Search Results (150)

Scavenging domestic ducks significantly contribute to the transmission and maintenance of highly pathogenic H5N1 clade 2.3.4.4b avian influenza viruses in Bangladesh, a strain of growing global concern due to its broad host range, high pathogenicity, and spillover potential. This study investigates the molecular epidemiology and pathology of HPAI H5N1 viruses in unvaccinated scavenging ducks in Bangladesh, with the goal of assessing viral evolution and associated disease outcomes. Between June 2022 and March 2024, 40 scavenging duck flocks were investigated for HPAI outbreaks. Active HPAIV H5N1 infection was detected in 35% (14/40) of the flocks using RT-qPCR. Affected ducks exhibited clinical signs of incoordination, torticollis, and paralysis. Pathological examination revealed prominent meningoencephalitis, encephalopathy and encephalomalacia, along with widespread lesions in the trachea, lungs, liver, and spleen, indicative of systemic HPAIV infection. A phylogenetic analysis of full-genome sequences confirmed the continued circulation of clade 2.3.2.1a genotype G2 in these ducks. Notably, two samples of 2022 and 2023 harbored HPAIV H5N1 of clade 2.3.4.4b, showing genetic similarity to H5N1 strains circulating in Korea and Vietnam. A mutation analysis of the HA protein in clade 2.3.4.4b viruses revealed key substitutions, including T156A (loss of an N-linked glycosylation site), S141P (antigenic site A), and E193R/K (receptor-binding pocket), indicating potential antigenic drift and receptor-binding adaptation compared to clade 2.3.2.1a. The emergence of clade 2.3.4.4b with the first report of neurological and systemic lesions suggests ongoing viral evolution with increased pathogenic potential for ducks. These findings highlight the urgent need for enhanced surveillance and biosecurity to control HPAI spread in Bangladesh. Full article

Feline calicivirus (FCV) is a highly contagious pathogen widely circulating in cat populations. FCV has been shown to be able to evade the host immune response through different mechanisms. As a result, following the acute phase of infection, some cats remain persistently infected or experience reinfection cycles with variants of the same strain or with distinct field FCVs. These animals may become asymptomatic carriers, assuming a critical role in virus transmission and posing a significant risk to susceptible cats, particularly in high-density settings. Typical clinical signs of FCV infection include upper respiratory tract disease, oral ulcerations, salivation, and gingivostomatitis. In some cases, FCV infection has also been linked to a range of other clinical manifestations, including severe virulent systemic disease with high mortality rates. Indeed, FCV diversity and evolution have led to the emergence of new genetic, antigenic, and phenotypic variants, challenging disease control. This review provides a comprehensive synthesis of FCV, including its molecular biology, epidemiology, pathogenesis and clinical manifestations. Additionally, the role of vaccination and direct prophylaxis is critically evaluated. An integrated approach is essential to mitigate FCV transmission and disease burden in feline populations. Full article

Echovirus 30 (E-30), a member of the Enterovirus B species, is frequently linked to neurological illnesses such as aseptic meningitis, encephalitis, and hand, foot, and mouth disease. In this study, we present the complete-genome analysis of an Echovirus 30 strain isolated from cerebrospinal fluid (CSF) and stool samples of a pediatric encephalitis case in Kerala, India, during 2023. A comparative genomic investigation was carried out using a dataset of 111 human E-30 isolates, encompassing 116,991 mutation records. This analysis revealed six distinct non-synonymous amino acid substitutions uniquely present in the isolate PQ472410.1, which may be associated with pathogenicity and/or neurotropic behavior. To the best of our knowledge, this represents the first complete-genome sequence report of E-30 from an encephalitis case in India. These findings contribute valuable information to the understanding of E-30’s molecular epidemiology and evolution and offer vital data for enhancing surveillance and response strategies against enteroviral infections. Full article

