Virology Journal最新文献

{"title":"Full genome sequencing, evolutionary dynamics, and pathogenicity evaluation of chicken infectious anemia virus with emphasis on Upper Egypt reveals genetic variability linked to vaccinal strains.","authors":"Eman Abd Elmenum Shosha, Ibrahim Eldaghayes, Ali Mahmoud Zanaty, Mohammed A Gamaleldin, Mervat Masoud Mohamed, A N Gamal Maha, Doha Abd Alrahman Ahmed","doi":"10.1186/s12985-026-03257-4","DOIUrl":"10.1186/s12985-026-03257-4","url":null,"abstract":"<p><p>Despite intensive vaccination efforts, Chicken Infectious Anemia Virus (CIAV) remains a formidable threat to the Egyptian poultry industry, primarily through the emergence of vaccine-escape variants. While most studies have focused on Northern Egypt, there is a critical knowledge gap regarding the viral landscape in the Southern provinces. This study provides the most extensive surveillance to date, spanning 10 diverse Egyptian governorates with a strategic focus on Upper Egypt (2024-2025). Out of 400 collected samples, TaqMan-based qPCR revealed a high prevalence of 30% (120/400). Five representative isolates were selected for whole-genome sequencing and molecular characterization. The isolates were classified as Genotype II by phylogenetic analysis, showing a notable genetic divergence (85-87% amino acid similarity) from traditional Genotype I vaccine strains. Notably, comprehensive recombination analysis identified isolate PX96998 as a mosaic variant, with breakpoints indicating intra-genotypic recombination between closely related genotype II lineages, highlighting complex evolutionary dynamics in the field. Furthermore, 3D homology modeling of the VP1 protein identified critical structural alterations in functional loop regions, potentially hindering the binding affinity of neutralizing antibodies and facilitating immune evasion. In an experimental setting, the genotype II isolate demonstrated hypervirulence in SPF chickens, causing severe development retardation and extensive atrophy of lymphoid organs (p < 0.0001). Pathognomonic pale, fatty bone marrow with a sharp drop in PCV% to 18 ± 0.58% indicated severe aplastic anemia. By the fifth week after infection, there was a complete humoral collapse with undetectable ELISA titers due to the huge systemic replication revealed by viral load measurement, which peaked in the thymus (9.50 ± 0.25 log₁₀) and bone marrow (9.00 ± 0.22 log₁₀). These results were supported by histopathology, which revealed intranuclear inclusion bodies and systemic lymphocyte depletion. These findings support the highly pathogenic genotype II CIAV's dominance and aggressive evolution in Egypt. The emergence of recombinant variants with altered structural epitopes underscores the urgent need to replace outdated vaccination plans with genotype-matched immunogens in order to lessen the severe consequences on Egypt's poultry industry.</p>","PeriodicalId":23616,"journal":{"name":"Virology Journal","volume":"23 1","pages":""},"PeriodicalIF":4.0,"publicationDate":"2026-07-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13401295/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148585418","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A dried blood spot protocol for high-throughput semi-quantitative analysis of Epstein-Barr Virus VCA IgG and EBNA IgG serologies based on the Roche Elecsys system.","authors":"Raquel Rubio-Acero, Christina Reinkemeyer, Mona Niethammer, Melina Hufnagl, Kalina Kazandzhieva, Irene Charlotte Schoof, Simon Winter, Alberto Beyersdorff Filho, Jessica Hintze, Thomas Seeholzer, Jana-Kristin Heise, Stefanie Castell, Thomas P H Meyer, Mirjam Schunk, Michael Hoelscher, Noemi Castelletti, Andreas Wieser","doi":"10.1186/s12985-026-03219-w","DOIUrl":"10.1186/s12985-026-03219-w","url":null,"abstract":"<p><strong>Background: </strong>Epstein-Barr virus (EBV) is highly prevalent worldwide and has been linked to different cancers and autoimmune disorders, including Multiple sclerosis (MS). Primary infection typically occurs during early childhood or adolescence and often goes undetected. Serological studies allow the detection of EBV-specific antibodies after infection, but venous blood collection is resource-intense and thus limits sample size. To overcome these challenges, we developed a high-throughput, semi-automated serology protocol targeting antibodies against EBV in capillary blood samples (Dried Blood Spots, DBS).