.9 %), multivitamins (46.1 %), black seeds (26.7 %), garlic (Allium sativum) (15.4 %), omega-3 (22.1 %), vitamin D (22.2 %), echinacea (10.1 %), manuka honey (26.0 %), curcumin (13.6 %), ginger (22.5 %), royal jelly (12.9 %), and propolis (7.5 %) before and during the COVID-19 pandemic period. These supplements were used more frequently by subjects during the pandemic than before.

DISCUSSION AND CONCLUSION

The respondents' risk of these supplements' use may partially reflect the public's behavioral response during a pandemic. Future studies can document the health beliefs and motivations of nutritional supplement users.

Amino Acid Variation at Hemagglutinin Position 193 Impacts the Properties of H9N2 Avian Influenza Virus

Despite active control strategies, including the vaccination program in poultry, H9N2 avian influenza viruses possessing mutations in hemagglutinin (HA) were frequently isolated. In this study, we analyzed the substitutions at HA residue 193 (H3 numbering) of H9N2 and investigated the impact of these mutations on viral properties. Our study indicated that H9N2 circulating in the Chinese poultry have experienced frequent mutations at HA residue 193 since 2013, with viruses that carried asparagine (N) being replaced by those with alanine (A), aspartic acid (D), glutamic acid (E), glycine (G), and serine (S), etc. Our results showed the N193G mutation impeded the multiple cycles of growth of H9N2, and although most of the variant HAs retained the preference for human-like receptors as did the wild-type N193 HA, the N193E mutation altered the preference for both human and avian-like receptors. Furthermore, these mutations substantially altered the antigenicity of H9N2 as measured by both monoclonal antibodies and antisera. In vivo studies further demonstrated that these mutations showed profound impact on viral replication and transmission of H9N2 in chicken. Viruses with D, E, or S at residue 193 acquired the ability to replicate in lungs of the infected chickens, whereas virus with G193 reduced its transmissibility in infected chickens to those in direct contact. Our findings demonstrated that variations at HA residue 193 altered various properties of H9N2, highlighting the significance of the continued surveillance of HA for better understanding of the etiology and effective control of H9N2 in poultry. IMPORTANCE H9N2 are widespread and have sporadically caused clinical diseases in humans. Extensive vaccinations in poultry helped constrain H9N2; however, they might have facilitated the evolution of the virus. It is therefore of importance to monitor the variation of the circulating H9N2 and evaluate its risk to both veterinary and public health. Here, we found substitutions at position 193 of HA from H9N2 circulated since 2013 and assessed the impact of several mutations on viral properties. Our data showed these mutations resulted in substantial antigenic change. N193E altered the binding preference of HA for human-like to both avian and human-like receptors. More importantly, N193G impaired the growth of H9N2 and its transmission in chickens, whereas mutations from N to D, E, and S enhanced the viral replication in lungs of chickens. Our study enriched the knowledge about H9N2 and may help implement an effective control strategy for H9N2.

Experimental and clinical data analysis for identification of COVID-19 resistant ACE2 mutations

The high magnitude zoonotic event has caused by Severe Acute Respitarory Syndrome CoronaVirus-2 (SARS-CoV-2) is Coronavirus Disease-2019 (COVID-19) epidemics. This disease has high rate of spreading than mortality in humans. The human receptor, Angiotensin-Converting Enzyme 2 (ACE2), is the leading target site for viral Spike-protein (S-protein) that function as binding ligands and are responsible for their entry in humans. The patients infected with COVID-19 with comorbidities, particularly cancer patients, have a severe effect or high mortality rate because of the suppressed immune system. Nevertheless, there might be a chance wherein cancer patients cannot be infected with SARS-CoV-2 because of mutations in the ACE2, which may be resistant to the spillover between species. This study aimed to determine the mutations in the sequence of the human ACE2 protein and its dissociation with SARS-CoV-2 that might be rejecting viral transmission. The in silico approaches were performed to identify the impact of SARS-CoV-2 S-protein with ACE2 mutations, validated experimentally, occurred in the patient, and reported in cell lines. The identified changes significantly affect SARS-CoV-2 S-protein interaction with ACE2, demonstrating the reduction in the binding affinity compared to SARS-CoV. The data presented in this study suggest ACE2 mutants have a higher and lower affinity with SARS-Cov-2 S-protein to the wild-type human ACE2 receptor. This study would likely be used to report SARS-CoV-2 resistant ACE2 mutations and can be used to design active peptide development to inactivate the viral spread of SARS-CoV-2 in humans.

Influenza antivirals and their role in pandemic preparedness

Effective antivirals provide crucial benefits during the early phase of an influenza pandemic, when vaccines are still being developed and manufactured. Currently, two classes of viral protein-targeting drugs, neuraminidase inhibitors and polymerase inhibitors, are approved for influenza treatment and post-exposure prophylaxis. Resistance to both classes has been documented, highlighting the need to develop novel antiviral options that may include both viral and host-targeted inhibitors. Such efforts will form the basis of management of seasonal influenza infections and of strategic planning for future influenza pandemics. This review focuses on the two classes of approved antivirals, their drawbacks, and ongoing work to characterize novel agents or combination therapy approaches to address these shortcomings. The importance of these topics in the ongoing process of influenza pandemic planning is also discussed.

Comparative Surface Electrostatics and Normal Mode Analysis of High and Low Pathogenic H7N7 Avian Influenza Viruses

Influenza A viruses are rarely symptomatic in wild birds, while representing a higher threat to poultry and mammals, where they can cause a variety of symptoms, including death. H5 and H7 subtypes of influenza viruses are of particular interest because of their pathogenic potential and reported capacity to spread from poultry to mammals, including humans. The identification of molecular fingerprints for pathogenicity can help surveillance and early warning systems, which are crucial to prevention and protection from such potentially pandemic agents. In the past decade, comparative analysis of the surface features of hemagglutinin, the main protein antigen in influenza viruses, identified electrostatic fingerprints in the evolution and spreading of H5 and H9 subtypes. Electrostatic variation among viruses from avian or mammalian hosts was also associated with host jump. Recent findings of fingerprints associated with low and highly pathogenic H5N1 viruses, obtained by means of comparative electrostatics and normal modes analysis, prompted us to check whether such fingerprints can also be found in the H7 subtype. Indeed, evidence presented in this work showed that also in H7N7, hemagglutinin proteins from low and highly pathogenic strains present differences in surface electrostatics, while no meaningful variation was found in normal modes.