The Apolipoprotein L1 (APOL1) innate immunity gene product represents the sole member of the APOL gene family in humans capable of secretion into circulation, thereby mediating the trypanolysis of T. brucei brucei. Gain-of-function variants of the APOL1 gene originated and spread among human population groups to extend APOL1’s protective capacity to include also serum-resistant subspecies, such as T. brucei gambiense (S342G known as APOL1-G1) and T. brucei rhodesiense (N388_Y389del known as APOL1-G2). The biochemical pathways underlying the lytic activity of these evolutionary favored mutations against bloodstream trypanosomes have been elucidated with remarkable precision. However, the intricate molecular mechanisms by which such variants confer an increased susceptibility to renal cellular injury and consequent kidney disease remain incompletely defined. In the absence of a consistent mechanistic explanation for differential kidney injury, we propose pursuing three interrelated avenues of investigation informed by prior epidemiological and mechanistic evidence linking them to APOL1’s cytotoxicity: (1) Molecular evolution of APOL1 haplotypes in human populations, (2) APOL1 splicing and consequent splice isoforms, (3) Interaction of APOL1 with other APOL gene family members, prioritizing APOL3. In the current study, we use reanalysis of population genetics datasets to resolve the haplotype contexts of all protein-altering APOL1 variants, uncovering previously unrecognized variant–haplotype couplings. We further characterize distinct cellular physiological properties among APOL1 splice isoforms, stressing the importance of isoform vB and what can be learned from isoform vC. Finally, a native interaction, and its interface, between APOL1 and APOL3 is reported, and shown to be differentially modulated by G1 and G2. We contend that continuing studies integrating these three interrelated domains will substantially advance mechanistic insights into APOL1 variant-driven renal injury, and leverage the findings to provide a more cohesive framework to guide future research. Full article

Porcine reproductive and respiratory syndrome virus (PRRSV) poses a significant economic challenge to Japan’s swine industry. This review synthesizes the epidemiological evolution of PRRSV in Japan by examining the available scientific literature from its initial Type 2 isolation in 1993 to recent events. Endemic Type 2 strains, initially dominated by Cluster III (Lineage 4), have diversified significantly. This diversification was marked by key events including the emergence of vaccine-associated Cluster II (Lineage 5) and incursions of virulent Cluster IV/Lineage 1F (MN184A-like) strains and Type 1 virus around 2008. By 2018–2020, Clusters II and IV predominated nationwide, a trend strongly linked to widespread modified live virus (MLV) vaccination. The recent detection of the globally significant NADC34-like (Lineage 1A) strain underscores ongoing foreign incursion risks. Current MLV vaccines face challenges, including safety concerns and limited cross-protection against diverse field strains. Consequently, effective control requires integrated strategies, comprising optimized vaccination, stringent biosecurity, advanced molecular surveillance, improved diagnostics, and coordinated regional control programs guided by systematic herd classification and stakeholder partnerships. The development of next-generation vaccines and sustained multi-stakeholder collaboration are critical for mitigating the impact of PRRSV in Japan. Full article

Canine circovirus (CanineCV) is an emerging virus of interest in both domestic and wild carnivores that is scarcely reported in southeastern Europe. This study examined the presence, genetic diversity, and evolutionary characteristics of CanineCV in red foxes (Vulpes vulpes) and golden jackals (Canis aureus) from northwestern Serbia, a region marked by expanding mesopredator populations overlapping with human habitats. Out of 98 sampled animals, circoviral DNA was detected in 31.6%. Jackals were mostly positive for CanineCV genotype 4, while genotype 5, associated with wild carnivores, was dominant in foxes. Mixed genotype 4/genotype 5 infections were only found in jackals. Phylogenetic and haplotype analyses indicated that most jackal-derived CanineCV strains clustered along sequences from Europe, Africa, and the Americas, while genotype 5 sequences grouped separately from other genotype representatives. A recombinant strain was identified as a divergent lineage, and several sequences showed evidence of recombination between Rep and Cap genes. Despite Cap protein amino acid differences, purifying selection dominated, suggesting functional constraints on viral evolution. The results indicate that jackals may act as recombination hotspots and bridging hosts between viral lineages. This study provides insight into the molecular epidemiology of CanineCV in the Balkans, highlighting the importance of ongoing surveillance. Full article

