Genomic insights into the impact of typhoid conjugate vaccine introduction and the COVID-19 pandemic on Salmonella Typhi and Paratyphi A in Nepal

Integrated genomic analysis of Salmonella Typhi from Pakistan: Antimicrobial resistance determinants, pangenome structure, and reverse vaccinology-driven vaccine target discovery

Genomic and Antigenic Evolution of Influenza A(H3N2) After the COVID-19 Era: A Scoping Review with Focus on J and K Subclades and Implications for Vaccine Effectiveness

A scoping review was conducted across six databases in January 2026, including studies on genomic surveillance, antigenic characterization, and vaccine effectiveness (VE), which indicated diminished VE against drifted strains, though no consistent increase in clinical severity was observed.

Strategies and lessons learned from a type 1 circulating vaccine-derived poliovirus (cVDPV) outbreak affecting adult population: Madagascar, 2020-2023.

INTRODUCTION From 2020 to 2023, Madagascar experienced an outbreak of circulating vaccine-derived poliovirus type 1 (cVDPV1) that notably affected adults and was associated with high mortality among paralytic cases. This atypical epidemiological pattern required adapted surveillance approaches and tailored outbreak response strategies, including vaccination campaigns targeting adult populations. METHODS We conducted a descriptive analysis of the cVDPV1 outbreak in Madagascar between September 2020 and September 2023. Epidemiological data on confirmed and polio-compatible cases were reviewed, including age distribution, clinical presentation, and outcomes. We also documented outbreak response strategies, particularly vaccination campaigns and operational innovations implemented to reach adult populations. RESULTS A total of 54 confirmed cases of paralytic polio caused by cVDPV1 were reported during the study period, including two adults presenting with fever and paralysis. Between February 2022 and March 2023, 15 adult acute flaccid paralysis cases were classified as polio-compatible by the National Polio Eradication Committee due to missing (86%) or negative laboratory specimens. Mortality among these compatible adult cases was 56%. In response, Madagascar conducted vaccination campaigns using bivalent oral polio vaccine, targeting the entire population in four regions and children under 15 years in the rest of the country. Critical role of country leadership, strategic mobilization, and effective communication in driving success and influencing risk perception during the 2023 campaigns helped achieve high coverage among adults. CONCLUSIONS The cVDPV1 outbreak in Madagascar demonstrated the potential for significant adult involvement and high mortality in polio outbreaks. High vaccination coverage combined with targeted innovations and strong community engagement contributed to successful outbreak control. These findings highlight the importance of inclusive vaccination strategies and tailored approaches in similar settings.

Recent developments in typhoidal and non-typhoidal Salmonella vaccines.

PURPOSE OF REVIEW Typhoidal and invasive non-typhoidal Salmonella (iNTS) serovars remain leading causes of bloodstream infection, mortality and morbidity, particularly in South Asia and sub-Saharan Africa. The rising burden of antimicrobial resistance has strengthened the case for vaccination as a control strategy. This review summarises recent advances in Salmonella vaccine development, highlighting progress, remaining challenges and future directions. RECENT FINDINGS The introduction of typhoid conjugate vaccine (TCV) programmes across some endemic countries represents a major public health milestone. Important questions remain, however. These include the durability of protection, optimal booster strategies and performance in diverse epidemiological settings. Vaccine development for S. Paratyphi A and iNTS has also accelerated, with candidates including conjugate, outer membrane vesicle/GMMA and live-attenuated, platforms advancing through preclinical and early clinical evaluation. Multivalent vaccine strategies have attracted growing interest. However, the divergent epidemiology of typhoidal and non-typhoidal disease, including differences in age-specific risk and geographic distribution, raises important questions about whether a single combination product is suitable for all settings. SUMMARY The Salmonella vaccine landscape is evolving rapidly from a focus on typhoid alone toward broader protection against multiple clinically important serovars. Although recent progress is encouraging, important scientific, regulatory, and implementation challenges remain. The practical case for integrated Salmonella vaccine strategies will depend on careful matching of vaccine composition to the differing epidemiology, age-specific risks, and delivery contexts of typhoidal and nontyphoidal disease.

Changes in the Distribution of Respiratory Pathogens After the COVID-19 Pandemic.

