#Biodiversity and emerging infectious #threats: the microbial dark matter of Southwest #China

 

Abstract

Southwest China is a global biodiversity hotspot, and its complex and diverse ecosystems harbor vast amounts of “microbial dark matter.” This paper systematically examines the distribution characteristics of microbial dark matter in hosts such as arthropods, mammals, and birds, as well as in environments including soil, hot springs, and high-altitude lakes, with a particular focus on the cross-species transmissibility and pathogenic potential of emerging pathogens. Research indicates that new microbial species in the Southwest exhibit significant geographic concentration and host specificity: Yunnan Province is a core hotspot, while the Tibet Autonomous Region contributes a wealth of microbial resources due to its extreme environments, with arthropods and mammals accounting for the highest proportion of novel species. Regarding public health risks, eight novel pathogens with evidence of human infection have been identified, spanning the three major groups of viruses, bacteria, and parasites. The cross-species transmission potential of some pathogens (such as DPRV rhabdovirus, PPV arenaviridae, Luxi hantavirus, Banna virus and a novel Babesia species) has been confirmed through serological surveys or molecular testing. Deepening the exploration of microbial dark matter and risk early warning in this region will provide critical scientific support for public health safety monitoring.

Source: 

Link: https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2026.1846062/full

____

#Nipah Virus Shedding in #Urine from Fruit #Bats, #SriLanka, 2018–2019

 

Abstract

Nipah virus causes outbreaks in humans with high case-fatality rates. In this study, we confirmed the presence of Nipah virus in Sri Lanka in Pteropus medius fruit bats, one of the known natural reservoir species. Sequences we generated were genetically related to Nipah virus strains from outbreaks in southern India.

Source: 

Link: https://wwwnc.cdc.gov/eid/article/32/7/25-1567_article

____

#Virus-host #interactions on #volcanic #ash from Mount #Etna

 

Abstract

Volcanic ash represents an extreme and dynamic habitat, yet it hosts diverse microbial communities with largely unexplored viral diversity. This study investigated bacterial and viral populations in volcanic ash from Mount Etna (Italy) collected during the eruption, focusing on microbial novelty, activity, and virus-host interactions. Taxonomic profiling revealed that Pseudomonas and Telluria were the dominant bacterial genera, both frequently detected in airborne environments. In contrast, enrichment cultures with volcanic ash were dominated by spore-forming members of the phylum Bacillota, highlighting their resilience under harsh conditions. Metagenomic analysis recovered 19 high-quality metagenome-assembled genomes, including four previously undescribed bacterial species. Replication rate estimates showed that certain taxa were metabolically active, particularly at one sampling site. The presence of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) systems with spacers matching viral sequences suggested viral predation pressure on volcanic ash. A total of 1139 viral operational taxonomic units (vOTUs) were identified, of only around half (660 vOTUs) showed similarities to known phages, underscoring the presence of novel viruses. Shared vOTUs across sites revealed the presence of both a core virome and site-specific viral populations. Virus-host predictions indicated frequent interactions with hosts from multiple Gammaproteobacterial genera. Additionally, a 336 kb jumbo phage genome exhibited extensive metabolic capabilities and genetic autonomy. Experimental work identified a unique lytic Bacillus-infecting phage (″Phoenix″) with limited propagation capacity. Furthermore, prophage induction experiments revealed active, morphologically diverse temperate phages across multiple bacterial host strains. Overall, these findings highlight volcanic ash as a reservoir of microbial and viral diversity, shaped by environmental extremes and dynamic ecological interactions.

Competing Interest Statement

The authors have declared no competing interest.

Funder Information Declared

Swedish Research Council, https://ror.org/03zttf063, 2023-03310_VR, 2022-06725

Source: 

Link: https://www.biorxiv.org/content/10.64898/2026.06.17.732739v1?rss=1

____

Lower limit of #detection of commercial respiratory virus RT – #PCR panels for #bovine #influenza #H5N1

 

Abstract

Objectives

The adaptation of clade 2.3.4.4b influenza A(H5N1) to dozens of mammalian species, including dairy cattle, raises concerns about potential spillover into humans. If the virus develops human-to-human transmissibility, sensitive diagnostics will be critical to containment efforts. We sought to determine the lower limit of detection of commercial influenza A tests for the circulating bovine-adapted strain of H5N1.

Methods

We determined the 95% lower limit of detection (LLOD) of 4 commercial respiratory virus panels for detecting inactivated bovine H5N1 (A/bovine/Ohio/B24OSU-439/2024). Two of the tested panels provide seasonal influenza A subtyping, the BioFire Respiratory Panel 2.1 (BioFire Diagnostics/BioMérieux) and the cobas eplex respiratory pathogen panel 2 (Roche Diagnostics), while 2 panels provide pan–influenza A detection, the Xpert Xpress CoV-2/Flu/RSV plus (Cepheid), and the Panther Fusion SARS-CoV-2/Flu A/B/RSV Assay (Hologic, Inc). Serial dilutions of H5 RNA (400-25 copies/mL) were prepared in respiratory virus–negative nasopharyngeal swab matrix, and 20 replicates were tested at each concentration. The 95% LLOD for each test was calculated using probit regression.

Results

All 4 tests detected H5 with 95% LLODs below 1000 H5 RNA copies/mL. Xpert demonstrated the highest analytical sensitivity (50 copies/mL; 95% CI, 39-160), followed by BioFire (297 copies/mL; 95% CI, 196-3955), Panther Fusion (531 copies/mL; 95% CI, 421-792), and eplex (883 copies/mL; 95% CI, 588-2741).

Conclusions

Existing commercial respiratory virus panels can effectively detect bovine H5N1. These platforms could support screening in the event of an H5N1 outbreak, followed by confirmation with specific H5 subtyping, as needed.

