Search Results (78)

Determining HIV-1 tropism provides the prognosis of HIV infection and is required before prescribing maraviroc, an entry inhibitor that blocks the interaction between the viral gp120 and the CCR5 coreceptor. However, existing prediction algorithms have been developed primarily for the globally most prevalent subtypes (B, C, and CRF01_AE) and often show reduced performance for other HIV-1 genetic variants. Sub-subtype A6 and circulating recombinant form CRF63_02A6 dominate the HIV-1 epidemic in Russia and other Former Soviet Union (FSU) countries, yet the reliability of tropism prediction for these viruses remains virtually unexplored. We phenotypically determined the tropism of 25 clinical isolates (11 R5, 1 X4, and 7 dual-tropic R5/X4) using U87.CD4.CCR5 and U87.CD4.CXCR4 cell lines and performed a comparative analysis of eight existing genotypic tools (Geno2pheno, WebPSSM, T-CUP 2.0, the Delobel/Garrido rules, and others) or their modifications on a combined dataset that included Los Alamos National Laboratory (LANL) reference sequences (subtypes A, B, C, CRF01_AE, and CRF02_AG) and our laboratory-derived isolates. Most models achieved high accuracy for globally prevalent subtypes (≈95% for B, C, and CRF01_AE) but showed markedly reduced performance for sub-subtype A6 (best accuracy among existing models, 85%) and CRF63_02A6 (best accuracy, 72%), with a poor balance between sensitivity and specificity. To address this problem, we developed HIV-V3Augur, an ensemble stacking model based on the Random Forest and Support Vector Machine (SVM) machine learning algorithms, trained on Pseudo Amino Acid Composition (PseAAC) and Relative Synonymous Codon Usage (RSCU) features with 10-fold stratified cross-validation. HIV-V3Augur achieved an accuracy of 77%, sensitivity of 79%, and specificity of 79% on sub-subtype A6, and on CRF63_02A6 it reached an accuracy of 95%, sensitivity of 87%, and specificity of 100%. Cross-validation demonstrated that HIV-V3Augur represents a balanced genotypic tropism prediction tool for understudied HIV-1 variants circulating in the FSU region. HIV-V3Augur can be used locally through a graphical user interface. Full article

Schistosomiasis remains a major public health concern in Nigeria. We molecularly characterized Schistosoma eggs obtained from human urine to identify species and assess the presence of hybrid schistosomes in Abuja, Nigeria. Urine samples were collected from 1887 participants aged five years and above. Samples were examined for Schistosoma eggs using light microscopy. A total of 507 (26.9%) were positive for any form of Schistosoma while 91 (4.8%) had atypical Schistosoma eggs. DNA extracted from pooled ova was analyzed using metagenomic sequencing, read mapping, phylogenetic analysis, and BLASTn confirmation. Molecular analyses identified genetic signatures associated with both S. haematobium and S. bovis within pooled human urine samples, indicating the co-circulation of multiple schistosome species in the study area. Phylogenetic analyses based on trans-ITS and mitochondrial COX1 markers supported the presence of distinct nuclear and mitochondrial schistosome lineages. However, because sequencing was performed on pooled egg samples, the findings cannot distinguish between true recombinants and mixed infections involving co-circulating parental species. These findings highlight the potential complexity of schistosome transmission dynamics in endemic communities and underscore the need for enhanced molecular surveillance, especially single-parasite genomic approaches, and integrated One Health investigations to better understand schistosome transmission and its implications for control and elimination efforts in Nigeria. Full article