Noninvasive Mechanical Ventilation in Patients with Viral Pneumonia-Associated Acute Respiratory Distress Syndrome: An Observational Retrospective Study

OBJECTIVES

Appropriate mechanical ventilation may change the prognosis of patients with viral pneumonia-associated acute respiratory distress syndrome (ARDS). This study aimed to identify the factors associated with the success of noninvasive ventilation in the management of patients with ARDS secondary to respiratory viral infection.

METHODS

In this retrospective cohort study, all patients with viral pneumonia-associated ARDS were divided into the noninvasive mechanical ventilation (NIV) success group and the NIV failure group. The demographic and clinical data of all patients were collected. The factors associated with the success of noninvasive ventilation were identified by the logistic regression analysis.

RESULTS

Among this cohort, 24 patients with an average age of 57.9 ± 17.0 years received successful NIVs, and NIV failure occurred in 21 patients with an average age of 54.1 ± 14.0 years. The independent influencing factors for the success of the NIV were the acute physiology and chronic health evaluation (APACHE) II score (odds ratio (OR): 1.83, 95% confidence interval (CI): 1.10-3.03) and lactate dehydrogenase (LDH) (OR: 1.011, 95% CI: 1.00-1.02). When the oxygenation index (OI) is <95 mmHg, APACHE II > 19, and LDH > 498 U/L, the sensitivity and specificity of predicting a failed NIV were (66.6% (95% CI: 43.0%-85.4%) and 87.5% (95% CI: 67.6%-97.3%)); (85.7% (95% CI: 63.7%-97.0%) and 79.1% (95% CI: 57.8%-92.9%)); (90.4% (95% CI: 69.6%-98.8%) and 62.5% (95% CI: 40.6%-81.2%)), respectively. The areas under the receiver operating characteristic curve (AUC) of the OI, APACHE II scores, and LDH were 0.85, which was lower than the AUC of the OI combined with LDH and the APACHE II score (OLA) of 0.97 (P=0.0247).

CONCLUSIONS

Overall, patients with viral pneumonia-associated ARDS receiving successful NIV have lower mortality rates than those for whom NIV failed. In patients with influenza A-associated ARDS, the OI may not be the only indicator of whether NIV can be used; a new indicator of NIV success may be the OLA.

Microbial diversity and antimicrobial susceptibility in endotracheal tube biofilms recovered from mechanically ventilated COVID-19 patients

In patients with acute respiratory failure, mechanical ventilation through an endotracheal tube (ET) may be required to correct hypoxemia and hypercarbia. However, biofilm formation on these ETs is a risk factor for infections in intubated patients, as the ET can act as a reservoir of microorganisms that can cause infections in the lungs. As severely ill COVID-19 patients often need to be intubated, a better knowledge of the composition of ET biofilms in this population is important. In Spring 2020, during the first wave of the COVID-19 pandemic in Europe, 31 ETs were obtained from COVID-19 patients at Ghent University Hospital (Ghent, Belgium). Biofilms were collected from the ET and the biofilm composition was determined using culture-dependent (MALDI-TOF mass spectrometry and biochemical tests) and culture-independent (16S and ITS1 rRNA amplicon sequencing) approaches. In addition, antimicrobial resistance was assessed for isolates collected via the culture-dependent approach using disc diffusion for 11 antimicrobials commonly used to treat lower respiratory tract infections. The most common microorganisms identified by the culture-dependent approach were those typically found during lung infections and included both presumed commensal and potentially pathogenic microorganisms like Staphylococcus epidermidis, Enterococcus faecalis, Pseudomonas aeruginosa and Candida albicans. More unusual organisms, such as Paracoccus yeei, were also identified, but each only in a few patients. The culture-independent approach revealed a wide variety of microbes present in the ET biofilms and showed large variation in biofilm composition between patients. Some biofilms contained a diverse set of bacteria of which many are generally considered as non-pathogenic commensals, whereas others were dominated by a single or a few pathogens. Antimicrobial resistance was widespread in the isolates, e.g. 68% and 53% of all isolates tested were resistant against meropenem and gentamicin, respectively. Different isolates from the same species recovered from the same ET biofilm often showed differences in antibiotic susceptibility. Our data suggest that ET biofilms are a potential risk factor for secondary infections in intubated COVID-19 patients, as is the case in mechanically-ventilated non-COVID-19 patients.

Concurrent pigeon paramyxovirus-1 and Acinetobacter baumannii infection in a fatal case of pneumonia

Pigeon paramyxovirus type 1 (PPMV-1), an antigenic variant of avian paramyxovirus type 1 (APMV-1), mainly infects pigeons. PPMV-1 genotype VI is the dominant genotype infecting pigeons in China. Human infection of avian paramyxovirus was rarely reported, and usually developed mild symptoms, such as conjunctivitis. We detected PPMV-1 in the lower respiratory sample from a fatal case with severe pneumonia; this patient aged 64 years presented cough, fever, and haemoptysis for 8 days and was admitted to hospital on Dec 26, 2020. He developed acute respiratory distress syndrome and sepsis in the following days and died of multiple organ failure on Jan 7, 2021. Sputum and blood culture reported multidrug-resistant Acinetobacter baumannii (ABA) for samples collected on days 22 and 19 post-illness, respectively. However, clinical metagenomic sequencing further reported PPMV-1 besides ABA in the bronchoalveolar lavage fluid. The PPMV-1 genome showed 99.21% identity with a Chinese strain and belonged to VI genotype by BLAST analysis. Multiple basic amino acids were observed at the cleavage site of F protein (113RKKRF117), which indicated high virulence of this PPMV-1 strain to poultry. The patient had close contact with pigeons before his illness, and PPMV-1 nucleic acid was detected from the pigeon feather. PPMV antibody was also detected in the patient serum 20 days after illness. In conclusion, concurrent PPMV-1 genotype VI.2.1.1.2.2 and ABA infection were identified in a fatal pneumonia case, and cross-species transmission of PPMV-1 may occur between infected pigeons and the human being.

Intestinal microbiota analysis and network pharmacology reveal the mechanism by which Lianhua Qingwen capsule improves the immune function of mice infected with influenza A virus

Objective

Lianhua Qingwen capsule (LHQW) can attenuate lung injury caused by influenza virus infection. However, it is unclear whether the intestinal microbiota plays a role in LHQW activity in ameliorating viral infectious pneumonia. This study aimed to investigate the role of intestinal microbiota in LHQW activity in ameliorating viral infectious pneumonia and its possible mechanisms.