Source: 

Link: https://academic.oup.com/ajcp/article-abstract/165/6/aqag067/8709618?redirectedFrom=fulltext

____

Mass #mortality of southern elephant #seals during multi-species #outbreak of HPAI #H5N1 on sub - #Antarctic Heard Island

 

Abstract

High pathogenicity avian influenza (HPAI) has spread across the sub-Antarctic, causing significant wildlife impacts. We report its first detection in an Australian external territory, Heard Island and McDonald Islands, which supports over one million breeding seabirds and seals. Drone and ground surveys (October 2025, January 2026), combined with viral genome analysis, confirmed infection with Influenza A H5N1 clade 2.3.4.4b at Heard Island. Drone surveys revealed mass mortality in southern elephant seals, with 8,573 pups (62%) recorded dead across Heard Island by the final surveys. Mortality increased at an average rate of 5.6% per day in a subset of harems, and the highest observed mortality in a harem was 97%. Based on the average (76%) mortality in the final surveys, total estimated pup mortality at Heard Island was 13,359 (from a total population of 17,364 pups), though this may be an underestimate as mortality was ongoing at this time. HPAI was detected in six of nine species tested and, we suspect, led to elevated mortality in king and gentoo penguins. Phylogenetic analysis indicates the virus was introduced from Crozet Islands, with an estimated arrival around August 2025. These data show the continued easterly spread of HPAI around the sub-Antarctic, with severe but heterogeneous impacts across taxa. Our results demonstrate the value of drones for large scale monitoring, underscoring the need for continued and enhanced HPAI surveillance across the Southern Ocean.

Competing Interest Statement

The authors have declared no competing interest.

Source: 

Link: https://www.biorxiv.org/content/10.64898/2026.06.16.732752v1

____

The Winners Take It All? #Global Evolutionary #Success of #H5Nx #Reassortants in the 2020–2024 #Panzootic

 

Abstract

Avian influenza viruses undergo frequent genetic reassortment, which can coincide with phenotypic changes in transmission, pathogenicity, and host species niche. Since 2020, clade 2.3.4.4b H5 high pathogenicity avian influenza viruses (HPAIVs) have driven a global panzootic, causing mass mortality in wild birds, poultry, and, for the first time, repeated spillover infections in a variety of mammalian species. This worldwide resurgence of H5 HPAIV has coincided with a dramatic increase in the number of circulating reassortant strains; however, the scale, impact and drivers of these reassortants remain unclear. Here, we combined statistical and phylodynamic modelling to reconstruct the global evolutionary dynamics of H5Nx viruses across four epizootic seasons (2020-2024). We identified 209 genetically distinct reassortants, stratified into three transmission categories based on their phylogenetic and epidemiological profiles. Accounting for sampling depth and HPAIV incidence, we estimated that reassortants emerged most frequently from Asia, but `major' reassortants associated with increased host range, inter-seasonal persistence, and long-range dissemination, more frequently emerged from Europe. Altogether, reassortant emergence followed an episodic pattern in which most reassortants were transient, but 2% seeded large clusters of secondary reassortants soon after their own emergence. Statistical modelling revealed that reassortant success was strongly shaped by ecological factors, including sustained circulation in specific wild bird orders and detection across a wider range of host niches. Collectively, our findings uncover global reassortment dynamics in H5 HPAIVs and identify key virological and ecological drivers underpinning the emergence and spread of successful reassortants. These insights support the importance of enhanced surveillance to track evolution of H5 HPAIV and identify traits relevant for consideration in pandemic risk assessment.

Competing Interest Statement

The authors have declared no competing interest.

Funder Information Declared

Biotechnology and Biological Sciences Research Council, BB/V011286/1, BB/X006204/1, BB/X006166/1, BB/Y007271/1, BB/Y007298/1

Biotechnology and Biological Sciences Research Council - Institute Strategic Grants, BBS/E/RL/230002C, BBS/E/RL/230002D

Medical Research Council, MR/Y015045/1, MR/Y03368X/1

National Natural Science Foundation of China, https://ror.org/01h0zpd94, 32061123001, 32425053, 32200416

National Key Research and Development Program of China, 2023YFC2307500, 2024YFE0106000

European Union, 727922, 874850, 101094685, 101084171, 874735

Fonds National de la Recherche Scientifique, F.4515.22

Fonds voor Wetenschappelijk Onderzoek — Vlaanderen, G098321N

Source: 

Link: https://www.biorxiv.org/content/10.1101/2025.07.19.665680v2

____

#Pathogens #analysis and modeling of #mortality #risk in #sepsis patients with #COVID19 and without COVID-19

 

Abstract

This study compared isolate-level pathogen profiles, antimicrobial susceptibility, clinical characteristics, and mortality predictors between sepsis patients with and without coronavirus disease 2019 (COVID-19), and developed cohort-specific nomograms for in-hospital mortality. This retrospective intensive care unit (ICU) cohort included 608 adults with sepsis: 158 in group COVID-19 and 450 in group non–COVID-19. All patients were assessed for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detection status. Patient-level comparisons and mortality modeling used the full cohort, whereas microbiological analyses were restricted to 235 eligible bacterial or fungal isolates from baseline cultures after exclusion of colonizers, contaminants, clinically non-causative organisms, and duplicates. Candidate predictors were selected by least absolute shrinkage and selection operator (LASSO) regression and entered into multivariable logistic regression; coefficients were pooled using Rubin’s rules when multiple imputation was performed. External validation used MIMIC-IV with fixed internal coefficients. Gram-negative organisms predominated, mainly Acinetobacter baumannii and Klebsiella pneumoniae, with substantial antimicrobial resistance. The COVID-19 and non–COVID-19 models showed apparent internal area under the curve values of 0.938 and 0.871, conservative optimism-corrected values of 0.913 and 0.871, and external validation AUC values of 0.841 and 0.859, respectively. Cohort-specific nomograms may provide supplementary risk-stratification information in critically ill patients with sepsis.

Source: 

Link: https://www.nature.com/articles/s41598-026-58450-w

____

#Antibodies to #influenza A virus #hemagglutinin and #neuraminidase limit egress and alter the physical properties of released virus particles

 

Abstract

Influenza A virus (IAV)-specific antibodies neutralize mature virions by inhibiting functional sites or, in some cases, by promoting virion aggregation. Many antibodies also act on infected cells to reduce virion yields, but the underlying mechanisms and effects on the physical properties and function of released virus particles remain incompletely characterized. Here we use flow virometry to acquire high-sensitivity yield and size measurements of virus particles released in the presence of antibodies. Combined with digital-droplet PCR and electron microscopy, this approach enables comprehensive characterization of antibody-induced changes in particle genome-content and morphology. We show that antibodies rapidly and dynamically alter released particle distributions, reducing yields and inducing the production of larger particles. Both effects result in part from aggregation induced by crosslinking of viral antigen on the infected-cell surface and inhibition of viral NA. However, yield reduction is not fully explained by aggregation, and a subset of induced larger particles are elongated virions. Finally, particles formed in the presence of HA stem-binding antibody, which does not inhibit attachment of mature virions, show reduced attachment in subsequent rounds of infection. Altogether, we uncover an unappreciated mechanism by which antibodies interfere with viral infection that occurs only during budding and release. Our work highlights the necessity of studying how the immune response shapes virus populations in the context of active infection processes.

