#Host type governs #influenza evolutionary #strategy across reservoir and #spillover hosts

 

Abstract

Despite its high propensity for host switching, the evolutionary mechanisms underlying influenza host adaptation remain unclear. H3Nx influenza viruses are uniquely generalist, with long-term lineages that circulate in avian, human, swine, equine, and canine hosts. Using 13,295 H3Nx sequences, we quantified host-specific adaptive evolution and developed a pipeline to map reassortment events onto trees with measures of statistical uncertainty. We find that while H3Nx viruses in mammals undergo adaptive evolution in HA and NA, viruses in birds experience very little directional selection. Instead, avian lineages exhibit high rates of reassortment, frequently generating novel reassortant lineages that persist transiently and turn over rapidly. 29.8-47.4% of all avian reassortant lineages are purged within the first year of circulation, and reassortment shows no fitness benefit in birds. In contrast, reassorted lineages in swine are more likely to persist long-term, suggesting that reassortment in swine may be broadly beneficial. Segment-specific reassortment patterns were also distinct between avian and mammalian viruses, with NA reassorting more frequently than expected in birds, but less frequently than expected in swine. Reassortment events are enriched between mammalian, but not avian, host switches, suggesting that reassortment may be most beneficial for mediating host switches among mammalian species. Together, our data suggest that host differences drive fundamentally different evolutionary outcomes for influenza viruses, transitioning from reassortment-dominant evolution in their avian reservoir, to varying degrees of adaptation upon establishment in mammals.

Competing Interest Statement

The authors have declared no competing interest.

Funder Information Declared

Pew Charitable Trusts

Margaret Q. Landenberger Research Foundation

National Institute of Allergy and Infectious Diseases

National Institutes of Health

Department of Health and Human Services

United States Department of Agriculture

Agricultural Research Service

Source: 

Link: https://www.biorxiv.org/content/10.64898/2026.09.15.751820v1

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Increased #receptor #binding and #spike glycosylation, remodeled immune #escape of surging #SARS-CoV-2 subvariant BA.3.2.2/RE.2.2/Cicada

 

Significance

SARS-CoV-2 evolved into distinct phylogenetic clades, generating a series of mutant strains. Notably, variants such as BA.1, BA.2.86, and BA.3.2 deserve special attention as they emerged abruptly at high detection frequencies during specific periods and harbored extensive mutations in the spike protein relative to contemporaneously prevalent strains, often accompanied by unique phenotypic characteristics. In this study, we primarily evaluated the structural and functional features of the BA.3.2.2 S protein, revealing its distinct traits in receptor binding, immune evasion, cross-species transmission, and glycosylation evolution. We observed constrained viral immune escape, as certain antibodies that were nonneutralizing against previously dominant subvariants exhibited neutralizing activity against recently emerged BA.3.2.2. These findings provide mechanistic insights for viral surveillance, vaccines, and therapeutics development.

Abstract

SARS-CoV-2 continues to evolve. The subvariant BA.3.2 (Cicada), a derivative of the Omicron BA.3 subtype first detected in late 2024, harbors multiple spike protein mutations, ORF7 and ORF8 deletions, and has recently evolved sublineages (BA.3.2.1 and BA.3.2.2), rendering it a critical target for epidemiological surveillance. The BA.3.2.2 sublineage, represented by RE.2.2, shows a marked upward trend in late 2025. Using surface plasmon resonance, we found that RE.2.2’s spike (S) protein receptor-binding domain (RBD) exhibits relatively high affinity for human receptor angiotensin-converting enzyme 2, with structural analysis identifying the R493Q reverse mutation as the key determinant. Pseudovirus infection and antibody neutralization assays demonstrated that RE.2.2 exhibited a distinct neutralization profile compared to contemporaneous dominant subvariants. Notably, several antibodies that previously lacked neutralizing activity (e.g., S2K146 and L4.65) to other subvariants regained neutralizing potency against RE.2.2, which was associated with key mutations including G446D. Profiling of RE.2.2 RBD binding to ACE2 orthologs across species showed no significant difference in species tropism from the representative Omicron BA.1. Importantly, RE.2.2 exhibits the newly emerged N-linked glycosylation at spike protein N529 (absent in all other subvariants), a modification potentially associated with immune evasion or spike protein conformational dynamics. In addition, we corroborated the “O-follow-N” glycosylation observation as previously reported, where O-linked glycans preferentially localize near N-glycosylation sites, implying coordinated glycan organization as an extra layer of spike regulation. These findings illuminate the evolutionary characteristics, functional changes, and the constrained virus immune escape of BA.3.2.2 (RE.2.2), providing critical insights into antibody development and variant surveillance.