BACKGROUND Diverse quarantine measures against the coronavirus disease 2019 (COVID-19) pandemic have affected the distribution patterns of respiratory pathogens. This study analyzed changes in the incidence and distribution of major respiratory pathogens during the COVID-19 pandemic and after the endemic declaration. In addition, the study aimed to provide a basis for future community-centered infectious disease response strategies by identifying co-infection patterns and whether pathogens re-emerge after mitigation. METHODS In this retrospective study, the results of 105,619 respiratory pathogen tests, including FilmArray® Respiratory Panel (BioFire Diagnostics) assay (FilmArray RP), influenza tests, and COVID-19 tests, were collected at a Korean university hospital during the COVID-19 pandemic (Period I: March 2021 through April 2023) and endemic (Period II: May 2023 through February 2025). The changes in the distribution of major pathogens, age and gender characteristics, seasonality, and co-infection patterns were compared between the two periods. RESULTS The overall positivity rate for the FilmArray RP significantly increased from 64.4% in Period I to 71.1% in Period II (p < 0.001). In the age-specific analysis, age group 3 (4 months to 2 years) had the highest positivity rate in Period II (82.7%). Human rhinovirus/enterovirus was the most frequently detected pathogen, whereas respiratory syncytial virus cases increased in number, but decreased in proportion to all positive cases in Period II. The prevalence of adenoviruses and Mycoplasma pneumoniae has significantly increased since the pandemic. Human metapneumovirus has shifted its seasonality from autumn to summer and spring, whereas parainfluenza virus 3 has shifted from autumn to spring and summer. Among all positive cases, co-infections significantly increased to 17.6% and 22.3% during Periods I and II, respectively (p < 0.001). CONCLUSIONS This study revealed significant changes in the incidence, seasonality, age characteristics, and co-infection patterns of respiratory pathogens after the mitigation of COVID-19. These changes result from the re-emergence of pathogens that were suppressed during the pandemic, immune vaccination, and the resumption of social activities, suggesting the need to establish an age- and pathogen-specific surveillance system for future infec-tious disease responses.

Genomic surveillance of enterovirus D68 circulating in 2025 reveals the emergence of a novel A2/B3 recombinant lineage

ABSTRACT Enterovirus D68 (EV-D68) has re-emerged over the past decade as a significant respiratory pathogen associated with severe respiratory disease and acute flaccid myelitis. Its circulation has typically followed a biennial pattern, with predominance in late summer and early fall, a pattern that was temporarily disrupted during the COVID-19 pandemic. Surveillance in 2025 revealed off-season circulation of EV-D68. This study describes the genomic characteristics of the 2025 EV-D68 viruses and the clinical features of affected patients. Between May and December 2025, remnant respiratory specimens positive for rhinovirus/enterovirus were screened for EV-D68 and subjected to whole-genome sequencing. Phylogenetic analyses were performed using maximum-likelihood methods. Recombination was assessed using subgenomic phylogenies, SimPlot similarity and BootScan analyses, and read-level inspection. Among 1,321 patients tested, 147 (11.1%) were EV-D68-positive, and 119 (81.0%) yielded complete genomes. EV-D68 positivity increased in July 2025, peaked in August (~21%), and remained elevated through September and October, exceeding levels observed in 2024. Patients had a median age of 36 years, with infections disproportionately affecting older adults. Phylogenetic analysis demonstrated exclusive circulation of subclade A2. Five genomes formed a distinct recombinant lineage (A2-Re). Subgenomic phylogenies showed clustering with A2 viruses in the P1 region and with B3 viruses in the P2–P3 regions. SimPlot and BootScan analyses identified a recombination breakpoint near the 2A/2B junction (~nt 3,700). The recombinant lineage was associated with temporally clustered cases in September–October. These findings demonstrate recombination between distinct EV-D68 subclades and underscore the importance of whole-genome surveillance for accurate viral characterization. Continued genomic monitoring is essential for detecting emerging variants with potential implications for transmissibility, pathogenicity, and public health preparedness. IMPORTANCE This study highlights an increased off-season circulation of Enterovirus D68 (EV-D68) and a higher burden of disease in adults in 2025. The identification of a novel A2–B3 recombinant lineage provides evidence of ongoing viral evolution through recombination, a mechanism that may alter transmissibility, virulence, or immune responses. Detection of this lineage in temporally clustered cases suggests local transmission and underscores the potential for rapid spread of newly emerged variants. These findings emphasize the limitations of partial genomic approaches and the critical role of whole-genome sequencing in accurately characterizing circulating strains and identifying recombination events. Enhanced genomic surveillance is essential to detect emerging variants in real time, inform diagnostic assay performance, and support public health responses. Continued monitoring of EV-D68 evolution will be important for anticipating changes in disease burden, guiding clinical awareness, and strengthening preparedness for future outbreaks. This study highlights an increased off-season circulation of Enterovirus D68 (EV-D68) and a higher burden of disease in adults in 2025. The identification of a novel A2–B3 recombinant lineage provides evidence of ongoing viral evolution through recombination, a mechanism that may alter transmissibility, virulence, or immune responses. Detection of this lineage in temporally clustered cases suggests local transmission and underscores the potential for rapid spread of newly emerged variants. These findings emphasize the limitations of partial genomic approaches and the critical role of whole-genome sequencing in accurately characterizing circulating strains and identifying recombination events. Enhanced genomic surveillance is essential to detect emerging variants in real time, inform diagnostic assay performance, and support public health responses. Continued monitoring of EV-D68 evolution will be important for anticipating changes in disease burden, guiding clinical awareness, and strengthening preparedness for future outbreaks.