Competing Interest Statement

T.I. is involved on a patent related to the flow virometry methodology: PCT/US2022/042125, status pending. The authors declare no other competing interests.

Funder Information Declared

Intramural Research Program of the National Institutes of Health (NIH), ZIAAI001385

G. Harold & Leila Y. Mathers Foundation, https://ror.org/02a7hjv13

Source: 

Link: https://www.biorxiv.org/content/10.64898/2026.06.15.729605v1

____

#Genomic #wastewater #surveillance of seasonal and #zoonotic #influenza A viruses in #California during the 2024-2025 flu season

 

Abstract

Wastewater genomic surveillance provides an opportunity to detect human and animal influenza A virus (IAV). We aimed to implement an IAV genomic surveillance framework agnostic to subtype, which enables recovery of IAV from multiple hosts and estimation of proportions across subtypes. We conducted IAV genomic surveillance in wastewater during the 2024-2025 flu season at multiple sites in California and compared these data with available human clinical IAV sequences and test positivity. We applied a custom whole-genome, multi-host IAV probe enrichment panel and adapted our custom expectation-maximization (EM) algorithm to deconvolute IAV mixtures in wastewater and infer subtype relative abundances. Absolute IAV concentrations were quantified using RT-PCR-based assays. H5N1 wastewater and clinical sequences were further characterized by constructing a whole-genome maximum-likelihood phylogenetic tree. Finally, we performed variant analysis to examine amino acid substitutions detected in wastewater. Our IAV probe enrichment method and EM algorithm successfully enriched all eight segments of three circulating IAV subtypes and accurately estimated subclade relative abundances for mixed IAV samples. Seasonal human H1N1pdm09 and H3N2 were detected throughout the study period from both wastewater and clinical sequencing data, with H1N1 subclades 6B.1A.5a.2a.1 and 6B.1A.5a.2a co-circulating, and H3N2 dominated by subclade 3C.2a1b.2a.2a.3a.1. Wastewater surveillance consistently detected H5N1 clade 2.3.4.4b across three monitored wastewater sites, while clinical H5N1 detections, from anywhere in CA, were sporadic and rare. Whole-genome phylogenetic analysis revealed that wastewater H5N1 sequences clustered with reference sequences associated with dairy cow and avian infections, while all human clinical H5N1 sequences clustered exclusively with reference sequences associated with dairy cow infections. Amino acid substitutions were identified across viral segments, and no mutations associated with mammalian adaptation were observed from wastewater samples.

Competing Interest Statement

The authors have declared no competing interest.

Source: 

Link: https://www.medrxiv.org/content/10.64898/2026.06.10.26355323v1

____

Seasonal #vaccine-induced #immunity shows preserved cross-reactivity to #H3N2 subclade K in adults

 

Summary

Background

Influenza A subclade K viruses caused high infection rates in the 2025/2026 Northern Hemisphere season, raising concerns about antigenic drift and reduced vaccine effectiveness.

Methods

We measured antibody responses in matched human pre- and post-vaccination sera, selected from two observational cohort studies of adults, against both a vaccine-like as well as subclade K isolates.

Findings

Pre-existing immunity to subclade K variants was noted with seasonal influenza vaccination further boosting titres two-fold against subclade K and three-fold against the vaccine-like strain, consistent with limited antigenic divergence between subclade K isolates and the vaccine. These findings contrast with ferret-based predictions of marked antigenic drift and align with the observed vaccine effectiveness in adults.

Interpretation

Our results underscore the importance of incorporating human serologic data in influenza surveillance to better inform vaccine strain selection and anticipate vaccine performance in immunologically experienced populations.

Funding

NIAID Centers for Excellence in Influenza Research and Response (75N93021C00014); NIAID VIVA HIPC (U19 AI168631); Mount Sinai Center for Vaccine Research and Pandemic Preparedness; institutional support from the Mount Sinai Center for Vaccine Research and Pandemic Preparedness and the Medical University of Vienna.

Source: 

Link: https://www.thelancet.com/journals/ebiom/article/PIIS2352-3964(26)00203-3/fulltext

____

#Coronavirus Disease Research #References (AMEDEO, June 13 '26)

 

Clin Infect Dis

1. BRITT NS, Khader K, He T, Prinzi AM, et al
   Clinical Impact of the BIOFIRE(R) FILMARRAY(R) Pneumonia Panel in the Veterans Affairs Healthcare System: A Difference-in-Differences Study.
   Clin Infect Dis. 2026 Jun 12:ciag328. doi: 10.1093.
   PubMed         Abstract available
   
   

   
   Infect Control Hosp Epidemiol

2. NERBY J, Berg W, McFarren M, Rhame F, et al
   Collaborative approaches to masking: statewide threshold development and performance across three respiratory seasons.
   Infect Control Hosp Epidemiol. 2026 Jun 11:1-7. doi: 10.1017/ice.2026.10487.
   PubMed         Abstract available
   
   

   
   Int J Infect Dis

3. CHEN H, Manu EK
   Shifting patterns of acute respiratory infection mortality in Australia: Changing contributions of COVID-19, influenza and respiratory syncytial virus and persistent Indigenous inequalities.
   Int J Infect Dis. 2026 Jun 8:108866. doi: 10.1016/j.ijid.2026.108866.
   PubMed         Abstract available
   
   

   
   Intensive Care Med

4. MEYBOHM P, Baron DM, Fries D, Lasocki S, et al
   Patient blood management in general intensive care patients.
   Intensive Care Med. 2026 Jun 8. doi: 10.1007/s00134-026-08491.
   PubMed         Abstract available
   
   

