The Ecology and Evolution of Influenza Viruses

Evaluation of global distribution, genetic evolution, and mammalian infectivity and pathogenicity of H13 and H16 avian influenza viruses

H13 and H16 subtype avian influenza viruses (AIVs) typically infect Charadriiformes, are widely distributed throughout coastal regions worldwide, and pose a risk of spill-over to mammals. Systematic research on the epidemiology, transmission dynamics, and biological characteristics of these subtypes remains limited. To address this gap, we analyzed 20 years of wild bird influenza surveillance data from China integrated with global influenza database information to reconstruct the global spatiotemporal distribution, transmission dynamics and public health implications of H13 and H16. During influenza surveillance, 28 H13 and 19 H16 viruses were isolated. The phylogenetic trees for the H13 and H16 viruses revealed that both subtypes could be classified into three distinct groups. Viruses from H13 Group A, H13 Group C, and H16 Group C demonstrated frequent genetic exchanges and intercontinental transmission on a global scale. Mapping host migration revealed overlap between virus spread and host migration pathways. Our results suggest that host migration is a key driver of widespread distribution, cross-regional spread, and gene exchange for some H13 and H16 lineages. Virus isolates exhibit high genetic diversity with rich genotypic variation. Most isolates carry mammalian-adaptive mutations, such as the G228S mutation in the HA protein. H13 and H16 isolates of multiple genotypes infected mice without prior adaptation and exhibited varying tissue tropism. In summary, these findings indicate that host migration patterns are closely associated with the evolution of H13 and H16 AIVs. The potential risk of mammalian infection is highlighted, as viruses carrying mammalian-adaptive mutations may lead to new infection cases.

Refinement of imidazo[2,1-a]pyrimidines in pursuit of potential drug candidates against group 2 influenza A viruses

We discovered a series of imidazo[1,2-a]pyrimidines as potent, group 2 selective inhibitors of influenza A viruses (IAVs) that target the hemagglutinin-mediated viral entry process. Preliminary hit-to-lead optimization efforts afforded promising IAV inhibitors with improved activity against infectious H7N7 and H3N2 viruses. We now report a more comprehensive cycle of structure-activity relationship studies and optimization of metabolic stability, and overall druglike properties of this series of imidazo[1,2-a]pyrimidines, which allowed in the identification of two lead compounds that show promise as preclinical candidates. Compounds 10 and 12 inhibited pseudotyped H7N1 with EC50 values of 0.09 and 0.47 μM, respectively. They were among the most potent compounds in the viral replication assay when tested against infectious H3N2 IAV, and they also demonstrated remarkable activity against avian influenza viruses; these data designated these imidazo[1,2-a]pyrimidines as potent broad-spectrum group 2 IAV inhibitors. Compounds 10 and 12 exhibit dissimilar but desirable drug metabolism and pharmacokinetics (DMPK) profiles, and therefore they offer different options for specific and effective patient treatment.

Seroprevalence of anti-influenza antibodies in humans and characterization of seasonal influenza viruses isolated in Russia during the 2023-2024 flu season

The 2023-2024 flu season in Russia was dominated by influenza A(H3N2) viruses. In this study, we isolated seasonal influenza viruses from human respiratory specimens, analyzed their genetic and antigenic properties, and assessed their susceptibility to neuraminidase inhibitors. In total, we isolated 207 influenza virus isolates. Of them, 95.2% were subtyped as A(H3N2), 1.9% as A(H1N1)pdm09, and 2.9% as B/Victoria influenza viruses. The hemagglutinin sequences of the A(H3N2) isolates showed that they belonged to several subclades within the 2a.3a.1 genetic group, with the J2 subclade being predominant. Despite their genetic diversity, all A(H3N2) strains tested using a hemagglutination inhibition assay were antigenically similar to the egg-propagated vaccine strain A/Darwin/09/2021(H3N2). The B/Victoria virus isolates belonged to the C.5 and C.5.7 subclades of the genetic group V1A.3a.2 and were antigenically similar to cell- and egg-propagated variants of the vaccine strain B/Austria/1359417/2021. All of the A(H1N1)pdm09 isolates belonged to the 6B.1A.5a.2a genetic clade and were well-recognized by a ferret antiserum raised against a cell-propagated A/Wisconsin/67/2022(H1N1pdm09)-like reference strain. All of the tested isolates were susceptible to oseltamivir and zanamivir, including two A(H1N1)pdm09 strains with an NA-S247N substitution. Seroprevalence analysis showed that 60%, 54%, and 46% of the human blood samples tested were seropositive for the A(H3N2), A(H1N1)pdm09 and B/Victoria antigens from the 2022-2023 vaccine.

Making sense of the virome in light of evolution and ecology

Understanding the patterns and drivers of viral prevalence and abundance is of key importance for understanding pathogen emergence. Over the last decade, metagenomic sequencing has exponentially expanded our knowledge of the diversity and evolution of viruses associated with all domains of life. However, as most of these 'virome' studies are primarily descriptive, our understanding of the predictors of virus prevalence, abundance and diversity, and their variation in space and time, remains limited. For example, we do not yet understand the relative importance of ecological predictors (e.g. seasonality and habitat) versus evolutionary predictors (e.g. host and virus phylogenies) in driving virus prevalence and diversity. Few studies are set up to reveal the factors that predict the virome composition of individual hosts, populations or species. In addition, most studies of virus ecology represent a snapshot of single species viromes at a single point in time and space. Fortunately, recent studies have begun to use metagenomic data to directly test hypotheses about the evolutionary and ecological factors which drive virus prevalence, sharing and diversity. By synthesizing evidence across studies, we present some over-arching ecological and evolutionary patterns in virome composition, and illustrate the need for additional work to quantify the drivers of virus prevalence and diversity.

The Auditory Brainstem Response Diagnoses Alzheimer-Like Disease in the 5xFAD Mouse Model

Early and accurate diagnosis of Alzheimer's disease (AD) will be key for effective personalized treatment plans ( Cummings, 2023). Significant difficulties in auditory processing have been frequently reported in many patients with mild cognitive impairment, the prodromal form of AD ( Tarawneh et al., 2022), making it an outstanding candidate as AD diagnostic biomarker. However, the efficiency of diagnosis with this parameter has not been explored. Here we show that when male mice with amyloidosis begin to show memory decline, changes in the auditory brainstem response (ABR) to clicks enable the reliable diagnosis of disease using a machine learning algorithm. Interpretation of the machine learning diagnosis revealed that the upper levels of the auditory pathway, including the inferior colliculus, were the probable sources of the defects. Histological analyses show that in these locations, neuroinflammation and plaque deposition temporally correlate with behavioral changes consistent with memory loss. While these findings are tempered by the caveat that they derive from amyloidosis mice, we propose that ABR measurements be evaluated as an additional rapid, low-cost, noninvasive biomarker to assist the diagnostic testing of early-stage AD.

A human-infecting H10N5 avian influenza virus: Clinical features, virus reassortment, receptor-binding affinity, and possible transmission routes

BACKGROUND

In late 2023, the first human case caused by an H10N5 avian influenza virus (AIV) was diagnosed in China. H10Ny AIVs have been identified in various poultry and wild birds in Eurasia, the Americas, and Oceania.

METHODS

We analyzed the clinical data of the H10N5 AIV-infected patient, isolated the virus, and evaluated the virus receptor-binding properties together with the H10N8 and H10N3 AIVs identified in humans and poultry. The genomic data of the human-infecting H10N5 strain and avian H10Ny AIVs (n = 48, including 16 strains of H10N3 and 2 strains of H10N8) from live poultry markets in China, during 2019-2021, were sequenced. We inferred the genetic origin and spread pattern of the H10N5 AIV using the phylodynamic methods. In addition, given all available nucleotide sequences, the spatial-temporal dynamics, host distribution, and the maximum-likelihood phylogenies of global H10 AIVs were reconstructed.

FINDINGS

The first H10N5 AIV-infected human case co-infected with seasonal influenza H3N2 virus was identified. Unfortunately, the patient died after systematic treatments. The H10N5 virus predominantly bound avian-type receptor, without any known mammalian-adapted mutations. Phylodynamic inference indicated that the H10N5 AIV was generated by multiple reassortments among viruses from Korea and Japan, central Asia, and China in late 2022, acquiring the seven gene segments from H10N7 or other low pathogenic AIVs in wild Anseriformes, except for the PA gene from H5N2 AIVs in Domestic Anseriformes. The HA gene of the H10N5 virus belongs to the North American lineage, which was probably introduced into Asia by migratory birds, subsequently forming local circulation.