Human immunodeficiency virus type 1 exhibits extensive genetic diversity, which has important implications for molecular epidemiology, recombinant-pattern assessment, and antiretroviral resistance surveillance. In Mexico, HIV-1 molecular surveillance has historically relied mainly on partial pol gene sequencing, limiting the ability to compare lineage assignments across gag, pol, and env regions. We analyzed plasma samples from 40 treatment-naïve adults receiving care at a tertiary-care hospital in Mexico using a commercial amplicon-based multiregion HIV-1 genomic sequencing workflow. DeepChek^® was used as the primary workflow for read processing, mutation calling, region-level subtype assignment, and antiretroviral resistance interpretation. Resistance interpretation was restricted to antiretroviral target regions with sufficient coverage, mainly reverse transcriptase, protease, integrase, and capsid, when available. Drug resistance mutations were identified in 6/40 participants (15.0%) when mutation-level resistance findings in RT, PR, and IN were considered; one additional sample showed a capsid inhibitor-nonsusceptible NGS call. NNRTI-associated findings were identified in 2/40 patients (5.0%), whereas NRTI- and PI-associated findings were identified in 1/40 patients (2.5%). Accessory or secondary INSTI-associated substitutions were detected in 2/40 patients (5.0%). Region-level subtype analysis revealed frequent discordant assignments across amplified segments, which is consistent with complex mosaic profiles; however, these findings are interpreted as region-level subtypes and recombinant-pattern assignments rather than continuous whole-genome recombination maps. One sample had insufficient RT/PROT/INT coverage for drug resistance interpretation in the complete DeepChek report and was retained only for regions meeting quality thresholds. These findings support the value of multiregion HIV-1 sequencing for local molecular surveillance while emphasizing the need for transparent region-level coverage reporting, cautious interpretation of recombinant-pattern calls, and transparent repository reporting. Full article

The re-emergence of Coxsackievirus A6 (CV-A6) as a predominant pathogen in hand, foot, and mouth disease (HFMD) underscores the need for ongoing molecular surveillance to clarify local evolutionary dynamics. This study aimed to characterize the genetic features of CV-A6 strains circulating in Baotou, Inner Mongolia, from 2023 to 2024. Throat swabs collected from HFMD patients were screened using real-time quantitative PCR; the VP1 region and complete genomes of representative CV-A6-positive samples were amplified and sequenced. Phylogenetic and recombination analyses were subsequently performed. Among 266 clinical specimens, 169 (63.53%) tested positive for enterovirus, of which 146 (86.39%) were identified as CV-A6. The local epidemic displayed an autumn–winter seasonality and predominantly affected children aged 4–6 years. Phylogenetic reconstruction of 133 VP1 sequences revealed that all Baotou CV-A6 isolates belonged to subgenotype D3c, and analysis of complete genomes identified a predominant recombinant form. These findings demonstrate that the D3c subgenotype, characterized by a specific recombinant structure, was responsible for HFMD outbreaks in Baotou during the study period, providing essential molecular evidence for regional public health strategies and vaccine development. Full article

Human Immunodeficiency Virus Type 1 (HIV-1), the causative agent of the acquired immune deficiency syndrome (AIDS), originated from zoonotic transmissions of simian immunodeficiency viruses (SIVs) infecting African great apes, following complex cross-species transmission events and virus–host co-evolution. These processes were accompanied by multiple viral adaptations, particularly within structural and accessory genes, enabling evasion of host restriction factors and long-term viral persistence. In 1988, an antisense open reading frame (ORF) overlapping the env gene was proposed and subsequently confirmed by the identification of antisense transcripts and the antisense protein (ASP). An “intact” ASP ORF (defined as >150 codons) is predominantly conserved in pandemic HIV-1 group M viruses and shows evidence of positive selection, suggesting a selective advantage. Increasing evidence supports the hypothesis that the asp gene emerged de novo during the evolution of group M and contributed to viral adaptation and global spread in humans. This review combines a narrative review of the literature with original in silico analyses of HIV-1 and SIV sequences retrieved from the Los Alamos National Laboratory database. We systematically reassessed the distribution, length variability and conservation of the ASP ORF across HIV-1 groups (M, N, O, P), subtypes, circulating recombinant forms (CRFs), unique recombinant forms (URFs) and related SIV lineages. Our updated analyses confirmed the strong association between the presence of an “intact” ASP ORF and pandemic HIV-1 group M lineages, while revealing rare but notable antisense ORFs in selected SIVcpz and SIVgor strains. By integrating evolutionary, epidemiological and sequence-based evidence, we aim to clarify the origin and maintenance of the ASP ORF and to contextualize its emergence within the broader framework of overlapping gene evolution, de novo gene birth and the selective pressures shaping viral fitness and pandemic potential. Full article

