Influenza Virus-Host Co-evolution. A Predator-Prey Relationship?

SARS-CoV-2 Prevalence and Variant Surveillance among Cats in Pittsburgh, Pennsylvania, USA

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infects many mammals, and SARS-CoV-2 circulation in nonhuman animals may increase the risk of novel variant emergence. Cats are highly susceptible to SARS-CoV-2 infection, and there were cases of virus transmission between cats and humans. The objective of this study was to assess the prevalence of SARS-CoV-2 variant infection of cats in an urban setting. We investigated the prevalence of SARS-CoV-2 variant infections in domestic and community cats in the city of Pittsburgh (n = 272). While no cats tested positive for SARS-CoV-2 viral RNA, 35 cats (12.86%) tested SARS-CoV-2-antibody-positive. Further, we compared a cat-specific experimental lateral flow assay (eLFA) and species-agnostic surrogate virus neutralization assay (sVNT) for SARS-CoV-2 antibody detection in cats (n = 71). The eLFA demonstrated 100% specificity compared to sVNT. The eLFA also showed 100% sensitivity for sera with >90% inhibition and 63.63% sensitivity for sera with 40-89% inhibition in sVNT. Using a variant-specific pseudovirus neutralization assay (pVNT) and antigen cartography, we found the presence of antibodies to pre-Omicron and Omicron SARS-CoV-2 variants. Hence, this approach proves valuable in identifying cat exposure to different SARS-CoV-2 variants. Our results highlight the continued exposure of cats to SARS-CoV-2 and warrant coordinated surveillance efforts.

Investigating host-virus interaction mechanism and phylogenetic analysis of viral proteins involved in the pathogenesis

Since the emergence of yellow fever in the Americas and the devastating 1918 influenza pandemic, biologists and clinicians have been drawn to human infecting viruses to understand their mechanisms of infection better and develop effective therapeutics against them. However, the complex molecular and cellular processes that these viruses use to infect and multiply in human cells have been a source of great concern for the scientific community since the discovery of the first human infecting virus. Viral disease outbreaks, such as the recent COVID-19 pandemic caused by a novel coronavirus, have claimed millions of lives and caused significant economic damage worldwide. In this study, we investigated the mechanisms of host-virus interaction and the molecular machinery involved in the pathogenesis of some common human viruses. We also performed a phylogenetic analysis of viral proteins involved in host-virus interaction to understand the changes in the sequence organization of these proteins during evolution for various strains of viruses to gain insights into the viral origin's evolutionary perspectives.

Facilitating Antiviral Drug Discovery Using Genetic and Evolutionary Knowledge

Over the course of human history, billions of people worldwide have been infected by various viruses. Despite rapid progress in the development of biomedical techniques, it is still a significant challenge to find promising new antiviral targets and drugs. In the past, antiviral drugs mainly targeted viral proteins when they were used as part of treatment strategies. Since the virus mutation rate is much faster than that of the host, such drugs feature drug resistance and narrow-spectrum antiviral problems. Therefore, the targeting of host molecules has gradually become an important area of research for the development of antiviral drugs. In recent years, rapid advances in high-throughput sequencing techniques have enabled numerous genetic studies (such as genome-wide association studies (GWAS), clustered regularly interspersed short palindromic repeats (CRISPR) screening, etc.) for human diseases, providing valuable genetic and evolutionary resources. Furthermore, it has been revealed that successful drug targets exhibit similar genetic and evolutionary features, which are of great value in identifying promising drug targets and discovering new drugs. Considering these developments, in this article the authors propose a host-targeted antiviral drug discovery strategy based on knowledge of genetics and evolution. We first comprehensively summarized the genetic, subcellular location, and evolutionary features of the human genes that have been successfully used as antiviral targets. Next, the summarized features were used to screen novel druggable antiviral targets and to find potential antiviral drugs, in an attempt to promote the discovery of new antiviral drugs.

Abnormal Airway Mucus Secretion Induced by Virus Infection

The airway mucus barrier is a primary defensive layer at the airway surface. Mucins are the major structural components of airway mucus that protect the respiratory tract. Respiratory viruses invade human airways and often induce abnormal mucin overproduction and airway mucus secretion, leading to airway obstruction and disease. The mechanism underlying the virus-induced abnormal airway mucus secretion has not been fully studied so far. Understanding the mechanisms by which viruses induce airway mucus hypersecretion may open new avenues to treatment. In this article, we elaborate the clinical and experimental evidence that respiratory viruses cause abnormal airway mucus secretion, review the underlying mechanisms, and also discuss the current research advance as well as potential strategies to treat the abnormal airway mucus secretion caused by SARS-CoV-2.