INTERPRETATION

Unlike the human-infecting H10N3 and H10N8 AIVs acquiring six internal protein-coding genes from H9N2 AIVs in domestic poultry, the human-infecting H10N5 AIV was generated through multiple reassortments among viruses mainly carried by wild Anseriformes. Furthermore, worldwide distribution, inter-continental transmission, and genetic exchanges between Eurasian and North American lineages call for more concerns about influenza surveillance on H10Ny AIVs, especially in the flyway overlapping areas.

Genomic Characterization and Phylogenetic Analysis of Five Avian Influenza H5N1 Subtypes from Wild Anser indicus in Yunnan, China

Highly pathogenic avian influenza (HPAI) H5 viruses have been found to have a substantial geographic distribution since they were first reported in Guangdong Province, China. The emergence of new genotypes threatens the poultry industry and human health worldwide. Here, we report five HPAI H5N1 variants isolated from Anser indicus in Yunnan Province, China. A phylogenetic analysis of the hemagglutinin (HA) gene showed that all isolates belong to the highly pathogenic H5 clade 2.3.4.4b and formed two distinct genetic clusters. Bayesian phylogenetic analysis also revealed that the viruses were initially disseminated from wild birds to Anser indicus, implying that infected birds most likely contributed to viral transmission in the region. Genomic sequence analysis revealed several amino acid substitutions, also implying that the infected birds contributed to the spread of the virus throughout the region. Substitutions in the HA glycoprotein increased the virus's binding affinity to human α-2,6 sialic acid residues. Substitutions in the PB1, PA, and PB2 motifs increased viral polymerase activity and replication in hosts, whereas substitutions in the NP, M1, and NS motifs increased viral pathogenicity in chickens and mice.

Evolutionary dynamics and molecular epidemiology of H1N1 pandemic 2009 influenza A viruses across swine farms in Denmark

Transmission of influenza A viruses (IAVs) between pigs and humans can trigger pandemics but more often cease as isolated infections without further spread in the new host species population. In Denmark, a major pig-producing country, the first two detections of human infections with swine-like IAVs were reported in 2021. These zoonotic IAVs were reassortants of the H1N1 pandemic 2009 lineage ("H1N1pdm09," H1 lineage 1A, clade 1A.3.3.2) introduced to swine farms in Denmark through humans approximately 11 years prior. However, predicting the likelihood and outcome of such IAV spillovers is challenging without a better understanding of the viral determinants. This study traced the evolution of H1N1pdm09 from 207 sequenced genomes as the virus propagated across Danish swine farms over a decade. H1N1pdm09 diverged into several genetically distinct viral populations, largely prompted by reassortments with neuraminidase (NA) segments from other enzootic IAV lineages. The genomic segments encoding the viral envelope glycoproteins, hemagglutinin (HA) and NA, evolved at the fastest rates, while the M and NS genomic segments were among the lowest evolutionary rates. The two zoonotic IAVs emerged from separate viral populations and shared the highest number of amino acid mutations in the PB2 and HA proteins. Acquisition of additional predicted glycosylation sites on the HA proteins of the zoonotic IAVs may have facilitated infection of the human patients. Ultimately, the analysis provides a foundation from which to further explore viral genetic indicators of host adaptation and zoonotic risk.

Antivirotics based on defective interfering particles: emerging concepts and challenges

Viruses are obligate parasites, that use the host's internal metabolic systems for their own reproduction. This complicates the search for molecular targets to prevent the spread of viral infection without disrupting the vital functions of human cells. Defective interfering particles (DIPs) are natural competitors of viruses for important resources of viral reproduction. DIPs emerge during infection, originate from the normal viral replication process and inhibit its progression, making them an interesting candidate for antiviral therapy. Here we describe the biology of DIPs, advances in DIP-based antiviral technology, analyze their therapeutic potential and provide a systemic overview of existing preventive and therapeutic antiviral strategies.

Are we serologically prepared against an avian influenza pandemic and could seasonal flu vaccines help us?

The current situation with H5N1 highly pathogenic avian influenza virus (HPAI) is causing a worldwide concern due to multiple outbreaks in wild birds, poultry, and mammals. Moreover, multiple zoonotic infections in humans have been reported. Importantly, HPAI H5N1 viruses with genetic markers of adaptation to mammals have been detected. Together with HPAI H5N1, avian influenza viruses H7N9 (high and low pathogenic) stand out due to their high mortality rates in humans. This raises the question of how prepared we are serologically and whether seasonal vaccines are capable of inducing protective immunity against these influenza subtypes. An observational study was conducted in which sera from people born between years 1925-1967, 1968-1977, and 1978-1997 were collected before or after 28 days or 6 months post-vaccination with an inactivated seasonal influenza vaccine. Then, hemagglutination inhibition, viral neutralization, and immunoassays were performed to assess the basal protective immunity of the population as well as the ability of seasonal influenza vaccines to induce protective responses. Our results indicate that subtype-specific serological protection against H5N1 and H7N9 in the representative Spanish population evaluated was limited or nonexistent. However, seasonal vaccination was able to increase the antibody titers to protective levels in a moderate percentage of people, probably due to cross-reactive responses. These findings demonstrate the importance of vaccination and suggest that seasonal influenza vaccines could be used as a first line of defense against an eventual pandemic caused by avian influenza viruses, to be followed immediately by the use of more specific pandemic vaccines.IMPORTANCEInfluenza A viruses (IAV) can infect and replicate in multiple mammalian and avian species. Avian influenza virus (AIV) is a highly contagious viral disease that occurs primarily in poultry and wild water birds. Due to the lack of population immunity in humans and ongoing evolution of AIV, there is a continuing risk that new IAV could emerge and rapidly spread worldwide, causing a pandemic, if the ability to transmit efficiently among humans was gained. The aim of this study is to analyze the basal protection and presence of antibodies against IAV H5N1 and H7N9 subtypes in the population from different ages. Moreover, we have evaluated the humoral response after immunization with a seasonal influenza vaccine. This study is strategically important to evaluate the level of population immunity that is a major factor when assessing the impact that an emerging IAV strain would have, and the role of seasonal vaccines to mitigate the effects of a pandemic.

Long Non-Coding RNA THRIL Promotes Influenza Virus Replication by Inhibiting the Antiviral Innate Immune Response

Long non-coding RNAs (lncRNAs) have been recognized for their crucial roles in the replication processes of various viruses. However, the specific functions and regulatory mechanisms of many lncRNAs in influenza A virus (IAV) pathogenesis remain poorly understood. In this study, we identified lncRNA THRIL and observed a significant reduction in its expression following IAV infection in A549 cells. The treatment of cells with the viral mimic poly (I:C), or with type I and type III interferons, resulted in a substantial decrease in THRIL expression. Furthermore, THRIL overexpression significantly enhanced IAV replication, while its silencing markedly reduced IAV replication. Additionally, IAV infection led to notable reductions in the expression levels of type I and type III interferons in cell lines overexpressing THRIL compared to control groups; conversely, cell lines with THRIL knockdown exhibited significantly higher interferon levels than control groups. Moreover, THRIL was found to inhibit the expression of several critical interferon-stimulated genes (ISGs), which are essential for an effective antiviral response. Notably, our findings demonstrated that THRIL impaired the activation of IRF3, a key transcription factor in the interferon signaling pathway, thereby suppressing host innate immunity. These results highlight THRIL's potential as a therapeutic target for antiviral strategies.

Impact of Oseltamivir and Diabetes Development

Background/Objectives: Influenza is a major global health challenge, causing thousands of deaths annually. Antiviral drugs, particularly oseltamivir, a neuraminidase inhibitor, have become essential therapeutic options due to their oral bioavailability and efficacy. Previous studies suggest a potential association between oseltamivir use and the onset of diabetes mellitus. However, further investigation is needed to establish a definitive link. Methods: This retrospective cohort study utilized data from the Taiwan National Health Insurance Research Database (NHIRD), including 1,631,968 patients (815,984 oseltamivir users) between 1 January 2009 and 28 December 2018. All statistical analyses were performed using SAS 9.4M8 software (SAS Institute Inc., Cary, NC, USA). Results: Cox proportional hazards regression and multivariate analyses revealed a statistically significant association between oseltamivir use and overall diabetes risk (HR = 1.027, p = 0.0186). While no significant association was observed for Type 1 diabetes (HR = 1.021; p = 0.06795), oseltamivir users showed a higher incidence of Type 2 diabetes (HR = 1.024; p < 0.05). Oseltamivir was also linked to increased risks of comorbidities, including dyslipidemia (HR = 1.295, p < 0.0001), chronic liver disease (HR = 1.446, p < 0.0001), hypertension (HR = 1.586, p < 0.0001), and obesity (HR = 2.949, p < 0.0001). Conclusions: Oseltamivir is associated with an increased risk of Type 2 diabetes but not Type 1, and related comorbidities.