Research design and methods

A mouse model of influenza A viral pneumonia was established by intranasal administration in BALB/c mice. Detection of influenza virus in the lungs, pathological examination of the lungs and small intestine, and biochemical detection of inflammatory indices were performed. The effects of LHQW on intestinal microbiota were evaluated by 16S rRNA gene sequencing. The key components and targets of LHQW were screened via network pharmacology and verified through molecular docking, molecular dynamics simulation, and free binding energy calculations.

Results

Body weight decreased, inflammatory factor levels were disturbed, and the lung and intestinal mucosal barriers were significantly injured in the infected group. The alpha diversity of the intestinal microbiota decreased, and the abundance of Bacteroidetes, Muribaculaceae_unclassified, and Streptococcus decreased significantly. LHQW treatment reduced the viral load in the lungs, rescued body weight and survival, alleviated lung and intestinal mucosal barrier injury, reversed the reduction in the intestinal microbiota alpha diversity, and significantly increased the abundance of Bacteroidetes and Muribaculaceae. Network pharmacological analysis showed that six active herbal medicinal compounds from LHQW could regulate the intestinal microbiota and inhibit the immune-inflammatory response through the Toll-like receptor (TLR) and nuclear factor-κB (NF-κB) signalling pathways in the lungs.

Conclusion

These results suggest that LHQW is effective for treating influenza A virus infectious pneumonia, and the mechanism is associated with the regulation of the TLR4/NF-κB signalling pathway in the lungs by restoring intestinal microbiota and repairing the intestinal wall.

Comparison of clinical characteristics between COVID-19 and H7N9 fatal cases: An observational study

Objective

The outbreak of COVID-19 in 2020 is reminiscent of the H7N9 outbreak in 2013, which poses a huge threat to human health. We aim to compare clinical features and survival factors in fatal cases of COVID-19 and H7N9.

Methods

Data on confirmed COVID-19 and H7N9 fatal cases identified in mainland China were analyzed to compare demographic characteristics and clinical severity. Survival curves were estimated by the Kaplan-Meier method and compared using log-rank tests and a restricted mean survival time model. A Cox regression model was used to identify survival factors in fatal cases of COVID-19 and H7N9.

Results

Similar demographic characteristics were observed in fatal cases of COVID-19 and H7N9. The proportion of fatal cases of H7N9 receiving antibiotics, antiviral drugs, and oxygen treatment was higher than that of COVID-19. The potential protective factors for fatal COVID-19 cases were receiving antibiotics (HR: 0.37, 95% CI: 0.22-0.61), oxygen treatment (HR: 0.66, 95% CI: 0.44-0.99), and corticosteroids (HR: 0.46, 95% CI: 0.35-0.62). In contrast, antiviral drugs (HR: 0.21, 95% CI: 0.08-0.56) and corticosteroids (HR: 0.45, 95% CI: 0.29-0.69) were the protective factors for H7N9 fatal cases.

Conclusion

The proportion of males, those having one or more underlying medical condition, and older age was high in COVID-19 and H7N9 fatal cases. Offering antibiotics, oxygen treatment, and corticosteroids to COVID-19 cases extended the survival time. Continued global surveillance remains an essential component of pandemic preparedness.

Clinical Characteristics and Risk Factors among Patients with Positive COVID-19 Test Admitted to ICU

Background

Studies that show common characteristics among ICU-admitted patients due to COVID-19 are available on the net, but such studies in Saudi Arabia are limited.

Methods

A descriptive cross-sectional study establishing common comorbidities and risk factors among critically ill patients who tested positive for COVID-19 at the National Guard Hospital from March 2, 2020, to March 20, 2021. The data were obtained from the BEST Care System of King Abdulaziz Medical City, computed, and analyzed using SPSS.

Results

Three hundred eighty-five COVID-19 patients admitted to the intensive care unit (ICU) were included in this study. The mean age was 60.85 ± 20.46, 60.85% were males, and 39.2% were females. There was statistically significant positive relationship between severity of the symptoms and age (P = 0.002). The mean duration of hospital stay in the sample was 21.85 ± 28.47. More than one-third (37.4%) of cases admitted to the hospital died while about two-thirds of the cases were discharged after complete recovery. Two hundred ninety (75.3%) of the patients who were admitted to the National Guard Health Affairs (Riyadh, Saudi Arabia) had respiratory disease. Two hundred twelve patients (55.1%) had diabetes mellitus, while the number of hypertensive patients was 203 (52.7%). There was a significant positive relation among patients with gastrointestinal tract infection (GIT) risk factors and the severity of the symptoms of COVID-19 (P = 0.000). In addition, there was a strong significant relation between hypertension patients and the severity of the COVID-19 symptoms (P = 0.017).

Conclusion

COVID-19 patients who have GIT and hypertension have been found to be at an increased risk of COVID-19 symptom severity. Old age was also found to have an increased risk for COVID-19 symptom severity.

Comparison of acute respiratory distress syndrome in patients with COVID-19 and influenza A (H7N9) virus infection

OBJECTIVES

We aimed to compared the clinical features of acute respiratory distress syndrome (ARDS) induced by COVID-19 and H7N9 virus infections.

METHODS

Clinical data of 100 patients with COVID-19 and 46 patients with H7N9 were retrospectively analyzed.

RESULTS

Elevated inflammatory indices and coagulation disorders were more common in COVID-19-ARDS group than in the H7N9-ARDS group. The median interval from illness onset to ARDS development was shorter in H7N9-ARDS. The PaO₂/FiO₂ level was lower in H7N9-ARDS, whereas the Sepsis-related Organ Failure Assessment score was higher in COVID-19-ARDS. The proportion of patients with disseminated intravascular coagulation and liver injury in COVID-19-ARDS and H7N9-ARDS was 45.5% versus 3.1% and 28.8% versus 50%, respectively (P <0.05). The mean interval from illness onset to death was shorter in H7N9-ARDS. A total of 59.1% patients with H7N9-ARDS died of refractory hypoxemia compared with 28.9% with COVID-19-ARDS (P = 0.014). Patients with COVID-19-ARDS were more likely to die of septic shock and multiple organ dysfunction compared with H7N9-ARDS (71.2% vs 36.4%, P = 0.005).