Differentiation of Chest CT Findings Between Influenza Pneumonia and COVID-19: Interobserver Agreement Between Radiologists

OBJECTIVES

To investigate the chest CT and clinical characteristics of COVID-19 pneumonia and H1N1 influenza, and explore the radiologist diagnosis differences between COVID-19 and influenza.

MATERIALS AND METHODS

This cross-sectional study included a total of 43 COVID-19-confirmed patients (24 men and 19 women, 49.90 ± 18.70 years) and 41 influenza-confirmed patients (17 men and 24 women, 61.53 ± 19.50 years). Afterwards, the chest CT findings were recorded and 3 radiologists recorded their diagnoses of COVID-19 or of H1N1 influenza based on the CT findings.

RESULTS

The most frequent clinical symptom in patients with COVID-19 and H1N1 pneumonia were dyspnea (96.6%) and cough (62.5%), respectively. The CT findings showed that the COVID-19 group was characterized by GGO (88.1%), while the influenza group had features such as GGO (68.4%) and consolidation (66.7%). Compared to the influenza group, the COVID-19 group was more likely to have GGO (88.1% vs. 68.4%, p = 0.032), subpleural sparing (69.0% vs. 7.7%, p <0.001) and subpleural band (50.0% vs. 20.5%, p = 0.006), but less likely to have pleural effusion (4.8% vs. 33.3%, p = 0.001). The agreement rate between the 3 radiologists was 65.8%.

CONCLUSION

Considering similarities of respiratory infections especially H1N1 and COVID-19, it is essential to introduce some clinical and para clinical modalities to help differentiating them. In our study we extracted some lung CT scan findings from patients suspected to COVID-19 as a newly diagnosed infection comparing with influenza pneumonia patients.

Digital Feast and Physical Famine: The Altered Ecosystem of Anatomy Education due to the Covid-19 Pandemic

This article explores the effects of the coronavirus disease 2019 (Covid-19) pandemic on the evolution of both physical and digital cadavers within the unique ecosystem of the anatomy laboratory. A physical cadaver is a traditional and established learning tool in anatomy education, whereas a digital cadaver is a relatively recent phenomenon. The Covid-19 pandemic presented a major disturbance and disruption to all levels and types of education, including anatomy education. This article constructs a conceptual metaphor between a typical anatomy laboratory and an ecosystem, and considers the affordances, constraints, and changing roles of physical and digital cadavers within anatomy education through an ecological lens. Adaptation of physical and digital cadavers during the disturbance is analyzed, and the resiliency of digital cadaver technology is recognized. The evolving role of the digital cadaver is considered in terms of increasing accessibility and inclusivity within the anatomy laboratory ecosystem of the future.

Time-delayed and stochastic effects in a predator-prey model with ratio dependence and Holling type III functional response

In this article, we derive and analyze a novel predator-prey model with account for maturation delay in predators, ratio dependence, and Holling type III functional response. The analysis of the system's steady states reveals conditions on predation rate, predator growth rate, and maturation time that can result in a prey-only equilibrium or facilitate simultaneous survival of prey and predators in the form of a stable coexistence steady state, or sustain periodic oscillations around this state. Demographic stochasticity in the model is explored by means of deriving a delayed chemical master equation. Using system size expansion, we study the structure of stochastic oscillations around the deterministically stable coexistence state by analyzing the dependence of variance and coherence of stochastic oscillations on system parameters. Numerical simulations of the stochastic model are performed to illustrate stochastic amplification, where individual stochastic realizations can exhibit sustained oscillations in the case, where deterministically the system approaches a stable steady state. These results provide a framework for studying realistic predator-prey systems with Holling type III functional response in the presence of stochasticity, where an important role is played by non-negligible predator maturation delay.

