ETIDIOH - NEW

Abstract The avian influenza virus (AIV) primarily affects birds and poses an increasing concern due to its growing adaptability to other hosts , heightening zoonotic risks . The adaptability is a key factor in AIV to infect multiple non-avian species, including humans , companion animals , aquatic mammals , carnivores , and other mammals. The virus is evolving through genetic mutations and reassortments , leading to the emergence of AIV strains with enhanced virulence and adaptability in mammals. This highlights the critical need to understand the genetic factors of AIV, including mutations in polymerase proteins , surface antigens , and other regulatory proteins, as well as the dynamics of AIV- host interactions and environmental factors such as temperature, humidity, water salinity, and pH that govern the cross-species adaptability of the virus. This review provides comprehensive insights into the molecular/genetic changes AIV undergoes to adapt in mammalian hosts including bovines,...

Significance We explored how H5Nx influenza viruses , which can infect many different birds and mammals, could adapt to infect humans by altering the hemagglutinin (HA). HA must change to bind human-type receptors for transmission between people. We compared two strains from viruses isolated in 2016 and found that one ( 2.3.4.4e ) can switch to human receptor binding with a single mutation , while another ( 2.3.4.4b ) might require more complex changes to bind simple human-type receptors. These findings highlight the potential for specific strains to evolve and become a pandemic threat, underscoring the importance of monitoring mutations that could lead to human-type receptor adaptation. Abstract H5Nx viruses continue to wreak havoc in avian and mammalian species worldwide . The virus distinguishes itself by the ability to replicate to high titers and transmit efficiently in a wide variety of hosts in diverse climatic environments. Fortunately, transmission to and between humans is sca...

Highlights •  The present analysis addresses the paucity of genetic information available for the recently emerged KFDV strains. •  As the virus is classified as a highly dangerous pathogen, it is essential to expand the existing genetic information. •  Continuous surveillance of the virus is essential for the development of a vaccine. •  The present study presents new findings on the KFD virus strains that were introduced into circulation in the period 2018-2020. •  The nanopore sequencing technology is presented as a proof of concept for the provision of early warnings in the field. Abstract The future of infectious agent detection and molecular characterization lies in field-forward, on-site strategies . The lack of genomic information for recently circulating Kyasanur Forest Disease virus strains is critical. Kyasanur Forest Virus Disease virus PCR-positive samples from 2018 to 2020 were selected for sequencing. Detailed molecular phylogenetic analyses were ...

Abstract H5N1 influenza has been circulating in birds from Eurasia and Africa for more than 146 years , but human infection has been sporadic. H5N1 (clade 2.3.4.4b) has recently infected hundreds of species of wild and domestic birds and mammals in North America . Furthermore, as of February 26, 2025, H5N1 has infected 70 humans in the United States , and one infection proved lethal . Furthermore, in attempts to control H5N1 in the United States, 10s of millions of egg-laying chickens have died or been culled . These efforts have led to very high egg prices in the United States. We have developed an analytical bioinformatics and genomics workflow to understand better how H5N1 is circulating in North America and adapting to new host species . Our workflow consists of: 1) Phylogenetic analyses of large viral sequence datasets to identify subclades of viral lineages causing the current outbreaks in humans and farm animals and closely related viral background lineages. 2) Next, we transfer...

Significance The dominance of the H9N2 subtype of avian influenza virus (AIV) within the influenza A virus family has raised questions regarding the factors influencing its epidemiological dominance . This study concentrates on the role of five major evolutionary patterns of the matrix protein M1 in the replication and transmission of H9N2 AIVs. The findings indicate a strong correlation between the epidemiological dominance of H9N2 AIVs and the specific M1 patterns , particularly M1P5. It highlights the significance of genetic patterns in M1 for understanding the adaptive differences and turnover of epidemiological dominant H9N2 AIVs. Abstract The H9N2 subtype of avian influenza virus (AIV) emerges as a significant member of the influenza A virus family. However, the varying degrees of epidemiological dominance among different lineages or clades of H9N2 AIVs have not been fully clarified. The matrix protein M1 , a key structural component of the virion , plays a crucial role in mainta...