   
   J Infect

5. HARRIS R, Thirard R, McBrien C, Middleditch A, et al
   Immunogenicity and safety of co-administration of a recombinant shingles vaccine with an mRNA COVID-19 or adjuvanted influenza vaccine: a randomised controlled trial.
   J Infect. 2026 Jun 4:106784. doi: 10.1016/j.jinf.2026.106784.
   PubMed         Abstract available
   
   
6. WANG X, Yin J, Xu B, Guanhua X, et al
   Clinical epidemiological characteristics of hospitalized pediatric Mycoplasma pneumoniae pneumonia in China.
   J Infect. 2026 Jun 10:106793. doi: 10.1016/j.jinf.2026.106793.
   PubMed         Abstract available
   
   
7. TRUONG T, Radin JM, Li L, Ordonez-Mena JM, et al
   Burden and economic impact of RSV hospitalisations among English adults, 2023/24.
   J Infect. 2026;93:106792.
   PubMed         Abstract available
   
   

   
   J Med Virol

8. USHIJIMA H, Onda-Shimizu Y, Kotaki T, Nishimura S, et al
   Co-Circulation and Mixed Infections of Classic and Melbourne Human Astroviruses Among Pediatric Acute Gastroenteritis Patients in Japan, 2018-2024.
   J Med Virol. 2026;98:e71002.
   PubMed         Abstract available
   
   
9. AYDIN U, Duzenci D, Akkoc RF, Karatas A, et al
   Serum Histatin Levels in COVID-19: Association With Disease Severity and Immune Status.
   J Med Virol. 2026;98:e71009.
   PubMed         Abstract available
   
   
10. CHEN R, Kong W, Li C, Zhang J, et al
    TXD-198 Exhibits Inhibitory Activity Against SARS-CoV-2 by Upregulating ANO1.
    J Med Virol. 2026;98:e71004.
    PubMed         Abstract available
    
    
11. DENG J, Lin Q, Zeng Z, Huang H, et al
    Post-Pandemic Influenza Resurgence in Guangzhou, China: Impact of COVID-19 Interventions and Immune Alterations.
    J Med Virol. 2026;98:e71012.
    PubMed         Abstract available
    
    
12. FU JYL, Lim SK, Jalalonmuhali M, Bador MK, et al
    Immune Pressure From Plasma From Immunocompromised and Healthy Individuals Drives Differential SARS-CoV-2 Evolution and Escape Mutation Emergence.
    J Med Virol. 2026;98:e71016.
    PubMed         Abstract available
    
    

    
    J Travel Med

13. LUBBERT C, Fruhwein M, Dinjer CS, Machler C, et al
    Assessment of the healthcare burden of dengue disease in Germany: a retrospective analysis of statutory health insurance data (2014-2023).
    J Travel Med. 2026 Jun 11:taag047. doi: 10.1093.
    PubMed         Abstract available
    
    

    
    J Virol

14. YANG Y, Su Z, Zhang X, Tan Y, et al
    PPP2R5B regulates ANPEP expression and TGEV entry via dephosphorylation of HSF1 at Ser304/Ser308.
    J Virol. 2026 Jun 11:e0016626. doi: 10.1128/jvi.00166.
    PubMed         Abstract available
    
    
15. YO MS, Kaku Y, Kosugi Y, Tolentino JE, et al
    Genetic diversity of pangolin coronaviruses reveals a key immuno-evasive substitution at spike residue 519.
    J Virol. 2026 Jun 10:e0035226. doi: 10.1128/jvi.00352.
    PubMed         Abstract available
    
    
16. PENG M, Liu L, Li X, Yu X, et al
    Pre-pandemic contraction, phase-specific rate variation, and site-specific antigenic adaptation shape influenza A(H3N2) evolutionary dynamics in Hubei, China.
    J Virol. 2026 Jun 10:e0055626. doi: 10.1128/jvi.00556.
    PubMed         Abstract available
    
    
17. ARTUSA V, Limanaqi F, Santacroce E, Clerici M, et al
    Alpha-synuclein at the crossroads of host-virus interactions: immunological roles beyond the nervous system.
    J Virol. 2026 Jun 9:e0019126. doi: 10.1128/jvi.00191.
    PubMed         Abstract available
    
    
18. VARGAS DA, Albornoz LL, Pena-Morales M, Ortiz Rojas HJ, et al
    Within-host SARS-CoV-2 diversity in immunocompromised patients during acute infection.
    J Virol. 2026 Jun 9:e0222425. doi: 10.1128/jvi.02224.
    PubMed         Abstract available
    
    
19. YU H-M, Zhu M-L, Zhao Y-L, Tan J-X, et al
    Research progress on the association between viruses and cardiac diseases.
    J Virol. 2026 Jun 9:e0038326. doi: 10.1128/jvi.00383.
    PubMed         Abstract available
    
    
20. LI S, Luo H, Zhang K, Wu C, et al
    The cholesterol transporter Niemann-Pick C1 facilitates the entry of porcine epidemic diarrhea coronavirus.
    J Virol. 2026 Jun 9:e0030126. doi: 10.1128/jvi.00301.
    PubMed         Abstract available
    
    
21. ZHANG Q, Xin J, Wang C, Zhang X, et al
    Cleavage of TOM1 by the SARS-CoV-2 main protease NSP5 prevents autophagic degradation of viral envelope.
    J Virol. 2026 Jun 12:e0043426. doi: 10.1128/jvi.00434.
    PubMed         Abstract available
    
    

    
    Lancet Infect Dis

22. XIE Y, Choi T, Al-Aly Z
    Seasonal influenza versus COVID-19 hospitalisation risk during the 2025-26 influenza season.
    Lancet Infect Dis. 2026 Jun 10:S1473-3099(26)00289.
    PubMed        
    
    

    
    Travel Med Infect Dis

23. MIHAI I, Bonnaud L, Arregle F, Doudier B, et al
    Purulent meningococcal pericarditis with cardiac tamponade in a Hajj pilgrim: A diagnostic challenge of anchoring bias on MERS-CoV.
    Travel Med Infect Dis. 2026;72:103001.
    PubMed         Abstract available
    

#Influenza and Other Respiratory Viruses Research #References (AMEDEO, June 13 '26)

 

Arch Virol

1. SMATTI MK, Al-Khatib H, Suleman M, Nizar M, et al
   Functional and structural characterization of the SARS-CoV-2 spike N481K mutation.
   Arch Virol. 2026;171:198.
   PubMed         Abstract available
   
