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The poor prognosis observed in elderly individuals infected with severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) remains a serious clinical burden and the underlying mechanism is unclear, which necessities detailed investigation of disease characteristics and research for efficient countermeasures. To simulate lethal coronavirus disease 2019 (COVID‐19) in senescent human patients, 80‐week‐old male hamsters are intranasally inoculated with different doses of SARS‐CoV‐2 Omicron BA.5 variant. Exposure to a low dose of the Omicron BA.5 variant results in early activation of the innate immune response, followed by rapid viral clearance and minimal lung damage. However, a high dose of BA.5 results in impaired interferon signaling, cytokine storm, uncontrolled viral replication, and severe lung injury. To decrease viral load and reverse the deterioration of COVID‐19, a new bio‐mimic decoy called CoVR‐MV is used as a preventive or therapeutic agent. Administration of CoVR‐MV as a preventive or therapeutic intervention in the early stages of infection can effectively suppress viral load, regulate the immune response, and rescue animals from death and critical illness. These findings underscore the risk associated with SARS‐CoV‐2 Omicron BA.5 exposure in senescent hamsters and highlight the importance of early intervention to prevent disease progression. [ABSTRACT FROM AUTHOR]

Highly pathogenic coronavirus (CoV) infection induces a defective innate antiviral immune response coupled with the dysregulated release of proinflammatory cytokines and finally results in acute respiratory distress syndrome (ARDS). A timely and appropriate triggering of innate antiviral response is crucial to inhibit viral replication and prevent ARDS. However, current medical countermeasures can rarely meet this urgent demand. Here, an antiviral nanobiologic named CoVR‐MV is developed, which is polymerized of CoVs receptors based on a biomimetic membrane vesicle system. The designed CoVR‐MV interferes with the viral infection by absorbing the viruses with maximized viral spike target interface, and mediates the clearance of the virus through its inherent interaction with macrophages. Furthermore, CoVR‐MV coupled with the virus promotes a swift production and signaling of endogenous type I interferon via deregulating 7‐dehydrocholesterol reductase (DHCR7) inhibition of interferon regulatory factor 3 (IRF3) activation in macrophages. These sequential processes re‐modulate the innate immune responses to the virus, trigger spontaneous innate antiviral defenses, and rescue infected Syrian hamsters from ARDS caused by SARS‐CoV‐2 and all tested variants. [ABSTRACT FROM AUTHOR]

Background: Influenza infection is often measured by a fourfold antibody titer increase over an influenza season (ie seroconversion). However, this approach may fail when influenza seasons are less distinct as it does not account for transient effects from recent infections. Here, we present a method to determine seroconversion for non‐paired sera, adjusting for changes in individuals' antibody titers to influenza due to the transient impact of recent exposures, varied sampling times, and laboratory processes. Methods: We applied our method using data for five H3N2 strains collected from 942 individuals, aged 2‐90 years, during the first two study visits of the Fluscape cohort study (2009‐2012) in Guangzhou, China. Results: After adjustment, apparent seroconversion rates for non‐circulating strains decreased while we observed a 20% increase in seroconversion rates to recently circulating strains. When examining seroconversion to the most recently circulating strain (A/Brisbane/20/2007) in our study, participants aged under 18, and over 64 had the highest seroconversion rates compared to other age groups. Conclusions: Our results highlight the need for improved methods when using antibody titers as an endpoint in settings where there is no clear influenza "off" season. Methods, like those presented here, that use titers from circulating and non‐circulating strains may be key. [ABSTRACT FROM AUTHOR]

Background: Avian influenza A (H7N9) remains circulating in China. For countries at risk of introduction of H7N9, such as Vietnam, early detection of H7N9 virus is essential for the early containment of the virus. Insulated isothermal reverse transcriptase PCR (iiRT‐PCR) is a portable PCR system that can be deployed under field conditions to identify pathogens at the sampling site. Applying PCR at the sampling site will greatly reduce the time to obtain a diagnostic result which allows the veterinary authority to take immediate action to contain disease spreading. Objective: To determine analytical and diagnostic sensitivity and specificity of the portable iiRT‐PCR for H7N9 virus detection. Methods: A panel of 59 virus isolates, including H7N9, avian influenza viruses of subtype H1 to H13, swine and human influenza viruses, Newcastle disease virus, and infectious bursal disease virus, were tested by H7 and N9 iiRT‐PCR reagents, using probes and primers specific to H7 or N9, in comparison with laboratory‐based real‐time RT‐PCR assays to determine analytical sensitivity and specificity. Fifty oropharyngeal samples from experimentally infected chicken and ducks with H7N9 and 50 non‐infected control swabs were tested by the H7 iiRT‐PCR to determine diagnostic sensitivity and specificity. Results: The H7 and N9 iiRT‐PCR reagents yielded comparable levels of analytical sensitivity and specificity with real‐time RT‐PCR for the detection of H7N9 virus. Diagnostic sensitivity and specificity of H7 iiRT‐PCR were 98% and 100%, respectively. Conclusion: The observed high sensitivity and specificity of iiRT‐PCR for H7N9 detection show its potential for early detection of H7N9 in risk‐based surveillance. [ABSTRACT FROM AUTHOR]