Abstract Using a phylogenetic framework to characterize natural selection , we investigate the hypothesis that zoonotic viruses require adaptation prior to zoonosis to sustain human-to-human transmission . Examining the zoonotic emergence of Ebola virus, Marburg virus, influenza A virus, SARS-CoV, and SARS-CoV-2 , we find no evidence of a change in the intensity of natural selection immediately prior to a host switch , compared with typical selection within reservoir hosts . We conclude that extensive pre-zoonotic adaptation is not necessary for human-to-human transmission of zoonotic viruses. In contrast, the reemergence of H1N1 influenza A virus in 1977 showed a change in selection, consistent with the hypothesis of passage in a laboratory setting prior to its reintroduction into the human population, purportedly during a vaccine trial. Holistic phylogenetic analysis of selection regimes can be used to detect evolutionary signals of host switching or laboratory passage, providing ins...

ABSTRACT Since 2020, H5N1 highly pathogenic avian influenza (HPAI) viruses of clade 2.3.4.4b have been rapidly spreading in wild birds but have also caused a large number of mammalian infections and more than 70 known human cases . Importantly, this H5N1 clade has also crossed the species barrier into dairy cattle in the US in late 2023/early 2024. The neuraminidase (NA) protein of the N1 subtype can feature truncations in its stalk domain, which have been identified as putative virulence factors in poultry but seem to have a negative impact on transmission in mammals. Since its emergence, the vast majority of HPAI H5N1 A/goose/Guangdong/1/1996-lineage isolates have featured this truncated version of the NA stalk domain. Here, we report that this changed with the 2020 expansion of clade 2.3.4.4b H5N1 and that the majority of isolates—including the strains circulating in dairy cattle—feature a long NA stalk domain . Source: mBio,  https://journals.asm.org/doi/10.1128/mbio.03989-24 _...

Abstract Equine influenza (EI) is a highly contagious respiratory disease caused by the equine influenza virus (EIV), posing a significant threat to equine populations worldwide . EIV exhibits considerable antigenic variability due to its segmented genome, complicating long-term disease control efforts. Although infections are rarely fatal , EIV’s high transmissibility results in widespread outbreaks, leading to substantial morbidity and considerable economic impacts on veterinary care, quarantine, and equestrian activities. The H3N8 subtype has undergone significant antigenic evolution , resulting in the emergence of distinct lineages , including Eurasian and American , with the Florida sublineage being particularly prevalent. Continuous genetic surveillance and regular updates to vaccine formulations are necessary to address antigenic drift and maintain vaccination efficacy. Additionally, rare cross-species transmissions have raised concerns regarding the zoonotic potential of EIV. T...

Abstract Enveloped viruses such as influenza A virus (IAV) often produce a mixture of virion shapes , ranging from 100 nm spheres to micron-long filaments. Spherical virions use fewer resources, while filamentous virions resist cell-entry pressures such as antibodies . While shape changes are believed to require genetic adaptation , the mechanisms of how viral mutations alter shape remain unclear. Here we find that IAV dynamically adjusts its shape distribution in response to environmental pressures . We developed a quantitative flow virometry assay to measure the shape of viral particles under various infection conditions (such as multiplicity, replication inhibition and antibody treatment) while using different combinations of IAV strains and cell lines. We show that IAV rapidly tunes its shape distribution towards spheres under optimal conditions but favours filaments under attenuation . Our work demonstrates that this phenotypic flexibility allows IAV to rapidly respond to environm...

Abstract Viral infections are characterized by dispersal from an initial site to secondary locations within the host. How the resultant spatial heterogeneity shapes within-host genetic diversity and viral evolutionary pathways is poorly understood. Here, we show that virus dispersal within and between the nasal cavity and trachea maintains diversity and is therefore conducive to adaptive evolution , whereas dispersal to the lungs gives rise to population heterogeneity . We infected ferrets either intranasally or by aerosol with a barcoded influenza A/California/07/2009 (H1N1) virus . At 1, 2, or 4 days postinfection, dispersal was assessed by collecting 52 samples from throughout the respiratory tract of each animal. Irrespective of inoculation route, barcode compositions across the nasal turbinates and trachea were similar and highly diverse, revealing little constraint on the establishment of infection in the nasal cavity and descent through the trachea. Conversely, infection of the ...

