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  • Cross-sectional study on protective antibodies against influenza A virus subtypes and cross-protection against influenza A(H3N2) subclade K, Portugal, August 2025
    Publication . Guiomar, Raquel; Henriques, Camila; Pereira da Silva, Susana; Gomes, Licínia; Dias, Daniela; Verdasca, Nuno; Portuguese Laboratory Network for the Diagnosis of Influenza and Respiratory Viruses; Nunes, Baltazar; Rodrigues, Ana Paula
    The 2025/26 season was marked by co-circulation of influenza A subtypes, with the first detection of A(H3N2) subclade K in September 2025. In August 2025 in Portugal, 14.8% (95% CI: 12.2-17.8) of 886 persons tested had cross-protective antibodies against this subclade. The overall seroprevalence against circulating A(H1N1)pdm09 strains was 28.1% (95% CI: 24.4-32.0). These data highlight the presence of previous cross-reactive antibodies and the possible advantage of vaccination in the extent of detectable antibodies against influenza viruses.
    2026-02Artigo científico Acesso aberto Ver mais
  • Rapid drug resistance prediction in positive clinical samples using an extensive targeted next-generation sequencing panel
    Publication . Rosendal, Ebba; Isidro, Joana; Carneiro, Sofia; Gomes, João Paulo; Macedo, Rita
    Tuberculosis (TB) remains a global health challenge, exacerbated by the emergence of drug-resistant strains. Most methods for drug susceptibility testing (DST) are culture-dependent and time consuming, possibly delaying optimal TB-treatment. This study aimed to develop an extensive targeted next-generation sequencing (tNGS) approach for rapid genotypic DST directly from clinical samples. We designed a tNGS panel comprising 30 amplicons targeting 19 genomic regions associated with resistance to 20 antibiotics. This method was applied to 71 smear-positive (0-3+) pulmonary TB clinical samples collected at the Portuguese National Reference Laboratory. DNA was extracted and amplified using multiplex PCRs, followed by sequencing on Oxford Nanopore Technologies MinION platform. Sequencing data were using TB-Profiler and the tNGS results compared to phenotypic DST and whole genome sequencing (WGS) data from corresponding isolates. The tNGS demonstrated high concordance with both phenotypic and WGS-based DST across different sample types and smear positivity levels. For first-line drugs, tNGS showed 88% categorical agreement (CA) with pDST, increasing to 97% when excluding undetermined results. Compared to WGS across all analysed antibiotics, tNGS achieved 92% CA, increasing to >99% when excluding undetermined results. Validation of the tNGS panel showed 90% (1,895/2,076) of amplicons reaching >10x coverage at all analysed positions and 43 (61%) samples with all complete amplicons above this threshold. Non-specific amplification of contaminant bacterial DNA was minimal, with most mapped off-target reads being of human origin. This method enables comprehensive resistance prediction directly from clinical samples and signifies an important development in TB diagnostics and resistance monitoring.
    2026-02-12Artigo científico Acesso aberto Ver mais