</p><p><strong>Methods: </strong>Paired serum and DBS samples were obtained from 417 participants aged 18-25 years. We used Roche Elecsys^® EBV nuclear antigen-1 EBNA IgG and Elecsys^® EBV viral capsid antigen VCA IgG assays, established for serum, to detect antibodies against EBV anti-EBNA‑1 IgG and anti-VCA IgG in DBS. Cut-off Indices (COI) for the DBS assays were determined using a classification tree.</p><p><strong>Results: </strong>Of the 416 valid paired serum samples, 78.6% (327/416) were anti-VCA-positive and 76.4% (318/416) anti-EBNA-positive. Discrepant results were observed in 3.6% (15/416) of participants. Based on combined assay results, 20.7% (86/416) of the samples were classified as EBV-negative. The serum COI values revealed that most of the negative cases clustered well below the cutoff, while positive cases spanned a broad range of higher values. Overall, 98.8% (326/330) of participants classified as positive based on serum testing (n = 330) were also classified as positive in DBS (n = 326), corresponding to the sensitivity of DBS relative to serum results. Likewise, 96.5% (83/86) of participants classified as serum-negative participants (n = 86) were also negative in DBS (n = 83), corresponding to the specificity of DBS relative to serum results. Among the 416 participants, only 4/330 (1.2%) were false negatives and 3/86 (3.5%) were false positives in DBS. The newly established assays were validated in a self-sampling cohort of 295 participants.</p><p><strong>Conclusion: </strong>We established DBS-specific cutoff values to detect antibodies against EBV in DBS, achieving high sensitivity (98.8%) and specificity (96.5%) relative to the corresponding venous blood assay. Furthermore, we derived a correction formula to convert semi-quantitative DBS values to serum-equivalents, enabling comparison with other studies and standardized datasets. The DBS-based approach allows sero-status assessment in a large population and thus e.g. simplifies the identification of suitable participants for clinical trials.</p>","PeriodicalId":23616,"journal":{"name":"Virology Journal","volume":"23 1","pages":""},"PeriodicalIF":4.0,"publicationDate":"2026-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13401283/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148585363","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Generation and immunological evaluation of SARS-CoV-2 membrane protein virus-like particles.","authors":"Akash Kumar, Krishna Kishore Inampudi, Vikas Kumar, Rajan Singh, Ghanshyam P Sinha, Mohammad K Parvez, Deepak Sehgal","doi":"10.1186/s12985-026-03256-5","DOIUrl":"10.1186/s12985-026-03256-5","url":null,"abstract":"<p><strong>Background: </strong>The emergence of the SARS-CoV-2 pandemic led to the spread of highly transmissible variants, such as the Delta variant, which originated in India, underscoring the urgent need to develop new antivirals, therapeutics, and vaccines. In our previous study, we showed that Membrane-Envelope Virus-like Particles exhibit antigenicity and neutralization activity. Hence, our present study was conducted to evaluate whether the M protein alone can form VLPs that elicit an immune response.</p><p><strong>Methods: </strong>Using computational methods, we identified key interacting residues in M-protein that contribute to VLP formation and interact with other structural proteins, including Spike (S), Nucleocapsid (N), and Envelope (E). The SARS-CoV-2-M protein was expressed in Sf-21 insect cells, and the resulting VLPs were purified, analyzed for shape and size, and characterized using DLS, FESEM, and TEM. The purified VLPs were injected into BALB/c mice to evaluate their immune response compared with uninfected controls.</p><p><strong>Results: </strong>The biophysical analysis confirms that the particles are round and have a size of ~ 180-200 nm. The serum levels of IgG, IgM, and IgA were found to be higher in immunized mice than in uninfected mice. Further qRT-PCR analysis demonstrated the levels of IFN-γ, IL-2, and IL-12, indicating a TH1-biased immune response against the M protein.