The simulations examined how the timing and extent of infection-acquired immunity could affect the apparent performance of Shigella vaccines. In high-incidence settings, repeated exposure may allow unvaccinated infants to accumulate natural immunity, potentially bringing their immune status closer to that of vaccinated infants. A trial conducted after this convergence could therefore record a lower vaccine efficacy than the vaccine would achieve in a fully immunologically naïve population. The magnitude of the effect depended on the trial design and on assumptions about the natural history of Shigella, including how quickly immunity develops and how long it persists.

Researchers modeled trials in settings with low, medium and high disease burdens. For each setting, they evaluated six combinations of surveillance and statistical analysis: active surveillance for Shigella infection or symptom-based reporting, each paired with a single-outcome model, a stratified recurrent-outcome model or a crude recurrent-outcome Cox proportional hazards model. The analysis measured bias in vaccine-efficacy estimates, the coverage of nominal 95% confidence intervals and the false-negative rate. Active infection surveillance with a single-outcome model was the only approach that remained unbiased throughout the scenarios tested. Among the other five approaches, the single-outcome model paired with symptom-based reporting performed least poorly.

Bias generally increased in higher-burden settings, where the accumulation of natural immunity was expected to be more pronounced. The results for realistically sized trials were also less favorable at higher-burden sites: confidence-interval coverage was worse, and the false-negative rate was higher. These findings identify a specific measurement challenge for late-stage Shigella vaccine trials rather than evidence that the vaccines themselves are ineffective. They also do not establish the size of the discrepancy in an actual trial, because the estimates are conditional on simulated inputs and limited published information about Shigella immunity and natural history. The study’s conclusion is that observed efficacy is likely to understate true efficacy in some circumstances, while careful design is needed to reduce that bias.

Subject of Research: Simulation analysis of how natural immunity and trial design affect estimates of Shigella vaccine efficacy

Article Title: Analysis of the impact of naturally-acquired immunity on Shigella vaccine performance to inform clinical trials: A simulation-based modeling study

Article References: Amin, A. B., Garcia Quesada, M., Trudell, D., Dean, N. E., Lopman, B. A., Platts-Mills, J. A., & Rogawski McQuade, E. T. (2026). Analysis of the impact of naturally-acquired immunity on Shigella vaccine performance to inform clinical trials: A simulation-based modeling study. PLOS Medicine, 23(10), e1004878. https://doi.org/10.1371/journal.pmed.1004878

Image Credits: AI Generated

DOI: 10.1371/journal.pmed.1004878

Keywords: Shigella, vaccine efficacy, natural immunity, clinical trials, epidemiology, simulation modeling, active surveillance, diarrheal disease, statistical bias, Analysis, impact, naturally-acquired

The team enrolled 337 healthy infants shortly after birth and followed them through their two-dose Rotarix series, administered at 2 and 4 months of age according to routine immunization schedules at each site. Of these, 328 infants, or 97.3 percent, completed visits through 6 months. To measure vaccine response, the researchers used two complementary indicators. The first was seroconversion, defined as at least a threefold increase in serum rotavirus-specific IgA between the pre-vaccination visit at a median of 54 days of life and the post-vaccination visit at a median of 188 days. The second was vaccine-strain shedding, detected by polymerase chain reaction in stool collected within 14 days after the second dose. Overall, 153 of 328 infants, or 46.6 percent, seroconverted. Shedding was less common: of 216 infants with stool analyzed after the second dose, only 79, or 36.6 percent, had detectable vaccine virus. Neither measure differed significantly between countries, a striking result given that absolute IgA levels did vary by site.

To understand what distinguished responders from non-responders, the team sequenced shotgun metagenomes from 816 stool samples collected at 1, 2, and 4 months of life, ultimately analyzing 765 high-quality samples from 324 infants. As expected, microbial richness increased with age, and community composition differed by delivery mode, diet, and country. But the critical signal emerged in the first month. Marginal PERMANOVA testing revealed that seroconversion status correlated with gut community composition at month 1, explaining roughly 1.1 percent of variation in Aitchison distance, while no relationship existed at months 2 or 4. Functional diversity based on MetaCyc pathway profiles showed the same temporal restriction. When the researchers applied distance-based redundancy analysis conditioned on country, delivery mode, diet, and age, they recovered a gradient inverse to seroconversion, and Klebsiella was the top contributor, explaining 8.6 percent of total variation along the first axis.