CONCLUSION

Patients with H7N9 were more susceptible to develop severe ARDS and showed a more acute disease course. COVID-19-ARDS was associated with severe inflammatory response and coagulation dysfunction, whereas liver injury was more common in H7N9-ARDS. The main causes of death between patients with the two diseases were different.

In Silico Drug Repurposing of FDA-Approved Drugs Highlighting Promacta as a Potential Inhibitor of H7N9 Influenza Virus

Influenza virus infections continue to be a significant and recurrent public health problem. Although vaccine efficacy varies, regular immunisation is the most effective method for suppressing the influenza virus. Antiviral drugs are available for influenza, although two of the four FDA-approved antiviral treatments have resulted in significant drug resistance. Therefore, new treatments are being sought to reduce the burden of flu-related illness. The time-consuming development of treatments for new and re-emerging diseases such as influenza and the high failure rate are increasing concerns. In this context, we used an in silico-based drug repurposing method to repurpose FDA-approved drugs as potential therapies against the H7N9 virus. To find potential inhibitors, a total of 2568 drugs were screened. Promacta, tucatinib, and lurasidone were identified as promising hits in the DrugBank database. According to the calculations of MM-GBSA, tucatinib (−54.11 kcal/mol) and Promacta (−56.20 kcal/mol) occupied the active site of neuraminidase with a higher binding affinity than the standard drug peramivir (−49.09 kcal/mol). Molecular dynamics (MD) simulation studies showed that the C-α atom backbones of the complexes of tucatinib and Promacta neuraminidase were stable throughout the simulation period. According to ADME analysis, the hit compounds have a high gastrointestinal absorption (GI) and do not exhibit properties that allow them to cross the blood–brain barrier (BBB). According to the in silico toxicity prediction, Promacta is not cardiotoxic, while lurasidone and tucatinib show only weak inhibition. Therefore, we propose to test these compounds experimentally against the influenza H7N9 virus. The investigation and validation of these potential H7N9 inhibitors would be beneficial in order to bring these compounds into clinical settings.

Hematological features and risk factors of hospitalized COVID-19 patients: A retrospective analysis

Background:

Coronavirus disease 2019 (COVID-19) became pandemic in 2020 and recently, mutated coronaviruses have emerged in many countries. The aim of this study was to identify the clinical characteristics and risk factors for critical illness in hospitalized COVID-19 patients in Zhengzhou for clinical prevention and management.

Materials and methods:

A total of 70 patients hospitalized with COVID-19 were enrolled between 21 January and 29 February 2020, in Zhengzhou, China. Clinical characteristics, hematological findings, neutrophil lymphocyte ratio (NLR), platelet lymphocyte ratio (PLR), and inflammatory index on admission were obtained from medical records, COVID-19 patients with different outcomes were compared.

Results:

The median age was 55 years. Forty-three (61.0%) patients were classified as having severe or critical cases. Eighteen (25.7%) patients died in hospital and the remaining 52 were discharged. Patients who died tend to be old with expectoration and chronic obstructive pulmonary disease. Compared to survivor, non-survivor had significantly higher numbers of leucocytes and neutrophils, NLR, aspartate aminotransferase (AST), γ-glutamyl transpeptidase, total bilirubin, direct bilirubin, lactate dehydrogenase (LDH), prothrombin time, D-dimer, C-reactive protein, and decreased platelets, lymphocytes, uric acid, and albumin (ALB). Logistic regression analysis identified leucocytes, platelets, PLR, NLR, AST, and ALB as independent predictive factors for poor outcomes. The area under curve of the combination of leucocytes, PLR, NLR, and AST was 0.87, with a sensitivity of 0.83 and specificity of 0.81.

Conclusion:

Our results identified risk factors among COVID-19 patients for in-hospital mortality. Leucocytes, PLR, NLR, and AST could have important reference value for predicting prognosis, especially in low-resource countries.

Characterization of the Cross-Species Transmission Potential for Porcine Deltacoronaviruses Expressing Sparrow Coronavirus Spike Protein in Commercial Poultry

Avian species often serve as transmission vectors and sources of recombination for viral infections due to their ability to travel vast distances and their gregarious behaviors. Recently a novel deltacoronavirus (DCoV) was identified in sparrows. Sparrow deltacoronavirus (SpDCoV), coupled with close contact between sparrows and swine carrying porcine deltacoronavirus (PDCoV) may facilitate recombination of DCoVs resulting in novel CoV variants. We hypothesized that the spike (S) protein or receptor-binding domain (RBD) from sparrow coronaviruses (SpCoVs) may enhance infection in poultry. We used recombinant chimeric viruses, which express S protein or the RBD of SpCoV (icPDCoV-SHKU17, and icPDCoV-RBDISU) on the genomic backbone of an infectious clone of PDCoV (icPDCoV). Chimeric viruses were utilized to infect chicken derived DF-1 cells, turkey poults, and embryonated chicken eggs (ECEs) to examine permissiveness, viral replication kinetics, pathogenesis and pathology. We demonstrated that DF-1 cells in addition to the positive control LLC-PK1 cells are susceptible to SpCoV spike- and RBD- recombinant chimeric virus infections. However, the replication of chimeric viruses in DF-1 cells, but not LLC-PK1 cells, was inefficient. Inoculated 8-day-old turkey poults appeared resistant to icPDCoV-, icPDCoV-SHKU17- and icPDCoV-RBDISU virus infections. In 5-day-old ECEs, significant mortality was observed in PDCoV inoculated eggs with less in the spike chimeras, while in 11-day-old ECEs there was no evidence of viral replication, suggesting that PDCoV is better adapted to cross species infection and differentiated ECE cells are not susceptible to PDCoV infection. Collectively, we demonstrate that the SpCoV chimeric viruses are not more infectious in turkeys, nor ECEs than wild type PDCoV. Therefore, understanding the cell and host factors that contribute to resistance to PDCoV and avian-swine chimeric virus infections may aid in the design of novel antiviral therapies against DCoVs.