We present an r package, ggtree, which provides programmable visualization and annotation of phylogenetic trees., ggtree can read more tree file formats than other softwares, including newick, nexus, NHX, phylip and jplace formats, and support visualization of phylo, multiphylo, phylo4, phylo4d, obkdata and phyloseq tree objects defined in other r packages. It can also extract the tree/branch/node-specific and other data from the analysis outputs of beast, epa, hyphy, paml, phylodog, pplacer, r8s, raxml and revbayes software, and allows using these data to annotate the tree., The package allows colouring and annotation of a tree by numerical/categorical node attributes, manipulating a tree by rotating, collapsing and zooming out clades, highlighting user selected clades or operational taxonomic units and exploration of a large tree by zooming into a selected portion., A two-dimensional tree can be drawn by scaling the tree width based on an attribute of the nodes. A tree can be annotated with an associated numerical matrix (as a heat map), multiple sequence alignment, subplots or silhouette images., The package ggtree is released under the artistic-2.0 license. The source code and documents are freely available through bioconductor (). [ABSTRACT FROM AUTHOR]

Background Serum antibody to influenza can be used to identify past exposure and measure current immune status. The two most common methods for measuring this are the hemagglutination inhibition assay ( HI) and the viral neutralization assay ( NT), which have not been systematically compared for a large number of influenza viruses. Methods A total of 151 study participants from near Guangzhou, China, were enrolled in 2009 and provided serum. HI and NT assays were performed for 12 historic and recently circulating strains of seasonal influenza A. We compared titers using Spearman correlation and fit models to predict NT using HI results. Results We observed high positive mean correlation between HI and NT assays (Spearman's rank correlation, ρ=.86) across all strains. Correlation was highest within subtypes and within close proximity in time. Overall, an HI=20 corresponded to NT=10, and HI=40 corresponded to NT=20. Linear regression of log( NT) on log( HI) was statistically significant, with age modifying this relationship. Strain-specific area under a curve ( AUC) indicated good accuracy (>80%) for predicting NT with HI. Conclusions While we found high overall correspondence of titers between NT and HI assays for seasonal influenza A, no exact equivalence between assays could be determined. This was further complicated by correspondence between titers changing with age. These findings support generalized comparison of results between assays and give further support for use of the hemagglutination inhibition assay over the more resource intensive viral neutralization assay for seasonal influenza A, although attention should be given to the effect of age on these assays. [ABSTRACT FROM AUTHOR]

Avian H7N9 influenza viruses may pose a further threat to humans by reassortment with human viruses, which could lead to generation of novel reassortants with enhanced polymerase activity. We previously established a novel statistical approach to study the polymerase activity of reassorted v RNPs (Influenza Other Respir Viruses. 2013;7:969-78). Here, we report the use of this method to study recombinant v RNPs with subunits derived from human H1N1, H3N2, and H7N9 viruses. Our results demonstrate that some reassortant v RNPs with subunits derived from the H7N9 and other human viruses can have much higher polymerase activities than the wild-type levels. [ABSTRACT FROM AUTHOR]

Please cite this paper as: Pepin et al. (2012) Multiannual patterns of influenza A transmission in Chinese live bird market systems. Influenza and Other Respiratory Viruses DOI: 10.1111/j.1750-2659.2012.00354.x. Background Avian influenza viruses (AIV) cause huge economic losses in poultry industries and pose a substantial threat to human health. However, predicting AIV epizootics and emergence in humans is confounded by insufficient empirical data on the ecology and dynamics of AIV in poultry systems. To address this gap, we quantified incidence patterns for 13 hemagglutinin subtypes of AIV using 6 years of surveillance data that were collected from ten different species of poultry and three different types of poultry holdings (contexts) - retail, wholesale, or farms. Methods We collected 42 646 samples in Shantou, China between 2000 and 2006. We screened samples for hemagglutinin subtypes 1-13 of AIV and Avian Paramyxovirus-type-1 (APMV-1) using monospecific antisera in hemagglutination inhibition tests. We analyzed the data to determine seasonality patterns, subtype-host, and subtype-subtype interactions as well as subtype bias in incidence in different contexts. Results H3, H6, H9, and APMV-1 were the most prevalent. No significant seasonality was found when all subtypes were considered together. For most AIV subtypes and APMV-1, there was subtype specificity for host, context, and coinfection partner. H5 showed the most generalized host usage pattern, followed by H9 and H6. Conclusion Subtype-specific patterns because of host, context, and other subtypes suggest that risk assessments that exclude these details are likely inaccurate. Surveillance should include longitudinal sampling of multiple host species in multiple contexts. Quantitative models of control strategies must consider multiple subtypes, hosts, and source contexts to assess the effectiveness of interventions. [ABSTRACT FROM AUTHOR]