Source: 

Link: https://doi.org/10.1073/pnas.2614163123

____

Increased #receptor #binding and #spike #glycosylation, remodeled immune escape of surging #SARS-CoV-2 subvariant BA.3.2.2/RE.2.2/Cicada

 

Significance

SARS-CoV-2 evolved into distinct phylogenetic clades, generating a series of mutant strains. Notably, variants such as BA.1, BA.2.86, and BA.3.2 deserve special attention as they emerged abruptly at high detection frequencies during specific periods and harbored extensive mutations in the spike protein relative to contemporaneously prevalent strains, often accompanied by unique phenotypic characteristics. In this study, we primarily evaluated the structural and functional features of the BA.3.2.2 S protein, revealing its distinct traits in receptor binding, immune evasion, cross-species transmission, and glycosylation evolution. We observed constrained viral immune escape, as certain antibodies that were nonneutralizing against previously dominant subvariants exhibited neutralizing activity against recently emerged BA.3.2.2. These findings provide mechanistic insights for viral surveillance, vaccines, and therapeutics development.

Abstract

SARS-CoV-2 continues to evolve. The subvariant BA.3.2 (Cicada), a derivative of the Omicron BA.3 subtype first detected in late 2024, harbors multiple spike protein mutations, ORF7 and ORF8 deletions, and has recently evolved sublineages (BA.3.2.1 and BA.3.2.2), rendering it a critical target for epidemiological surveillance. The BA.3.2.2 sublineage, represented by RE.2.2, shows a marked upward trend in late 2025. Using surface plasmon resonance, we found that RE.2.2’s spike (S) protein receptor-binding domain (RBD) exhibits relatively high affinity for human receptor angiotensin-converting enzyme 2, with structural analysis identifying the R493Q reverse mutation as the key determinant. Pseudovirus infection and antibody neutralization assays demonstrated that RE.2.2 exhibited a distinct neutralization profile compared to contemporaneous dominant subvariants. Notably, several antibodies that previously lacked neutralizing activity (e.g., S2K146 and L4.65) to other subvariants regained neutralizing potency against RE.2.2, which was associated with key mutations including G446D. Profiling of RE.2.2 RBD binding to ACE2 orthologs across species showed no significant difference in species tropism from the representative Omicron BA.1. Importantly, RE.2.2 exhibits the newly emerged N-linked glycosylation at spike protein N529 (absent in all other subvariants), a modification potentially associated with immune evasion or spike protein conformational dynamics. In addition, we corroborated the “O-follow-N” glycosylation observation as previously reported, where O-linked glycans preferentially localize near N-glycosylation sites, implying coordinated glycan organization as an extra layer of spike regulation. These findings illuminate the evolutionary characteristics, functional changes, and the constrained virus immune escape of BA.3.2.2 (RE.2.2), providing critical insights into antibody development and variant surveillance.

Source: 

Link: https://www.pnas.org/doi/10.1073/pnas.2614163123

____

#Genome-informed structural #analysis of #polymerase and glycoprotein #adaptation in #H5N1 clade 2.3.4.4b

 

Abstract

Importance

Understanding the molecular mechanisms driving H5N1 clade 2.3.4.4b is critical for pandemic preparedness.

Objective

To characterize the molecular drivers of viral fitness and mammalian adaptability in recent H5N1 viruses by integrating evolutionary dynamics with structural simulations.

Methods

This study analyzed 2,398 H5Nx genomes (2000–2024) through phylogenetic and selective pressure analyses. HA/NA structures were predicted with AlphaFold 3 and evaluated by AutoDock4 docking, whereas polymerase–ANP32A/B complexes were modeled using template-based methods and their binding free energies were estimated using MM/GBSA. Polymerase–ANP32E complexes were predicted with AlphaFold 3 and similarly evaluated by MM/GBSA. The binding affinities (ΔG) for the sialic acid (SA) receptors and human ANP32 proteins were quantified through molecular mechanics/generalized born surface area calculations.

Results

Clade 2.3.4.4b showed significant antigenic drift in the HA receptor binding site, reducing affinity for α2,3-SA and α2,6-SA receptors. On the other hand, the emergence of a full-length stalk N1 NA with second sialic acid-binding site mutations (e.g., N366S) compensated for reduced HA affinity by enhancing the NA binding stability. In the polymerase complex, both the PB2-627E/631L variant (−144.00 kcal/mol; unadjusted p = 0.0058) and the known mammalian-adaptive 627K/631M variant (−144.67 kcal/mol; unadjusted p = 0.0165) showed more favorable predicted human ANP32B binding free energies than the ancestral 627E/631M state (−136.46 kcal/mol).

Conclusions and Relevance

The co-occurrence of HA, NA, PB1, and PB2 signatures was associated with clade expansion and produced structural predictions consistent with altered receptor or ANP32 interactions; experimental validation is required before inferring effects on fitness or zoonotic risk.