Divergent Viruses Discovered in Swine Alter the Understanding of Evolutionary History and Genetic Diversity of the Respirovirus Genus and Related Porcine Parainfluenza Viruses

Paramyxoviridae is a rapidly growing family of viruses, whose potential for cross-species transmission makes it difficult to predict the harm of newly emerging viruses to humans and animals. To better understand their diversity, evolutionary history, and co-evolution with their hosts, we analyzed a collection of porcine parainfluenza virus (PPIV) genomes to reconstruct the species classification basis and evolutionary history of the Respirovirus genus. We sequenced 17 complete genomes of porcine respirovirus 1 (also known as porcine parainfluenza virus 1; PPIV-1), thereby nearly tripling the number of currently available PPIV-1 genomes. We found that PPIV-1 was widely prevalent in China with two divergent lineages, PPIV-1a and PPIV-1b. We further provided evidence that a new species, porcine parainfluenza virus 2 (PPIV-2), had recently emerged in China. Our results pointed to a need for revising the current species demarcation criteria of the Respirovirus genus. In addition, we used PPIV-1 as an example to explore recombination and diversity of the Respirovirus genus. Interestingly, we only detected heterosubtypic recombination events between PPIV-1a and PPIV-1b with no intrasubtypic recombination events. The recombination hotspots highlighted a diverse geography-dependent genome structure of paramyxovirus infecting swine in China. Furthermore, we found no evidence of co-evolution between respirovirus and its host, indicating frequent cross-species transmission. In summary, our analyses showed that swine can be infected with a broad range of respiroviruses and recombination may serve as an important evolutionary mechanism for the Respirovirus genus’ greater diversity in genome structure than previously anticipated.

IMPORTANCE Livestock have emerged as critically underrecognized sources of paramyxovirus diversity, including pigs serving as the source of Nipah virus (NiV) and swine parainfluenza virus type 3, and goats and bovines harboring highly divergent viral lineages. Here, we identified a new species of Respirovirus genus named PPIV-2 in swine and proposed to revise the species demarcation criteria of the Respirovirus genus. We found heterosubtypic recombination events and high genetic diversity in PPIV-1. Further, we showed that genetic recombination may have occurred in the Respirovirus genus which may be associated with host range expansion. The continued expansion of Respirovirus genus diversity in livestock with relatively high human contact rates requires enhanced surveillance and ongoing evaluation of emerging cross-species transmission threats.

The importance of association of comorbidities on COVID-19 outcomes: a machine learning approach

BACKGROUND

The individual influence of a variety of comorbidities on COVID-19 patient outcomes has already been analyzed in previous works in an isolated way. We aim to determine if different associations of diseases influence the outcomes of inpatients with COVID-19.

METHODS

Retrospective cohort multicenter study based on clinical practice. Data were taken from the SEMI-COVID-19 Registry, which includes most consecutive patients with confirmed COVID-19 hospitalized and discharged in Spain. Two machine learning algorithms were applied in order to classify comorbidities and patients (Random Forest -RF algorithm, and Gaussian mixed model by clustering -GMM-). The primary endpoint was a composite of either, all-cause death or intensive care unit admission during the period of hospitalization. The sample was randomly divided into training and test sets to determine the most important comorbidities related to the primary endpoint, grow several clusters with these comorbidities based on discriminant analysis and GMM, and compare these clusters.

RESULTS

A total of 16,455 inpatients (57.4% women and 42.6% men) were analyzed. According to the RF algorithm, the most important comorbidities were heart failure/atrial fibrillation (HF/AF), vascular diseases, and neurodegenerative diseases. There were six clusters: three included patients who met the primary endpoint (clusters 4, 5, and 6) and three included patients who did not (clusters 1, 2, and 3). Patients with HF/AF, vascular diseases, and neurodegenerative diseases were distributed among clusters 3, 4 and 5. Patients in cluster 5 also had kidney, liver, and acid peptic diseases as well as a chronic obstructive pulmonary disease; it was the cluster with the worst prognosis.

CONCLUSION

The interplay of several comorbidities may affect the outcome and complications of inpatients with COVID-19.

Inactivated Rabies Virus Vectored MERS-Coronavirus Vaccine Induces Protective Immunity in Mice, Camels, and Alpacas

Middle East respiratory syndrome coronavirus (MERS-CoV) is an emergent coronavirus that has caused frequent zoonotic events through camel-to-human spillover. An effective camelid vaccination strategy is probably the best way to reduce human exposure risk. Here, we constructed and evaluated an inactivated rabies virus-vectored MERS-CoV vaccine in mice, camels, and alpacas. Potent antigen-specific antibody and CD8⁺ T-cell responses were generated in mice; moreover, the vaccination reduced viral replication and accelerated virus clearance in MERS-CoV-infected mice. Besides, protective antibody responses against both MERS-CoV and rabies virus were induced in camels and alpacas. Satisfyingly, the immune sera showed broad cross-neutralizing activity against the three main MERS-CoV clades. For further characterization of the antibody response induced in camelids, MERS-CoV-specific variable domains of heavy-chain-only antibody (VHHs) were isolated from immunized alpacas and showed potent prophylactic and therapeutic efficacies in the Ad5-hDPP4-transduced mouse model. These results highlight the inactivated rabies virus-vectored MERS-CoV vaccine as a promising camelid candidate vaccine.

Impact of the R292K Mutation on Influenza A (H7N9) Virus Resistance towards Peramivir: A Molecular Dynamics Perspective

In March 2013, a novel avian influenza A (H7N9) virus emerged in China. By March 2021, it had infected more than 1500 people, raising concerns regarding its epidemic potential. Similar to the highly pathogenic H5N1 virus, the H7N9 virus causes severe pneumonia and acute respiratory distress syndrome in most patients. Moreover, genetic analysis showed that this avian H7N9 virus carries human adaptation markers in the hemagglutinin and polymerase basic 2 (PB2) genes associated with cross-species transmissibility. Clinical studies showed that a single mutation, neuraminidase (NA) R292K (N2 numbering), induces resistance to peramivir in the highly pathogenic H7N9 influenza A viruses. Therefore, to evaluate the risk for human public health and understand the possible source of drug resistance, we assessed the impact of the NA-R292K mutation on avian H7N9 virus resistance towards peramivir using various molecular dynamics approaches. We observed that the single point mutation led to a distorted peramivir orientation in the enzyme active site which, in turn, perturbed the inhibitor's binding. The R292K mutation induced a decrease in the interaction among neighboring amino acid residues when compared to its wild-type counterpart, as shown by the high degree of fluctuations in the radius of gyration. MM/GBSA calculations revealed that the mutation caused a decrease in the drug binding affinity by 17.28 kcal/mol when compared to the that for the wild-type enzyme. The mutation caused a distortion of hydrogen bond-mediated interactions with peramivir and increased the accessibility of water molecules around the K292 mutated residue.