Infectious bronchitis virus (IBV) is a chicken pathogen present in commercial poultry farms worldwide. It is classified within the species Avian coronavirus, genus Gammacoronavirus. As with other members of the family Coronaviridae, it has a single positive-sense RNA genome with 27.6 Kb and presents viral particles with a typical crown-like aspect due to the spike (S) transmembrane glycoprotein. IBV has a remarkable capacity for genetic recombination and mutation, resulting in many genotypes and antigenic variants over evolutionary time. Currently, it is classified into nine genetic types (GI to GIX) and 41 (1 to 41) lineages disseminated worldwide. In South America, IBV was first identified in early commercial poultry production ventures in Brazil in the 1950s. Since then, this virus has been frequently detected in commercial South American poultry farms, being classified into serotypes in the first decades and genotypes more recently. IBVs of the Massachusetts (Mass) serotype were initially detected and vaccine strains of this serotype were used extensively on commercial poultry farms. Other serotypes/genotypes were identified later, with almost all of them classified in the current genetic type I (GI). In addition, five GI lineages (GI-1, -11, -13, -16, and -23) have been associated with the main infectious bronchitis outbreaks in the continent, with some variations in the occurrence according to the countries and the period of time. Molecular epidemiological surveillance of IBV genetic types and lineages is necessary to anticipate potential outbreaks, revealing patterns of viral evolution and dissemination, as well as to guide the selection of appropriate vaccine strains and immunization programs. Full article

The predominant clonal evolution (PCE) model is often misunderstood. Contrary to common belief, it is not restricted to strict mitotic clonality. Instead, it encompasses processes such as selfing, strong homogamy, and various forms of parthenogenesis, as widely acknowledged by researchers studying clonality. Moreover, the PCE model does not claim that genetic recombination is entirely absent or devoid of epidemiological and evolutionary significance. In this review, I will explore the reciprocal relationship between PCE and molecular epidemiology (strain typing) and discuss the implications of PCE for revising the subspecific nomenclature of Trypanosoma cruzi. Full article

Background/Objectives: The surveillance of viral strain evolution is needed during prophylactic HPV vaccination programs against cervical cancer and necessitates safely archiving and storing cervical samples while maintaining the long-term stability of HPV DNA to carry out molecular diagnosis. The present proof-of-concept study aimed to assess DNA stability for HPV molecular detection from veils resuspended in a universal transport medium (UTM) and conserved at different temperatures after long-term storage. Methods: The detection and quantification of HPV DNA were evaluated in female genital secretions self-collected using veils and conserved in Cyt-All^® UTM at −30 °C, +4 °C, and +25 °C after long-term 27-month storage. Results: A slight degradation of the ubiquitous single-copy cellular DNA TOP3 gene was assessed using multiplex real-time PCR (BMRT Human Papillomavirus Genotyping Real Time PCR Kit, Bioperfectus Technologies Co., Ltd., Taizhou, Jiangsu, China) at positive temperatures (+4 °C and +25 °C) but not at a frozen temperature (−30 °C) after 27 months of storage. Nevertheless, HPV DNA preservation was sufficient at the three storage temperatures to detect and quantify HPV DNA, with a similar rate of HPV detection, a similar level of cumulative HPV viral loads, high sensitivity and specificity, and perfect concordance in HPV genotype detection after the long period of 27 months of storage. Finally, the conservation of genital samples for a prolonged period in the Cyt-All^® medium, even at room temperature, allows for the detection and quantification of any HPV and HR-HPV with high accuracy. Conclusions: The combination of veil-based self-sampling of female genital secretions and their elution and conservation in UTM may be used in the field to carry out longitudinal molecular epidemiology surveys of circulating HPV. Full article

