Search Results (71)

Dengue fever represents a significant public health challenge in Saudi Arabia, yet comprehensive molecular characterization of circulating serotypes remains limited. This study combines epidemiological and phylogenetic analyses to understand dengue virus (DENV) dynamics in the Kingdom. A systematic review and meta-analysis of dengue epidemiological data from Saudi Arabia (1992–2026) was the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. All available DENV envelope (E) gene sequences from Saudi human cases (1992–2023) were retrieved from GenBank and Global Initiative on Sharing All Influenza Data (GISAID). Phylogenetic trees were constructed using maximum likelihood with 1000 bootstrap replicates and best-fit models. Selection pressure was analyzed using SLAC, FEL, FUBAR, and MEME methods, while glycosylation sites were predicted with NetNGlyc and NetOGlyc. The pooled seroprevalence from 25 studies (n = 32,393) was 40.71% (95% CI: 26.96–56.10%). DENV-2 predominated (80.25%), followed by DENV-1 and DENV-3, with DENV-4 remaining rare (0.42%). Males (67–78%) and adults aged 25–44 years were most affected. Phylogenetic analysis of 50 Saudi isolates showed DENV-1 strains clustered within American–African (1994) and Asian (2004–2011) genotypes, all DENV-2 within the Cosmopolitan genotype, and all DENV-3 within Genotype III (bootstrap support 99–100%). Selection pressure analysis indicated pervasive positive selection in DENV-2, episodic selection across serotypes, and strong purifying selection in the E gene. Several amino acid substitutions with potential functional importance were identified. No DENV-4 E gene sequences from Saudi Arabia are publicly available. Dengue in western Saudi Arabia is characterized by DENV-2 predominance, co-circulation of three serotypes, and multiple introductions. The absence of DENV-4 sequences highlights critical surveillance gaps. Sustained molecular surveillance, expanded genomic sequencing, and data sharing are essential for effective prevention and vaccine preparedness. Full article

Adolescents and young people (AYP) experience a disproportionate burden of both mental health conditions and HIV, particularly in low- and middle-income countries (LMICs)-nations classified by the World Bank as having lower or middle economies. Mental health problems such as depression, anxiety, and substance use increase HIV (Human Immunodeficiency Virus that attacks the human immune system and leads to various illnesses when untreated) risk, and negatively affect treatment adherence and outcomes. However, mental health remains insufficiently integrated into HIV research and programming. Evidence on how mental health services are operationally integrated into HIV prevention and treatment for this population is limited and fragmented. This scoping review mapped existing evidence on the integration of mental health services into HIV treatment programs for AYP in LMICs, guided by PRISMA-ScR (a guideline used for reporting scoping reviews in research) and the Person–Concept–Context framework, a framework used to define specific research question in research. In this case, the population was adolescents and young people (10–24 years) receiving HIV prevention or treatment services, the concept referring to the integration of mental health interventions such as screening, assessment and counseling within HIV services, and the context focused on low- and middle-income countries (LMICs). PubMed, MEDLINE, Scopus and PsycINFO databases were searched for studies published between 2014 and 2024. Eligible studies reported mental health screening, assessment, treatment, or referral within HIV services for AYP in LMICs. Two reviewers independently screened studies, assessed full texts, and extracted data. Of 634 records identified, ten (10) studies met the inclusion criteria. All were conducted in Sub-Saharan Africa and primarily used qualitative or pilot designs. Four integration approaches were identified: routine mental health screening within HIV services, task-shifting to trained lay providers, peer-led and community-based psychosocial support, and culturally adapted, youth-centered psychological interventions. Common barriers included stigma, low mental health literacy, limited training and supervision, staffing constraints, and weak referral systems. Existing evidence is limited, remains exploratory, preliminary, and largely focused on feasibility and implementation experiences, suggesting that integrating mental health services within adolescent HIV care in LMICs may be feasible and acceptable when approaches are contextually adapted and participatory. Full article