Unveiling the role of long non-coding RNAs in chicken immune response to highly pathogenic avian influenza H5N1 infection

Avian influenza viruses (AIVs) pose a significant threat to global poultry production, necessitating effective control strategies to mitigate economic losses and ensure animal welfare. Long non-coding RNAs (lncRNAs) have emerged as crucial regulators of immune responses, yet their roles in AIV-infected chickens remain poorly understood. This study aimed to investigate the expression profiles of lncRNAs and their targets in Vietnamese Ri chickens infected with the highly pathogenic AIV (HPAIV) H5N1. Through RNA sequencing, we identified novel lncRNAs and analyzed differentially expressed (DE) transcripts at 1 and 3 days post-infection (dpi) in chicken lung tissue. Our results revealed a higher number of DE lncRNAs and mRNAs at 1 dpi and 3 dpi, respectively, compared to control, with resistant chickens exhibiting a notably stronger immune response than susceptible chickens at 3 dpi. Functional analysis implicated these lncRNAs in immune-related pathways crucial for host responses to H5N1 viral infection. Furthermore, we identified lncRNA-mRNA interactions associated with antiviral responses and immune function. Notably, several genes involved in antiviral resistance and immune responses showed higher expression in resistant chickens, confirming their stronger antiviral response. Overall, our study provides insights into the role of lncRNAs in the host's response to HPAIV H5N1 infection in chickens and highlights potential candidates for further investigation into host-pathogen interactions. These findings could drive the development of novel control strategies for AIVs, significantly enhancing poultry health and biosecurity.

Longitudinal Active Avian Influenza Surveillance in Bangladesh From 2017-2022 Reveals Differential IAV and H5 Infection and Viral Burden Associated With Bird Species, Sex, and Age

Influenza viruses are a major global health burden with up to 650,000 associated deaths annually. Beyond seasonal illness, influenza A viruses (IAVs) pose a constant pandemic threat due to novel emergent viruses that have evolved the ability to jump from their natural avian hosts to humans. Because of this threat, active surveillance of circulating IAV strains in wild and domestic bird populations is vital to our pandemic preparedness and response strategies. Here, we report on IAV surveillance data collected from 2017 to 2022 from wild and domestic birds in Bangladesh. We note evidence to suggest that male birds show a higher risk of IAV, including highly pathogenic avian influenza (HPAI) A(H5) virus, positivity than female birds. The data was stratified to control for selection bias and confounding variables to test the hypothesis that male birds are at a higher risk of IAV positivity relative to female birds. The association of IAV and A(H5) largely held in each stratum, and double stratification suggested that the phenomena was largely specific to ducks. Finally, we show that chickens, male birds, and juvenile birds generally have higher viral loads compared to their counterparts. These observations warrant further validation through active surveillance across various populations. Such efforts could significantly contribute to the enhancement of pandemic prediction and risk assessment models.

Detection and phylogenetic analysis of contemporary H14N2 Avian influenza A virus in domestic ducks in Southeast Asia (Cambodia)

Avian influenza virus (AIV) in Asia is a complex system with numerous subtypes and a highly porous wild birds-poultry interface. Certain AIV subtypes, such as H14, are underrepresented in current surveillance efforts, leaving gaps in our understanding of their ecology and evolution. The detection of rare subtype H14 in domestic ducks in Southeast Asia comprises a geographic region and domestic bird population previously unassociated with this subtype. These H14 viruses have a complex evolutionary history involving gene reassortment events. They share sequence similarity to AIVs endemic in Cambodian ducks, and Eurasian low pathogenicity and high pathogenicity H5Nx AIVs. The detection of these H14 viruses in Southeast Asian domestic poultry further advances our knowledge of the ecology and evolution of this subtype and reinforces the need for continued, longitudinal, active surveillance in domestic and wild birds. Additionally, in vivo and in vitro risk assessment should encompass rare AIV subtypes, as they have the potential to establish in poultry systems.

Cistanche deserticola polysaccharide-functionalized dendritic fibrous nano-silica as oral delivery system for H9N2 vaccine to promote systemic and mucosal immune response

Most infectious diseases are caused by pathogens that invade the body tissues through mucosal tract. Therefore, it is essential to develop effective vaccines administered through the mucosa as a first-line of defense against major infectious diseases. Oral delivery of vaccines is currently of great interest due to its potential to elicit both mucosal and systemic immune responses, high compliance rate and non-invasive nature. However, their development is limited by the challenging gastrointestinal (GI) environment, the low permeability of the mucus barrier, and the lack of effective and safe mucosal adjuvants. Currently, nanoparticle-based strategies show significant potential for improving oral vaccine delivery systems. Herein, the dendritic fibrous nano-silica (DFNS) grafted with Cistanche deserticola polysaccharide (CDP) nanoparticles (CDP-DFNS) were developed for oral delivery of H9N2 antigen. CDP-DFNS induced the activation of macrophages, thereby enhancing antigen uptake in vitro. Additionally, CDP-DFNS/H9N2 significantly activated the dendritic cells (DCs) in Peyer's patches (PPs), and T/B cells in mesenteric lymph nodes (MLNs). Moreover, CDP-DFNS/H9N2 enhanced the HI titers and levels of H9N2-specific antibody IgG, secretory IgA (SIgA) and H9N2-specific IgA in intestinal and respiratory mucosa, as well as Th-associated cytokines. Our results indicate that CDP-DFNS could be a promising oral vaccine adjuvant delivery system.

Computational screening of phytocompounds from C. amboinicus identifies potential inhibitors of influenza A (H3N2) virus by targeting hemagglutinin

The H3N2 subtype of the influenza A virus continues to be a notable public health issue due to its association with seasonal epidemics and severe human morbidity. The constrained effectiveness of current antiviral medications, combined with the inevitable emergence of drug-resistant variants, mandates the exploration of innovative therapeutic approaches. This study focuses on the identification of phytocompounds from Coleus amboinicus with the potential to target hemagglutinin, viral protein involved in viral entry by binding to sialyl glycoconjugates receptors on the surface of host cells. Molecular docking studies were carried out to assess the efficacy of C. amboinicus phytocompounds with hemagglutinin receptor-binding site. The study revealed that among the 84 signature phytocompounds, isosalvianolic acid and salvianolic acid C showed the highest docking scores and favourable intermolecular interactions. Pharmacokinetic analysis and Pan-assay interference compounds (PAINS) filtering confirmed that isosalvianolic acid meets the criteria outlined in Lipinski's rule of five, exhibits favourable ADMET profiles and passes PAINS filters. Furthermore, the molecular dynamics simulations followed by radius of gyration (Rg), solvent accessible surface area (SASA), and MM-PBSA calculations for binding free energy, verified the stability of the docked complexes. Together, the study identifies isosalvianolic acid as a promising inhibitor of the H3N2 virus by binding to hemagglutinin, indicating its potential as a strategy for therapeutic intervention.

Phylogenetic Insights into H7Nx Influenza Viruses: Uncovering Reassortment Patterns and Geographic Variability

Influenza A viruses (IAVs), which belong to the Orthomyxoviridae family, are RNA viruses characterized by a segmented genome that allows them to evolve and adapt rapidly. These viruses are mainly transmitted by wild waterfowl. In this study, we investigated the evolutionary processes of H7Nx (H7N1, H7N2, H7N3, H7N4, H7N5, H7N6, H7N7, H7N8, H7N9) viruses, which pose a significant pandemic risk due to the known cases of human infection and their potential for rapid genetic evolution and reassortment. The complete genome sequences of H7Nx influenza viruses (n = 3239) were compared between each other to investigate their phylogenetic relationships and reassortment patterns. For the selected viruses, phylogenetic trees were constructed for eight genome segments (PB2, PB1, PA, HA, NP, NA, M, NS) to assess the genetic diversity and geographic distribution of these viruses. Distinct phylogenetic clades with remarkable geographic patterns were found for the different segments. While the viruses were consistently grouped by subtype based on the NA segment sequences, the phylogeny of the other segment sequences, with the exception of the NS segment, showed distinct grouping patterns based on geographic origin rather than formal subtype assignment. Reassortment events leading to complex phylogenetic relationships were frequently observed. In addition, multiple cases of previously undescribed reassortments between subtypes were detected, emphasizing the fluidity of H7Nx virus populations. These results indicate a high degree of genetic diversity and reassortment within H7Nx influenza viruses. In other words, H7Nx viruses exist as constantly changing combinations of gene pools rather than stable genetic lineages.