</p><p><strong>Conclusion: </strong>Our study demonstrates that the highly conserved M protein can self-assemble into VLPs and elicit humoral and cellular immune response. Furthermore, our study indicates that while M-protein VLPs elicit significant antibodies and cytokine responses, they do not induce detectable neutralizing activity when given alone.</p>","PeriodicalId":23616,"journal":{"name":"Virology Journal","volume":" ","pages":""},"PeriodicalIF":4.0,"publicationDate":"2026-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13440007/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148473155","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"NGS-diagnosed HBV encephalitis with isolated left parietal lobe involvement: a case report.","authors":"Zihan Zhou, Zhangning Zhou, Longqi Zhang","doi":"10.1186/s12985-026-03253-8","DOIUrl":"10.1186/s12985-026-03253-8","url":null,"abstract":"<p><strong>Background: </strong>Viral encephalitis refers to the inflammation of the brain parenchyma caused by viral infection, usually manifested as fever, unconsciousness, seizures, and meningeal irritation symptoms. The non-specific clinical manifestations, combined with incomplete medical history, often lead to missed diagnoses and inappropriate treatments.</p><p><strong>Case presentation: </strong>We present a case of Hepatitis B virus (HBV) encephalitis, manifesting as isolated left parietal lobe involvement. The patient is a chronic hepatitis B virus carrier who did not receive antiviral therapy. Upon onset, the main symptoms were unconsciousness, fever, and seizures. He was diagnosed with HBV encephalitis thru next-generation sequencing (NGS) testing of the cerebrospinal fluid (CSF). After antiviral treatment with entecavir and general symptomatic treatment, the patient's clinical symptoms disappeared, and a follow-up brain MRI showed that the lesion had almost completely resolved.</p><p><strong>Conclusions: </strong>Central nervous system (CNS) infections caused by HBV are incredibly uncommon in clinical practice. This case highlights that the clinical manifestations of HBV encephalitis are nonspecific and prone to being missed, while neuroimaging often reveals an isolated lesion. Early application of NGS for accurate pathogen diagnosis is crucial to reduce misdiagnosis.</p>","PeriodicalId":23616,"journal":{"name":"Virology Journal","volume":" ","pages":""},"PeriodicalIF":4.0,"publicationDate":"2026-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13539874/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148473200","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Exploration of viral diversity in Aedes mosquitoes employing different shotgun metagenomic data analysis pipelines.","authors":"Ekta Gupta, Shashi Sharma, Sachin Narayan Tikar, Paban Kumar Dash","doi":"10.1186/s12985-026-03249-4","DOIUrl":"10.1186/s12985-026-03249-4","url":null,"abstract":"<p><p>Metagenomics or metaviromics is emerging as a powerful technology for pathogen surveillance and pandemic preparedness. Mosquitoes are important vectors for transmission of many emerging viruses responsible for numerous outbreaks. Monitoring mosquitoes becomes essential to investigate its virome which leads to understanding of disease dynamics and allow preventive actions. In this study, shotgun metagenomic methodology using Ion GeneStudio S5 System was optimized for exploration of viral diversity. A total of 1913 Aedes larvae were collected from Central India during post monsoon season of 2024. Aedes larvae reared to adulthood and processed for sequencing using Ion Torrent S5 platform. Computational analyses were performed using three bioinformatic pipelines: Chan Zuckerberg ID (CZ ID), Genome Detective Platform and the Galaxy Platform. A mock database of 11 known viruses was created as well as publicly available NCBI Sequence Read Archive (SRA) datasets were used to validate all three pipelines. In terms of detection accuracy, Genome Detective and CZ ID performed exceptionally well and therefore may be suitable for future mosquito virome surveillance studies. We found presence of viruses viz. Alphamesonivirus cavallynense and Phasivirus phasiense dominating in all samples. Dengue virus was detected in one sample by CZ ID, whereas Wenzhou sobemo-like virus, Hubei mosquito virus 2, Cell fusing agent virus found most commonly among samples. Other viruses found like Aedes anphevirus (AeAV; genus Glybovirus), Aedes totivirus, Verdadero virus and Chaq-like virus. Variation in the result among different pipelines are likely attributable to incorporation of different viral reference databases, classification algorithms, metrics and analysis parameters. To the best of our knowledge, this study represents the first metagenomic study of mosquitoes using Ion GeneStudio S5 platform in India. The findings provide a comparative evaluation of the metagenomic pipelines and elucidates detailed information of each pipeline and its working for future studies.