The widespread distribution and genetic diversity of porcine circovirus type 2 (PCV2) seriously threatens the swine industry worldwide. This study investigates the molecular epidemiology of PCV2 in Henan Province (2020–2023) through PCR screening (385 samples) and whole-genome sequencing (34 strains). The overall detection rate was 71.17% (274/385), with annual rates of 81.16% (112/138) in 2020, 72.41% (84/116) in 2021, 62.50% (55/88) in 2022, and 53.49% (23/43) in 2023, indicating a declining trend. Phylogenetic analysis revealed the dominance of the PCV2d genotype, comprising 82.4% (28/34) of sequenced strains. Evolutionary analysis identified strong negative selection pressure on ORF2, with an elevated substitution rate of 1.098 × 10⁻³ ssy. These findings provide critical insights into the predominance and adaptive evolution of PCV2d, and significantly improve our understanding of its genetic diversity and evolutionary dynamics. Full article

West Nile Virus (WNV), a mosquito-borne pathogen, is a growing public health challenge across Europe. Environmental and anthropogenic factors have led to the spread of the virus to higher geographic latitudes, as well as to increased viral circulation and genetic diversity. Aims: This study aimed to describe the epidemiological, clinical, and laboratory characteristics of WNV cases in Bulgaria during 2024 and to investigate WNV phylogenetics. Epidemiological, clinical and laboratory data from 32 patients with confirmed or probable WNV infections were collected and analysed. Complete viral genomes were obtained from two samples using whole genome sequencing (WGS). Phylogenetic analysis was performed using the Nextstrain WNV analysis pipeline. Severe disease was observed in 21 patients, with three fatalities reported in older males with comorbidities. Phylogenetic analysis revealed that Bulgarian strains clustered within the Central/Southern European clade of lineage 2, closely related to Greek strains. Evidence suggested localised viral evolution following cross-border introduction from Greece. Our study provides a detailed clinical and laboratory characterization of the human WNV cases detected in Bulgaria in 2024. Improved diagnostic workflows, expanded laboratory resources and increased molecular surveillance are essential to better understand the burden of WNV infections in Bulgaria, as well as to follow the evolution and spread of the virus. Full article

Having spanned thousands of kilometers from Africa through Europe, the Middle East, Central Asia through to the south eastern part of Eurasia in the recent decade, lumpy skin disease virus has now become entrenched in China, Thailand, Vietnam, and South Korea. In light of discovered findings on recombination, cluster 2.5 lineage strains are now dominant and continue to spread throughout Southeast Asia. To gain a better picture of the phylogenetic landscape in the field, whole genome sequencing of 11 LSDV isolates from Russia and Mongolia collected from 2021 to 2023 has been attempted to see the dynamics of recombination signals, as was shown for LSDV circulating in 2017–2019 in Russia and Kazakhstan. Deep sequencing performed direct from skin nodules along with data retrieved from Genbank provides the most recent update on molecular epidemiology of LSDV and demonstrates that no more mosaic variant of LSDV has been observed, and cluster 2.5 lineage is now the dominant lineage currently on the rise in the region with its own patterns of monophyletic evolution. These discoveries may help future investigations aimed at epidemiological surveillance and virus tracking in the context of currently identified lineages worldwide. Full article