Source: 

Link: https://vetsci.org/DOIx.php?id=10.4142/jvs.26088

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#Influenza A virus #H5N1 genotypes #B3.13 and D1.1 show #temperature-dependent restriction of #replication in primary #human respiratory epithelial cell cultures derived from the upper and lower respiratory tract

 

Abstract

H5N1 clade 2.3.4.4b avian influenza A viruses pose a significant threat to wild animal populations, domesticated animals, and potentially, the human population. For H5N1s to infect and transmit among mammalian species, mutations for improved utilization of mammalian receptors and enhanced replication at the lower temperatures of the upper respiratory tract need to be acquired. A human H1N1pdm09-like virus was compared to H5N1 genotypes B3.13 and D1.1 for replication at 33ºC, 37ºC, and 39ºC – temperatures consistent with the upper and lower respiratory tract in humans, and dairy cow udder tissue. All H5N1 viruses had increased plaque sizes on MDCK cells at 37ºC and 39ºC compared to H1N1pdm09. In primary, differentiated human nasal and bronchial epithelial cultures, all H5N1 viruses show restricted infectious virus production compared to H1N1 at 33ºC. While H5N1 D1.1 also showed restricted replication at 37ºC and 39ºC, the H5N1 B3.13 replicated to nearly equivalent titers as H1N1pdm09. All H5N1 viruses demonstrated similar cell tropism in cells from the upper and lower respiratory tract, infecting more ciliated than non-ciliated cells relative to H1N1pdm09. H1N1, H5N1 B3.13 D1.1 infection induced similar innate immune factors, with nasal epithelial cells producing higher levels compared to bronchial epithelial cells. These data suggest that genotype B3.13 and D1.1 H5N1 viruses show different temperature dependent replication patterns compared to H1N1pdm09.

Source: 

Link: https://www.biorxiv.org/content/10.64898/2026.08.27.747488v1

____

West African Clade C #MERS-CoV Strains BF785 and Mor213 Induce More Robust #Interferon and Inflammatory Signaling Compared to Clade A in #Human Respiratory Cells

 

Abstract

Clade A Middle East respiratory syndrome coronavirus (MERS-CoV) spilled over from camels into humans in Saudi Arabia in 2012 and caused pneumonia and severe respiratory disease, with a 37% case fatality rate. While clade A and B viruses are closely related phylogenetically, clade B MERS-CoV strains have since outcompeted clade A strains and continue to circulate in camels and humans in the Middle East and cause outbreaks in humans. Clade C strains circulate in camels across the African continent but have not been reported to cause disease in humans. We have shown that a number of East African clade C isolates are less able to utilize the TMPRSS2-mediated pathway for viral entry in both cell lines and primary nasal epithelial cultures, which may underlie the reduced replication of East African clade C strains in humans. However, the reduced replicative capacity of West African strains in human cells appears to be independent of viral entry, suggesting an alternative basis for their attenuation. Here, we report that West African clade C MERS-CoV isolates with deletions in ORF4b encoding a key accessory protein, NS4b, induced significantly more robust interferon and inflammatory responses than clade A MERS in human respiratory cell lines and primary bronchial air–liquid interface cultures. The replication deficit for the West African strain BF785, which has a complete deletion of ORF4b, was partially rescued when RNASEL was knocked out in A549 cells. These findings demonstrate that complete loss of NS4b results in stronger innate immune activation than partial truncation and suggests that differential selection on NS4b may contribute to the varying phenotypes of clade C MERS-CoV strains circulating in African camels.

Source: 

Link: https://www.mdpi.com/1999-4915/18/9/935

____

Serum Escape Landscape of #SARS-CoV-2 #Omicron JN.1 and XEC RBD Under #COVID19 #Vaccine Breakthrough #Immunity in #China

 

Abstract

Population immune pressure from vaccination and prior infection continues to drive the evolution of SARS-CoV-2. Systematic characterization of RBD mutations under complex immune backgrounds is essential for understanding viral adaptation and evolutionary trajectories. Here, we applied a deep mutational scanning (DMS) to comprehensively map the neutralization escape landscape of the Omicron variant JN.1 and its descendant lineage XEC, under immune pressure from individuals who experienced Omicron breakthrough infections following three doses of inactivated vaccines. A neutralization escape map for the single amino acid substitutions in the RBD of JN.1 or XEC was generated, and the escape efficiency of each mutation was determined. The results show that RBD escape mutations are hierarchically organized: low-intensity signals are widespread, whereas high-intensity escape is confined to a few key sites. These escape mutations are not confined solely to the receptor-binding motif (RBM) but are broadly distributed across the entire RBD. Many escape sites could accommodate multiple amino acid substitutions. Integration of DMS data with genomic surveillance of circulating variants from 2024 to 2025 revealed significant overlap between experimentally identified escape sites and mutations observed in natural isolates. This overlap increased substantially in 2025, with site concordance rising from 27.17% and 26.81% to 45.09% and 47.10% for JN.1 and XEC, respectively. The natural prevalence of these escape mutations is further shaped by factors such as receptor-binding affinity, protein stability, and epistatic interactions. Overall, our findings suggest that SARS-CoV-2 antigenic evolution follows the pattern of multiple pathways within a constrained space, providing new insights into the adaptive mechanisms of Omicron-derived variants under hybrid immune pressure.