Recombinant Influenza A Viruses Expressing Reporter Genes from the Viral NS Segment

Studying influenza A viruses (IAVs) requires secondary experimental procedures to detect the presence of the virus in infected cells or animals. The ability to generate recombinant (r)IAV using reverse genetics techniques has allowed investigators to generate viruses expressing foreign genes, including fluorescent and luciferase proteins. These rIAVs expressing reporter genes have allowed for easily tracking viral infections in cultured cells and animal models of infection without the need for secondary approaches, representing an excellent option to study different aspects in the biology of IAV where expression of reporter genes can be used as a readout of viral replication and spread. Likewise, these reporter-expressing rIAVs provide an excellent opportunity for the rapid identification and characterization of prophylactic and/or therapeutic approaches. To date, rIAV expressing reporter genes from different viral segments have been described in the literature. Among those, rIAV expressing reporter genes from the viral NS segment have been shown to represent an excellent option to track IAV infection in vitro and in vivo, eliminating the need for secondary approaches to identify the presence of the virus. Here, we summarize the status on rIAV expressing traceable reporter genes from the viral NS segment and their applications for in vitro and in vivo influenza research.

Different effects of air pollutant concentrations on influenza A and B in Sichuan, China

BACKGROUND

The detrimental effects of air pollution on the respiratory system are well documented. Previous research has established a correlation between air pollutant concentration and the frequency of outpatient visits for influenza-like illness. However, studies investigating the variations in infection among different influenza subtypes remain sparse. We aimed to determine the correlation between air pollutant levels and different influenza subtypes in Sichuan Province, China.

METHODS

A generalized additive model and distributed lag nonlinear model were employed to assess the association between air pollutants and influenza subtypes, utilizing daily influenza data obtained from 30 hospitals across 21 cities in Sichuan Province. The analysis considered the temporal effects and meteorological factors. The study spanned from January 1, 2017, to December 31, 2019. To provide a more precise evaluation of the actual impact of air pollution on different subtypes of influenza, we also performed subgroup analyses based on factors such as gender, age, and geography within the population.

RESULTS

During the investigation, 17,462 specimens from Sichuan Province tested positive for influenza. Among these, 12,607 and 4855 were diagnosed with Flu A and B, respectively. The related risk of influenza A infection significantly increased following exposure to PM2.5 on Lag2 days (RR=1.008, 95 % confidence interval [CI]: 1.000-1.016), SO2 and CO on Lag1 days (RR=1.121, 95 % CI: 1.032-1.219; RR=1.151, 95 % CI: 1.030-1.289), and NO2 on Lag0 day (RR=1.089, 95 % CI: 1.035-1.145). PM10 and SO2 levels on Lag0 day, PM2.5 levels on Lag1 day, and CO levels on Lag6 day, with a reduced risk of influenza B (RR=0.987, 95 % CI: 0.976-0.997; RR=0.817, 95 % CI: 0.676-0.987; RR=0.979, 95 % CI: 0.970-0.989; RR=0.814, 95 % CI: 0.561-0.921).

CONCLUSION

The findings from the overall population and subgroup analyses indicated that the impact of air pollutant concentrations on influenza A and B is inconsistent, with influenza A demonstrating greater susceptibility to these pollutants. Minimizing the levels of SO2, CO, NO2, and PM2.5 can significantly decrease the likelihood of contracting influenza A. Analyzing the influence of environmental contaminants on different influenza subtypes can provide insights into seasonal influenza trends and guide the development of preventive and control strategies.

First detection of influenza A virus subtypes H1N1 and H3N8 in the Antarctic region: King George Island, 2023

RELEVANCE

Influenza A virus is characterized by a segmented single-stranded RNA genome. Such organization of the virus genome determines the possibility of reassortment, which can lead to the emergence of new virus variants. The main natural reservoir of most influenza A virus subtypes are wild waterfowl. Seasonal migrations gather waterfowl from all major migration routes to nesting areas near the northern and southern polar circles. This makes intercontinental spread of influenza A viruses possible. Objective ‒ to conduct molecular genetic monitoring and study the phylogenetic relationships of influenza A virus variants circulating in Antarctica in 2023.

MATERIALS AND METHODS

We studied 84 samples of biological material obtained from birds and marine mammals in April‒May 2023 in coastal areas of Antarctica. For 3 samples, sequencing was performed on the Miseq, Illumina platform and phylogenetic analysis of the obtained nucleotide sequences of the influenza A virus genomes was performed.

RESULTS

The circulation of avian influenza virus in the Antarctic region was confirmed. Heterogeneity of the pool of circulating variants of the influenza A virus (H3N8, H1N1) was revealed. Full-length genomes of the avian influenza virus were sequenced and posted in the GISAID database (EPI_ISL_19032103, 19174530, 19174467).

CONCLUSION

The study of the genetic diversity of influenza A viruses circulating in the polar regions of the Earth and the identification of the conditions for the emergence of new genetic variants is a relevant task for the development of measures to prevent biological threats.

Influenza sequence validation and annotation using VADR

Tens of thousands of influenza sequences are deposited into the GenBank database each year. The software tool FLu ANnotation tool (FLAN) has been used by GenBank since 2007 to validate and annotate incoming influenza sequence submissions and has been publicly available as a webserver but not as a standalone tool. Viral Annotation DefineR (VADR) is a general sequence validation and annotation software package used by GenBank for norovirus, dengue virus and SARS-CoV-2 virus sequence processing that is available as a standalone tool. We have created VADR influenza models based on the FLAN reference sequences and adapted VADR to accurately annotate influenza sequences. VADR and FLAN show consistent results on the vast majority of influenza sequences, and when they disagree, VADR is usually correct. VADR can also accurately process influenza D sequences as well as influenza A H17, H18, H19, N10 and N11 subtype sequences, which FLAN cannot. VADR 1.6.3 and the associated influenza models are now freely available for users to download and use. Database URL: https://bitbucket.org/nawrockie/vadr-models-flu.

Evolutionary characterization of the establishment of H6 influenza viruses in domestic geese in China: implications for the position of the host in the ecosystem

Geese, both wild and domestic, are generally considered part of the natural reservoir for influenza A viruses. The highly pathogenic H5 Goose/Guangdong avian influenza virus lineage that is still causing outbreaks worldwide was first detected in domestic geese in 1996. However, while wild geese might have a somewhat restricted role in the influenza ecosystem, the role of domestic geese is little studied. Here, 109 H6 viruses isolated from domestic geese during 2001-2018 in southern China had their phylogeny, evolutionary dynamics, and molecular signatures characterized to examine the role of domestic geese. Our findings demonstrated that all geese H6 viruses were derived from H6 viruses established in ducks and that they subsequently formed three distinct hemagglutinin lineages. Rapid evolution of the hemagglutinin genes was not detected after the duck-to-goose transmissions of H6 viruses that then circulated in geese. Despite long-term persistence in geese, H6 viruses were rarely observed to transmit back to ducks or terrestrial poultry and never exchanged genes with viruses from other subtypes. Most geese H6 viruses maintained the primary molecular signatures of their duck precursors. This study raises the possibility that, rather than being part of the natural reservoir, domestic geese might be more like an aberrant host species for influenza A viruses, and perhaps a "dead-end" host.