</p>","PeriodicalId":23616,"journal":{"name":"Virology Journal","volume":" ","pages":""},"PeriodicalIF":4.0,"publicationDate":"2026-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13656711/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148457066","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"RRM2B is associated with low-level viremia during entecavir therapy in pediatric chronic hepatitis B and promotes profibrotic signaling in vitro.","authors":"Yuanzhen Zhang, Aoxue Tan, Tingting Wu, Yunan Chang, Xiaorong Peng, Kai Zhu, Qiqin Tang, Hongmei Xu","doi":"10.1186/s12985-026-03246-7","DOIUrl":"10.1186/s12985-026-03246-7","url":null,"abstract":"<p><strong>Background: </strong>Low-level viremia (LLV) during nucleos(t)ide analogue therapy for chronic hepatitis B (CHB) is clinically relevant, but its biological basis in children remains unclear. We investigated the clinical features of pediatric LLV and sought host factors linking incomplete virological suppression to stress adaptation and profibrotic signaling.</p><p><strong>Methods: </strong>Children with CHB who initiated entecavir therapy between 2019 and 2024 were retrospectively enrolled. LLV and maintained virological response (MVR) were defined by serum HBV DNA at week 48. Longitudinal trajectories were analyzed using generalized estimating equation models. Public liver transcriptomic datasets were integrated to identify CHB-associated host candidates, which were prioritized by machine learning and validated in pediatric samples. Functional studies were performed in an entecavir-based LLV-like HepG2.2.15 model.</p><p><strong>Results: </strong>Among 109 children with CHB, 27.5% developed LLV. Compared with the MVR group, LLV was associated with higher baseline HBV pregenomic RNA (HBV pgRNA) and smaller declines in HBV DNA, aminotransferases, and APRI, with the earliest divergence at week 12. Integrated transcriptomic and machine-learning analyses identified 5,080 differentially expressed genes enriched in oxidative stress- and DNA damage-related pathways and prioritized RRM2B as a candidate host factor. RRM2B was elevated in pediatric LLV samples and correlated positively with HBV pgRNA. In vitro, low-dose entecavir induced an LLV-like state characterized by increased RRM2B, reactive oxygen species, γ-H2AX, and PI3K/AKT signaling. RRM2B silencing further suppressed HBV DNA replication, reduced oxidative stress and DNA damage, and attenuated LLV-like hepatocyte-derived TGF-β1 secretion and subsequent profibrotic activation of LX-2 cells.</p><p><strong>Conclusions: </strong>RRM2B is associated with pediatric LLV and may be involved in stress-related and profibrotic host responses under conditions of incomplete virological suppression.</p>","PeriodicalId":23616,"journal":{"name":"Virology Journal","volume":" ","pages":""},"PeriodicalIF":4.0,"publicationDate":"2026-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13640231/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148424602","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genetic variation of human papillomavirus type 39 E6 and E7 genes in central China.","authors":"Keying Qin, Yang Yang, Zicong Lin, Yangying Wu, Ping Luo, Xiaoru Gao, Bing Mei","doi":"10.1186/s12985-026-03250-x","DOIUrl":"10.1186/s12985-026-03250-x","url":null,"abstract":"<p><strong>Background: </strong>Persistent infection with high-risk human papillomavirus (HR-HPV) is a key driver of cervical carcinogenesis. Human papillomavirus type 39 (HPV-39) infection is relatively prevalent in central China. However, data regarding the genetic variability of HPV-39 in this region remain limited.