Differential abundance analysis sharpened the picture. At month 1, the species Klebsiella michiganensis and Phytobacter ursingii were overrepresented in the guts of vaccine non-responders, and these findings were reproducible across multiple statistical methodologies. No species at months 2 or 4 were associated with seroconversion status. The functional profile of non-responders was equally distinctive: 61 MetaCyc pathways were enriched in non-responders, dominated by aromatic compound degradation, particularly of toluene and catechol, alongside ureide biosynthesis, trimethylamine degradation, and catabolism of arginine, ornithine, asparagine, glutamate, and threonine. Crucially, pathways involved in lipopolysaccharide, or LPS, biosynthesis were overrepresented in non-responders, with no LPS pathways enriched in responders. Gene-level analysis of KEGG orthologs stratified by species confirmed that Klebsiella species carrying LPS biosynthetic genes were enriched in non-responders, directly linking the taxonomic and functional signatures.

To capture the overall ecological configuration of the infant gut, the researchers applied Dirichlet Multinomial Mixture modeling to cluster communities into discrete gut community types at each time point. At month 1, one type, designated cs-GCT3, was enriched in Klebsiella, while another, cs-GCT6, was depleted in both Klebsiella and Escherichia. After accounting for country, diet, and breastfeeding, seroconversion status was significantly associated with month 1 gut type. Seroconverters had lower odds of belonging to the Klebsiella-dominant cs-GCT3 and the highest odds of belonging to cs-GCT6, which contained the greatest absolute percentage of seroconverters at 74.0 percent. Proportionally fewer cs-GCT3 infants, only 16 percent, were seropositive after vaccination. The Klebsiella-dominant type was also less likely to show vaccine virus shedding than any other type except cs-GCT2, which was enriched in both Klebsiella and Escherichia. These patterns were restricted to month 1, indicating that the gut configuration in the first weeks of life, not the composition at the time of vaccination, predicted later response.

The researchers then turned to fecal calprotectin, a clinical biomarker of intestinal inflammation, to test whether these microbial patterns corresponded to an inflamed gut. Calprotectin did not differ between countries at month 1, but by month 2 it was elevated in Peruvian infants compared to those in Panama and the United States. More tellingly, infants with vaccine virus shedding detected after the second dose had significantly lower calprotectin at month 1, linking reduced early inflammation with enhanced mucosal replication of the vaccine virus. Differential abundance analysis showed that calprotectin at month 1 was negatively associated with Bifidobacterium longum and, more weakly, Bifidobacterium saguini, though not with Klebsiella or Escherichia. Calprotectin was also elevated at month 1 among infants in the Klebsiella- and Escherichia-enriched cs-GCT2 compared to the demographically similar but pathobiont-depleted cs-GCT1.

The mechanistic hypothesis that emerges from these data centers on LPS, the endotoxic outer membrane component of Gram-negative bacteria. Klebsiella overabundance in the first month of life was accompanied by enrichment of LPS biosynthetic potential, and the authors propose that this drives a pro-inflammatory mucosal environment that impedes vaccine take. The discussion in the paper situates the finding within a broader literature: neonatal antibiotic exposure in an Australian cohort was associated with decreased antibody responses to multiple vaccines through reductions in Bifidobacterium, while oral vaccine failure in Indian infants has been linked to Enterobacteriaceae enrichment and Bifidobacterium depletion. Non-polio enterovirus colonization and increased gut inflammation have similarly been tied to reduced poliovirus and rotavirus vaccine responses in South Asia and Central America. Animal models reinforce the framework, with neonatal microbiome disruption in mice impairing both mucosal and systemic vaccine responses in a manner that could be rescued through microbial restoration.

Notably, the high-response gut type cs-GCT6 was not characterized by enrichment of genera typically considered probiotic. The authors suggest that protection against vaccine hypo-responsiveness may result from exclusion of pro-inflammatory taxa rather than enrichment of beneficial ones, a subtle but important reframing. Consistent with this, probiotic supplementation did not improve Rotarix immunogenicity among infants in India in a prior randomized study, and reduced Proteobacteria abundance at birth correlated with improved vaccine shedding following neonatal rotavirus vaccination in Indonesia and Malawi. The relationship between shedding and seroconversion also appears paradoxical here: the authors propose that an inflamed gut may reflect neutrophil-driven clearance of the vaccine virus without concurrent generation of effective adaptive immune memory, since enhanced neutrophil activity can suppress immune memory through competition with dendritic cells for antigen or inhibition of IgA production.