MicroRNAs for Virus Pathogenicity and Host Responses, Identified in SARS-CoV-2 Genomes, May Play Roles in Viral-Host Co-Evolution in Putative Zoonotic Host Species

Our recent study identified seven key microRNAs (miR-8066, 5197, 3611, 3934-3p, 1307-3p, 3691-3p, 1468-5p) similar between SARS-CoV-2 and the human genome, pointing at miR-related mechanisms in viral entry and the regulatory effects on host immunity. To identify the putative roles of these miRs in zoonosis, we assessed their conservation, compared with humans, in some key wild and domestic animal carriers of zoonotic viruses, including bat, pangolin, pig, cow, rat, and chicken. Out of the seven miRs under study, miR-3611 was the most strongly conserved across all species; miR-5197 was the most conserved in pangolin, pig, cow, bat, and rat; miR-1307 was most strongly conserved in pangolin, pig, cow, bat, and human; miR-3691-3p in pangolin, cow, and human; miR-3934-3p in pig and cow, followed by pangolin and bat; miR-1468 was most conserved in pangolin, pig, and bat; while miR-8066 was most conserved in pangolin and pig. In humans, miR-3611 and miR-1307 were most conserved, while miR-8066, miR-5197, miR-3334-3p and miR-1468 were least conserved, compared with pangolin, pig, cow, and bat. Furthermore, we identified that changes in the miR-5197 nucleotides between pangolin and human can generate three new miRs, with differing tissue distribution in the brain, lung, intestines, lymph nodes, and muscle, and with different downstream regulatory effects on KEGG pathways. This may be of considerable importance as miR-5197 is localized in the spike protein transcript area of the SARS-CoV-2 genome. Our findings may indicate roles for these miRs in viral–host co-evolution in zoonotic hosts, particularly highlighting pangolin, bat, cow, and pig as putative zoonotic carriers, while highlighting the miRs’ roles in KEGG pathways linked to viral pathogenicity and host responses in humans. This in silico study paves the way for investigations into the roles of miRs in zoonotic disease.

Proteomics in Influenza Research: The Emerging Role of Posttranslational Modifications

Influenza viruses continue evolving and have the ability to cause a global pandemic, so it is very important to elucidate its pathogenesis and find new treatment methods. In recent years, proteomics has made important contributions to describing the dynamic interaction between influenza viruses and their hosts, especially in posttranslational regulation of a variety of key biological processes. Protein posttranslational modifications (PTMs) increase the diversity of functionality of the organismal proteome and affect almost all aspects of pathogen biology, primarily by regulating the structure, function, and localization of the modified proteins. Considerable technical achievements in mass spectrometry-based proteomics have been made in a large number of proteome-wide surveys of PTMs in many different organisms. Herein we specifically focus on the proteomic studies regarding a variety of PTMs that occur in both the influenza viruses, mainly influenza A viruses (IAVs), and their hosts, including phosphorylation, ubiquitination and ubiquitin-like modification, glycosylation, methylation, acetylation, and some types of acylation. Integration of these data sets provides a unique scenery of the global regulation and interplay of different PTMs during the interaction between IAVs and their hosts. Various techniques used to globally profiling these PTMs, mostly MS-based approaches, are discussed regarding their increasing roles in mechanical regulation of interaction between influenza viruses and their hosts.

Closely related reovirus lab strains induce opposite expression of RIG-I/IFN-dependent versus -independent host genes, via mechanisms of slow replication versus polymorphisms in dsRNA binding σ3 respectively

The Dearing isolate of Mammalian orthoreovirus (T3D) is a prominent model of virus-host relationships and a candidate oncolytic virotherapy. Closely related laboratory strains of T3D, originating from the same ancestral T3D isolate, were recently found to exhibit significantly different oncolytic properties. Specifically, the T3DPL strain had faster replication kinetics in a panel of cancer cells and improved tumor regression in an in vivo melanoma model, relative to T3DTD. In this study, we discover that T3DPL and T3DTD also differentially activate host signalling pathways and downstream gene transcription. At equivalent infectious dose, T3DTD induces higher IRF3 phosphorylation and expression of type I IFNs and IFN-stimulated genes (ISGs) than T3DPL. Using mono-reassortants with intermediate replication kinetics and pharmacological inhibitors of reovirus replication, IFN responses were found to inversely correlate with kinetics of virus replication. In other words, slow-replicating T3D strains induce more IFN signalling than fast-replicating T3D strains. Paradoxically, during co-infections by T3DPL and T3DTD, there was still high IRF3 phosphorylation indicating a phenodominant effect by the slow-replicating T3DTD. Using silencing and knock-out of RIG-I to impede IFN, we found that IFN induction does not affect the first round of reovirus replication but does prevent cell-cell spread in a paracrine fashion. Accordingly, during co-infections, T3DPL continues to replicate robustly despite activation of IFN by T3DTD. Using gene expression analysis, we discovered that reovirus can also induce a subset of genes in a RIG-I and IFN-independent manner; these genes were induced more by T3DPL than T3DTD. Polymorphisms in reovirus σ3 viral protein were found to control activation of RIG-I/ IFN-independent genes. Altogether, the study reveals that single amino acid polymorphisms in reovirus genomes can have large impact on host gene expression, by both changing replication kinetics and by modifying viral protein activity, such that two closely related T3D strains can induce opposite cytokine landscapes.