Antiviral Activity of Angelica Tenuissima Nakai against Influenza A Virus

The influenza A virus poses a serious threat to human health and is an important global public health issue. The drugs currently used for treatment are becoming increasingly ineffective against influenza A viruses and require the development of new antiviral drugs. Angelica tenuissima Nakai (ATN), a traditional herbal medicine belonging to the Umbelliferae family, exhibits a broad range of pharmacological activities, including inflammation, headache, and cold symptoms. In the present study, based on target protein identification, functional enrichment analysis, and gene set comparisons, we first suggested that ATN has potential therapeutic effects against influenza A virus infection. Next, methylthiazol tetrazolium (MTT) and sulforhodamine B colorimetric (SRB) assay results revealed that ATN exhibited low cytotoxicity in Madin-Darby canine kidney (MDCK) cells. The antiviral properties of ATN were observed against H1N1 and H3N2 virus strains. Microscopy confirmed the increased survival rate of the host cells. Further time-of-addition experiments revealed that the addition of ATN before virus adsorption showed similar results to the whole period of treatment. The pre- and co-treated groups showed lower levels of viral RNA (M1 protein). The results of this study suggest that ATN exhibits antiviral properties against the influenza A virus. These therapeutic properties of ATN can serve as a theoretical basis for further research on the applicability of ATN in the development of antiviral agents.

The Alarming Situation of Highly Pathogenic Avian Influenza Viruses in 2019-2023

Avian influenza viruses (AIVs) have the potential to cause severe illness in wild birds, domestic poultry, and humans. The ongoing circulation of highly pathogenic avian influenza viruses (HPAIVs) has presented significant challenges to global poultry industry and public health in recent years. This study aimed to elucidate the circulation of HPAIVs during 2019 to 2023. Specifically, we assess the alarming global spread and continuous evolution of HPAIVs. Moreover, we discuss their transmission and prevention strategies to provide valuable references for future prevention and control measures against AIVs.

Viral aptamer screening and aptamer-based biosensors for virus detection: A review

Virus-induced infectious diseases have a detrimental effect on public health and exert significant influence on the global economy. Therefore, the rapid and accurate detection of viruses is crucial for effectively preventing and diagnosing infections. Aptamer-based detection technologies have attracted researchers' attention as promising solutions. Aptamers, small single-stranded DNA or RNA screened via systematic evolution of ligands by exponential enrichment (SELEX), possess a high affinity towards their target molecules. Numerous aptamers targeting viral marker proteins or virions have been developed and widely employed in aptamer-based biosensors (aptasensor) for virus detection. This review introduces SELEX schemes for screening aptamers and discusses distinctive SELEX strategies designed explicitly for viral targets. Furthermore, recent advances in aptamer-based biosensing methods for detecting common viruses using different virus-specific aptamers are summarized. Finally, limitations and prospects associated with developing of aptamer-based biosensors are discussed.

Protection against the H1N1 influenza virus using self-assembled nanoparticles formed by lumazine synthase and bearing the M2e peptide

There is an urgent need for influenza vaccines that offer broad cross-protection. The highly conserved ectodomain of the influenza matrix protein 2 (M2e) is a promising candidate; however, its low immunogenicity can be addressed. In this study, we developed influenza vaccines using the Lumazine synthase (LS) platform. The primary objective of this study was to determine the protective potential of M2e proteins expressed on Lumazine synthase (LS) nanoparticles. M2e-LS proteins, produced through the E. coli system, spontaneously assemble into nanoparticles. The study investigated the efficacy of the M2e-LS nanoparticle vaccine in mice. Mice immunized with M2e-LS nanoparticles exhibited significantly higher levels of intracellular cytokines than those receiving soluble M2e proteins. The M2e-LS protein exhibited robust immunogenicity and provided 100% protection against cross-clade influenza.

Influenza in feral cat populations: insights from a study in North-East Italy

Influenza A virus (IAV) can cause high morbidity and mortality in domestic and wild avian species and it is able to infect mammals as well. IAV in cats is sporadic and self-limiting but the recent findings of high pathogenicity avian influenza virus (HPAIV) with genetic signatures of mammalian adaptation, in domestic cats, has raised new concerns about the potential role of cats in the virus ecology. The present study aimed to investigate the circulation of IAV in companion animals' shelters in North-eastern Italy. All samples were collected from feral cats living in feline colonies that were hosted in the companion animals' shelters for the requisite period to administer the veterinary treatments. Between 2021 and 2022, 389 oropharyngeal swabs and 279 sera were collected. All swabs tested negative for IAV and the only one ELISA positive serum sample resulted H5 positive by HI test with a titer of 1:80. Despite the sporadic occurrence of influenza in cats, continuous monitoring is crucial due to the evolving zoonotic nature of the virus.

The V223I substitution in hemagglutinin reduces the binding affinity to human-type receptors while enhancing the thermal stability of the H3N2 canine influenza virus

Given the intimate relationship between humans and dogs, the H3N2 canine influenza viruses (CIVs) pose a threat to public health. In our study, we isolated four H3N2 CIVs from 3,758 dog nasal swabs in China between 2018 and 2020, followed by genetic and biological analysis. Phylogenetic analysis revealed 15 genotypes among all available H3N2 CIVs, with genotype 15 prevailing among dogs since around 2017, indicating the establishment of a stable virus lineage in dogs. Molecular characterization identified many mammalian adaptive substitutions, including HA-G146S, HA-N188D, PB2-I292T, PB2-G590S, PB2-S714I, PB1-D154G, and NP-R293K, present across the four isolates. Notably, analysis of HA sequences uncovered a newly emerged adaptive mutation, HA-V223I, which is predominantly found in human and swine H3N2 viruses, suggesting its role in mammalian adaptation. Receptor-binding analysis revealed that the four H3N2 viruses bind both avian and human-type receptors. However, HA-V223I decreases the H3N2 virus's affinity for human-type receptors but enhances its thermal stability. Furthermore, attachment analysis confirmed the H3N2 virus binding to human tracheal tissues, albeit with reduced affinity when the virus carries HA-V223I. Antigenic analysis indicated that the current human H3N2 vaccines do not confer protection against H3N2 CIVs. Collectively, these findings underscore that the potential threat posed by H3N2 CIVs to human health still exists, emphasizing the necessity of close surveillance and monitoring of H3N2 CIVs in dogs.

Resurgence of seasonal influenza driven by A/H3N2 and B/Victoria in succession during the 2023-2024 season in Beijing showing increased population susceptibility

During the COVID-19 pandemic, non-pharmaceutical interventions were introduced to reduce exposure to respiratory viruses. However, these measures may have led to an "immunity debt" that could make the population more vulnerable. The goal of this study was to examine the transmission dynamics of seasonal influenza in the years 2023-2024. Respiratory samples from patients with influenza-like illness were collected and tested for influenza A and B viruses. The electronic medical records of index cases from October 2023 to March 2024 were analyzed to determine their clinical and epidemiological characteristics. A total of 48984 positive cases were detected, with a pooled prevalence of 46.9% (95% CI 46.3-47.5). This season saw bimodal peaks of influenza activity, with influenza A peaked in week 48, 2023, and influenza B peaked in week 1, 2024. The pooled positive rates were 28.6% (95% CI 55.4-59.6) and 18.3% (95% CI 18.0-18.7) for influenza A and B viruses, respectively. The median values of instantaneous reproduction number were 5.5 (IQR 3.0-6.7) and 4.6 (IQR 2.4-5.5), respectively. The hospitalization rate for influenza A virus (2.2%, 95% CI 2.0-2.5) was significantly higher than that of influenza B virus (1.1%, 95% CI 0.9-1.4). Among the 17 clinical symptoms studied, odds ratios of 15 symptoms were below 1 when comparing influenza A and B positive inpatients, with headache, weakness, and myalgia showing significant differences. This study provides an overview of influenza dynamics and clinical symptoms, highlighting the importance for individuals to receive an annual influenza vaccine.

Binding Evolution of the Dengue Virus Envelope Against DC-SIGN: A Combined Approach of Phylogenetics and Molecular Dynamics Analyses Over 30 Years of Dengue Virus in Brazil

The Red Queen Hypothesis (RQH), derived from Lewis Carroll's "Through the Looking-Glass", postulates that organisms must continually adapt in response to each other to maintain relative fitness. Within the context of host-pathogen interactions, the RQH implies an evolutionary arms race, wherein viruses evolve to exploit hosts and hosts evolve to resist viral invasion. This study delves into the dynamics of the RQH in the context of virus-cell interactions, specifically focusing on virus receptors and cell receptors. We observed multiple virus-host systems and noted patterns of co-evolution. As viruses evolved receptor-binding proteins to effectively engage with cell receptors, cells countered by altering their receptor genes. This ongoing mutual adaptation cycle has influenced the molecular intricacies of receptor-ligand interactions. Our data supports the RQH as a driving force behind the diversification and specialization of both viral and host cell receptors. Understanding this co-evolutionary dance offers insights into the unpredictability of emerging viral diseases and potential therapeutic interventions. Future research is crucial to dissect the nuanced molecular changes and the broader ecological consequences of this ever-evolving battle. Here, we combine phylogenetic inferences, structural modeling, and molecular dynamics analyses to describe the epidemiological characteristics of major Brazilian DENV strains that circulated from 1990 to 2022 from a combined perspective, thus providing us with a more detailed picture on the dynamics of such interactions over time.