Source: 

Link: https://www.mdpi.com/2076-2607/14/9/1872

____

Emerging Haemagglutinin #Mutations in #Bovine-origin #H5N1 Influenza Viruses from #Humans and #Cattle Retain Avian #Receptor Binding with Increased Stability

 

Abstract

The current H5N1 panzootic has seen an unprecedented host range expansion, including sustained circulation in US dairy cattle, detected in March 2024. By July 2026, infections had been reported on more than 1,150 dairy farms across 19 states. Although the outbreak initially centred in Texas, California has emerged as the principal focus of transmission and accounts for most human infections associated with exposure to infected dairy cattle. Continued transmission in cattle and repeated spillover into humans increase opportunities for acquisition of mammalian-adaptive mutations that could elevate zoonotic and pandemic risk. The haemagglutinin (HA) protein plays a central role in modulating virus receptor binding and airborne transmission. Here, we characterised the receptor-binding and stability phenotypes of HA mutations identified in viruses circulating in Californian dairy cattle. Receptor-binding specificity was assessed using bio-layer interferometry and pseudotype virus entry assays. All tested HA variants maintained a preference for avian-type α2,3-linked sialic acid receptors. We evaluated HA stability using fusion and thermostability assays. All mutants exhibited fusion pH values >5.5, outside the range associated with efficient airborne transmission in humans (pH 5.0-5.5). However, mutations D88G and S94N increased pH stability, with fusion pH values of 5.6 and 5.7, respectively, compared with 5.9 for wild-type HA. Viruses harbouring both mutations displayed increased thermostability. These findings demonstrate that cattle-origin H5N1 viruses retain avian-like receptor specificity despite acquiring mutations that modestly enhance HA stability. Evolution of H5N1 viruses in dairy cattle underscores the importance of genomic and phenotypic surveillance to identify mutations that may increase zoonotic risk.

Competing Interest Statement

The authors have declared no competing interest.

Funder Information Declared

Biotechnology and Biological Sciences Research Council, BB/X006166/1, BB/Y007298/1, BB/X006204/1 BB/Y007271/1, APP104179,, BBS/E/PI/230001B, BBS/E/PI/230001C, BBS/E/PI/230002B, BBS/E/PI/230002C), BBS/E/PI/23NB0004, BBS/E/PI/23NB0003, BB/S011269/1

Medical Research Council, https://ror.org/03x94j517, MR/Y03368X/1,

Source: 

Link: https://www.biorxiv.org/content/10.64898/2026.08.18.745528v1

____

Enhanced #Pathogenicity and Contact #Transmissibility of #Human-origin Avian #Influenza #H5N1 Clade 2.3.4.4b Genotype B3.13 Compared to D1.1 in #Ferrets

 

Abstract

Since its emergence in 2020, multiple genotypes of the H5N1 clade 2.3.4.4b have been identified, with B3.13 and D1.1 emerging in the USA as two major and concerning genotypes. However, their relative pathogenicity and transmissibility in mammals have not been fully elucidated. We compared the pathogenicity and transmissibility of the first two human H5N1 clade 2.3.4.4b cases caused by B3.13 in Texas (A/Texas/37/2024; HPhTX B3.13) and D1.1 in Louisiana (A/Louisiana/12/2024; HPhLA D1.1) in a ferret model of infection and transmission. HPhTX B3.13 infection resulted in more severe clinical disease and enhanced viral shedding, with evidence of increased transmission relative to HPhLA D1.1. Histopathological analysis revealed more extensive lung pathology in animals infected with HPhTX B3.13, consistent with increased viral loads and inflammatory responses. Importantly, both genotypes showed no significant differences in reactivity to ferret sera raised against candidate vaccine virus (CVV) strains, receptor binding properties, or neuraminidase (NA) activity and thermostability. Whole-genome sequencing revealed no adaptive mutations in HPhTX B3.13 following infection or transmission. In contrast, HPhLA D1.1 showed rapid acquisition of the mammalian-adaptive mutation E627K in infected ferrets and both E627K and Q194K in the only fatal contact animal. Both mutations were associated with enhanced polymerase activity and computational analyses suggested that they enhance interactions with the mammalian host factors ANP32A and B. Our findings indicate that B3.13 is already well adapted for mammalian infection and transmission whereas D1.1 retains evolutionary potential through the rapid acquisition of adaptive mutations, highlighting important genotype-specific differences relevant to zoonotic risk assessment and pandemic preparedness.

Competing Interest Statement

The A.G.-S. laboratory has received research support from Avimex, Dynavax, Pharmamar, and Accurius, outside of the reported work within the last three years. A.G.-S. has consulting agreements for the following companies involving cash and/or stock within the last three years: Castlevax, Amovir, Vivaldi Biosciences, Contrafect, Avimex, Pagoda, Accurius, Applied Biological Laboratories, Pharmamar, CureLab Oncology, CureLab Veterinary, Virofend, Prosetta and A.A.C.T., outside of the reported work. A.G.-S. has been an invited speaker in meeting events within the last three years organized by Seqirus, Novavax and Hipra. A.G.-S. is inventor on patents and patent applications on the use of antivirals and vaccines for the treatment and prevention of virus infections and cancer, owned by the Icahn School of Medicine at Mount Sinai, New York, outside of the reported work. The Icahn School of Medicine at Mount Sinai has licensed some of these inventions to Medimmune, Avimex, Leinco Technologies, Castlevax, Virofend, Kerafast, Cell Signaling, EMD Millipore, Genentech, Paratus and Nura Bio, and as a result receives financial compensation. Subject to Mount Sinai receiving such financial consideration, AG-S will receive a portion of that consideration pursuant to the terms of the Mount Sinai Intellectual Property Policy. All other authors declare no commercial or financial conflict of interest.