HLA-associated protection of lymphocytes during influenza virus infection

Background

Heterozygosity at HLA class I loci is generally considered beneficial for host defense. We report here an element of HLA class I homozygosity that may or may not help preserve its existence in populations but which could indicate a new avenue for antiviral research.

Methods

Lymphocytes from serologically HLA-homozygous or -heterozygous donors were examined for synthesis of influenza virus proteins and RNA after exposure to virus as peripheral blood mononuclear cells. The virus-exposed lymphocytes were also examined for internalization of the virus after exposure, and for susceptibility to virus-specific cytotoxic T lymphocytes in comparison with virus-exposed monocytes/macrophages and unseparated peripheral blood mononuclear cells. Results were compared using two-tailed Fisher’s exact test.

Results

Serologically-defined HLA-A2-homozygous lymphocytes, in contrast to heterozygous lymphocytes, did not synthesize detectable influenza virus RNA or protein after exposure to the virus. HLA-A2-homozygous lymphocytes, including both homozygous and heterozygous donors by genetic sequence subtyping, did internalize infectious virus but were not susceptible to lysis by autologous virus-specific cytotoxic T lymphocytes (“fratricide”). Similar intrinsic resistance to influenza virus infection was observed with HLA-A1- and HLA-A11-homozygous lymphocytes and with HLA-B-homozygous lymphocytes.

Conclusions

A significant proportion of individuals within a population that is characterized by common expression of HLA class I alleles may possess lymphocytes that are not susceptible to influenza virus infection and thus to mutual virus-specific lysis. Further study may identify new approaches to limit influenza virus infection.

Beyond the fear: Nurses' experiences caring for patients with Middle East respiratory syndrome: A phenomenological study

AIM AND OBJECTIVES

To explore the experiences of Korean nurses who had directly cared for patients with Middle East respiratory syndrome (MERS) and to derive the structure and meaning of these experiences.

BACKGROUND

In 2015, the MERS epidemic struck Korea, and ill-prepared nurses had to care for patients with MERS. Nurses experienced conflict between their fear of the disease and their work and professional ethic.

DESIGN

We employed a phenomenological qualitative approach.

METHODS

Inductive, qualitative, in-depth interviews were performed with 17 nurses. The study process followed the Consolidated Criteria for Reporting Qualitative Research (COREQ) checklist.

RESULTS

The qualitative inductive content analysis generated seven theme clusters and 18 themes. The theme clusters were "Fear of Uncertainty," "Beyond Hesitation," "A Scene Like a Battlefield," "Chaotic Nursing Identity," "Buttresses for Sustainability," "Lingering Trauma" and "Expanded Horizon of Nursing." The final analysis revealed that the core theme was "Beyond the fear of uncertainty."

CONCLUSIONS

This study contrives a more in-depth, holistic understanding by describing the experiences of nurses who directly cared for patients with MERS-the first large-scale infectious disease in Korea. Although nurses saw themselves as vital caregivers, they were frightened of the disease, had to work in a harsh environment, experienced various internal conflicts and had to deal with varying forms of uncertainty.

RELEVANCE TO CLINICAL PRACTICE

This study sheds light on the nursing situation during crises involving serious infectious diseases; to combat these, more medical facilities are needed, and staff should be proactively guided on how to care for patients. It can serve as part of a good foundation for further study of medical staff during recurring epidemics.

A Comparison of Clinical and Chest CT Findings in Patients With Influenza A (H1N1) Virus Infection and Coronavirus Disease (COVID-19)