   

   
   J Infect

2. HARRIS R, Thirard R, McBrien C, Middleditch A, et al
   Immunogenicity and safety of co-administration of a recombinant shingles vaccine with an mRNA COVID-19 or adjuvanted influenza vaccine: a randomised controlled trial.
   J Infect. 2026 Jun 4:106784. doi: 10.1016/j.jinf.2026.106784.
   PubMed         Abstract available
   
   
3. CORRAO G, Sguazzini E, Gori A, Monti E, et al
   All-cause mortality within seven days of COVID-19 vaccination: A matched cohort and self-controlled case series study in Lombardy, Italy.
   J Infect. 2026;93:106769.
   PubMed         Abstract available
   
   
4. GUINOVART LJ, Westrhenen SEMH, Schuurman R, Bruijning-Verhagen PCJL, et al
   Symptomatology of SARS-CoV-2 versus seasonal coronavirus infection in healthy young children.
   J Infect. 2026 May 20:106762. doi: 10.1016/j.jinf.2026.106762.
   PubMed         Abstract available
   
   

   
   J Infect Dis

5. LIU F, Gross FL, Li Z, House SL, et al
   Birth cohort effects in adults associated with influenza A(H1N1)pdm09 vaccine effectiveness.
   J Infect Dis. 2026 Jun 8:jiag294. doi: 10.1093.
   PubMed         Abstract available
   
   

   
   J Virol

6. LIU Z, Fan M, Zeng Y, Zheng Y, et al
   Gga-miR-92-targeted TNFRSF1B inhibits the replication of influenza A virus by degrading TRAF3.
   J Virol. 2026 Jun 12:e0067426. doi: 10.1128/jvi.00674.
   PubMed         Abstract available
   
   
7. XU S, Zhang Q, Xie X, Zhou M, et al
   A neutralizing nanobody targeting a conserved lateral patch on HA1 confers protection against multiple H7 avian influenza viruses.
   J Virol. 2026 Jun 11:e0056326. doi: 10.1128/jvi.00563.
   PubMed         Abstract available
   
   
8. PENG M, Liu L, Li X, Yu X, et al
   Pre-pandemic contraction, phase-specific rate variation, and site-specific antigenic adaptation shape influenza A(H3N2) evolutionary dynamics in Hubei, China.
   J Virol. 2026 Jun 10:e0055626. doi: 10.1128/jvi.00556.
   PubMed         Abstract available
   
   

   
   PLoS Comput Biol

9. LIN Z, Gao Y, Sun W
   Supervised deep learning with gene functional annotation for cell classification.
   PLoS Comput Biol. 2026;22:e1014327.
   PubMed         Abstract available
   
   
10. KWON J, Li K, Warren JL, Pandya S, et al
    Utilizing virus genomic surveillance to predict vaccine effectiveness.
    PLoS Comput Biol. 2026;22:e1014329.
    PubMed         Abstract available
    
    

    
    PLoS One

11. TAM VCW, Yeung NCY, Kwok AWL
    Getting over the hurdles to save lives: Incorporating perceived barriers into theory of planned behaviour (TPB) model to predict stated intention among Hong Kong trained laymen.
    PLoS One. 2026;21:e0350392.
    PubMed         Abstract available
    
    
12. KONDO K, Morita I, Sakuma S, Ohsawa I, et al
    Changes in tobacco sales before, during, and after the COVID-19 pandemic in Japan: An interrupted time series analysis.
    PLoS One. 2026;21:e0350820.
    PubMed         Abstract available
    
    
13. WOODGATE RL, Mary-Quigley L, Bell A, Bennett M, et al
    Youth's mental health journeys through the COVID-19 pandemic using arts-based methods in virtual environments.
    PLoS One. 2026;21:e0349860.
    PubMed         Abstract available
    
    
14. KARAMI B, Rezaeian S, Bagherinia M, Shakiba E, et al
    Social support and health related quality of life among older people in covid-19 pandemic: The mediating role of resilience.
    PLoS One. 2026;21:e0342982.
    PubMed         Abstract available
    
    
15. YANG RJ, Wang M, Lyu L, You JL, et al
    Pathogen spectrum and epidemiology of respiratory tract infections in Quzhou, Eastern China, from November 2023 to July 2024: A post?COVID?19 surveillance study.
    PLoS One. 2026;21:e0346441.
    PubMed         Abstract available
    
    
16. BOLSHOV O, Chumachenko D
    Reinforcement learning for policymaking in epidemic control: A scoping review.
    PLoS One. 2026;21:e0351176.
    PubMed         Abstract available
    
    
17. LIU C, Liu H, Wei Y, Ye J, et al
    Modeling the effects of meteorological factors and media-driven public awareness on seasonal influenza outbreaks.
    PLoS One. 2026;21:e0342962.
    PubMed         Abstract available
    
    
18. LIU F, Lai T, Xu W, Li G, et al
    ViralMultiNet: A structure-aware multimodal framework for viral protein function prediction in wastewater surveillance.
    PLoS One. 2026;21:e0349393.
    PubMed         Abstract available
    
    
19. MOUNCHID PM, Shukla S, Steinert JI
    The interplay of economic shocks and cultural practices in child marriage: Comparative evidence from India and Zambia during the COVID-19 pandemic.
    PLoS One. 2026;21:e0346851.
    PubMed         Abstract available
    
    

    
    Proc Natl Acad Sci U S A

20. ZHU Z, Fragkias M, Suh JW, McCoshan E, et al
    The Urban Pulse: Diagnosing the urbanization process as spiky, cyclical, and asynchronous.
    Proc Natl Acad Sci U S A. 2026;123:e2537770123.
    PubMed         Abstract available
    
    
21. SKELLY AN, Fan C, Keeffe JR, Okten AB, et al
    mRNA delivery of a class 1/4 SARS-CoV-2 neutralizing antibody protects against diverse sarbecoviruses in a lethal mouse challenge model.
    Proc Natl Acad Sci U S A. 2026;123:e2536870123.
    PubMed         Abstract available
    
    

    
    Vaccine

22. WU X, Tao Y, Sun Y, Chen J, et al
    Cost-effectiveness of free influenza vaccination policy for Chinese older adults: a modeling analysis using real-world data.
    Vaccine. 2026;88:128782.
    PubMed         Abstract available
    