Background: Hemagglutinin (HA) is the primary surface protein of the influenza A virus, determining its subtype and antigenic properties. Traditional subtype classification methods rely on DNA or amino acid sequence analysis, which does not account for protein spatial folding. Methods: In this work, we propose EpitopeGNN—a graph neural network (GNN) that constructs a residue interaction network (RIN) from the 3D structure of HA and classifies the virus subtype. The model was trained on 249 structures from the Protein Data Bank (PDB), containing H1N1, H3N2, H5N1, and other subtypes. Results: After rigorous sequence redundancy reduction (92% identity), the model maintained 95–100% accuracy on non-redundant data, significantly outperforming sequence-only baselines (the best baseline achieved 85% for multi-class and 92.3% for binary classification). A significant correlation was found between the obtained structural embeddings and phylogenetic distances (r = 0.38, p < 0.001), confirming their biological relevance and opening opportunities for structural monitoring of virus evolution, as well as rapid analog searching for novel strains. Conclusions: We developed a new graph neural network that classifies influenza A virus subtypes directly from the 3D structure of hemagglutinin using residue interaction networks and physicochemical features, which can serve as a foundation for predicting influenza virus receptor specificity and epitope immunogenicity. Full article

Bovine leukemia virus (BLV) is an oncogenic retrovirus and the etiological agent of enzootic bovine leukosis (EBL), which is spread worldwide. This study presents data on the genetic diversity of BLV in the Novosibirsk region of Russia. ELISA-positive samples were selected from six districts of the Novosibirsk region (Dovolnoye, Barabinsk, Tatarsk, Toguchin, Bolotnoye, and Kochenyovo districts). To assess the diversity of circulating BLV genotypes, samples were collected from settlements and districts that were geographically distant from each other and had no shared pasture lands. In total, 1410 bp fragments encoding the env gene region were obtained from 417 BLV-positive samples. Phylogenetic analysis classified 325 BLV strains (77.9%) as genotype 4 (G4) and 92 strains (22.1%) as genotype 7 (G7). A pairwise identity matrix was constructed for 268 amino acid residues. Pairwise identity of BLV amino acid sequences in the gp51 region ranged from 96.6% to 100% for G4 and from 97.4% to 100% for G7. Multiple alignment of the amino acid sequences identified 74 mutations found in the Russian BLV variants. Through the addition of 417 novel env BLV sequences to GenBank, this study significantly expands the foundational data and knowledge of BLV molecular epidemiology in Russia. Full article

Cassava brown streak disease (CBSD), caused by cassava brown streak virus (CBSV; Ipomovirus brunusmanihotis) and Ugandan cassava brown streak virus (UCBSV; Ipomovirus manihotis) (family Potyviridae, genus Ipomovirus), is increasingly becoming a threat to cassava production in several parts of Africa, especially in Eastern, Central and Southern Africa. In Kenya, the disease continues to wreak havoc on cassava production leading to a significant reduction in crop yields and economic losses of up to USD 1 billion. Variation in virus populations make the control of CBSD challenging as virus genomic variation can affect the accuracy of diagnostic tests, lead to resistance breaking isolates and jeopardize strategies of breeding for resistance. CBSV and UCBSV populations obtained from cassava fields in Kenya were characterized. In total, 44 new complete sequences of CBSV and UCBSV were assembled and 40 sequences successfully submitted to GenBank. Single Nucleotide Polymorphism (SNP) analysis revealed that the cylindrical inclusion protein (CI) is the most stable region across the genome of CBSV and UCBSV. In contrast, protein 1 (PI) and the coat protein (CP) were the most hypervariable regions. Phylogenetic analysis showed three major geographical groupings for both UCBSV and CBSV isolates, suggesting a continued spread of the viruses through human-mediated movement of infected planting materials. The data obtained in this study can support the development of disease management strategies through improved molecular diagnostic tests and targets for breeding for resistance against CBSD. Full article