Molecular Markers and Mechanisms of Influenza A Virus Cross-Species Transmission and New Host Adaptation

Influenza A viruses continue to be a serious health risk to people and result in a large-scale socio-economic loss. Avian influenza viruses typically do not replicate efficiently in mammals, but through the accumulation of mutations or genetic reassortment, they can overcome interspecies barriers, adapt to new hosts, and spread among them. Zoonotic influenza A viruses sporadically infect humans and exhibit limited human-to-human transmission. However, further adaptation of these viruses to humans may result in airborne transmissible viruses with pandemic potential. Therefore, we are beginning to understand genetic changes and mechanisms that may influence interspecific adaptation, cross-species transmission, and the pandemic potential of influenza A viruses. We also discuss the genetic and phenotypic traits associated with the airborne transmission of influenza A viruses in order to provide theoretical guidance for the surveillance of new strains with pandemic potential and the prevention of pandemics.

IAVCP (Influenza A Virus Consensus and Phylogeny): Automatic Identification of the Genomic Sequence of the Influenza A Virus from High-Throughput Sequencing Data

Recently, high-throughput sequencing of influenza A viruses has become a routine test. It should be noted that the extremely high diversity of the influenza A virus complicates the task of determining the sequences of all eight genome segments. For a fast and accurate analysis, it is necessary to select the most suitable reference for each segment. At the same time, there is no standardized method in the field of decoding sequencing results that allows the user to update the sequence databases to which the reads obtained by virus sequencing are compared. The IAVCP (influenza A virus consensus and phylogeny) was developed with the goal of automatically analyzing high-throughput sequencing data of influenza A viruses. Its goals include the extraction of a consensus genome directly from paired raw reads. In addition, the pipeline enables the identification of potential reassortment events in the evolutionary history of the virus of interest by analyzing the topological structure of phylogenetic trees that are automatically reconstructed.

Development of semisynthetic saponin immunostimulants

Many natural saponins demonstrate immunostimulatory adjuvant activities, but they also have some inherent drawbacks that limit their clinical use. To overcome these limitations, extensive structure-activity-relationship (SAR) studies have been conducted. The SAR studies of QS-21 and related saponins reveal that their respective fatty side chains are crucial for potentiating a strong cellular immune response. Replacing the hydrolytically unstable ester side chain in the C28 oligosaccharide domain with an amide side chain in the same domain or in the C3 branched trisaccharide domain is a viable approach for generating robust semisynthetic saponin immunostimulants. Given the striking resemblance of natural momordica saponins (MS) I and II to the deacylated Quillaja Saponaria (QS) saponins (e.g., QS-17, QS-18, and QS-21), incorporating an amide side chain into the more sustainable MS, instead of deacylated QS saponins, led to the discovery of MS-derived semisynthetic immunostimulatory adjuvants VSA-1 and VSA-2. This review focuses on the authors' previous work on SAR studies of QS and MS saponins.

Avian flu: «for whom the bell tolls»?

The family Orthomyxoviridae consists of 9 genera, including Alphainfluenzavirus, which contains avian influenza viruses. In two subtypes H5 and H7 besides common low-virulent strains, a specific type of highly virulent avian virus have been described to cause more than 60% mortality among domestic birds. These variants of influenza virus are usually referred to as «avian influenza virus». The difference between high (HPAI) and low (LPAI) virulent influenza viruses is due to the structure of the arginine-containing proteolytic activation site in the hemagglutinin (HA) protein. The highly virulent avian influenza virus H5 was identified more than 100 years ago and during this time they cause outbreaks among wild and domestic birds on all continents and only a few local episodes of the disease in humans have been identified in XXI century. Currently, a sharp increase in the incidence of highly virulent virus of the H5N1 subtype (clade h2.3.4.4b) has been registered in birds on all continents, accompanied by the transmission of the virus to various species of mammals. The recorded global mortality rate among wild, domestic and agricultural birds from H5 subtype is approaching to the level of 1 billion cases. A dangerous epidemic factor is becoming more frequent outbreaks of avian influenza with high mortality among mammals, in particular seals and marine lions in North and South America, minks and fur-bearing animals in Spain and Finland, domestic and street cats in Poland. H5N1 avian influenza clade h2.3.4.4b strains isolated from mammals have genetic signatures of partial adaptation to the human body in the PB2, NP, HA, NA genes, which play a major role in regulating the aerosol transmission and the host range of the virus. The current situation poses a real threat of pre-adaptation of the virus in mammals as intermediate hosts, followed by the transition of the pre-adapted virus into the human population with catastrophic consequences.

Influenza A virus antibodies in dogs, hunting dogs, and backyard pigs in Campeche, Mexico

AIMS

This study aimed to identify exposure to human, swine, and avian influenza A virus subtypes in rural companion and hunting dogs, backyard pigs, and feral pigs.

METHODS AND RESULTS

The study took place in a region of southeastern Mexico where the sampled individuals were part of backyard production systems in which different domestic and wild species coexist and interact with humans. We collected blood samples from pigs and dogs at each of the sites. We used a nucleoprotein enzyme-linked immunosorbent assay to determine the exposure of individuals to influenza A virus. Haemagglutination inhibition was performed on the positive samples to determine the subtypes to which they were exposed. For data analysis, a binomial logistic regression model was generated to determine the predictor variables for the seropositivity of the individuals in the study. We identified 11 positive individuals: three backyard pigs, four companion dogs, and four hunting dogs. The pigs tested positive for H1N1 and H1N2. The dogs were positive for H1N1, H1N2, and H3N2. The model showed that dogs in contact with backyard chickens are more likely to be seropositive for influenza A viruses.

CONCLUSIONS

We demonstrated the essential role hunting dogs could play as intermediate hosts and potential mixing vessel hosts when exposed to human and swine-origin viral subtypes. These results are relevant because these dogs interact with domestic hosts and humans in backyard systems, which are risk scenarios in the transmission of influenza A viruses. Therefore, it is of utmost importance to implement epidemiological surveillance of influenza A viruses in backyard animals, particularly in key animals in the transmission of these viruses, such as dogs and pigs.

Influenza sequence validation and annotation using VADR

Tens of thousands of influenza sequences are deposited into the GenBank database each year. The software tool FLAN has been used by GenBank since 2007 to validate and annotate incoming influenza sequence submissions, and has been publicly available as a webserver but not as a standalone tool. VADR is a general sequence validation and annotation software package used by GenBank for Norovirus, Dengue virus and SARS-CoV-2 virus sequence processing that is available as a standalone tool. We have created VADR influenza models based on the FLAN reference sequences and adapted VADR to accurately annotate influenza sequences. VADR and FLAN show consistent results on the vast majority of influenza sequences, and when they disagree VADR is usually correct. VADR can also accurately process influenza D sequences as well as influenza A H17, H18, H19, N10 and N11 subtype sequences, which FLAN cannot. VADR 1.6.3 and the associated influenza models are now freely available for users to download and use.

Impact of oseltamivir on the risk of cancer

Purpose

Mounting evidence has revealed the anti-cancer activity of various anti-viral drugs. Oseltamivir phosphate (OP), namely Tamiflu®, is routinely used to combat influenza infections. Although evidence has indicated the anti-cancer effects of OP in vitro and in vivo, little information is known about the effect of OP use on cancers in humans.

Methods

A nationwide population-based cohort study involving 13,977,101 cases with 284,733 receiving OP was performed to examine the association between OP use and cancers using the National Health Insurance Research Database in Taiwan between 2009 and 2018.