Funder Information Declared

NIH/NIAID, 75N93021C00014

Horizon Europe Program, KAPPA-FLU no. 101084171

Source: 

Link: https://www.biorxiv.org/content/10.64898/2026.08.10.744032v1

____

#Antibody #evasion and receptor binding of #SARS-CoV-2 variants #PQ.16.1.1 and RK.1

 

{Excerpt}

Since its rapid global spread beginning in late 2024, the SARS-CoV-2 variant NB.1.8.1 has progressively displaced older omicron variants, and has established near-total dominance in Asia. More recently, two NB.1.8.1-derived sublineages, PQ.16.1.1 and RK.1, have emerged and expanded substantially, particularly in China and Singapore (...). Specifically, the sublineage PQ.16.1.1 acquired the amino acid substitutions Asp253Gly (within the N-terminal domain), alongside Asn417Thr, Asp420Asn, and Ile478Thr (within the receptor-binding domain) relative to the parental NB.1.8.1 strain (...). Concurrently, the RK.1 sublineage (formally classified as a descendant of the PQ.17.7.2.1 branch) acquired Asp420Asn, His445Pro, and Ile478Thr (...). Furthermore, PQ.16.1.1 has continued to evolve into the SV series sublineages (predominantly SV.2 and SV.2.1), which have maintained all receptor-binding domain mutations, including Asp420Asn, and have subsequently come to dominate the circulating SARS-CoV-2 strains in Singapore (...).

(...)

In summary, the convergent acquisition of the Asp420Asn substitution in NB.1.8.1 sublineages again illustrates a classic SARS-CoV-2 receptor-binding domain evolution trade-off: a sacrifice in hACE2 receptor engagement in exchange for profound, targeted evasion of class 1 neutralising antibodies. (...) Given the increased evasion of class 1 antibodies by these Asp420Asn-carrying sublineages, these variants will likely spread from Asia and begin to prevail in countries where mRNA vaccination is common and populations are enriched with class 1 neutralising antibodies. 

Source: 

Link: https://www.thelancet.com/journals/laninf/article/PIIS1473-3099(26)00429-9/fulltext?rss=yes

____

Identification and characterization of #PB2 #mutations associated with #mammalian #adaptation of highly pathogenic #H5N1 avian #influenza viruses

 

Abstract

The highly pathogenic avian influenza virus (HPAIV) subtype H5N1 has been continuously circulating among wild bird populations and domestic poultry. It’s ongoing circulation has led to outbreaks in poultry and U.S. dairy cattle populations, as well as sporadic severe infections in individuals engaged in poultry and dairy farming. These occurrences have raised concerns about the potential evolution of this virus into a pandemic strain. To elucidate the molecular determinants facilitating H5N1 cross-species adaptation and to evaluate its implications for public health, we conducted serials of sequence analysis and specific-site mutations on the viral polymerase subunit PB2 to determine its effect on polymerase activity and viral infectivity. The results showed that three mutations in the PB2 protein (E362G, D441N and M631L) were presented cooperative effects associated with enhanced viral replication in mammalian cells. Compared to the original isolated strain of the 2.3.4.4b clade, A/chicken/NL/FAV-0033/2021, these three mutations were predominantly identified in isolates obtained from cattle and other mammalian hosts between 2021 and 2024. The M631L mutation, identified as the primary determinant of increased polymerase activity in mammalian cells, significantly enhanced the binding affinity of PB2 to ANP32A. The mutation E362G and D441N did not increased polymerase activity and viral replication significantly but enhanced binding affinity of PB2 to ANP32A. The combined mutations with E362G, D441N and M631L resulted in a significantly increased polymerase activity and viral replication in H5N1 virus, and significantly elevated viral loads and aggravated pulmonary pathology in lungs of mice with H5N1 infection. These findings indicate that the PB2-M631L mutation constitutes a crucial molecular marker for the adaptation of H5N1 to mammalian hosts, whereas the E362G and D441N mutations likely function as supportive modulatory factors that optimize this host-adaptation process.