Cryo-electron microscopy (cryo-EM) has revolutionized structural virology, enabling routine structure determination at 2–4 Å resolution, with exceptional cases reaching 1.56 Å. The structural diversity of viruses across vertebrate, plant, and insect hosts provides fundamental insights into infection mechanisms, host–pathogen coevolution, and therapeutic target identification. However, analysis of Electron Microscopy Data Bank entries reveals notable disparities in structural coverage: among 11,717 eukaryotic virus structures (excluding bacteriophages), vertebrate viruses constitute 97.6% (n = 11,432) of deposited entries, while plant viruses (1.0%; n = 117) and insect viruses (1.4%; n = 168) remain significantly underrepresented. This bias stems from distinct technical barriers including size limitations for giant viruses exceeding 200 nm, the loss of asymmetric information during symmetry-imposed processing, and the morphological complexity of filamentous and pleomorphic viruses. Each barrier has driven the development of specialized methodological solutions: block-based local refinement overcomes through-focus variations in giant viruses, cryo-electron tomography (cryo-ET) validates and reveals asymmetric features lost in symmetrized reconstructions, and subtomogram averaging enables structural analysis of pleomorphic assemblies. This review synthesizes recent methodological advances, critically evaluates their capacity to address specific technical barriers, and proposes strategies for expanding structural investigations across underrepresented host systems to achieve comprehensive understanding of viral structural biology. Full article

Tick-borne encephalitis virus (TBEV) causes tick-borne encephalitis (TBE), a severe disease of the human central nervous system. Currently, the data on the genetic variants of TBEV in Kyrgyzstan are practically absent. Therefore, the aim of this study was to analyze and describe the genetic diversity of TBEV in this region. The complete genome sequences of seven TBEV strains from the collection of the Scientific Centre for Family Health and Human Reproduction Problems (Irkutsk, Russia) were determined. These strains, isolated from Ixodes persulcatus ticks from Kyrgyzstan, were sequenced using the next generation sequencing approach on a MiSeq high-performance sequencer (Illumina, San Diego, CA, USA). A molecular genetic analysis of the obtained sequences, along with sequences of two previously isolated TBEV strains from Kyrgyzstan available in the GenBank database, demonstrated that the Siberian subtype of three genetic lineages (Zausaev, Vasilchenko and Bosnia) is predominantly distributed in Kyrgyzstan. The Far Eastern subtype of TBEV is also present. To date, this location probably represents the southernmost boundary of these TBEV subtypes’ ranges. Full article

Background/Objectives: Serological and molecular screening for Hepatitis B virus (HBV) has been essential in reducing the risk of transfusion-transmitted infection, particularly in regions of high endemicity. This retrospective study aimed to analyze the epidemiological profile and laboratory outcomes of 259 blood donors deemed ineligible after initial reactive or inconclusive screening for HBV markers. Methods: Donors were summoned for revaluation at the HEMOPA Foundation, in Belém, Pará, between February 2015 and July 2016. Demographic data, risk factors, and results for HBsAg, anti-HBc, anti-HBs, and HBV DNA obtained at the donation and return time points were collected. Results: The mean age was 37 ± 11.25 years, with a predominance of males (56.8%) and first-time donors (76%). At the return time point, 63.7% presented a profile indicative of resolved HBV infection and 3.5% of active infection, 6.6% were susceptible to HBV infection, and 1.9% presented vaccine-induced HBV immunity. Cases of Occult Hepatitis B Infection (OBI, 0.4%) and Window Period (WP, 0.4%) were also identified. Conclusions: The findings reveal a high prevalence of resolved HBV infection among ineligible donors, particularly first-time donors, and reinforce the importance of combined serological and molecular screening, as well as the need for vaccination and health education strategies for at-risk populations. As a public blood bank located in the Amazon region, we highlight that local epidemiological specificities must be considered in the formulation of public health policies that are sensitive to the regional context. Full article

Mouse papillomavirus (MmuPV1) is the first papillomavirus known to infect laboratory mice, making it an irreplaceable tool for research on papillomaviruses. Despite wide use, standardized techniques for conducting MmuPV1 animal research are lacking. In this report, we describe an unexpected MmuPV1 outbreak causing recurrent papillomatosis in a specific pathogen-free animal research facility. The infected mice displayed characteristic papillomatosis lesions from the muzzles, tails, and feet with histological signs including anisocytosis, epithelial dysplasia, and typical koilocytosis. Etiology studies showed that the papilloma tissues exhibited MmuPV1 infection with expression of viral early and late genes detected by RNA-ISH using MmuPV1 antisense probe to viral E6E7 region and antisense probe to viral L1 region. The viral L1 protein was detected by an anti-MmuPV1 L1 antibody. PCR amplification and cloning of the entire viral genome showed that the origin of the outbreak virus, named MmuPV1 Bethesda strain (GenBank Acc. No. PX123224), could be traced to the MmuPV1 virus previously used in studies at the same facility. Our data indicate that MmuPV1 could exist in a contaminated environment for a long period of time, and a standardized international animal protocol discussing how to handle MmuPV1 studies is urgently needed. Full article