Infiltration of inflammatory macrophages and neutrophils and widespread pyroptosis in lung drive influenza lethality in nonhuman primates

Severe influenza kills tens of thousands of individuals each year, yet the mechanisms driving lethality in humans are poorly understood. Here we used a unique translational model of lethal H5N1 influenza in cynomolgus macaques that utilizes inhalation of small-particle virus aerosols to define mechanisms driving lethal disease. RNA sequencing of lung tissue revealed an intense interferon response within two days of infection that resulted in widespread expression of interferon-stimulated genes, including inflammatory cytokines and chemokines. Macaques with lethal disease had rapid and profound loss of alveolar macrophages (AMs) and infiltration of activated CCR2⁺ CX3CR1⁺ interstitial macrophages (IMs) and neutrophils into lungs. Parallel changes of AMs and neutrophils in bronchoalveolar lavage (BAL) correlated with virus load when compared to macaques with mild influenza. Both AMs and IMs in lethal influenza were M1-type inflammatory macrophages which expressed neutrophil chemotactic factors, while neutrophils expressed genes associated with activation and generation of neutrophil extracellular traps (NETs). NETs were prominent in lung and were found in alveolar spaces as well as lung parenchyma. Genes associated with pyroptosis but not apoptosis were increased in lung, and activated inflammatory caspases, IL-1β and cleaved gasdermin D (GSDMD) were present in bronchoalveolar lavage fluid and lung homogenates. Cleaved GSDMD was expressed by lung macrophages and alveolar epithelial cells which were present in large numbers in alveolar spaces, consistent with loss of epithelial integrity. Cleaved GSDMD colocalized with viral NP-expressing cells in alveoli, reflecting pyroptosis of infected cells. These novel findings reveal that a potent interferon and inflammatory cascade in lung associated with infiltration of inflammatory macrophages and neutrophils, elaboration of NETs and cell death by pyroptosis mediates lethal H5N1 influenza in nonhuman primates, and by extension humans. These innate pathways represent promising therapeutic targets to prevent severe influenza and potentially other primary viral pneumonias in humans.

Influenza can cause acute lung injury and death, but the mechanisms resulting in lethal influenza in humans are not well understood. We used a novel model of lethal influenza in nonhuman primates caused by aerosol infection with highly pathogenic avian influenza virus that closely resembles human disease to define how the virus causes severe pneumonia. We found that a potent innate immune response starting with high-level production of interferons and inflammatory factors in the lung drives severe disease. Inflammatory cells including macrophages and neutrophils were recruited into lung because of this early response, which in turn led to release of neutrophil extracellular traps that blocked lung alveoli. In addition, a particularly inflammatory form of cell death known as pyroptosis occurred in lungs during lethal influenza. These new findings show that an intense interferon response leading to an inflammatory cascade of macrophages and neutrophils, release of neutrophil extracellular traps, and cell death by pyroptosis is responsible for acute lung injury in lethal influenza. These innate pathways could be targeted by drugs to prevent lung injury in critically ill influenza patients.

Effect of intravenous thrombolysis combined with mild hypothermia on the levels of IL-1β, IL-6, ICAM-1 and MMP-2 in patients with acute cerebral infarction and clinical significance

The present study aimed to explore the effects and clinical importance of serum interleukin (IL) IL-1β, IL-6, C-reactive protein (CRP), intercellular adhesion molecule (ICAM)-1 and matrix metalloproteinase (MMP)-2 in patients with acute cerebral infarction undergoing intravenous thrombolysis during simultaneous hypothermia therapy. A total of 80 patients with acute cerebral infarction who were treated at our hospital were randomly selected. They were divided into groups A and B. The two groups were treated with intravenous thrombolysis, while group B received sub-hypothermia treatment. Prior to treatment and at 7 days after treatment, 5 ml of venous blood was collected and stored in a freezer at -80˚C. IL-1β, IL-6, CRP, ICAM-1 and MMP-2 levels were detected by ELISA and compared between the groups and time-points. The results were as follows: i) At 7 days after treatment, the levels of IL-1β, IL-6, CRP, ICAM-1 and MMP-2 in group B were significantly decreased compared with those in group A (P<0.05), while there was no significant difference of these levels between group A and B before treatment (P>0.05). The incidence of adverse reactions in group A and group B was 35 and 20% respectively, and the mortality rate was 10 and 5%, respectively. There were no significant differences in adverse events and mortality between the two groups (P>0.05). In addition, a positive correlation of the level of IL-1β, IL-6, CRP, ICAM-1 and MMP-2 with the National Institutes of Health Stroke Scale score was determined in the patients prior to treatment. In conclusion, mild hypothermia treatment in addition to intravenous thrombolysis significantly reduced the levels of IL-1β, IL-6, CRP, ICAM-1 and MMP-2 in patients with acute cerebral infarction and reduced inflammation, and should therefore be incorporated in clinical practice.

Subcellular Proteomic Analysis Reveals Dysregulation in Organization of Human A549 Cells Infected with Influenza Virus H7N9

Background:

H7N9 influenza virus poses a high risk to human beings and proteomic evaluations of these infections may help to better understand its pathogenic mechanisms in human systems. Objective: To find membrane proteins related to H7N9 infection.

Methods:

Here, we infected primary human alveolar adenocarcinoma epithelial cells (A549) cells with H7N9 (including wild and mutant strains) and then produced enriched cellular membrane isolations which were evaluated by western blot. The proteins in these cell membrane fractions were analyzed using the isobaric Tags for Relative and Absolute Quantitation (iTRAQ) proteome technologies.

Results:

Differentially expressed proteins (n = 32) were identified following liquid chromatography-tandem mass spectrometry, including 20 down-regulated proteins such as CD44 antigen, and CD151 antigen, and 12 up-regulated proteins such as tight junction protein ZO-1, and prostaglandin reductase 1. Gene Ontology database searching revealed that 20 out of the 32 differentially expressed proteins were localized to the plasma membrane. These proteins were primarily associated with cellular component organization (n = 20), and enriched in the Reactome pathway of extracellular matrix organization (n = 4).

Conclusion:

These findings indicate that H7N9 may dysregulate cellular organization via specific alterations to the protein profile of the plasma membrane.