Results

The cohort study found that OP users showed a significantly lower incidence of lung cancer, colon cancer, liver, and intrahepatic bile duct cancer, oral cancer, pancreas cancer, esophagus cancer, stomach cancer, and prostate cancer. Additionally, OP users exhibited a lower risk of cancer-related mortality (adjusted HR=0.779; 95% confidence interval [CI] 0.743-0.817; p<0.001) and a reduced risk of developing liver cancer (adjusted HR=0.895; 95% CI 0.824-0.972; p=0.008), esophagus cancer (adjusted HR=0.646; 95% CI 0.522-0.799; p<0.001) and oral cancer (adjusted HR=0.587; 95% CI 0.346-0.995; p=0.048). Notably, OP users had a significant reduction in liver cancer occurrence over a 10-year period follow-up and a lower cancer stage at liver cancer diagnosis.

Conclusion

These findings first suggest the beneficial effects and therapeutic potential of OP use for certain cancers, especially liver cancer.

Targeted genomic sequencing of avian influenza viruses in wetland sediment from wild bird habitats

Diverse influenza A viruses (IAVs) circulate in wild birds, including highly pathogenic strains that infect poultry and humans. Consequently, surveillance of IAVs in wild birds is a cornerstone of agricultural biosecurity and pandemic preparedness. Surveillance is traditionally done by testing wild birds directly, but obtaining these specimens is labor intensive, detection rates can be low, and sampling is often biased toward certain avian species. As a result, local incursions of dangerous IAVs are rarely detected before outbreaks begin. Testing environmental specimens from wild bird habitats has been proposed as an alternative surveillance strategy. These specimens are thought to contain diverse IAVs deposited by a broad range of avian hosts, including species that are not typically sampled by surveillance programs. To enable this surveillance strategy, we developed a targeted genomic sequencing method for characterizing IAVs in these challenging environmental specimens. It combines custom hybridization probes, unique molecular index-based library construction, and purpose-built bioinformatic tools, allowing IAV genomic material to be enriched and analyzed with single-fragment resolution. We demonstrated our method on 90 sediment specimens from wetlands around Vancouver, Canada. We recovered 2,312 IAV genome fragments originating from all eight IAV genome segments. Eleven hemagglutinin subtypes and nine neuraminidase subtypes were detected, including H5, the current global surveillance priority. Our results demonstrate that targeted genomic sequencing of environmental specimens from wild bird habitats could become a valuable complement to avian influenza surveillance programs.IMPORTANCEIn this study, we developed genome sequencing tools for characterizing avian influenza viruses in sediment from wild bird habitats. These tools enable an environment-based approach to avian influenza surveillance. This could improve early detection of dangerous strains in local wild birds, allowing poultry producers to better protect their flocks and prevent human exposures to potential pandemic threats. Furthermore, we purposefully developed these methods to contend with viral genomic material that is diluted, fragmented, incomplete, and derived from multiple strains and hosts. These challenges are common to many environmental specimens, making these methods broadly applicable for genomic pathogen surveillance in diverse contexts.

Genetics and Pathogenicity of Influenza A (H4N6) Virus Isolated from Wild Birds in Jiangsu Province, China, 2023

During the routine surveillance, we isolated nine H4N6 subtype avian influenza viruses (AIVs) in Jiangsu Province, China, in March 2023. Phylogenetic analysis revealed that nine H4N6 viruses belonged to the Eurasian lineage and underwent complex genetic recombination among Asian countries during their evolution. It is particularly noteworthy that the PB2 and PB1 genes of our representative virus were descended from clade 2.3.4.4b H5 high-pathogenic AIVs in Japan. Mutations of D3V and D622G in PB1, N66S in PB1-F2, N30D, I43M, and T215A in M1, and P42S and I106M in NS1 were observed in nine isolates, which may increase the pathogenicity of the viruses in mice. The receptor binding analysis showed that the tested H4N6 virus could bind to both avian-type and human-type receptors. Vitro infection kinetics revealed that the representative virus could efficiently replicate in mammalian cells, including MDCK and 293T cells. Pathogenicity tests in mice indicated that the representative virus could replicate in nasal turbinates and lungs without prior adaptation. Our data reveal the potential public health issues represented by H4N6 viruses from wild birds and highlight the need to strengthen routine surveillance of wild birds.

Development and application of a triplex real-time PCR assay for the detection of H3, H4, and H5 subtypes of avian influenza virus

Avian influenza virus (AIV) poses a significant threat to the poultry industry and public health. Among the diverse AIV subtypes, H3, H4, and H5 are frequently detected in waterfowl and live poultry markets (LPM). The expeditious and precise identification of these subtypes is imperative in impeding the dissemination of the disease. In this study, we have developed a triplex real-time PCR assay endowed with the capacity to simultaneously discriminate AIV subtypes H3, H4, and H5. This method showcases remarkable specificity, selectively amplifying H3, H4, and H5 AIV subtypes sans any cross-reactivity with other subtypes or common avian pathogens. Furthermore, this method exhibits high sensitivity, with a detection threshold of 2.1 × 102 copies/μL for H3, H4, and H5 AIV subtypes. Additionally, the assay demonstrates reproducibility, as evidenced by intra- and interassay variability, with a coefficient of variation below 1.5%. A total of 338 cloacal swabs were collected from LPM to evaluate the performance of our assay. The obtained results evinced a high level of concordance with the sequencing data. In summary, our study has developed a triplex real-time PCR method that can be employed in laboratory-based testing and surveillance of AIV. This assay holds promise in augmenting our ability to detect and monitor AIV subtypes, thereby facilitating timely interventions and safeguarding both the poultry industry and public health.

A sequence-based machine learning model for predicting antigenic distance for H3N2 influenza virus

Introduction

Seasonal influenza A H3N2 viruses are constantly changing, reducing the effectiveness of existing vaccines. As a result, the World Health Organization (WHO) needs to frequently update the vaccine strains to match the antigenicity of emerged H3N2 variants. Traditional assessments of antigenicity rely on serological methods, which are both labor-intensive and time-consuming. Although numerous computational models aim to simplify antigenicity determination, they either lack a robust quantitative linkage between antigenicity and viral sequences or focus restrictively on selected features.

Methods

Here, we propose a novel computational method to predict antigenic distances using multiple features, including not only viral sequence attributes but also integrating four distinct categories of features that significantly affect viral antigenicity in sequences.

Results

This method exhibits low error in virus antigenicity prediction and achieves superior accuracy in discerning antigenic drift. Utilizing this method, we investigated the evolution process of the H3N2 influenza viruses and identified a total of 21 major antigenic clusters from 1968 to 2022.

Discussion

Interestingly, our predicted antigenic map aligns closely with the antigenic map generated with serological data. Thus, our method is a promising tool for detecting antigenic variants and guiding the selection of vaccine candidates.

Reassortant H9N2 canine influenza viruses containing the pandemic H1N1/2009 ribonucleoprotein complex circulating in pigs acquired enhanced virulence in mice

The reassortment between avian H9N2 and Eurasian avian-like (EA) H1N1 viruses may have potentially changed from avian-to-mammals adaptation. This study generated 20 reassortant viruses with the introduction of H1N1/2009 internal genes from EA H1N1 virus into H9N2 virus. 12 of these recovered the replication capability both in the lungs and turbinate samples. 10 of 12 obtained PA gene segments from the ribonucleoprotein (RNP) complexes of the EA H1N1 virus, and 3 exhibited extreme virulence. Specially, the combination of PB2, PA and NP genes could overcome the species-specific restriction in human cells. Analysis of the polymerase activities found that introduction of the PA gene resulted in increased polymerase activity. These findings indicated that RNP complexes from EA H1N1 virus could confer an adaptation advantage and high compatibility to avian H9N2 virus. This raises new concerns for public health due to the possible coexistence of H9N2 and EA H1N1 viruses in dogs.

Design of new chemical entities targeting both native and H275Y mutant influenza a virus by deep reinforcement learning

Influenza virus remains a major public health challenge due to its high morbidity and mortality and seasonal surge. Although antiviral drugs against the influenza virus are widely used as a first-line defense, the virus undergoes rapid genetic changes, resulting in the emergence of drug-resistant strains. Thus, new antiviral drugs that can outwit resistant strains are of significant importance. Herein, we used deep reinforcement learning (RL) algorithm to design new chemical entities (NCEs) that are able to bind to the native and H275Y mutant (oseltamivir-resistant) neuraminidases (NAs) of influenza A virus with better binding energy than oseltamivir. We generated more than 66211 NCEs, which were prioritized based on the filtering rules, structural alerts, and synthetic accessibility. Then, 18 NCEs with better MM/PBSA scores than oseltamivir were further analyzed in molecular dynamics (MD) simulations conducted for 100 ns. The MD experiments showed that 8 NCEs formed very stable complexes with the binding pocket of both native and H275Y mutant NAs of H1N1. Furthermore, most NCEs demonstrated much better binding affinity to group 2 (N2, N3, and N9) and influenza B virus NAs than oseltamivir. Although all 8 NCEs have non-sialic acid-like structures, they showed a similar binding mode as oseltamivir, indicating that it is possible to find new scaffolds with better binding and antiviral properties than sialic acid-like inhibitors. In conclusion, we have designed potential compounds as antiviral candidates for further synthesis and testing against wild and mutant influenza virus.Communicated by Ramaswamy H. Sarma.