Our knowledge of the molecular data on viruses infecting potato (Solanum tuberosum) and its weeds in Indonesia still needs to be expanded. Thirteen potato leaves, together with one carrot (Daucus carota subsp. sativus) and one Oxalis latifolia leaves grew adjacent to potato fields were sampled in West, Central, and East Java Provinces of Indonesia to be tested using RT-PCR with universal primers to monitor the presence of potyviruses, carlaviruses, and begomoviruses in the surveyed regions. According to the test results and BLAST nucleotide analysis, four potato samples were found to be infected by potato virus Y (PVY, Potyvirus). All samples tested negative for carlaviruses and begomoviruses. Both phylogenetic trees constructed by MEGA11 software based on partial coat protein and partial coat protein + 3′-UTR sequences demonstrated that the four new PVY isolates belong to strain N. Nucleotide and amino acid homology analysis determined that all four new and 12 other strain N isolates registered in NBCI GenBank were identical at the observed genome region, suggested the same origin of Indonesian isolates. This study improved our understanding of the variation in PVY isolates in Indonesia and highlighted the need for tight surveillance since the country imports most of its tubers used as planting material. Full article

Chandipura virus (CHPV) is an arthropod-borne virus linked to encephalitis in humans, primarily in India. Its evolutionary dynamics and transmission pathways remain poorly understood due to limited genomic data. This study analyzed 23 publicly available CHPV genomes, including isolates from humans, sandflies, and a hedgehog, retrieved from GenBank. Phylogenetic analyses were conducted to explore host-specific and geographic evolutionary patterns. Phylogenetic analysis revealed distinct evolutionary lineages. Human-derived genomes collected in India between 2003 and 2024 formed a well-supported monophyletic clade, suggesting a unique evolutionary lineage. In contrast, sandfly-derived genomes exhibited diverse clustering patterns. Notably, Kenyan sandfly isolates from 2016–2017 were phylogenetically closer to human-derived sequences, suggesting possible shared evolutionary pressures. These findings provide preliminary insights into CHPV evolution and emphasize the need for enhanced genomic surveillance in both human and non-human populations. Expanding genomic data is essential to validate these observations and inform public health strategies. Full article

Hepatitis B virus (HBV) is a major public health concern responsible for hepatitis and hepatocellular carcinoma (HCC) worldwide. In Mozambique, HBsAg prevalence is high and endemic, and despite the strategies to mitigate the spread of the disease, the HCC incidence is still high and one of the highest in the world. There is still limited data on the serological profile and molecular epidemiology of HBV in Mozambique given the burden of this disease. In this study, we aimed to describe the serological and molecular characterization of HBV among blood donors. We conducted a cross-sectional survey from November 2014 to October 2015 at the Blood Bank of the Hospital Central de Maputo. Serological testing and molecular testing were performed. The frequency of HBV infection was estimated at 4.4% and was higher among males (79.1%), individuals aged 25–39 years (55.2%), and replacement donors (89.6%). The median viral load of HBV-positive blood donors was 1288.5 IU/mL, and 43.8% had a viral load higher than 2000 IU/mL. Most of the sequenced samples (94.3%) belonged to subgenotype A1. These findings underscore the importance of ongoing surveillance to inform effective HBV control strategies and present evidence about the burden of HBV among blood donors, which definitely requires attention, and clinical blood banks in Mozambique and in similar settings. Full article