</p><p><strong>Methods: </strong>To characterize the genetic variation of the HPV-39 E6 and E7 genes in central China, samples with single type HPV-39 infection were identified by HPV genotyping prior to amplification. The E6 and E7 genes were amplified by polymerase chain reaction (PCR), followed by Sanger sequencing. The obtained sequences were subjected to variation, phylogenetic, selective pressure, and T-cell epitope analyses.</p><p><strong>Results: </strong>A total of 33 single nucleotide variants were identified in the E6 and E7 sequences, including 13 synonymous mutations and 20 non-synonymous mutations. Among which, six were novel non-synonymous mutations. Phylogenetic analysis based on HPV-39 E6 and E7 sequences demonstrated that most sequences (56/71) showed sequence similarity to lineage A. No positively selected site was detected in HPV-39 E6 or E7 genes. The predicted T-cell epitopes in the E6 sequence were influenced by non-conservative substitutions at positions H5Y, P7S, T19R, Q26H, E46D, A87G, L102S, and L151P; whereas those in the E7 sequence were affected by substitutions at positions L8V, D14H, D14E, H50Q, D57E, R87Q, Q88E, Q88D, L89V, Q91K, and F93C. A predicted candidate T-cell epitope spanning residues 70-78 (KFYAKIREL), restricted by HLA-C*06:02, was identified within the HPV-39 E6 sequence.</p><p><strong>Conclusion: </strong>This study describes the genetic variations of HPV-39 E6 and E7 genes in central China and provides regional molecular epidemiological data on HPV-39 sequence diversity. The identified sequence variations may be useful for future studies investigating HPV-39 evolution and host immune interactions.</p>","PeriodicalId":23616,"journal":{"name":"Virology Journal","volume":" ","pages":""},"PeriodicalIF":4.0,"publicationDate":"2026-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13637306/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148424627","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Etiological surveillance of viral gastroenteritis in children aged less than 5 years in Tehran Province, Iran, 2023-2024.","authors":"Somayeh Sadat Hosseini Fakhr, Hassan Karami, Motahareh Shafiei, Zahra Ahmadi, Zahra Fereydouni, Somayeh Jalilvand, Zabihollah Shoja, Ali Maleki","doi":"10.1186/s12985-026-03245-8","DOIUrl":"10.1186/s12985-026-03245-8","url":null,"abstract":"<p><strong>Background: </strong>Acute gastroenteritis (AGE) is a primary cause of death in children less than five years old in low- and middle-income countries (LMIC), mostly caused by viral intestinal infections. While the disease poses a significant global burden, further investigation is needed to clarify the role of enteric viruses in disease pathogenesis. This work aimed to study the frequency of five major enteropathogenic viruses-Rotavirus (RV), Norovirus (NoV), Adenovirus (AdV), Sapovirus (SaV), and Astrovirus (AstV)- in stool samples of young children in Tehran, Iran, during 2023-2024.</p><p><strong>Methods: </strong>A cross-sectional study was conducted on 203 stool samples collected from children under 5 years of age clinically diagnosed with AGE. Viral genomic RNA was extracted and amplified for the most common AGE viruses using the RT-qPCR assay.</p><p><strong>Results: </strong>Out of 203 tested samples, 101 (49.8%) were positive for at least one of the viruses assessed. The most frequently detected enteropathogenic viral agents in children under 5 years were RV and AdV, while AstV was rarely detected. The positivity rate varies by age, gender, and season. Mixed infections were determined in 16 (7.9%) patients, with a predominance of RV and AdV. Infection with enteric viruses can occur throughout the year (peaking during mild-to-cold months), with fever, diarrhea, and nausea/vomiting being the most common symptoms among children.</p><p><strong>Conclusions: </strong>Enteric viruses, particularly AdV and RV, contribute greatly to AGE among children in Iran. Continuous surveillance and long-term monitoring of enteropathogenic agents is essential to provide insight into the local circulation and characterization of AGE-causing viruses, guiding the implementation of targeted interventions and public health strategies to mitigate the risk of future outbreaks in the region.