Source: 

Link: https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2026.1867604/full

____

Loss-of-function #mutation in #Omicron #variants reduces #spike protein expression and attenuates #SARS-CoV-2 infection

 

Abstract

SARS-CoV-2 Omicron variants emerged in 2022 with >30 novel mutations in the spike alone. While most studies focus on receptor binding domain changes, mutations in the C-terminus of S1 (CTS1), adjacent to the furin cleavage site, have largely been ignored. Here, we examine three Omicron mutations in CTS1: H655Y, N679K, and P681H. Generating a SARS-CoV-2 triple mutant (YKH), we find that the mutant increases spike processing, consistent with prior reports for H655Y/P681H. In addition, the YKH mutant induces attenuated disease, but augments viral loads in male golden Syrian hamsters. Next, we generate a single N679K mutant, finding it reduces viral replication in Calu3 human respiratory cells and induces less disease in male golden Syrian hamsters. Mechanistically, the N679K mutant has increased spike processing but also reduces spike in purified virions; spike decreases are further exacerbated in infected Calu3 cell lysates. Importantly, exogenous spike expression reveals that N679K reduces overall spike protein in the context of the epidemic strain. Although a loss-of-function mutation, transmission competition demonstrates that N679K confers a replication advantage in the upper airway, potentially impacting transmissibility. Together, the data show that N679K reduces overall spike protein during Omicron infection, which has implications for infection, immunity, and transmission.

Source: 

Link: https://www.nature.com/articles/s41467-026-76680-4

____

Assessment of Quantitative #Genetic #Distances Supports the Separation of #H17N10 and #H18N11 Subtypes of #Influenza a Virus into a Distinct Species

 

Abstract

The taxonomic status of the H17N10 and H18N11 influenza A viruses isolated from bats remains unclear due to the absence of quantitative classification criteria at this taxonomic level. A total of 3328 representative IAV genomes, encompassing all eight protein-coding segments, were analysed. Various genetic distance-based metrics were assessed at the pairwise level, including intra- and intergroup nucleotide distances, dN/dS ratios, and transition/transversion ratios, to facilitate the differentiation of the Alphainfluenzavirus genus into distinct taxa. Pairwise distances for seven of the eight segments (PB2, PB1, PA, NP, M, NA, NS) consistently differentiated the H17–H18 group from H1–H16. Across segments, intergroup nucleotide divergence was consistently above a lower bound of ~25%, with segment-specific values extending to higher levels (up to ~40% in PB2 and PA), while intragroup divergence remained substantially lower. The HA segment did not conform to this pattern, which is consistent with the hypothesis of ancient reassortment. The distribution of pairwise dN/dS values for the PB2, PB1, PA, and NP segments is evidently bimodal. Intergroup comparisons were consistently higher across all segments, whereas intragroup values remained lower. A similar lower boundary of approximately 0.12 was observed across segments, while the upper range of intergroup values varied by gene. Overall, the results support a consistent gene-specific separation pattern. Previously demonstrated absence of reassortment compatibility between bat viruses (H17–H18) and canonical influenza A (H1–H16) viruses indicates that these lineages have evolved independently over an extended period. These consistent genomic patterns provide support for the hypothesis that H17N10 and H18N11 viruses may represent a separate species within the genus Alphainfluenzavirus.

Source: 

Link: https://www.mdpi.com/1999-4915/18/8/838

____

#Mutations in severe #human #H5N1 cases facilitate #evasion from human mucus and #antivirals

 

Abstract

In late 2024, two individuals in Canada and the United States were treated in intensive care for acute respiratory distress caused by infection with the avian Influenza A Virus H5N1 2.3.4.4b genotype D1.1. Viral sequence data obtained from sampling these patients indicated mixed alleles at haemagglutinin (HA) positions 190 and 226. Mutations at these positions are key determinants of HA usage of α2,6-linked sialic acids (SA), the most abundant influenza receptors in human upper respiratory tracts. Thus, these mutations raised concerns about human adaptation and pandemic potential of the H5N1 virus. In this study, we investigated the impact of the mutations at residues 190 and 226 in H5 HA. We studied the receptor binding properties, cell entry phenotypes and fitness impacts of the mutations using recombinant proteins, pseudotyped lentiviruses, and in the context of influenza viruses using reverse genetics. The mutations did not confer any detectable α2,6-linked sialic acid receptor usage either alone or in combination. Rather, viruses carrying these mutations exhibit weakened binding towards α2,3-linked sialic acid receptors. This correlated with an enhanced capacity to evade human airway mucus, and a reduced susceptibility to oseltamivir and zanamivir. This research underscores that in addition to the way HA interacts with SA as entry receptors, other factors that impact the HA/NA balance might influence the evolutionary trajectory of a zoonotic virus in the human respiratory tract. This study presents a new paradigm for the evolutionary drivers of HA, where reduced sialic acid binding can serve as an advantage for escape from host barriers and antivirals.

Competing Interest Statement

The authors have declared no competing interest.