    
23. BIETZ A, Sandow P, Hartmann C, Steffan L, et al
    Real-time in-season monitoring of adult influenza vaccination coverage rates in Germany: results from a repeated cross-sectional online survey.
    Vaccine. 2026;88:128765.
    PubMed         Abstract available
    
    
24. SONG L, He G, Cui Y, Tan R, et al
    Optimized flagellin enhances systemic and mucosal immune responses induced by SARS-CoV-2 virus-like particle vaccines.
    Vaccine. 2026;87:128767.
    PubMed         Abstract available
    
    
25. FAIJUE DD, Bouaddi O, Segui AO, Morias B, et al
    Catch-up and life-course vaccination policies for adult and adolescent migrants in low-and-middle income countries: A policy analysis.
    Vaccine. 2026;85:128645.
    PubMed         Abstract available
    
    
26. FORNS J, Pajouheshnia R, Aurelius T, Bouck Z, et al
    Risk of thrombosis with thrombocytopaenia syndrome (TTS) after vaccination with AZD1222: a European VAC4EU post-authorisation safety study.
    Vaccine. 2026;86:128723.
    PubMed         Abstract available
    
    
27. POWELL A, Suwalowska H, Sankoh O, Guo C, et al
    Recent enough to matter: Perceived temporal proximity, anxiety, and COVID-19 vaccine intent.
    Vaccine. 2026;85:128717.
    PubMed         Abstract available
    
    
28. DALEXIS RD, Beogo I, Kibret TC, Cenat JM, et al
    Racial disparities in coverage and determinants of childhood diphtheria, tetanus, and pertussis (DTaP) vaccination in Canada: a post-COVID-19 pandemic analysis.
    Vaccine. 2026;85:128679.
    PubMed         Abstract available
    
    
29. KOIRALA A, Prasad SA, Tjiam MC, Britton PN, et al
    SARS-CoV-2 Ancestral and Omicron variant immunity in Australian children in 2023, a seroprevalence study.
    Vaccine. 2026;85:128705.
    PubMed         Abstract available
    
    
30. XU Y, Nyberg F, Marking U, Gisslen M, et al
    Rare adverse events after COVID-19 vaccination among Swedish older adults-evidence from a nationwide register-based study.
    Vaccine. 2026;85:128724.
    PubMed         Abstract available
    
    
31. DANCHIN M, Rak A, Vasiliadis S, Wang B, et al
    Maternal preferences for infant respiratory syncytial virus (RSV) preventives: an Australian discrete choice experiment.
    Vaccine. 2026;85:128710.
    PubMed         Abstract available
    
    
32. KOHLI M, Maschio M, Lee A, Kissler S, et al
    The cost-effectiveness of vaccination against COVID-19 in at-risk populations and older adults in the United Kingdom: Projections using a dynamic transmission model.
    Vaccine. 2026;85:128687.
    PubMed         Abstract available
    
    
33. TRANG TPH, Bazelier MT, Klungel OH, Bots SH, et al
    Quality and methodological heterogeneity of COVID-19 vaccine safety studies focusing on the myocarditis safety signal: A systematic review, meta-analysis and meta-regression.
    Vaccine. 2026;85:128722.
    PubMed         Abstract available
    
    
34. WANG R, Zhao Y, Yang J, Luo R, et al
    Systemic BCG administration induces transcription factor signature in CD4(+) T cells that cooperates with IL-12 signaling to drive antiviral Th1 differentiation.
    Vaccine. 2026;85:128720.
    PubMed         Abstract available
    
    

    
    Virology

35. KOVACS E, Rios Carrasco M, Guerreiro Cabana MF, de Vries RP, et al
    H5N1 2.3.4.4b HA E190D and Q226H mutations, picked up as minority variants in a patient, result in an inability to bind sialic acid.
    Virology. 2026;621:110949.
    PubMed         Abstract available
    
    

    
    Virus Res

36. TJARNHAGE E, Vatsveen TK, Raki M, Nemazee D, et al
    Repurposing ALK Inhibitors as Influenza and Corona Virus Antivirals Targeting Lymphocyte Tyrosine Kinase (LTK).
    Virus Res. 2026 Jun 9:199759. doi: 10.1016/j.virusres.2026.199759.
    PubMed         Abstract available
    

A neutralizing #nanobody targeting a conserved lateral patch on HA1 confers #protection against multiple #H7 avian #influenza viruses

 

ABSTRACT

Human infections with H7 avian influenza viruses (AIVs) have been documented globally, involving multiple subtypes and geographic regions. However, effective therapeutics targeting H7 influenza viruses remain limited. Here, a panel of nanobodies targeting the HA1 domain of hemagglutinin (HA) was identified by yeast two-hybrid (Y2H) screening, and six candidates were subsequently validated to exhibit hemagglutination inhibition (HI) activity. Of these, a subset also displayed virus microneutralization (MN) activity, while all showed binding activity in ELISA assays. Among them, Nb74 exhibited inhibitory activity against four Chinese recombinant vaccine-matched strains (Rv1–Rv4), which were generated based on the HA sequences of the corresponding inactivated vaccine strains H7-Re1 to H7-Re4. The HI-IC50 values were 0.23, 0.57, 3.65, and 43.75 µg/mL, respectively, and the MN-IC50 values for Rv1–Rv3 were 0.02, 0.06, and 1.09 µg/mL. It also retained activity against diverse clinical isolates although HI potency varied among strains. In mouse challenge experiments, intratracheal administration of Nb74 conferred robust protection, achieving 100% and 80% survival against Rv1 and Rv2, respectively, when administered prophylactically (2 mg/kg) or therapeutically (4 mg/kg). Treated mice showed accelerated body weight recovery, reduced lung viral load, and alleviated pulmonary pathology. Mechanistic analyses indicated that Nb74 neutralizes virus by blocking viral attachment to the host. Furthermore, combined hydrogen-deuterium exchange mass spectrometry (HDX-MS) with escape mutant analysis mapped its epitope to a conserved lateral patch on the HA1 subunit, consistent with a conformational epitope. Overall, these results demonstrate the therapeutic promise of intratracheally delivered Nb74 and provide insights for H7 AIVs vaccine design.