Effects of Cigarette Smoking on Influenza Virus/Host Interplay

Cigarette smoking has been shown to increase the risk of respiratory infection, resulting in the exacerbation of infectious disease outcomes. Influenza viruses are a major respiratory viral pathogen, which are responsible for yearly epidemics that result in between 20,000 and 50,000 deaths in the US alone. However, there are limited general summaries on the impact of cigarette smoking on influenza pathogenic outcomes. Here, we will provide a systematic summarization of the current understanding of the interplay of smoking and influenza viral infection with a focus on examining how cigarette smoking affects innate and adaptive immune responses, inflammation levels, tissues that contribute to systemic chronic inflammation, and how this affects influenza A virus (IAV) disease outcomes. This summarization will: (1) help to clarify the conflict in the reports on viral pathogenicity; (2) fill knowledge gaps regarding critical anti-viral defenses such as antibody responses to IAV; and (3) provide an updated understanding of the underlying mechanism behind how cigarette smoking influences IAV pathogenicity.

Virus infection induced pulmonary fibrosis

Pulmonary fibrosis is the end stage of a broad range of heterogeneous interstitial lung diseases and more than 200 factors contribute to it. In recent years, the relationship between virus infection and pulmonary fibrosis is getting more and more attention, especially after the outbreak of SARS-CoV-2 in 2019, however, the mechanisms underlying the virus-induced pulmonary fibrosis are not fully understood. Here, we review the relationship between pulmonary fibrosis and several viruses such as Human T-cell leukemia virus (HTLV), Human immunodeficiency virus (HIV), Cytomegalovirus (CMV), Epstein–Barr virus (EBV), Murine γ-herpesvirus 68 (MHV-68), Influenza virus, Avian influenza virus, Middle East Respiratory Syndrome (MERS)-CoV, Severe acute respiratory syndrome (SARS)-CoV and SARS-CoV-2 as well as the mechanisms underlying the virus infection induced pulmonary fibrosis. This may shed new light on the potential targets for anti-fibrotic therapy to treat pulmonary fibrosis induced by viruses including SARS-CoV-2.

Pathogenesis and Treatment of Cytokine Storm Induced by Infectious Diseases

Cytokine storm is a phenomenon characterized by strong elevated circulating cytokines that most often occur after an overreactive immune system is activated by an acute systemic infection. A variety of cells participate in cytokine storm induction and progression, with profiles of cytokines released during cytokine storm varying from disease to disease. This review focuses on pathophysiological mechanisms underlying cytokine storm induction and progression induced by pathogenic invasive infectious diseases. Strategies for targeted treatment of various types of infection-induced cytokine storms are described from both host and pathogen perspectives. In summary, current studies indicate that cytokine storm-targeted therapies can effectively alleviate tissue damage while promoting the clearance of invading pathogens. Based on this premise, "multi-omics" immune system profiling should facilitate the development of more effective therapeutic strategies to alleviate cytokine storms caused by various diseases.

The viral distribution and pathological characteristics of BALB/c mice infected with highly pathogenic Influenza H7N9 virus

Background

The highly pathogenic Influenza H7N9 virus is believed to cause multiple organ infections. However, there have been few systematic animal experiments demonstrating the virus distribution after H7N9 virus infection. The present study was carried out to investigate the viral distribution and pathological changes in the main organs of mice after experimental infection with highly pathogenic H7N9 virus.

Methods

Infection of mice with A/Guangdong/GZ8H002/2017(H7N9) virus was achieved via nasal inoculation. Mice were killed at 2, 3, and 7 days post infection. The other mice were used to observe their illness status and weight changes. Reverse transcription polymerase chain reaction and viral isolation were used to analyse the characteristics of viral invasion. The pathological changes of the main organs were observed using haematoxylin and eosin staining and immunohistochemistry.

Results

The weight of H7N9 virus-infected mice increased slightly in the first two days. However, the weight of the mice decreased sharply in the following days, by up to 20%. All the mice had died by the 8th day post infection and showed multiple organ injury. The emergence of viremia in mice was synchronous with lung infection. On the third day post infection, except in the brain, the virus could be isolated from all organs (lung, heart, kidney, liver, and spleen). On the seventh day post infection, the virus could be detected in all six organs. Brain infection was detected in all mice, and the viral titre in the heart, kidney, and spleen infection was high.

Conclusion

Acute diffuse lung injury was the initial pathogenesis in highly pathogenic H7N9 virus infection. In addition to lung infection and viremia, the highly pathogenic H7N9 virus could cause multiple organ infection and injury.

Survey on COVID-19-related mortality associated with occupational infection during the first phase of the pandemic: A systematic review

According to the Centre for Disease Control and Prevention in 2020, a cluster of pneumonia cases of unknown etiology caused by the severe acute respiratory syndrome (SARS)-coronavirus 2 was reported in Wuhan, China. The present review examined the literature to reveal the incidence of novel coronavirus-2019 disease (COVID-19) infections, underlying comorbidities, workplace infections and case fatality rates. A review was performed to identify the relevant publications available up to May 15, 2020. Since the early stages of the COVID-19 outbreak, the case fatality rate among healthcare workers (HCWs) has stood at 0.69% worldwide and 0.4% in Italy. Based on the current information, most patients have exhibited good prognoses in terms of after-effects or sequelae and low mortality rate. Patients that became critically ill were primarily in the elderly population or had chronic underlying diseases, including diabetes and hypertension. Among all working sectors, HCWs, since they are front-line caregivers for patients with COVID-19, are considered to be in the high-risk population. Increased age and a number of comorbidity factors have been associated with increased risk of mortality in patients with COVID-19. The most frequent complications of COVID-19 reported that can cause fatality in patients were SARS, cardiac arrest, secondary infections and septic shock, in addition to acute kidney failure and liver failure. Overcoming the COVID-19 pandemic is an ongoing challenge, which poses a threat to global health that requires close surveillance and prompt diagnosis, in coordination with research efforts to understand this pathogen and develop effective countermeasures.

Comparative study of hematological and radiological feature of severe/critically ill patients with COVID-19, influenza A H7N9, and H1N1 pneumonia

OBJECTIVES

This study aimed to explore clinical indexes for management of severe/critically ill patients with COVID-19, influenza A H7N9, and H1N1 pneumonia by comparing hematological and radiological characteristics.