ABSTRACT The evolution of SARS-CoV-2 pathogenicity has been a major focus of attention. However, the determinants of pathogenicity are still unclear. Various hypotheses have attempted to elucidate the mechanisms underlying the evolution of viral pathogenicity , but a definitive conclusion has yet to be reached. Here, we review the potential impact of all proteins in SARS-CoV-2 on the viral pathogenic process and analyze the effects of their mutations on pathogenicity evolution. We aim to summarize which virus-encoded proteins are crucial in influencing viral pathogenicity, defined as disease severity following infection. Mutations in these key proteins, which are the virulence factors in SARS-CoV-2, may be the driving forces behind the evolution of viral pathogenicity. Mutations in the S protein can impact viral entry and fusogenicity . Mutations in proteins such as NSP2, NSP5, NSP14, and ORF7a can alter the virus’s ability to suppress host protein synthesis and innate immunity . Mutat...

Abstract H7N9 avian influenza virus (AIV) first emerged in February 2013 in China , and early isolates were all low pathogenic (LP). After circulation for a few years in live poultry markets of China , LP H7N9 AIVs evolved into a highly pathogenic (HP) form in late 2016. Deduced amino acid sequence analysis of hemagglutinin (HA) gene revealed that all HP H7N9 AIVs have obtained four-amino-acid insertion at position 339-342 (H7 numbering), making the cleavage site from a monobasic motif (LP AIVs) to a polybasic form (HP AIVs). Notably, the polybasic cleavage site motifs are diversified, of which PEVPKRKRTAR↓GLF motif is prevalent. To elucidate the reasons accounting for its dominance, recombinant H7N9 virus carrying PEVPKRKRTAR↓GLF (rJT157-2) motif was generated based on LP H7N9 virus A/chicken/Eastern China/JT157/2016 (JT157). Besides, another two viruses containing PEVPKGKRTAR↓GLF (rJT157-1) and PEIPKRKRTAR↓GLF (rJT157-3) cleavage site motifs were also constructed as comparisons. We f...

Summary The ongoing circulation of highly pathogenic avian influenza (HPAI) A (H5N1) viruses , particularly clade 2.3.4.4b strains , poses a significant threat to animal and public health . Recent outbreaks in cattle highlight concerns about cross-species transmission and zoonotic spillover . Here, we found that the hemagglutinin (HA) protein from a cattle-infecting H5N1 virus has acquired slight binding to human-like α2-6-linked receptors while still exhibiting a strong preference for avian-like α2-3-linked sialic acid receptors. Immunohistochemical staining revealed HA binding to bovine pulmonary and mammary tissues , aligning with clinical observations. HA also binds effectively to human conjunctival, tracheal, and mammary tissues , indicating a risk for human transmission , notably in cases of conjunctivitis . High-resolution cryo-electron microscopy (cryo-EM) structures of this H5 HA in complex with either α2-3 or α2-6 receptors elucidate the molecular mechanisms underlying its re...

Summary H5Nx viruses remain a threat to human health . Over the past few years, the H5Nx clade 2.3.4.4b has rapidly spread to 6 continents, leading to massive avian and mammalian host deaths . In late March 2024, H5N1 was first identified in lactating dairy cows in the United States and has spread to 16 states, affected hundreds of herds , and caused over 50 known human infections . In this review, we discuss the origins of 2.3.4.4b H5N1 viruses and how they are evolving to better infect mammals, with an emphasis on receptor-binding characteristics . Understanding changes in receptor binding and mutations in the viral genome that allow for sustained spread in mammals can inform public health measures and prevent future influenza virus epidemics and pandemics. (...) Source: PLoS Pathogens,  https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1012847 _____

Abstract In a patient on immunosuppressant treatment , SARS-CoV-2 RNA was documented in different extra-respiratory samples over several months in the absence of positive determinations in upper respiratory samples . Whole -genome sequencing of these samples showed the acquisition of different single-nucleotide polymorphisms over time, suggesting viral evolution and thus viral viability. Source: Viruses,  https://www.mdpi.com/1999-4915/17/2/147 _____

Abstract The effectiveness of poultry vaccination in preventing the transmission of highly pathogenic avian influenza viruses (AIVs) has been debated, and its impact on wild birds remains uncertain. Here, we reconstruct the movements of H5 subtype AIV lineages among vaccinated poultry , unvaccinated poultry, and wild birds, worldwide, from 1996 to 2023. We find that there is a time lag in viral transmission among different host populations and that movements from wild birds to unvaccinated poultry were more frequent than those from wild birds to vaccinated poultry . Furthermore, our findings suggest that the HA (hemagglutinin) gene of the AIV lineage that circulated predominately in Chinese poultry experienced greater nonsynonymous divergence and adaptive fixation than other lineages. Our results indicate that the epidemiological, ecological, and evolutionary consequences of widespread AIV vaccination in poultry may be linked in complex ways and that much work is needed to better under...