Source: 

Link: https://journals.asm.org/doi/10.1128/jvi.00563-26

____

Immunogenicity and safety of AS03-adjuvanted A/Astrakhan/3212/2020 #H5N8 -like #influenza #vaccine in adults: Phase 1/2, observer-blinded, randomized trial

 

ABSTRACT

Influenza pandemics arise from novel influenza A viruses. Recent emergence of a new clade (2.3.4.4.b) of the highly pathogenic H5N1 in animals and humans highlighted its pandemic potential. We evaluated the immunogenicity and safety of GSK’s AS03-adjuvanted H5N8 vaccine in adults. In this phase 1/2, observer-blinded, age-stratified, randomized trial, healthy US adults (age, ≥18 y) received two intramuscular doses of hemagglutinin antigen (3.75 or 7.50 μg) with AS03A or AS03B, administered 21 d apart. Immunogenicity – seroprotection rates (SPRs), seropositivity, geometric mean titers (GMTs), geometric mean fold rise (GMFR), and seroconversion rates (SCRs) – was evaluated on day 43 using hemagglutination inhibition (HI) and microneutralization (MN) assays. Safety was monitored throughout the study. Of 520 enrolled participants, 518 were vaccinated. On day 43, the US Food and Drug Administration’s (FDA) Center for Biologics Evaluation and Research criteria for influenza vaccines were met. HI SPRs, seropositivity rates, SCRs, GMTs, and GMFR appeared to be higher in the AS03A vs AS03B group. Immune responses were generally higher in younger (aged 18–64 y) vs older (aged ≥65 y) adults. Immune responses were also detected in MN assays, with a correlation between HI and MN responses on day 43 across age groups and vaccine formulations. Safety was acceptable, with no increase in adverse events post-dose 2. Reactogenicity appeared more common in younger adults. The antigen-sparing potential of AS03 was demonstrated, with an acceptable safety profile. The benefit/risk profile was favorable for all formulations tested, including 3.75 µg AS03A (licensed in the US).

ClinicalTrials.gov registration: NCT05975840.

Source: 

Link: https://www.tandfonline.com/doi/full/10.1080/21645515.2026.2649314

____

Seasonal #influenza versus #COVID19 #hospitalisation #risk during the 2025–26 influenza season

 

{Excerpt}

(...)

Contemporary surveillance data have shown higher population rates of influenza infections and hospitalisations during the 2025–26 influenza season; however, these aggregate metrics cannot disentangle infection frequency from disease severity. This analysis extends that evidence by comparing outcomes on a per-infection basis among patients with multiplex-based, laboratory-confirmed infection, showing that seasonal influenza was associated with a 43% higher risk of hospitalisation than COVID-19, corresponding to approximately 48 additional hospitalisations per 1000 infected individuals. The higher severity associated with seasonal influenza during this season likely reflects a combination of factors, including the increased virulence of circulating influenza strains, mismatch between vaccine composition and dominant circulating influenza variants, and the continued attenuation of SARS-CoV-2 severity over successive waves.

(...)

Source: 

Link: https://www.thelancet.com/journals/laninf/article/PIIS1473-3099(26)00289-6/fulltext?rss=yes

____

#Neurological Manifestations in Adult #Survivors of #Ebola Virus Disease

 

Key Points

    ° Question: 

        - What neurological symptoms are present in adult survivors of Ebola virus disease (EVD) and how long are they present after infection?

    ° Findings:  

        - In this cohort study conducted in Liberia including 148 EVD survivors and 81 control individuals, survivors had a wide range of neurological symptoms during acute EVD (including headaches, altered mental status, and meningitis symptoms) and numerous neurological sequelae in convalescence (including headaches, memory loss, and neurological examination abnormalities). Seven years later, most survivors’ symptoms and findings had improved, but many still had neurological symptoms, most notably memory loss.

    ° Meaning:  

        - The findings indicate that many neurological symptoms, including those that can affect quality of life and socioeconomic burden, were associated with EVD, warranting close neurological follow-up of EVD survivors.

Abstract

Importance  

    Ebola virus disease (EVD) causes multiorgan damage and is highly fatal. EVD’s neurological impact among survivors remains poorly characterized due to limited neurological assessment capabilities in the remote regions where most outbreaks occur.

Objective  

    To characterize neurological sequelae in EVD survivors over more than 7 years’ longitudinal follow-up.

Design, Setting, and Participants  

    Under the Ebola Natural History Study (PREVAIL III; PIII), the Neurology Study of PIII was a prospective longitudinal cohort study in Liberia of adult Ebola survivors and control individuals conducted from September 2015 to March 2023 at the Partnership for Research on Vaccines and Infectious Diseases in Liberia (PREVAIL) site at John F. Kennedy Medical Center in Monrovia, Liberia. Data were analyzed from April 2023 to September 2025.

Exposures  

    Neurological evaluations were performed by trained neurologists biannually. Questionnaire and neurological examination data were collected on case report forms.

Main Outcomes and Measures  

    Neurological symptom prevalence and neurological examination scores were compared to those of control individuals. Tests for differences between survivors and control individuals were conducted using generalized linear mixed-effects models controlling for age and sex. Overdispersed Poisson models were used to test for computed neurological examination score differences. Neurological examination scores were developed for this study, representing the cumulative abnormalities on neurological examinations, denoted on standardized case report forms, with the general neurological examination score representing all examination abnormalities and the central nervous system score representing the central nervous system–specific abnormalities on examination.

Results  

    Analysis after serologic testing included 148 Ebola antibody-positive survivors (mean [SD] age, 34.8 [10.5] years; 74 [50%] female) and 81 antibody-negative contacts (mean [SD] age, 35.8 [12.6] years; 41 [51%] female). During acute infection, survivors reported headaches, altered mental status, and strokelike symptoms or meningoencephalitis (rarely). Survivors had significant neurological sequelae involving the entire neuraxis: cognitive dysfunction (83 [56.1%]), persistent headaches (98 [66.2%]), sleep abnormalities (40 [27.0%]), depression (73 [49.3%]), sexual dysfunction (48 [32.4%]), tremor (18 [20.3%]), fatigue (71 [51.1%]), cranial nerve abnormalities (60 [40.5%]), and sensory abnormalities (45 [30.4%]). Over 7 years’ follow-up, most survivors demonstrated improvement in neurological status. The final visit included 115 survivors (77.7%) and 61 close contacts (75.3%). Persistent symptoms at final evaluation in survivors compared to contacts were memory loss (66 [57.4%] vs 16 [26.2%], respectively; P < .001), irritability (42 [36.5%] vs 9 [14.8%], respectively; P = .006), and trouble concentrating (34 [29.6%] vs 6 [9.8%], respectively; P = .002).