METHODS

Severe/critically ill patients with COVID-19, H7N9, and H1N1 pneumonia were retrospectively enrolled. The demographic data, clinical manifestations, hematological parameters, and radiological characteristics were compared.

RESULTS

In this study, 16 cases of COVID-19, 10 cases of H7N9, and 13 cases of H1N1 who met severe/critically ill criteria were included. Compared with COVID-19, H7N9 and H1N1 groups had more chronic diseases (80% and 92.3% vs. 25%, p < 0.05), higher APACHE Ⅱ scores (16.00 ± 8.63 and 15.08 ± 6.24, vs. 5.50 ± 2.58, p < 0.05), higher mortality rates (40% and 46.2% vs. 0%, p < 0.05), significant lymphocytopenia (0.59 ± 0.31 × 10⁹ /L and 0.56 ± 0.35 × 10⁹ /L vs. 0.97 ± 0.33 × 10⁹ /L, p < 0.05), and elevated neutrophil-to-lymphocyte ratio (NLR; 14.67 ± 6.10 and 14.64 ± 10.36 vs. 6.29 ± 3.72, p < 0.05). Compared with the H7N9 group, ground-glass opacity (GGO) on chest CT was common in the COVID-19 group (p = 0.028), while pleural effusion was rare (p = 0.001).

CONCLUSIONS

The NLR can be used as a clinical parameter for the predication of risk stratification and outcome in COVID-19 and influenza A pneumonia. Manifestations of pleural effusion or GGO in chest CT may be helpful for the identification of different viral pneumonia.

Influenza A Viruses and Zoonotic Events-Are We Creating Our Own Reservoirs?

Zoonotic infections of humans with influenza A viruses (IAVs) from animal reservoirs can result in severe disease in individuals and, in rare cases, lead to pandemic outbreaks; this is exemplified by numerous cases of human infection with avian IAVs (AIVs) and the 2009 swine influenza pandemic. In fact, zoonotic transmissions are strongly facilitated by manmade reservoirs that were created through the intensification and industrialization of livestock farming. This can be witnessed by the repeated introduction of IAVs from natural reservoirs of aquatic wild bird metapopulations into swine and poultry, and the accompanied emergence of partially- or fully-adapted human pathogenic viruses. On the other side, human adapted IAV have been (and still are) introduced into livestock by reverse zoonotic transmission. This link to manmade reservoirs was also observed before the 20th century, when horses seemed to have been an important reservoir for IAVs but lost relevance when the populations declined due to increasing industrialization. Therefore, to reduce zoonotic events, it is important to control the spread of IAV within these animal reservoirs, for example with efficient vaccination strategies, but also to critically surveil the different manmade reservoirs to evaluate the emergence of new IAV strains with pandemic potential.

Altered Lipid Profile Is a Risk Factor for the Poor Progression of COVID-19: From Two Retrospective Cohorts

Background

The coronavirus disease 2019 (COVID-19) pandemic has spread worldwide. However, the impact of baseline lipid profile on clinical endpoints in COVID-19 and the potential effect of COVID-19 on lipid profile remain unclear.

Methods

In this retrospective cohort study, we consecutively enrolled 430 adult COVID-19 patients from two Chinese hospitals (one each in Chengdu and Wuhan). The lipid profile before admission and during the disease course and the clinical endpoint including in-hospital death or oropharyngeal swab test positive again (OSTPA) after discharge were collected. We used Kaplan-Meier and Cox regression to explore the lipid risk factors before admission associated with endpoints. Then, we assessed the lipid level change along with the disease course to determine the relationship between pathology alteration and the lipid change.

Results

In the Chengdu cohort, multivariable Cox regression showed that low-density lipoprotein cholesterol (LDL-C) dyslipidemia before admission was associated with OSTPA after discharge for COVID-19 patients (RR: 2.51, 95% CI: 1.19, 5.29, p = 0.006). In the Wuhan cohort, the patients with triglyceride (TG) dyslipidemia had an increased risk of in-hospital death (RR: 1.92, 95% CI: 1.08, 3.60, p = 0.016). In addition, in both cohorts, the lipid levels gradually decreased in the in-hospital death or OSTPA subgroups since admission. On admission, we also noticed the relationship between the biomarkers of inflammation and the organ function measures and this lipid level in both cohorts. For example, after adjusting for age, sex, comorbidities, smoking, and drinking status, the C-reactive protein level was negatively associated with the TC lipid level [β (SE) = -0.646 (0.219), p = 0.005]. However, an increased level of alanine aminotransferase, which indicates impaired hepatic function, was positively associated with total cholesterol (TC) lipid levels in the Chengdu cohort [β (SE) = 0.633 (0.229), p = 0.007].

Conclusions

The baseline dyslipidemia should be considered as a risk factor for poor prognosis of COVID-19. However, lipid levels may be altered during the COVID-19 course, since lipidology may be distinctly affected by both inflammation and organic damage for SARS-CoV-2.

Ultrasound and Influenza: The Spectrum of Lung and Cardiac Ultrasound Findings in Patients with Suspected Influenza A and B

In patients with influenza, cardiac and lung ultrasound may help determine the severity of illness and predict clinical outcomes. To determine the ultrasound characteristics of influenza and define the spectrum of lung and cardiac findings in patients with suspected influenza A or B, we conducted a prospective observational study in patients presenting to the emergency department at a tertiary care academic institution. An ultrasound protocol consisting of cardiac, lung and inferior vena cava scans was performed within 6 h of admission. We compared the ultrasound findings in cases with positive and negative influenza polymerase chain reaction, while controlling for comorbidities. We enrolled 117 patients, 41.9% of whom (49/117) tested positive for influenza. In those with influenza, ultrasound confirmed preserved left ventricular and right ventricular (RV) function in 81.3% of patients. The most common cardiac pathology was RV dilation (10.4%), followed by left ventricular systolic dysfunction (8.3%). Patients with negative influenza polymerase chain reaction with RV dysfunction demonstrated higher hospital admission than those those with normal RV function (45.1%, 23/51, vs. 17.9%, 5/28; p = 0.016). B-lines were prevalent in both influenza and non-influenza groups (40.8% and 69.1%, respectively; p = 0.013). Lung consolidation was identified in only 8.25% of patients with influenza. In conclusion, in patients with influenza we were unable to define distinct ultrasound features specific to influenza A or B, suggesting that ultrasound may not be beneficial in diagnosing influenza nor in evaluating its severity.