ABSTRACT The host range of HPAIV H5N1 was recently expanded to include ruminants , particularly dairy cattle in the United States (US). Shortly after, human H5N1 infection was reported in a dairy worker in Texas following exposure to infected cattle. Herein, we rescued the cattle-origin influenza A/bovine/Texas/24-029328-02/2024(H5N1, rHPbTX) and A/Texas/37/2024(H5N1, rHPhTX) viruses, identified in dairy cattle and human, respectively, and their low pathogenic forms , rLPbTX and rLPhTX, with monobasic HA cleavage sites . Intriguingly, rHPhTX replicated more efficiently than rHPbTX in mammalian and avian cells . Still, variations in the PA and NA proteins didn’t affect their antiviral susceptibility to PA and NA inhibitors. Unlike rHPbTX and rLPbTX, both rHPhTX and rLPhTX exhibited higher pathogenicity and efficient replication in infected C57BL/6J mice . The lungs of rHPhTX-infected mice produced higher inflammatory cytokines/chemokines than rHPbTX-infected mice. Our results highlight ...

Abstract The H9N2 subtype of avian influenza virus (AIV) is widely distributed among poultry and wild birds and is also a threat to humans . During AIV active surveillance in Liaoning province from 2015 to 2016, we identified ten H9N2 strains exhibiting different lethality to chick embryos . Two representative strains, A/chicken/China/LN07/2016 (CKLN/07) and A/chicken/China/LN17/2016 (CKLN/17), with similar genomic background but different chick embryo lethality, were chosen to evaluate the molecular basis for this difference. A series of reassortants between CKLN/07 and CKLN/17 were generated and their chick embryo lethality was assessed. We found that the isoleucine (I) residue at position 137 (H3 numbering) in the hemagglutinin (HA) was responsible for the chick embryo lethality of the H9N2 virus. Further studies revealed that the threonine (T) to I mutation at HA position 137 enhanced viral replication in vitro and in vivo . Moreover, the HA-T137I substitution in H9N2 avian influen...

Abstract The Eurasian avian-like (EA) H1N1 swine influenza virus (SIV) possesses the capacity to instigate the next influenza pandemic , owing to its heightened affinity for the human-type α-2,6 sialic acid (SA) receptor . Nevertheless, the molecular mechanisms underlying the switch in receptor binding preferences of EA H1N1 SIV remain elusive. In this study, we conduct a comprehensive genome-wide CRISPR/Cas9 knockout screen utilizing EA H1N1 SIV in porcine kidney cells. Knocking out the enzyme gamma glutamyl carboxylase (GGCX) reduces virus replication in vitro and in vivo by inhibiting the carboxylation modification of viral haemagglutinin (HA) and the adhesion of progeny viruses, ultimately impeding the replication of EA H1N1 SIV. Furthermore, GGCX is revealed to be the determinant of the D225E substitution of EA H1N1 SIV, and GGCX-medicated carboxylation modification of HA 225E contributes to the receptor binding adaption of EA H1N1 SIV to the α-2,6 SA receptor. Taken together, our...

Abstract Clade 2.3.4.4b H5N1 high pathogenicity avian influenza virus (HPAIV) has caused a panzootic affecting all continents except Australia , expanding its host range to several mammalian species . In March 2024, H5N1 HPAIV was first detected in dairy cattle and goats in the United States . Over 891 dairy farms across 16 states have tested positive until 25th December 2024, with zoonotic infections reported among dairy workers . This raises concerns about the virus undergoing evolutionary changes in cattle that could enhance its zoonotic potential . The Influenza glycoprotein haemagglutinin (HA) facilitates entry into host cells through receptor binding and pH-induced fusion with cellular membranes. Adaptive changes in HA modulate virus-host cell interactions. This study compared the HA genes of cattle and goat H5N1 viruses with the dominant avian-origin clade 2.3.4.4b H5N1 in the United Kingdom , focusing on receptor binding, pH fusion, and thermostability. All the tested H5N1 viru...