Conclusions and Relevance  

    The findings indicate that Ebola virus infection is associated with neurological complications in survivors, with increased health care burden and socioeconomic consequences. These neurological issues generally improved with time, but some persisted long-term. Close neurological follow-up of EVD survivors may be warranted.

Source: 

Link: https://jamanetwork.com/journals/jamaneurology/fullarticle/2850237#251071811

____

Evaluation of #antiviral #treatments for highly pathogenic avian #influenza virus #infections in #feline species

 

Abstract

In 2020, highly pathogenic avian influenza (HPAI) isolates from clade 2.3.4.4b emerged in Europe and spread globally, including in bovine hosts in the USA. Viruses from this clade cause minimal disease in dairy cattle, characterized by decreased milk production but low mortality rates. Infections have also occurred in feline hosts. In contrast to cows, infection of cats (and closely related species, including skunks and foxes) can result in severe neurological signs and mortality. Documented feline H5N1 infections from clade 2.3.4.4.b have a mortality rate of approximately 80% following rapid onset of clinical signs. No antiviral compounds have been tested in an experimental feline model; however, anecdotal clinical evidence suggests early treatment with oseltamivir may improve outcomes in felines with HPAI. Here, we show the in vitro efficacy of several influenza inhibitors in feline glial astrocyte (PG-4) and kidney (CRFK) cell culture models using the clade 2.3.4.4.b virus Tx2/24 (H5N1). The neuraminidase inhibitor oseltamivir carboxylate did not effectively inhibit viral replication in either cell line. The cap-dependent endonuclease inhibitor baloxavir exhibited the strongest inhibition of this virus, with EC50 values of 30 nM in PG-4 and 1 μM in CRFK cells. Amantadine and rimantadine, M2 ion channel inhibitors, were unable to completely inhibit viral replication in either cell line at any concentration utilized. The broad-spectrum nucleoside analog GS-441524 demonstrated little to no inhibition of viral replication in either cell line. Additionally, the mutagenic NHC analogs EIDD-1931 and EIDD-2801 successfully inhibited viral replication at the maximum tested concentration of 100 μM but exhibited significant cytotoxicity. Our findings suggest that baloxavir should be considered by veterinary clinicians as the first-line drug of choice when presented with felines or other species infected with HPAI.

Competing Interest Statement

The authors have declared no competing interest.

Funder Information Declared

Cornell Feline Health Center, Ithaca, US

Source: 

Link: https://www.biorxiv.org/content/10.64898/2026.06.09.730954v1

____

#Antigenic mapping of #H2 #influenza viruses recognized by #ferret and #human sera and predicting antigenically significant sites

 

ABSTRACT

Influenza viruses cause hundreds of thousands of infections globally every year. In the past century, seasonal influenza viruses have included H1N1, H2N2, and H3N2 strains. H2N2 influenza viruses circulated in the human population between 1957 and 1968. Previously, our group demonstrated a lack of H2N2 influenza virus immunity in individuals born after 1968, as well as the effectiveness of hemagglutinin (HA)-based vaccines for multiple influenza virus subtypes. In this study, H2 antigenic maps and radial graphs were generated using previously published data from H2 HA vaccinations of ferrets and seasonal influenza vaccinations of humans. The antigenic maps revealed a stark difference in the clustering of HA antigens between ferrets and humans, and the radial graphs showed that specific antigen recognition varies greatly among different influenza preimmune ferrets. These maps also revealed the significant impact that different pre-existing immunities have on antigenic recognition and clustering of antigens after vaccine boost. From these data, we predicted two possible antigenically significant sites containing various mutations that have not been previously reported, and showed that one of these sites is relevant using mouse antisera.

Source: 

Link: https://journals.asm.org/doi/10.1128/msphere.00022-26

____

Regional #Signals Preceding the 2026 #Bundibugyo Virus Disease #Outbreak

 

Highlights

    • Bundibugyo virus circulated undetected for months prior to outbreak declaration.

    • Four earlier regional hemorrhagic fever clusters flagged by open surveillance are unresolved.

    • These clusters warrant urgent reanalysis due to concern for regional spread.

Abstract

Background

The May 2026 Bundibugyo virus disease (BVD) outbreak in the Democratic Republic of the Congo was declared a Public Health Emergency of International Concern after substantial undetected community transmission. We describe regional surveillance signals detected by the Biothreats Emergence, Analysis, and Communications Network (BEACON), our open access event based surveillance program, in the weeks preceding outbreak declaration.

Methods

We reviewed BEACON reports of VHF-compatible illness clusters detected in the transboundary DRC-Uganda-Burundi-South Sudan region during March–April 2026, prior to the May 15 laboratory confirmation of BDBV.

Results

BEACON detected four temporally proximal VHF-compatible illness signals: (1) March 9, North Kivu Province—suspected Ebola case under investigation with unresolved laboratory results; (2) March 10, Kasaï Province—fatal hemorrhagic illness with secondary cases and negative Ebola PCR; (3) March 30, Burundi—35-case undiagnosed cluster near the DRC border with 5 deaths, negative testing for major filoviruses and >200 pathogens, pending metagenomic sequencing; (4) April 22, South Sudan—three suspected VHF cases with negative initial testing. All four signals shared a similar diagnostic phenotype: VHF-compatible presentation, mobilization of investigation teams, negative initial testing, and no publicly reported confirmed etiology. None were formally reported to have been resolved.

Conclusions

Our detection of four unresolved VHF signals preceding the confirmed BDBV outbreak highlights gaps in formal follow-up mechanisms for negative cases and fragmented regional diagnostic coordination. In light of confirmed BDBV circulation and Africa CDC's identification of 10 countries at high risk for spread, these preceding signals warrant urgent retrospective investigation and laboratory.

Source: 

Link: https://www.ijidonline.com/article/S1201-9712(26)00497-2/fulltext

____