The study has clear limitations. Seroconversion measured in blood represents systemic rather than localized gut response, and the degree of seroconversion may be confounded by pre-existing immunity, including transplacentally acquired maternal IgG, which the team did not assess. Human milk contains immunologic and compositional factors that may influence response, and the study was observational, so a causal relationship between gut microbiome and vaccine response cannot be established. Machine learning models built with LightGBM failed to predict seroconversion from microbiome data alone, with holdout area under the receiver operating characteristic curve not exceeding 50 percent at any time point, underscoring that context-specific ecological configurations rather than globally generalizable signatures drive outcomes. The Klebsiella-dominant gut type was also overrepresented by cesarean-delivered Panamanian infants, lacking a direct comparator among Peruvian infants.

Despite these caveats, the findings carry substantial implications for precision vaccine approaches. The authors argue that microbiome-targeted strategies, including synbiotic combinations, selective prebiotics to support Bifidobacterium, or phage-based depletion of Klebsiella, may offer greater specificity than broad probiotic supplementation, and that the timing of such interventions should align with the neonatal window during which the microbiome and immune system are most dynamically interacting. By identifying a microbial-metabolic-inflammatory axis centered on Klebsiella colonization and early-life gut inflammation, the study reframes oral vaccine failure not as a mystery of geography but as a consequence of which bacteria claim the infant gut in its first weeks, opening a concrete path toward interventions that could improve vaccine performance where it is needed most.

Subject of Research: Association between Klebsiella-dominant infant gut microbiome communities and impaired oral rotavirus vaccine response

Article Title: Klebsiella-dominant gut communities are associated with impeded oral rotavirus vaccine response in infants

Article References: Seymour, C. O., Ecklu-Mensah, G., Lee, Y., Nicols, A. R., Cheng, W. A., Jumarang, J. M., Marentes Ruiz, C. J., Navarro, J., Navarro, R., Rodriguez-Angeles, Y., Durand, D., Allard, S. M., Taylor, Z. W., De León, R. G., Ochoa, T. J., Gilbert, J. A., & Pannaraj, P. S. (2026). Klebsiella-dominant gut communities are associated with impeded oral rotavirus vaccine response in infants. Nature Communications, 17(1), Article 10783. https://doi.org/10.1038/s41467-026-78148-x

Image Credits: AI Generated

DOI: 10.1038/s41467-026-78148-x

Keywords: rotavirus vaccine, gut microbiome, Klebsiella, infants, seroconversion, lipopolysaccharide, fecal calprotectin, gut inflammation, Bifidobacterium, oral vaccines, Nature Communications, vaccine efficacy

The choice of platform matters. Whole-genome sequencing with nanopore devices allows laboratories to generate complete viral genomes rapidly and at relatively low cost, which is essential for surveillance programs that need to keep pace with a virus that evolves on a timescale of months. Rather than focusing solely on the hemagglutinin gene, the conventional workhorse of influenza phylogenetics, the Iranian team examined the entire genome, including the internal proteins that govern replication efficiency, host immune modulation, and antiviral susceptibility. This comprehensive approach is increasingly recognized as essential because changes outside the surface glycoproteins can influence viral fitness and virulence in ways that hemagglutinin-focused studies miss entirely.

The central finding concerns genetic distance from the vaccine strain. Viruses circulating during the 2024–2025 season showed slightly lower nucleotide similarity to the vaccine component, at 98.78 percent, than those from the 2023–2024 season, which stood at 99.13 percent. While a difference of roughly a third of a percentage point may appear trivial, in influenza virology such incremental drift is precisely what accumulates into antigenic change over successive seasons. The result confirms that the Iranian viral population was not static between the two seasons but continued to diverge slowly from the A/Wisconsin/67/2022 vaccine strain, mirroring the global pattern of antigenic drift that the World Health Organization monitors when it convenes its twice-yearly vaccine composition meetings.