Background: Proprotein convertase subtilisin/kexin type 9 (PCSK9) promotes low-density lipoprotein receptor degradation and thereby regulates plasma LDL cholesterol levels. Although PCSK9 is primarily produced by the liver, it has been detected in platelets; however, the origin and functional relevance of platelet-associated PCSK9 remain unclear. Methods: Washed platelets (WPs) were isolated from normolipidemic subjects. Endogenous platelet PCSK9 content was quantified by ELISA, and PCSK9 molecular forms were assessed by immunoblotting. The WPs were incubated with recombinant PCSK9 (recPCSK9), and platelet aggregation in response to arachidonic acid (AA) or thrombin (Thr) was evaluated. The effects of LDL- or HDL-bound PCSK9 on platelet aggregation were also examined. Results: Platelets from normolipidemic subjects contained measurable amounts of PCSK9 (0.84 ± 0.27 ng/mg protein), which increased to 2.91 ± 0.53 ng/mg protein following incubation with recPCSK9. Exposure to recPCSK9 significantly enhanced AA- and Thr-induced platelet aggregation. In contrast, LDL and HDL inhibited platelet aggregation independently of their PCSK9 content. Conclusions: Human platelets contain endogenous PCSK9 and can accumulate additional PCSK9 from the extracellular environment. Exogenous PCSK9 enhances platelet aggregation, supporting a potential prothrombotic role for circulating PCSK9 even in normolipidemic individuals. These findings provide new insight into the complex interplay between PCSK9, lipoproteins, and platelet function. Full article

HIV-1 diversified for decades within the Democratic Republic of the Congo (DRC) before spreading globally in the early 1980s. Thus, the DRC is home to some of the most ancestral and diverse HIV-1 strains. Recent serosurveys conducted from 2017 to 2019 in Kinshasa, DRC, indicated high prevalence of HIV-1, yet sequence data is lacking from this period. Given the history of circulating rare HIV-1 subtypes in the DRC, a viral whole-genome sequencing study was conducted to determine current diversity in the greater Kinshasa area. Next-generation sequencing (NGS) through metagenomic and target enrichment methods was conducted on 197 specimens collected from 2017 to 2019. A large array of HIV subtypes (A, B, C, D, F1, G, H, J, and K), circulating recombinant forms (CRF01_AE, CRF02_AG, CRF05_DF, CRF11_cpx, CRF13_cpx, CRF25_cpx, CRF 45_cpx, and CRF92_C2U), unique recombinant forms, and unclassifiable sequences were observed, with many branching in basal positions within, or outside of, many subtypes on phylogenetic trees. Incorporating these new sequences into Bayesian inference of phylogeny pushes back the dates of the most recent common ancestors of HIV-1 group M and the rare subtypes G, H, and J by between 3 and 7 years each. The DRC continues to harbor diverse and rare HIV-1 subtypes that could challenge diagnostic tests, treatments, and vaccines. In addition to shifting subtype emergence dates, the sequences from our study are evidence that rare strains continue to circulate and should be regularly monitored. Full article

