Viruses

A multivariant total subclass analysis has been performed for a control cohort (n=15) and a long COVID patient cohort (n=15) measuring the IgG1, IgG2, IgG3, IgG4 and IgE response to the following 14 variants of SARS-CoV-2: Wuhan, Alpha, Delta, BA.1, BA.2, BA.5, EG.5.1, XBB.1.5, BA.2.75, CH.1.1, BA.2.12.1, BQ.1.1, JN.1, and KP.3. Significant differences (p < 0.05 and p < 0.005) between concentrations of IgG subclasses by variant were found in 24% of variants and in mean-normalised distributions. ...

ObjectiveWest Nile virus lineage 2 (WNV-2) is a growing public health concern in Europe causing West Nile fever or West Nile neuroinvasive disease (WNND) with substantial morbidity and mortality; however, genomic data from Southern Italy are limited despite recent expansion of autochthonous transmission. The aim of the study was to characterise the phylogenetic and molecular features of the WNV-2 strain responsible for the first autochthonous human infection reported in Calabria (2023), and two ...

The emergence of vaccine covered serotypes causing invasive pneumococcal disease (IPD) is a serious concern worldwide. We investigated the unexpected rise of serotype 4 causing IPD primarily in non-vaccinated young adults after the COVID-19 pandemic that further spread to adults [&ge;] 65 years in recent years. For this purpose, we conducted a retrospective study of serotype 4 IPD cases (n=827) reported in Spain between 2009 and 2024. Whole-genome sequencing was performed to assess clonal lineag...

Herpes simplex virus (HSV) is an endemic pathogen, infecting most adults world-wide. HSV infection can cause a wide spectrum of disease outcomes, ranging from asymptomatic infection or mild lesions to rare cases of infectious keratitis, encephalitis, and death. HSV genome sequences have been shown to differ between individual patients, as well as within individuals. To date, the vast majority of publicly available HSV genomic data has come from Europe and North America. Our current understanding...

Influenza A(H3N2) subclade K virus was detected in Canada early in the 2025/26 influenza season, bearing an antigenic transition in the hemagglutinin (HA) glycoprotein. Analysis of 396 HA sequences from Canada showed antigenic divergence from 2025/26 influenza vaccine strains, consistent with partial mismatch. Phylodynamic analysis revealed sustained pre-vaccine transmission without clear post-vaccine expansion. Phylogenetic and phylogeographic analyses indicated interprovincial mixing within a ...

Severe Acute Respiratory Infection (SARI) remains a major global health burden, yet conventional diagnostics frequently fail to identify the causative pathogens. This study aimed to comprehensively characterize the respiratory microbial landscape in adult SARI and to evaluate the clinical utility of an optimized long-read metagenomic next-generation sequencing (mNGS) workflow. A total of 101 respiratory specimens from hospitalized adults in northern Thailand (November 2023 to April 2024) were an...

In the past decade, dengue fever has emerged as a major public health on Reunion Island in the Southwest Indian Ocean. During the 2018-2022 outbreak, an unusual increase in ocular complications was reported in some patients. To investigate a potential viral cause, we analysed 447 blood samples from hospitalized patients with and without ophthalmic symptoms. Genetic sequencing revealed the co-circulation of two strains of dengue virus serotype 1, both genetically linked to strains previously iden...

IntroductionSequence-based typing (SBT) has been the standard molecular typing method for understanding Legionella pneumophila genetic relationships. However, genome-scale typing approaches, namely core-genome (cg) or whole-genome (wg) multilocus sequence typing (MLST), provide higher discriminatory power. To advance these capabilities, the Legionella International Typing (LIT) workgroup was established to develop, evaluate, and disseminate a novel cgMLST schema with enhanced wgMLST resolution f...

Shigella flexneri 2a is the most common cause of shigellosis, a major public health concern in developing countries. Rapid and reliable diagnostic tools are critical for timely outbreak detection and management. Leveraging Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) technology, we developed a CRISPR-Cas12a-based assay for the rapid and specific detection of S. flexneri 2a and validated its performance using stool specimens from patients. Two guide RNAs targeting the gtrII ...

A new H3N2 variant (named subclade K) possesses several key hemagglutinin substitutions and is circulating widely during the 2025-2026 influenza season. In this report, we completed experiments to determine if the 2025-2026 seasonal influenza vaccine elicits antibodies in humans that recognize this variant. We find that H3N2 subclade K viruses are antigenically advanced; however, the 2025-2026 seasonal influenza vaccine elicited antibodies in many individuals that efficiently recognized these vi...