To translate raw sequence divergence into immunological terms, the researchers turned their attention to the epitope landscape of the hemagglutinin protein. Epitopes are the discrete regions of viral surface proteins that antibodies actually bind, and mutations concentrated within these regions are far more consequential for immune escape than changes elsewhere in the protein. The analysis revealed that epitope A, one of the five major antigenic sites on the globular head of hemagglutinin, was the most variable region during both seasons. This is consistent with decades of influenza research showing that epitope A sits at the immunodominant tip of the molecule, where antibody pressure is strongest and where substitutions are most readily tolerated structurally.

Using a computational method that estimates vaccine efficacy from the density of substitutions within epitope regions, the team calculated that vaccine protection against the dominant epitope ranged from 38.1 percent to 50.5 percent across the 2023–2025 period. These figures, while moderate, fall within the range typically observed for inactivated influenza vaccines in well-matched seasons, where real-world effectiveness against laboratory-confirmed infection often hovers between 40 and 60 percent. The authors interpret these estimates as acceptable and consistent with the WHO decision to retain A/Wisconsin/67/2022 as the H1N1 component of the 2025–2026 seasonal vaccine. In other words, despite measurable drift, the circulating Iranian viruses had not yet escaped the reach of vaccine-induced immunity.

Beyond the surface glycoproteins, the study documented several substitutions in the internal proteins of the viral genome, a dimension of influenza evolution that receives far less attention in routine surveillance. Among these, the I123V substitution in the non-structural protein NS1 was detected in both the vaccine strain and the analyzed Iranian isolates. NS1 is a multifunctional virulence factor that antagonizes the host interferon response, and substitutions in this protein can modulate how effectively the virus suppresses innate immunity. The presence of the same substitution in both vaccine and circulating strains suggests it is a shared, likely stable feature of the clade rather than a marker of emerging virulence specific to the Iranian isolates.

Antiviral susceptibility is the other critical surveillance question, and here the news was largely reassuring. Neuraminidase inhibitors such as oseltamivir remain the mainstay of influenza antiviral therapy, and resistance mutations in the neuraminidase gene can rapidly undermine treatment, as occurred historically with seasonal H1N1 strains that acquired the H275Y substitution. The Iranian viruses remained largely susceptible to neuraminidase inhibitors throughout the study period, although one strain carried the S247N substitution, a change that has been associated with reduced inhibition in some influenza A viruses and therefore warrants continued monitoring. A single resistant-adjacent variant among thirty genomes does not signal a treatment crisis, but it illustrates exactly the kind of signal that whole-genome surveillance is designed to catch early.

Phylogenetic analysis placed 90 percent of the Iranian strains within clade 6B.1 A.5a.2a, the same subclade that dominated globally during the 2023–2025 seasons. This clustering demonstrates that Iran’s H1N1 population was fully integrated into the worldwide viral lineage structure, with no evidence of a locally divergent or geographically isolated evolutionary trajectory. The researchers also compared the topologies of phylogenetic trees built from different genomic segments, a standard approach for detecting reassortment, the process by which co-infecting viruses exchange entire segments and can generate strains with novel combinations of surface and internal genes. Despite minor topological differences among the trees, no reassortment was detected, indicating that the Iranian viruses evolved through gradual point mutation rather than segment exchange.

The broader significance of the study lies less in any single mutation than in the demonstration of what sustained national sequencing capacity can deliver. Iran sits at a crossroads of human migration and viral traffic, and genomic data from the region fill an important gap in the global influenza surveillance network, which has historically been concentrated in North America, Europe, and East Asia. By showing that circulating strains remained closely matched to the vaccine, that epitope-level drift was measurable but not yet consequential, and that antiviral susceptibility was preserved, the study provides exactly the kind of evidence that informs vaccine strain selection committees and public health planners. The authors emphasize that continued national surveillance within global frameworks is essential for monitoring antigenic change, assessing pandemic risk, guiding vaccine updates, and detecting antiviral resistance before it becomes widespread.