Arthritis in K/BxN mice is provoked by pathogenic autoantibodies to glucose-6-phosphate isomerase (G6PI), which is a ubiquitously expressed enzyme that is present in cells, in the circulation and on articular cartilage. When G6PI autoantibodies (auto-Abs) deposit on the articular cartilage of K/BxN mice, arthritis ensues due to the activation of various components of the innate immune system. Recent studies have investigated the in vivo efficacy of recombinant fragment-crystallizable (Fc) protein-based therapeutics. Many recombinant Fc proteins evaluated provide protection against inflammation in mouse models of arthritis, such as the K/BxN serum-transfer model. More recently, rFc-µTP-L309C, a recombinant human IgG1-Fc with an additional point mutation at position L309C fused to the human IgM tailpiece to form a hexamer, has been shown to ameliorate the arthritis in K/BxN mice. Additional studies have shown that rFc-µTP-L309C has multiple effects that work together to ameliorate the arthritis, including inhibition of neutrophil migration into the joint, inhibition of IL-1β production, downregulation of Th1 and Th17 cells, and increases in T regulatory cells and synovial fluid IL-10. In this work, rFc-µTP-L309C was shown to effectively prevent arthritis in the K/BxN serum-transfer model, significantly downregulate inflammatory cytokines/chemokines, and ameliorate the arthritis in the endogenous K/BxN model. This amelioration of the arthritis was associated with a significant decrease in autoantibody levels, which was independent of the neonatal Fc receptor (FcRn). rFc-µTP-L309C was shown to specifically inhibit G6PI autoantibody secretion from B-cells with a concomitant increase in TGFβ and decrease in B-cell activating factor (BAFF). These new findings suggest that rFc-µTP-L309C may provide a therapeutic benefit for other antibody-mediated autoimmune diseases through its effects on B-cells. Full article

Circulating recombinant forms (CRFs) are important components of the HIV-1 pandemic. Previous studies have reported the propagation of diverse HIV-1 CRFs of South American origin in Europe. Here, through protease-reverse transcriptase (Pr-RT) and integrase sequence analyses, we identify a Spanish cluster (BC3) branching with a Brazilian virus (10BR_RJ009) previously classified as CRF146_BC. In Pr-RT, BC3 comprised 14 viruses and was nested within a larger cluster, comprising 22 Brazilian viruses and 1 Spanish virus branching outside of BC3. Near full-length genome analyses of five BC3 viruses revealed mosaic structures identical to 10BR_RJ009, with two breakpoints delimiting a ~0.3 kb subtype B fragment within an otherwise subtype C genome. Two other Brazilian viruses previously classified as CRF146_BC (10BR_RJ039 and 01_BR_RGS69) had one and two additional short subtype B fragments, respectively, and failed to group with the 10BR_RJ009/BC3 cluster in subtype C fragments. Based on these results, we contend that 10BR_RJ009 and BC3 viruses, but not 10BR_RJ039 and 01_BR_RGS69, should be classified as CRF146_BC. Bayesian analyses estimated the CRF146_BC emergence in Brazil to be around 1999 and its introduction in Europe around 2011. CRF146_BC is the 10th CRF of South American origin reported to circulate in Europe, reflecting the relationship between South American and European HIV-1 epidemics. Full article

The extensive genetic diversity of HIV-1, also represented by the circulation of multiple subtypes and circulating recombinant forms (CRFs), poses significant challenges for accurate subtype classification, especially when sequencing is limited to partial genomic regions. This study evaluated the performance of four commonly used automated subtyping tools (Stanford HIVdb, COMET, REGA, and Geno2pheno) by comparing their outputs with molecular phylogenetic analysis (Mphy), considered the gold standard, using three NGS-derived sequence data sets: protease-reverse transcriptase (PR-RT), pol, and near full-length (NFL). One hundred plasma samples were processed to generate sequences of increasing length, which were analyzed to assess concordance, sensitivity, and specificity. NFL-based Mphy identified a higher proportion of circulating recombinant forms (51.6%) than PR-RT and pol (44.1%) and enabled the reclassification of 13 samples as more complex CRFs. Automated tools displayed good concordance with Mphy for PR-RT and pol, particularly for pure subtypes, whereas concordance decreased considerably for NFL sequences, especially among non-B subtypes and CRFs. Sensitivity varied substantially across tools and subtypes, while specificity remained consistently high. Overall, the findings indicate that whole genome or NFL sequencing enhances the detection of CRFs and that the accuracy of automated tools is strongly influenced by the completeness and updating of their reference databases. Full article