Madin–Darby Canine Kidney (MDCK) cells are a key cell line for influenza vaccine production, due to their high viral yield and low mutation resistance. In our laboratory, we established a tertiary cell bank (called M60) using a standard MDCK cell line imported from American Type Culture Collection (ATCC) in the USA. Due to their controversial tumourigenicity, we domesticated non-tumourigenic MDCK cells (named CL23) for influenza vaccine production via monoclonal screening in the early stage of this study, and the screened CL23 cells were characterised based on their low proliferative capacity, which had certain limitations in terms of expanding their production during cell resuscitation. It was thus our objective to enhance the proliferation efficiency of MDCK cells for influenza vaccine production following cell resuscitation, with a view to improving the production of non-tumourigenic MDCK cells for vaccines and enhancing the production of influenza virus lysate vaccines from MDCK cells through genetic intervention. We concentrated on the protein thrombosponin-1 (THBS1), which was markedly differentiated in the proteomics data of the two MDCK cells. By integrating this finding with related studies, we were able to ascertain that THBS1 exerts a significant influence on the level of cell proliferation and apoptosis. Consequently, our objective was to investigate the impact of THBS1 expression on MDCK cell apoptosis by verifying the differences in THBS1 expression between the two MDCK cells and by interfering with THBS1 expression in the MDCK cells. We found that the knockdown of THBS1 significantly increased the proliferation and apoptosis of CL23 cells without causing significant changes in cell migration and invasion, and its overexpression significantly decreased the proliferation of M60 cells and increased cell migration, invasion, and apoptosis. In addition, the TGF-β/Smad pathway target genes transforming growth factor-β1 (TGF-β1), mothers against decapentaplegic homolog 2 (Smad2), and mothers against decapentaplegic homolog 3 (Smad3), were significantly down-regulated in CL23 cells after THBS1 knockdown and up-regulated in M60 cells after overexpression, with consistent expression identified at both the mRNA and protein levels. The treatment of cells with TGF-β activators and inhibitors further demonstrated that THBS1 regulated MDCK cell proliferation and apoptosis through the TGF-β/Smad signalling pathway. Finally, we found that THBS1 also regulated H1N1 influenza virus replication. These findings enable a comprehensive understanding of the regulatory mechanisms of THBS1 regarding MDCK cell proliferation and apoptosis functions and the effects of influenza virus replication. Full article

The lack of data on the whole-genome analysis of genotype II African swine fever virus (ASFV) isolates significantly hinders our understanding of its molecular evolution, and as a result, the range of single nucleotide polymorphisms (SNPs) necessary to describe a more accurate and complete scheme of its circulation. In this regard, this study aimed to identify unique SNPs, conduct phylogenetic analysis, and determine the level of homology of isolates obtained in the period from 2019 to 2022 in the central and eastern regions of Russia. Twenty-one whole-genome sequences of genotype II ASFV isolates were assembled, analyzed, and submitted to GenBank. The isolates in eastern Russia form two clades, “Amur 2022” and “Asia”. Within the latter clade, five subclusters can be distinguished, each characterized by a unique set of SNPs and indels. The isolates from the central regions of Russia (2019; 2021) form the “Center of Russia” clade, with two subclusters, “Bryansk 2021” and “Center of Russia 2021” (bootstrap confidence index = 99). The presence of the previously unique genetic variant ASFV for the Kaliningrad region in the wild boar population of the Khabarovsk region (eastern Russia; 2021) has also been confirmed. Full article

The orange-spotted grouper (Epinephelus coioides) is an important mariculture fish in China. However, in recent years, with the rapid development of aquaculture activities, outbreaks of viral diseases have affected the grouper aquaculture industry, causing severe economic losses. In the present study, we isolated and identified a virus from diseased, orange-spotted groupers from an aquaculture farm in Hainan Province, China. The isolated virus was identified as orange-spotted grouper iridovirus, hence named the orange-spotted grouper iridovirus Hainan strain (OSGIV-HN-2018-001). OSGIV-HN-2018-001 induces a cytopathic effect after the infection of mandarin fish (Siniperca chuatsi) brain clonal passage (SBC) cells. In addition, the cytoplasm of the OSGIV-HN-2018-001-infected SBC cells was found to contain a large number of hexagonal virus particles with a diameter of approximately 134 nm. Using the Illumina NovaSeq system, we assembled the sequence data and annotated the complete genome of OSGIV-HN-2018-001 (GenBank accession number: PP974677), which consisted of 110,699 bp and contained 122 open reading frames (ORFs). Phylogenetic tree analysis showed that OSGIV-HN-2018-001 was most closely related to ISKNV-ASB-23. The cumulative mortality rate of groupers infected with OSGIV-HN-2018-001 reached 100% on day 8. The spleens were enlarged and blackened after the dissection of the dying groupers. These results contribute to the understanding of the molecular regulatory mechanism of the iridovirus infection and provide a basis for iridovirus prevention. Full article