For the coming seasons, the message is one of cautious continuity rather than alarm. The H1N1 viruses circulating in Iran between 2023 and 2025 drifted measurably, concentrated their changes in the most immunologically visible regions of hemagglutinin, and edged slightly further from the vaccine strain with each season, yet they remained recognizably the same clade 6B.1 A.5a.2a viruses that the current vaccine was designed to counter. The estimated epitope-based vaccine efficacy of roughly 38 to 50 percent suggests meaningful, if imperfect, protection, in line with expectations for a well-matched seasonal vaccine. As sequencing technology becomes cheaper and faster, studies of this kind are likely to become the norm rather than the exception, offering public health authorities a near-real-time view of viral evolution and a firmer scientific footing for the annual decisions that determine how well the world’s influenza vaccines match the viruses they must fight.

Subject of Research: Molecular evolution and epitope variation of influenza A(H1N1)pdm09 viruses in Iran based on whole-genome sequencing, 2023–2025

Article Title: Molecular evolution and epitope landscape of influenza A(H1N1) viruses in Iran: insights from whole-genome sequencing (2023–2025)

Article References: Ghadirali, M., Sadeghi, K., Nejati, A., Shabani, M., Zadheidar, S., Ahmadi, A. S., Abedi, A., Yavarian, J., Shafiei-Jandaghi, N. Z., & Mokhtari-Azad, T. (2026). Molecular evolution and epitope landscape of influenza A(H1N1) viruses in Iran: insights from whole-genome sequencing (2023–2025). Virology Journal. https://doi.org/10.1186/s12985-026-03331-x

Image Credits: AI Generated

DOI: 10.1186/s12985-026-03331-x

Keywords: influenza A(H1N1)pdm09, whole-genome sequencing, Oxford Nanopore Technology, antigenic drift, epitope landscape, vaccine efficacy, phylogenetic analysis, clade 6B.1 A.5a.2a, neuraminidase inhibitors, NS1 protein, influenza surveillance, Iran

The rationale for targeting mucins rests on their central role in tick biology. Mucins are heavily glycosylated proteins that, in ticks, contribute to the formation of the cement cone that anchors the mouthparts into the host skin during feeding, help modulate the host immune response at the bite site, and participate in assembling the peritrophic membrane that lines the tick gut and protects it from ingested blood and microbes. Because these functions are essential to feeding and survival, proteins involved in them are attractive vulnerabilities: antibodies circulating in the host’s blood would be ingested by the tick and could interfere with these processes from within the parasite.

Before committing to laboratory production, the team characterized Mucin-6 using bioinformatic tools. The predictions indicated a hydrophilic but intrinsically unstable protein with a molecular mass of 24.9 kilodaltons after removal of its signal peptide, the short N-terminal sequence that normally directs secretion. Importantly for vaccine design, the sequence was predicted to be rich in linear B-cell epitopes, the short stretches of amino acids that antibodies can recognize on a denatured or soluble protein. Abundant epitopes increase the likelihood that vaccination will elicit a robust and specific humoral response, which is the arm of immunity most relevant for an antigen that will be encountered by the tick through a blood meal.

To confirm that the gene is biologically relevant throughout the tick life cycle, the researchers used quantitative PCR to measure Mucin-6 expression across developmental stages and feeding states. The gene was transcribed at every stage examined, from larva to adult, with significantly higher expression in eggs. This broad and consistent expression profile matters for vaccine utility: an antigen expressed only in a narrow stage or feeding condition would leave windows in which the parasite is unprotected, whereas a constitutively expressed protein offers a target throughout the tick’s interaction with the vaccinated host.

With the sequence validated, the team moved to recombinant production. The Mucin-6 coding sequence was cloned into the pET28a expression vector and transformed into BL21(DE3) Escherichia coli, a standard laboratory strain engineered for high-level protein expression under T7 promoter control. On induction, the recombinant protein accumulated in inclusion bodies, the dense aggregates of misfolded protein that bacteria often form when expressing foreign or disulfide-rich proteins. The researchers recovered the protein from these bodies, renatured it to restore a soluble conformation, and purified it using nickel-nitrilotriacetic acid affinity chromatography, which exploits the histidine tag encoded by the pET28a vector. On SDS-PAGE, the purified recombinant Mucin-6 migrated at approximately 41 kilodaltons, larger than the predicted 24.9 kilodaltons of the mature protein, a discrepancy consistent with the tag and the anomalous electrophoretic behavior typical of mucin-like, compositionally biased proteins.