Nucleoprotein as a Promising Antigen for Broadly Protective Influenza Vaccines

Annual vaccination is considered as the main preventive strategy against seasonal influenza. Due to the highly variable nature of major viral antigens, such as hemagglutinin (HA) and neuraminidase (NA), influenza vaccine strains should be regularly updated to antigenically match the circulating viruses. The influenza virus nucleoprotein (NP) is much more conserved than HA and NA, and thus seems to be a promising target for the design of improved influenza vaccines with broad cross-reactivity against antigenically diverse influenza viruses. Traditional subunit or recombinant protein influenza vaccines do not contain the NP antigen, whereas live-attenuated influenza vaccines (LAIVs) express the viral NP within infected cells, thus inducing strong NP-specific antibodies and T-cell responses. Many strategies have been explored to design broadly protective NP-based vaccines, mostly targeted at the T-cell mode of immunity. Although the NP is highly conserved, it still undergoes slow evolutionary changes due to selective immune pressure, meaning that the particular NP antigen selected for vaccine design may have a significant impact on the overall immunogenicity and efficacy of the vaccine candidate. In this review, we summarize existing data on the conservation of the influenza A viral nucleoprotein and review the results of preclinical and clinical trials of NP-targeting influenza vaccine prototypes, focusing on the ability of NP-specific immune responses to protect against diverse influenza viruses.

Evidence for an ancient aquatic origin of the RNA viral order Articulavirales

The emergence of previously unknown disease-causing viruses in mammals is in part the result of a long-term evolutionary process. Reconstructing the deep phylogenetic histories of viruses helps identify major evolutionary transitions and contextualizes the emergence of viruses in new hosts. We used a combination of total RNA sequencing and transcriptome data mining to extend the diversity and evolutionary history of the RNA virus order Articulavirales, which includes the influenza viruses. We identified instances of Articulavirales in the invertebrate phylum Cnidaria (including corals), constituting a novel and divergent family that we provisionally named the "Cnidenomoviridae." We further extended the evolutionary history of the influenza virus lineage by identifying four divergent, fish-associated influenza-like viruses, thereby supporting the hypothesis that fish were among the first hosts of influenza viruses. In addition, we substantially expanded the phylogenetic diversity of quaranjaviruses and proposed that this genus be reclassified as a family-the "Quaranjaviridae." Within this putative family, we identified a novel arachnid-infecting genus, provisionally named "Cheliceravirus." Notably, we observed a close phylogenetic relationship between the Crustacea- and Chelicerata-infecting "Quaranjaviridae" that is inconsistent with virus-host codivergence. Together, these data suggest that the Articulavirales has evolved over at least 600 million years, first emerging in aquatic animals. Importantly, the evolution of the Articulavirales was likely shaped by multiple aquatic-terrestrial transitions and substantial host jumps, some of which are still observable today.

Evolution and Current Status of Influenza A Virus in Chile: A Review

The influenza A virus (IAV) poses a significant global threat to public health and food security. Particularly concerning is the avian influenza virus (AIV) subtype H5N1, which has spread from Europe to North and Central/South America. This review presents recent developments in IAV evolution in birds, mammals, and humans in Chile. Chile's encounter with IAV began in 2002, with the highly pathogenic avian influenza (HPAI) H7N3 virus, derived from a unique South American low pathogenic avian influenza (LPAI) virus. In 2016-2017, LPAI H7N6 caused outbreaks in turkey, linked to wild birds in Chile and Bolivia. The pandemic influenza A (H1N1) 2009 (H1N1pdm09) virus in 2009 decreased egg production in turkeys. Since 2012, diverse IAV subtypes have emerged in backyard poultry and pigs. Reassortant AIVs, incorporating genes from both North and South American isolates, have been found in wild birds since 2007. Notably, from December 2022, HPAI H5N1 was detected in wild birds, sea lions, and a human, along Chile's north coast. It was introduced through Atlantic migratory flyways from North America. These findings emphasize the need for enhanced biosecurity on poultry farms and ongoing genomic surveillance to understand and manage AIVs in both wild and domestic bird populations in Chile.

Phylodynamic approaches to studying avian influenza virus

Avian influenza viruses can cause severe disease in domestic and wild birds and are a pandemic threat. Phylodynamics is the study of how epidemiological, evolutionary, and immunological processes can interact to shape viral phylogenies. This review summarizes how phylodynamic methods have and could contribute to the study of avian influenza viruses. Specifically, we assess how phylodynamics can be used to examine viral spread within and between wild or domestic bird populations at various geographical scales, identify factors associated with virus dispersal, and determine the order and timing of virus lineage movement between geographic regions or poultry production systems. We discuss factors that can complicate the interpretation of phylodynamic results and identify how future methodological developments could contribute to improved control of the virus.

Analysis of avian influenza A (H3N8) viruses in poultry and their zoonotic potential, China, September 2021 to May 2022

BackgroundTwo human cases of avian influenza A (H3N8) virus infection were reported in China in 2022.AimTo characterise H3N8 viruses circulating in China in September 2021-May 2022.MethodsWe sampled poultry and poultry-related environments in 25 Chinese provinces. After isolating H3N8 viruses, whole genome sequences were obtained for molecular and phylogenetic analyses. The specificity of H3N8 viruses towards human or avian receptors was assessed in vitro. Their ability to replicate in chicken and mice, and to transmit between guinea pigs was also investigated.ResultsIn total, 98 H3N8 avian influenza virus isolates were retrieved from 38,639 samples; genetic analysis of 31 representative isolates revealed 17 genotypes. Viruses belonging to 10 of these genotypes had six internal genes originating from influenza A (H9N2) viruses. These reassorted viruses could be found in live poultry markets and comprised the strains responsible for the two human infections. A subset of nine H3N8 viruses (including six reassorted) that replicated efficiently in mice bound to both avian-type and human-type receptors in vitro. Three reassorted viruses were shed by chickens for up to 9 days, replicating efficiently in their upper respiratory tract. Five reassorted viruses tested on guinea pigs were transmissible among these by respiratory droplets.ConclusionAvian H3N8 viruses with H9N2 virus internal genes, causing two human infections, occurred in live poultry markets in China. The low pathogenicity of H3N8 viruses in poultry allows their continuous circulation with potential for reassortment. Careful monitoring of spill-over infections in humans is important to strengthen early-warning systems and maintain influenza pandemic preparedness.

A Fatal A/H5N1 Avian Influenza Virus Infection in a Cat in Poland

A European Shorthair male cat, neutered, approximately 6 years of age, was presented to the veterinary clinic due to apathy and anorexia. The cat lived mostly outdoors and was fed raw chicken meat. After 3 days of diagnostic procedures and symptomatic treatment, respiratory distress and neurological signs developed and progressed into epileptic seizures, followed by respiratory and cardiac arrest within the next 3 days. Post-mortem examination revealed necrotic lesions in the liver, lungs, and intestines. Notably, the brain displayed perivascular infiltration of lymphocytes and histiocytes. Few foci of neuronal necrosis in the brain were also confirmed. Microscopic examination of the remaining internal organs was unremarkable. The A/H5N1 virus infection was confirmed using a one-step real-time reverse transcription polymerase chain reaction (RT-qPCR). The disease caused severe neurological and respiratory signs, evidence of consolidations and the presence of numerous B lines, which were detected on lung ultrasound examination; the postmortem findings and detection of A/H5N1 viral RNA in multiple tissues indicated a generalized A/H5N1 virus infection. Moreover, a multidrug-resistant strain of Enterococcus faecium was isolated in pure culture from several internal organs. The source of infection could be exposure to infected birds or their excrements, as well as contaminated raw poultry meat but, in this case, the source of infection could not be identified.