Background and Objectives: Early-onset colorectal cancer (EO-CRC) has become a significant public health concern due to its alarming rise in incidence and the poor prognosis associated with this disease. The aim of our study was to identify epidemiological, clinical, and paraclinical characteristics that could explain the more aggressive evolution of EO-CRC compared to late-onset colorectal cancer (LO-CRC). Materials and Methods: We conducted a retrospective study over a two-year period, including 204 patients diagnosed with colorectal cancer (CRC). The patients were divided into two subgroups: those with EO-CRC and those with LO-CRC. Statistical analysis was performed using IBM SPSS Statistics, Version 29.0. Results: EO-CRC was identified in 11.3% of the patients included in the study. Compared to LO-CRC patients, EO-CRC patients exhibited a tendency for more distal tumor localization and a stenotic endoscopic appearance (43.5% vs. 29.3%). Regarding histopathological diagnosis, EO-CRC patients demonstrated a higher proportion of the mucinous histologic subtype (34.8% vs. 14.4%) and a significantly greater percentage of poorly differentiated tumors (39.1% vs. 14.5%; p = 0.010). Immunohistochemical results, available for a limited number of patients, revealed higher CDX2 positivity in LO-CRC patients (p = 0.012) and higher HER2 positivity in EO-CRC patients (p = 0.002). Smoking (p = 0.006) and hypertension (p = 0.002) were more prevalent in EO-CRC patients than in LO-CRC patients. Conclusions: Patients with EO-CRC exhibit distinct histopathological and molecular characteristics compared to those with LO-CRC, which may contribute to their poorer prognoses. The higher prevalence of the mucinous histological subtype, poor tumor differentiation, increased HER2 expression, and reduced CDX2 expression suggest potential molecular pathways driving the aggressive nature of EO-CRC. These findings highlight the need for tailored screening strategies and personalized therapeutic approaches in younger CRC patients. Future studies should further investigate the underlying mechanisms and potential biomarkers that could guide early diagnoses and targeted treatments. Full article

The Mpox virus (MPXV), a zoonotic pathogen from the Orthopoxvirus genus, has emerged as a significant global public health concern, especially after the unprecedented outbreak in 2022. This review synthesizes the MPXV’s molecular features, focusing on its genomic structure, replication mechanisms, immune evasion strategies, and implications for diagnostics and therapeutics. The study examines the virus’s genomic organization utilizing recent peer-reviewed literature, highlighting essential genes like OPG027 and D1L, which contribute to host adaptation, increased transmissibility, and immune evasion. Advances in molecular diagnostics, including real-time PCR and genome sequencing, are reviewed, emphasizing their critical role in outbreak monitoring and control. However, challenges persist, such as diagnostic limitations in resource-constrained settings and the lack of targeted vaccines and antivirals. This review discusses new antiviral candidates, confirmed through computational and in vitro techniques, identifying thymidine kinase and VP39 as key therapeutic targets. Emphasizing the need for genomic surveillance to track adaptive evolution, results show that particular mutations, such as in the OPG027 and D1L genes, increase the transmissibility and immune evasion of the MPXV. These molecular revelations highlight the urgent necessity for better diagnostics catered towards addressing present constraints and developing focused treatments that reduce the effect of the virus. This study emphasizes how these results underscore the need for combined public health plans to handle the changing MPXV epidemiology properly. Full article

Porcine reproductive and respiratory syndrome virus (PRRSV), an important pathogen affecting the pig industry, is an RNA virus with high genetic diversity. In this study, 12,299 clinical samples were collected from northern China during 2021–2023 to investigate the molecular epidemiological characteristics and genetic evolution of PRRSV. All samples were screened using qRT-PCR and further analyzed through ORF5 gene and whole-genome sequencing. The results showed that the positive rate of PRRSV in northern China was 18.42%, and positivity rates were relatively high in spring. The phylogenetic analysis of the ORF5 gene indicated that the 174 gene sequences were classified as PRRSV-2, predominantly found in Lineage 1.8 (L1.8), Lineage 1.5 (L1.5), and Lineage 8 (L8). L1.8 and L1.5 showed considerable polymorphism at decoy and neutralizing epitopes. Mutations of specific amino acids were present in L1.8 and L1.5 at T- and B-cell epitopes. Moreover, the 27 whole-genome sequences were analyzed. As indicated, 24 of them were exposed to gene recombination, and L1.8 provided the backbone for recombination events. The predominant recombination modes were L1.8 + L8.7 + L1.5/L3, with L1.5 and L3.5 generally yielding GP2~GP6 structural proteins. Recombination hotspots were primarily located within the ranges of 780~2200 (Nsp1~Nsp2), 5400~6200 (Nsp3~Nsp4), 7800~9000 (Nsp9), and 12,200~14,800 (ORF2~ORF6). This study enriches the epidemiological data of PRRSV in northern China, thereby providing theoretical references for the prevention and control of PRRSV in northern China. Full article