Funder Information Declared

Medical Research Council, https://ror.org/03x94j517, MR/Y03368X/1, MR/Y015061/1, CC2127

Biotechnology and Biological Sciences Research Council, BB/Y007298/1, APP104179, BBS/E/PI/23NB000, BBS/E/PI/23NB0003

Wellcome Trust, https://ror.org/029chgv08, CC2127, 218304/Z/19/Z

Department for Environment Food and Rural Affairs, BB/Y007298/1

The Pirbright Institute, BBS/E/PI/230002A, BBS/E/PI/230001C, BBS/E/PI/230002B

Cancer Research UK, CC2127

UK Research and Innovation, https://ror.org/001aqnf71, UKRI3602

Source: 

Link: https://www.biorxiv.org/content/10.64898/2026.07.28.740943v1

____

#H5N1 #influenza binding and cell entry via #human class II #MHC, and blocking by cross-reactive #antibodies

 

Abstract

Highly pathogenic avian influenza H5N1 clade 2.3.4.4b viruses are currently responsible for a multi-species outbreak affecting wild birds, poultry, numerous mammalian species, and humans. Influenza A viruses typically initiate infection through binding to sialic acid, although select bat and human influenza viruses can also exploit class II major histocompatibility complex (MHC–II) molecules for cell entry. Here we show that emerging H5N1 clade 2.3.4.4b viruses, but not historical H5 lineages, bind human MHC–II HLA-DR and mediate sialic acid-independent cell entry. Hemagglutinin binding to primary human immune cells varies with MHC–II expression and is further shaped by HLA–DR allelic variation, identifying host genetic determinants that may influence susceptibility to infection. Mammalian-adaptive substitutions within the hemagglutinin sialic acid receptor-binding domain reduce MHC–II binding, suggesting this interaction is remodeled during clade 2.3.4.4b H5 adaptation to a human host. Lastly, cross-reactive monoclonal antibodies isolated from clade 2.3.4.4b H5–naive humans can block the hemagglutinin–MHC–II interaction. These findings identify a previously unrecognized receptor pathway in contemporary H5N1 viruses and reveal that both human genetic variation and pre-existing humoral immunity can modulate this interaction, with implications for host range, cellular tropism, spillover risk, and therapeutic intervention.

Competing Interest Statement

S.D.B. has consulted for Regeneron, Sanofi, Novartis, Genentech, Pfizer, Visterra, and Otsuka on topics unrelated to the research presented here; owns stock in AbCellera Biologics; and is a scientific cofounder of Immunera, Inc.; S.E.H reports receiving consulting fees from Sanofi, Pfizer, Lumen, Novavax, and Merck.

Funder Information Declared

NIH/NIAID CEIRR contract, 75N93021C00015

NIH, 1U54CA260517

HIPC, U19AI057266

P01 grant, 5P01AI153559

David Crown Foundation endowment

Early Postdoc Mobility Fellowship Stipend from the Swiss

National Institutes of Health NRSA T32, T32OD011121

Source: 

Link: https://www.biorxiv.org/content/10.64898/2026.07.22.739677v1

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Evolving #dynamics of #H5Nx avian #influenza in #China revealed by long-term wild bird #surveillance

 

Abstract

H5Nx highly pathogenic avian influenza viruses pose persistent threats to poultry, wildlife, and public health. Over the past two decades, their geographic and host ranges have expanded across migratory networks whose epidemiological connectivity has become increasingly apparent through recent surveillance and genomic analyses. To elucidate these dynamics, we conduct long-term nationwide wild-bird surveillance in China, integrating active and passive monitoring. Our analyses reveal the maintenance, reassortment, and transmission of H5Nx viruses in wild birds, highlighting the value of sustained surveillance in capturing viral evolution. We identify distinct ecological patterns among major clades, with 2.3.4.4b showing the widest distribution and acting as the main lineage mediating intercontinental spread. Since 2020, most 2.3.4.4b viruses detected in wild birds in China have clustered with lineages originating outside China, consistent with repeated reintroduction rather than sustained local circulation. This shift underscores the growing role of migratory connectivity in shaping global viral exchange and the need for coordinated international active surveillance.

Source: 

Link: https://www.nature.com/articles/s41467-026-76039-9

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Characterization and evolutionary history of novel #SARS-CoV-2-related viruses in #bats from #Cambodia

 

Abstract

Circulating bat coronaviruses present a significant pandemic threat, yet our understanding of their genetic diversity and evolutionary dynamics remains limited. Over 3 years, we sampled 1,462 bats in Cambodia’s Steung Treng province, identifying extensive and diverse coronaviruses co-circulation. Using metatranscriptomic and amplicon sequencing, we generated 33 complete sarbecovirus genomes sequences, revealing novel lineages that cluster into four distinct groups, each associated with different Rhinolophus bat species. Our analysis highlights rapid migration and recombination of sarbecovirus lineages over short distances and timescales. Of note, the receptor-binding domains of two novel viral groups exhibit high similarity to SARS-CoV-2, and pseudovirus assays confirmed the ability of this spike protein to mediate entry into cells expressing human ACE2, suggesting a potential zoonotic risk. The observed genetic diversity underscores the urgent need for continuous surveillance to identify high-risk animal-to-human interfaces and inform pandemic preparedness.