Severe fever with thrombocytopenia syndrome (SFTS), caused by SFTS virus (SFTSV), is an emerging tick-borne disease in East Asia. SFTS monitoring has been carried out since 2010 in mainland China, but no confirmed human cases or infected vectors had been reported from the northern regions of Hebei Province. We intensified surveillance in this area by collecting serum samples from patients with fever of unknown origin (FUO) and ticks from local habitats. Subsequently, all collected samples were screened for SFTSV by qRT-PCR. SFTSV RNA was detected in two patient sera from Chengde (2.2%). In six, positive ticks were detected among the Haemaphysalis verticalis (8.6%) collected from Zhangjiakou; no positive ticks were detected among the ticks collected from Chengde. Complete viral genomes were recovered from positive tick samples via next-generation sequencing and subjected to a suite of bioinformatic analyses. Two complete genomes from Haemaphysalis verticalis formed a distinct clade with an Inner Mongolia strain across L/M/S (bootstrap = 1.0) and separate from genotypes A–F; pairwise p-distances to genotypes A–F were >0.11 across L/M/S, supporting designation of a distinct genotype. We designate this lineage as genotype G; no credible recombination was detected. Based on the L segment, molecular-clock analyses dated the genotype G lineage to the late 13th century, predating the crown age of genotypes A–F (~18th century) by more than 400 years. We provide the first evidence of SFTSV circulation in northern Hebei and identify a novel, deeply divergent lineage. This finding confirms the co-circulation of distinct viral lineages (G and F) within the province and provides critical new insights into the virus’s diversity and evolutionary history. These results expand the known range and genetic diversity of SFTSV, underscoring the need for enhanced surveillance and ecological investigation in emerging regions. It is necessary to strengthen public health education, improve the early diagnosis and treatment ability of medical workers, and provide a scientific basis for targeted public health interventions. Full article

Human immunodeficiency virus (HIV), comprising two distinct types, HIV-1 and HIV-2, remains one of the most significant global health challenges, originating from multiple cross-species transmissions of simian immunodeficiency viruses (SIVs) in the early 20th century. This review traces the evolutionary trajectory of HIV from zoonotic spillover to its establishment as a global pandemic. HIV-1, the principal strain responsible for AIDS, emerged from SIVcpz in Central African chimpanzees, with phylogenetic evidence indicating initial human transmission between the 1920s and 1940s in present day Democratic Republic of Congo. The virus disseminated through colonial trade networks, reaching the Caribbean by the 1960s before establishing endemic transmission in North America and Europe. HIV’s extraordinary genetic diversity—driven by high mutation rates (~10⁻⁵ mutations per base per replication cycle) and frequent recombination events—has generated multiple groups, subtypes, and circulating recombinant forms (CRFs) with distinct epidemiological patterns. HIV-1 Group M, comprising subtypes A through L, accounts for over 95% of global infections, with subtype C predominating in sub-Saharan Africa and Asia, while subtype B dominates in Western Europe and North America. The extensive genetic heterogeneity of HIV significantly impacts diagnostic accuracy, antiretroviral therapy efficacy, and vaccine development, as subtypes exhibit differential biological properties, transmission efficiencies, and drug resistance profiles. Contemporary advances, including next-generation sequencing (NGS) for surveillance, broadly neutralizing antibodies for cross-subtype prevention and therapy, and long-acting antiretroviral formulations to improve adherence, have transformed HIV management and prevention strategies. NGS enables near real-time surveillance of drug resistance mutations and inference of transmission networks where it is available, although access and routine application remain uneven across regions. Broadly neutralizing antibodies demonstrate cross-subtype efficacy, while long-acting formulations have the potential to improve treatment adherence. This review synthesizes recent evidence and offers actionable recommendations to optimize clinical and public health responses—including the routine use of genotypic resistance testing where feasible, targeted use of phylogenetic analysis for outbreak investigation, and the development of region-specific diagnostic and treatment algorithms informed by local subtype prevalence. While the understanding of HIV’s evolutionary dynamics has substantially improved and remains essential, translating this knowledge into universally implemented intervention strategies remains a key challenge for achieving the UNAIDS 95-95-95 targets and the goal of ending AIDS as a public health threat by 2030. Full article