The immunization trial used six New Zealand White rabbits randomly assigned to a vaccinated group of three and a phosphate-buffered saline control group of three. Each vaccinated rabbit received 500 micrograms of recombinant Mucin-6 formulated with Freund’s adjuvant in three subcutaneous injections spaced 14 days apart. Enzyme-linked immunosorbent assays tracked the antibody response, revealing titers that reached 1:512,000 by day 35, an exceptionally high level indicating strong recognition of the recombinant antigen. Fourteen days after the final booster, the researchers challenged each rabbit with 30 adult ticks, 15 males and 15 females, and measured the parameters that define tick vaccine efficacy: engorgement weight, egg mass, blood-feeding duration and egg-hatching rate.

The results showed a consistent, statistically significant burden on the parasites. Ticks that fed on immunized rabbits had engorged body weights reduced by 13.6 percent and egg masses reduced by 14.7 percent compared with ticks fed on control rabbits, both differences significant at P less than 0.05. Blood-feeding duration was prolonged by 8.3 percent, suggesting that antibodies disrupted the efficiency of feeding, forcing ticks to remain attached longer to obtain a full blood meal. Combining the effects on tick weight and fecundity, the authors calculated an overall vaccine efficacy of 26.3 percent. While modest compared with the best commercial anti-tick formulations, this figure represents a meaningful proof of concept for a single antigen tested in its first host species.

A critical question for any recombinant antigen is whether antibodies raised against the laboratory-produced protein also recognize the native version in the parasite. The team addressed this by western blot, incubating tick lysates with serum from the immunized rabbits. The anti-rMucin-6 serum bound native Mucin-6 in tick extracts, confirming that the recombinant protein preserved epitopes present in the authentic tick protein and that the antibodies generated in the vaccinated animals could, in principle, engage their target during a natural blood meal. This cross-recognition underpins the observed phenotypic effects and strengthens the case that Mucin-6, rather than an artifact of immunization, is the operative antigen.

The study sits within a broader effort to develop anti-tick vaccines that reduce both parasite loads and pathogen transmission without the drawbacks of chemical acaricides. The only commercially available tick vaccine, based on the gut antigen Bm86 against Rhipicephalus microplus, demonstrated decades ago that vaccinating the host can starve and sterilize ticks from within, but its efficacy varies across tick species and regions, driving the search for new antigens. Secreted proteins such as mucins, which are exposed to host antibodies in the ingested blood and are functionally indispensable, form a promising class of candidates. The Hainan team’s work adds Mucin-6 to this pipeline and demonstrates a complete workflow, from epitope prediction and expression profiling through prokaryotic production and a controlled animal challenge.

Limitations remain before Mucin-6 could approach practical deployment. The trial involved a small number of animals, a single antigen and a single host species, and Freund’s adjuvant is unsuitable for veterinary or human use, so future work would need to test the antigen with licensed adjuvants, in larger cohorts, and ideally in combination with other antigens to push efficacy higher. The authors, led by corresponding author Qingfeng Guan with co-first authors Jie Chen and Yongchuan Zhu, conclude that Mucin-6 merits further evaluation as a candidate vaccine antigen against R. linnaei. Given that tick-borne diseases continue to expand their geographic range with changing climates and livestock movements, even incremental gains from antigen discovery of this kind carry substantial implications for animal health and the economics of tick control.

Subject of Research: Evaluation of the tick protein Mucin-6 from Rhipicephalus linnaei as a recombinant anti-tick vaccine antigen

Article Title: Prokaryotic expression and vaccine potential of Mucin-6 from Rhipicephalus linnaei

Article References: Chen, J., Zhu, Y., Zhao, J., Wang, J., Han, Q., & Guan, Q. (2026). Prokaryotic expression and vaccine potential of Mucin-6 from Rhipicephalus linnaei. Parasites & Vectors. https://doi.org/10.1186/s13071-026-07675-9

Image Credits: AI Generated

DOI: 10.1186/s13071-026-07675-9

Keywords: Rhipicephalus linnaei, Mucin-6, anti-tick vaccine, recombinant protein, prokaryotic expression, vaccine efficacy, tick control, humoral immunity, B-cell epitopes, Parasites & Vectors, livestock health, vector biology