</p>","PeriodicalId":23616,"journal":{"name":"Virology Journal","volume":" ","pages":""},"PeriodicalIF":4.0,"publicationDate":"2026-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13637321/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148424635","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A highly sensitive amplicon sequencing workflow for genomic surveillance of Usutu virus.","authors":"Gábor Endre Tóth, Anna Nagy, Jaime A Costales, M Alejandra Camacho, Santiago F Burneo, Marike Petersen, Alexandra Bialonski, Heike Baum, Balázs Horváth, Anna Heitmann, Renke Lühken, Michael Schmidt, Jonas Schmidt-Chanasit, Zsófia Tauber, Dániel Cadar","doi":"10.1186/s12985-026-03251-w","DOIUrl":"10.1186/s12985-026-03251-w","url":null,"abstract":"<p><p>Genomic surveillance of Usutu virus (USUV) in blood donors is hampered by extremely low viral loads, which usually prevent reliable genome sequencing. We developed and validated a tiled amplicon-based sequencing protocol optimized for low-titer samples. Serial dilutions of four phylogenetically distinct USUV lineages showed ≥ 95% genome recovery above 100 RNA copies/µL and 65-98% recovery between 3 and 100 copies/µL. We applied the method to 27 USUV-positive blood donors from Germany (median 1.70 copies/µL), achieving lineage assignment in 74% and ≥ 70% genome coverage in 63% of samples. This approach enables routine genomic surveillance of USUV in blood donors.</p>","PeriodicalId":23616,"journal":{"name":"Virology Journal","volume":"23 1","pages":""},"PeriodicalIF":4.0,"publicationDate":"2026-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13352883/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148424666","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Major protease inhibitor drug resistance mutations among patients with virological failure on second-line antiretroviral therapy in Zimbabwe: a retrospective cross-sectional study.","authors":"Justin Mayini, Tendai Washaya, Justen Manasa, Edward Zumbika, Shungu Munyati, Ryman Shoko, Christine Dahlke, Vinie Kouamou","doi":"10.1186/s12985-026-03255-6","DOIUrl":"10.1186/s12985-026-03255-6","url":null,"abstract":"<p><strong>Background: </strong>Virological failure (VF) on protease inhibitor (PI)-based second-line antiretroviral therapy (ART) remains an important driver of HIV drug resistance (HIVDR) in sub-Saharan Africa. Despite widespread adoption of dolutegravir (DTG)-based first-line ART, many people living with HIV (PLWH) remain on PI-based second-line regimens. Data on major PI drug resistance mutations (DRMs) in Zimbabwe remain limited.</p><p><strong>Methods: </strong>We conducted a retrospective cross-sectional study of archived plasma specimens from PLWH with VF (viral load (VL) ≥ 1,000 copies/mL) receiving PI-based second-line ART in Zimbabwe between January 2021 and June 2025. HIV-1 protease and reverse transcriptase regions were Sanger-sequenced, and resistance was interpreted using the Stanford HIV Drug Resistance Database. Factors associated with major PI DRMs were evaluated using multivariable logistic regression.</p><p><strong>Results: </strong>Among 297 participants, 153 (51.5%, 95% confidence interval [CI] 45.8-57.2%) harboured major PI DRMs. The most frequent mutations were M46I (22.6%), V82A (19.2%), and I54V (17.2%). NRTI- and NNRTI-associated DRMs were present in 70.4% and 79.5% of participants, respectively, while 47.8% exhibited triple-class resistance. Predicted susceptibility to darunavir/ritonavir remained high (78.8%), despite resistance to atazanavir/ritonavir (45.5%) and lopinavir/ritonavir (50.8%). In multivariable analysis, increasing age (adjusted odds ratio [aOR] 1.04, P < 0.001), higher VL (aOR 1.55, P = 0.011) and male sex (aOR 1.59, P = 0.044) were independently associated with major PI DRMs.</p><p><strong>Conclusions: </strong>Major PI DRMs and multiclass HIVDR were common among PLWH with VF on PI-based second-line ART. Routine VL monitoring and early resistance testing are needed to detect and guide second-line ART failure in Zimbabwe.</p>","PeriodicalId":23616,"journal":{"name":"Virology Journal","volume":" ","pages":""},"PeriodicalIF":4.0,"publicationDate":"2026-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13647759/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148424697","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}