Human metapneumovirus (HMPV) is a significant cause of acute respiratory illness in both children and adults, yet its genomic epidemiology remains understudied compared to other respiratory viruses. Here, we report an expanded genomic surveillance of HMPV in the United States, utilizing 325 newly sequenced samples from two cohorts: the household-based HIVE study (2010-2022) in Michigan and the multicenter IVY network (2022-2025) of hospitalized adults. Our analyses revealed the continued predomi...

BackgroundWhile antimicrobial resistance is an increasingly urgent problem, with Escherichia coli infections representing a major priority, the development of effective vaccines has proven both challenging and largely unsuccessful. Given accumulating evidence supporting the immunosuppressive role of extracellular bacterial glyceraldehyde-3-phosphate dehydrogenase (GAPDH), we aimed to characterize individual susceptibility to E. coli infections based on the presence of naturally induced antibodie...

SARS-CoV-2 mutations play a key role in viral evolution, in immune escape, and potentially in disease severity. However, the clinical impact of most mutations remains poorly understood, particularly across different variants. A historical observational study was conducted using SARS-CoV-2 whole-genome sequencing data linked to clinical metadata from 175,503 COVID-19 cases in Israel. The dataset was stratified into four variant-specific periods: B.1.1.7, B.1.617.2, BA.1, and BA.2. Logistic regres...

Clade 2.3.4.4b highly pathogenic avian influenza A(H5N1) viruses continue to expand geographically and across mammalian hosts, raising concern about pandemic potential. The degree and specificity of pre-existing immunity in humans are key determinants of this risk. We analyzed hemagglutinin (HA)-and neuraminidase (NA)-specific antibody responses in 300 sera collected from adults in New York City. While HA directed binding antibodies to clade 2.3.4.4b H5 were low and hemagglutination-inhibiting a...

Carbapenem-resistant (CR) bacteria have emerged and been spreading beyond healthcare-associated facilities into the environment. It is recognized that toilet bowl water in patient rooms of healthcare-associated facilities can be one of internal reservoirs of CR bacteria. In accordance with this idea, toilet bowl water samples were collected from patient rooms in a tertiary healthcare-associated facility in North Macedonia, and meropenem (MEM)-resistant bacterial isolates were obtained from the t...

Malaria remains a major public health concern in Cameroon, with Plasmodium falciparum responsible for most morbidity and mortality, particularly among children under five. In response to rising cases, Cameroon began implementing the RTS,S/AS01 malaria vaccine in early 2024. Given the vaccines strain-specific efficacy, understanding antigenic diversity and complexity of infection (COI) is critical for evaluating long-term impact. We analyzed 100 P. falciparum-positive dried blood spots collected ...

Strengthening in-country sequencing capacity generated 28 Lassa virus genomes from human clinical cases, expanding our knowledge of Lassa fever in Guinea. Phylogeographic analysis revealed cross-border exchange between Liberia and the NZerekore region, and a Sierra Leone introduction into the Gueckedou area. Enhanced genomic surveillance is crucial to guide future public health actions.

We evaluated the BOSCH Vivalytic MPXV assay using serial dilutions of monkeypox virus clade Ib, a new offshoot of clade I identified in 2023. The assay detected viral DNA down to [~]100 copies/mL demonstrating comparable analytical sensitivity to our in-house reference PCR and to other commercial platform-based mpox molecular assays.

BackgroundDengue virus (DENV) appears to manipulate several cellular metabolic pathways to permit its replication and immune evasion in the host. Here, we employed high-resolution mass spectrometry (HR-MS) to investigate the serum metabolomic landscape of clinical DENV infection. MethodsSerum specimens from primary dengue (n=11), secondary dengue (n=9) samples, and healthy controls (n=10) were used for untargeted and targeted metabolomic quantification on a Waters Xevo G2-XS QTof Mass Spectrome...

In November 2025, a traveler from Cuba tested positive for chikungunya virus upon arrival to Mexico. The virus belonged to the East-Central-South-African lineage, clustering with a clade prevalent in Brazil. Ten years after the last chikungunya epidemic in Mexico, strengthened surveillance is required to anticipate transmission of this emergent lineage.