OBJECTIVE. The purpose of this study was to compare clinical and chest CT findings in patients with influenza A (H1N1) pneumonia and coronavirus disease (COVID-19) pneumonia. MATERIALS AND METHODS. Thirty patients with diagnosed influenza A (H1N1) virus infection (group A) and 30 patients with diagnosed COVID-19 (group B) were retrospectively enrolled in the present study. The clinical characteristics and chest CT findings of the two groups were compared. RESULTS. Fever, cough, expectoration, and dyspnea were the main symptoms in both groups with viral pneumonia, with cough and expectoration more frequently found in group A. Lymphopenia, an elevated C-reactive protein level, and an increased erythrocyte sedimentation rate were common laboratory test findings in the two groups. The median time from symptom onset to CT in group A and group B was 6 and 15 days, respectively, and the median total CT score of the pulmonary lobes involved was 6 and 13, respectively. Linear opacification, crazy-paving sign, vascular enlargement, were more common in group B. In contrast, bronchiectasis and pleural effusion were more common in group A. Other common CT features, including peripheral or peribronchovascular distribution, ground-glass opacities (GGOs), consolidation, subpleural line, air bronchogram, and bronchial distortion, did not show statistical significance. CONCLUSION. On CT, the significant differences between influenza A (H1N1) pneumonia and COVID-19 pneumonia were findings of linear opacification, crazy-paving sign, vascular enlargement, pleural thickening, and pleural effusion, which were more common in patients with COVID-19 pneumonia, and bronchiectasis and pleural effusion, which were more common in patients with influenza A (H1N1) pneumonia. Other imaging findings, including peripheral or peribronchovascular distribution, ground-glass opacities (GGO), consolidation, subpleural line, air bronchogram, and bronchial distortion, were not significantly different between the two patient groups.

Artificial Intelligence Empowers Radiologists to Differentiate Pneumonia Induced by COVID-19 versus Influenza Viruses

Background

Given the current pandemic, differentiation between pneumonia induced by COVID-19 or influenza viruses is of utmost clinical significance in the patients' management. For this purpose, this study was conducted to develop sensitive artificial intelligence (AI) models to assist radiologists to decisively differentiate pneumonia due to COVID-19 versus influenza viruses.

Methods

Cross sectional chest CT images (N=12744) from well-evaluated cases of pneumonias induced by COVID-19 or H1N1 Influenza viruses, and normal individuals were collected. We examined the computer tomographic (CT) chest images from 137 individuals. Various pre-trained convolutional neural network models, such as ResNet-50, InceptionV3, Wide ResNet, SqueezNet, VGG 16 and VGG 19 were fine-tuned on our datasets. The datasets were used for training (60%), validation (20%), and testing (20%) of the final models. Also, the predictive power and means of precision and recall were determined for each model.

Results

Fine-tuned ResNet-50 model differentiated the pneumonia due to COVID-19 or H1N1 influenza virus with accuracies of 96.7% and 92%, respectively This model outperformed all others, i.e., InceptionV3, Wide ResNet, SqueezNet, VGG 16 and VGG 19.

Conclusion

Fine-tuned and pre-trained image classifying models of AI enable radiologists to reliably differentiate the pneumonia induced by COVID-19 versus H1N1 influenza virus. For this purpose, ResNet-50 followed by InceptionV3 models proved more promising than other AI models. Also in the supplements, we share the source codes and our fine-tuned models for use by researchers and clinicians globally toward the critical task of image differentiation of patients infected with COVID-19 versus H1N1 Influenza viruses.

Long-term virus evolution in nature

Viruses spread to give rise to epidemics and pandemics, and some key parameters that include virus and host population numbers determine virus persistence or extinction in nature. Viruses evolve at different rates depending on the polymerase copying fidelity during genome replication and a number of environmental influences. Calculated rates of evolution in nature vary depending on the time interval between virus isolations. In particular, intrahost evolution is generally more rapid that interhost evolution, and several possible mechanisms for this difference are considered. The mechanisms by which the error-prone viruses evolve are very unlikely to render the operation of a molecular clock (constant rate of incorporation of mutations in the evolving genomes), although a clock is assumed in many calculations. Several computational tools permit the alignment of viral sequences and the establishment of phylogenetic relationships among viruses. The evolution of the virus in the form of dynamic mutant clouds in each infected individual, together with multiple environmental parameters renders the emergence and reemergence of viral pathogens an unpredictable event, another facet of biological complexity.

Virus-Host Coevolution with a Focus on Animal and Human DNA Viruses

Viruses have been infecting their host cells since the dawn of life, and this extremely long-term coevolution gave rise to some surprising consequences for the entire tree of life. It is hypothesised that viruses might have contributed to the formation of the first cellular life form, or that even the eukaryotic cell nucleus originates from an infection by a coated virus. The continuous struggle between viruses and their hosts to maintain at least a constant fitness level led to the development of an unceasing arms race, where weapons are often shuttled between the participants. In this literature review we try to give a short insight into some general consequences or traits of virus–host coevolution, and after this we zoom in to the viral clades of adenoviruses, herpesviruses, nucleo-cytoplasmic large DNA viruses, polyomaviruses and, finally, circoviruses.