Human noroviruses (HuNoVs) stand as the primary cause of acute viral gastroenteritis outbreaks worldwide, particularly impacting children under the age of five. In Russia, reports of norovirus gastroenteritis have surged, especially in the post-COVID-19 era starting in 2022, with elevated infection rates reported into 2024. These viruses exhibit significant mutational variability, leading to the emergence of recombinant strains that can evade immune responses. A comprehensive examination of the complete genome is crucial for understanding the evolution of norovirus genes and for predicting potential outbreaks. This research focuses on analyzing the genotypic composition of HuNoVs circulating in the Sverdlovsk region during 2024, using Sanger sequencing and next-generation sequencing (NGS). Biological samples were collected (n = 384) from patients diagnosed with norovirus infection within the region. Bioinformatics analysis targeted the nucleotide sequences of the ORF1/ORF2 fragment and the assembly of complete genomes for the GII.4 and GII.7 genotypes. In total, 220 HuNoVs were characterized, representing 57.3% of the collected samples. The main capsid variants forming the predominant genotypic profile included GII.4 (n = 88, 40%), GII.7 (n = 86, 39%), and GII.17 (n = 14, 6%). Using NGS, we successfully assembled 8 out of 10 complete genomes for noroviruses GII.4[P16] and GII.7[P7]. Non-synonymous substitutions appeared at amino acid sites corresponding to the subdomains of VP1 in these strains. This molecular–genetic analysis provides contemporary insights into the genotypic composition, circulation patterns, and evolutionary dynamics associated with the dominant genovariants GII.4[P16] and GII.7[P7]. Full article

Studies of HIV-1 molecular epidemiology describe significant differences in HIV infection spread across geographical areas. We examined 80 HIV-1 samples from the Jewish Autonomous Region of Russia in 2024. HIV-1 genome sequences for 12 samples revealed a novel HIV-1 called CRF173_63A6. HIV-1 CRF173_63A6 was found to have arisen through recombination between a specific Russian A6 subtype and the recombinant virus CRF63_02A6, which is responsible for the PWID-associated HIV outbreak in the Siberian region of Russia. Phylogenetic analysis of pol sequences previously deposited in Genbank showed that the CRF173_63A6 samples we described are grouped into a common phylogenetic cluster that includes 54 HIV-1 samples isolated in the JAR and other areas of the Russian Far East, indicating a wide distribution of this virus genovariant. This study once again proves the significant contribution of the key PWID group not only to the development of local Russian HIV epidemics, but also to the change in the characteristics of the circulating virus population. Full article

Background: The advent and continuous improvement in antiretroviral therapy (ART) have profoundly altered the clinical course of HIV infection, shifting the focus from AIDS-related complications to the management of age-related comorbidities and non-AIDS-related hospitalizations. In this evolving context, optimizing ART is essential, with genotypic resistance testing (GRT), particularly through next-generation sequencing (NGS), playing a pivotal role. Methods: This multicenter, retrospective cross-sectional study investigated HIV-1 subtypes, resistance mutations, and drug resistance profiles among 367 people living with HIV (PLWH) in Sicily, based on 384 GRTs performed at the Microbiology Laboratory of the University Hospital of Palermo. Results: Subtype B was the most prevalent (50%), followed by circulating recombinant forms (30%). Among treatment-naïve individuals, resistance-associated mutations were infrequent, with prevalence rates of 0.4% for NRTIs, 5.5% for NNRTIs, 1.3% for PIs, and 0.8% for INIs. Conversely, treatment-experienced individuals showed significantly higher resistance rates, especially to NRTIs (16.3%), NNRTIs (10.6%), and INIs (9.6%). No significant differences in resistance patterns were observed between B and non-B subtypes. Conclusions: This study provides the first regional overview of HIV drug resistance across Sicily. Despite the detection of resistance-associated mutations, the overall prevalence of clinically relevant resistance, particularly to currently recommended therapies, remains low, especially among treatment-naïve individuals. Full article