Source: 

Link: https://www.nature.com/articles/s41467-026-75954-1

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Within- and between-host #dynamics of highly pathogenic avian #influenza in domestic #birds from #Pennsylvania #farms and live bird #markets

 

Abstract

Since late 2021, highly pathogenic avian influenza viruses (HPAI) of the H5 subtype clade 2.3.4.4b have spread across the Americas, devastating wildlife, agricultural animals, and resulting in dozens of human spillovers. National surveillance strategies generally provide only a single representative sequence per poultry outbreak, precluding fine-scale geographic transmission inference or studies of within-outbreak evolution. We produced high-quality deep sequence data from 46 infected Galliformes and Anseriformes sampled from commercial farm and live bird market (LBM) outbreaks in Pennsylvania from 2023-2025. We found that H5N1 viruses were introduced into Pennsylvania at least 68 independent times. We recover independent origins of live bird market outbreaks within the same county 3 weeks apart, and transmission between Pennsylvania LBM and New York commercial birds, suggesting high transmission risk within the Northeast live bird market distribution system. Analyses of within-farm variant populations show frequent variant sharing between samples from the same outbreak, suggesting that variants are propagated among epidemiologically linked infections. We identified 9 known adaptive mutations in these samples, including one instance of PB2 D701N in a LBM chicken sample, suggesting that while rare, concerning mammalian adaptive mutations can be present within these domestic outbreaks. Our data suggest that domestic bird outbreaks support high circulating diversity and wide transmission bottlenecks, increasing the risk of minority variants arising and propagating between infections. These data can help inform targeted biosecurity measures and better quantify the risk of viral adaptation during agricultural outbreaks.

Competing Interest Statement

The authors have declared no competing interest.

Funder Information Declared

NIAID, NIH 75N93021C00015

Pew Charitable Trusts

Source: 

Link: https://www.biorxiv.org/content/10.64898/2026.07.17.739193v1

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Highly Pathogenic Avian #Influenza #H5N5 in a Polar #Bear and Atlantic #Walrus, #Svalbard, 2026, with Widespread Seroconversion in Polar Bears

 

Abstract

Highly pathogenic avian influenza virus (HPAIV) subtype H5N5 was detected in a one-year-old polar bear (Ursus maritimus) and an adjacent adult Atlantic walrus (Odobenus rosmarus rosmarus), both found deceased in Raudfjorden, Svalbard. This represents the first confirmed case of HPAI in a European polar bear and the second in an Atlantic walrus. Viral genomes were nearly identical and harbored PB2-E627V, a marker associated with mammalian adaptation. Several polar bears, including the deceased individual, had previously been observed feeding on the walrus carcass. Antibodies against H5 were detected in 75% of polar bears in 2023 (n=36) and 97% in 2024-2025 (n=65), suggesting extensive circulation of HPAIV in the population following the first detections in birds in Svalbard in 2022, whereas no antibodies were detected in samples from 2014-2022 (n=243).

Competing Interest Statement

The authors have declared no competing interest.

Funder Information Declared

Project OH4Surveillance, funded by the European Union, Grant Agreement No 101132473

Morris Animal Foundation, Grant ID# D25ZO-430; KJB

Norwegian Veterinary Institute, 12311 SvalVilt

Source: 

Link: https://www.biorxiv.org/content/10.64898/2026.07.20.739480v1

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#Genomic Characterization of #SARS-CoV-2 #NB.1.8.1 and #PQ.2 from the #Infants and Young #Children with #Gastrointestinal Symptoms

 

Abstract

Purpose: 

This study investigated the viral genomic characteristics of infants and young children who presented to our hospital with gastrointestinal symptoms during a local COVID-19 epidemic and were confirmed to have SARS-CoV-2 infection.

Patients and methods: 

Between May and August 2025, pharyngeal swab samples were collected from four infants and young children who presented to the outpatient department of Meizhou People’s Hospital in Meizhou, with gastrointestinal symptoms. Nucleic acid testing and whole-genome sequencing were performed. The viral mutation profile was analyzed, and the potential impact of mutations on protein function was predicted.

Results: 

Pangolin typing identified the NB.1.8.1 variant in three patients and the PQ.2 variant in one patient. Genome sequences from three of the four viral variants displayed varying degrees of mutation. The nonsynonymous mutations for both variants were concentrated in the spike protein. A comparison with the parental XDV.1.5.1 lineage revealed 14 specific mutations, with 7 nonsynonymous sites conserved across all gene sequences. Five of these mutation sites, NSP12: D284Y, ORF3a: L46F, ORF3a: F207C, N: Q9H, and N: Q384H, were predicted to be functionally deleterious and structurally destabilizing.

Conclusion: 

SARS-CoV-2 variants from specimens obtained from four infants and young children exhibited varying degrees of mutation, providing evidence for the ongoing evolution of emerging variants in pediatric patients. However, monitoring genomic changes of circulating variants requires further clinical specimens, which contributes to understanding the dynamic changes at mutation sites, thereby supporting epidemic prevention and control.

Source: 

Link: https://www.dovepress.com/genomic-characterization-of-sars-cov-2-nb181-and-pq2-from-the-infants--peer-reviewed-fulltext-article-IDR

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