Virology Journal最新文献

{"title":"Standardization, validation, and comparative evaluation of a convenient surrogate recombinant vesicular stomatitis virus plaque reduction test for quantification of Hantaan orthohantavirus (HTNV) neutralizing antibodies.","authors":"Jing Wei, Hui Zhang, Jiawei Pei, Qiqi Yang, Yuan Wang, Xiaolei Jin, He Liu, Liang Zhang, Hongwei Ma, Linfeng Cheng, Yangchao Dong, Yingfeng Lei, Yinlan Bai, Zhikai Xu, Pengbo Yu, Fanglin Zhang, Wei Ye","doi":"10.1186/s12985-024-02613-6","DOIUrl":"10.1186/s12985-024-02613-6","url":null,"abstract":"<p><p>Hantaan orthohantavirus (HTNV) is responsible for severe hemorrhagic fever with renal syndrome (HFRS), which has a case fatality rate of 1% to 10%. Currently, the inactive vaccine licensed in endemic areas elicit low levels of neutralizing antibodies (NAbs). Early NAbs administration is helpful for patients recovery from HFRS. Therefore, measuring NAbs is crucial for evaluating the immune response following infection or vaccination. The golden standard for HTNV NAbs measurement is the focus reduction neutralization test (FRNT), which typically requires skilled technicians and is performed under high biosafety containment facility. Here, we established a surrogate NAbs titration method with replication-competent vesicular stomatitis virus (VSV) bearing HTNV glycoprotein (rVSV-HTNV-GP) based plaque reduction neutralization test (PRNT). Then compared and correlated this method with the authentic HTNV based FRNT, and applied it to measure the NAbs level in 47 serum samples from HFRS patients, healthy donors and inactive vaccine recipients. We observed positive correlations between two neutralization assays among HFRS patients and inactive vaccine recipients (R² = 0.5994 and 0.3440, respectively) and confirmed the clear specificity with healthy donors without vaccinated and reproducibility with three more assays. Our results suggest that rVSV-HTNV-GP based PRNT is a reliable lower-biosafety level surrogate for HTNV NAbs evaluation, which is easy to perform with higher sensitivity.</p>","PeriodicalId":23616,"journal":{"name":"Virology Journal","volume":"22 1","pages":"31"},"PeriodicalIF":4.0,"publicationDate":"2025-02-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11806752/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143374391","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":"Impact of hepatic steatosis on the efficacy of antiviral treatment for chronic hepatitis B and the establishment of predictive model: a cohort study.","authors":"Guanghui Ren, Kaining Jia, Shi Yin, Yunpeng Guan, Qingwei Cong, Ying Zhu","doi":"10.1186/s12985-025-02642-9","DOIUrl":"10.1186/s12985-025-02642-9","url":null,"abstract":"<p><strong>Aim: </strong>Metabolic dysfunction-associated steatotic disease (MASLD) and chronic hepatitis B (CHB) are prevalent liver disorders. Ongoing discussions investigate the impact of MASLD on the therapeutic outcomes of CHB.</p><p><strong>Methods: </strong>A cohort of 320 CHB patients on antiviral therapy (including NAs and PEG IFNα) were included and categorized into CHB + MASLD (n = 125) and CHB group (n = 195). The treatment response rates, Kaplan-Meier survival analysis, and Cox regression were assessed between the two groups to investigate the impact of MASLD on antiviral responses in patients with CHB.</p><p><strong>Results: </strong>At weeks 24 and 48, the CHB + MASLD group displayed a higher HBsAg response rate than the CHB group (24 weeks: 11.5% vs. 3.8%, p = 0.026; 48 weeks: 24.4% vs. 8.4%, p = 0.001). The pgRNA response was also higher in the CHB + MASLD group at both time points (24 weeks: 30.9% vs. 19.7%, p = 0.163; 48 weeks: 48.8% vs. 28.3%, p = 0.049). Kaplan-Meier survival analysis revealed a shorter median time to HBsAg response at 48 weeks for the CHB + MASLD group (HR = 3.251, 40 weeks vs. 42.5 weeks, p = 0.002). This is particularly evident among individuals who are negative for HBeAg (48w: 24.2% vs 12.2%, p = 0.005). KM survival analysis demonstrated that the CHB + MASLD group was more likely to achieve HBsAg response (HR = 2.428, p = 0.039).COX regression analysis identified age (HR = 0.948, p = 0.005), antiviral regimen (NAs + PEG IFNα: HR = 5.33, p < 0.001; PEG IFNα: HR = 1.099, p = 0.93), baseline HBsAg level (HR = 0.648, p = 0.009), and MASLD presence (HR = 3.321, p = 0.002) as independent predictors for HBsAg response. Time-ROC analysis showed that these factors effectively predicted HBsAg decline (24 weeks: AUC = 0.902; 48 weeks: AUC = 0.890). The model demonstrated strong discriminative power, calibration, and clinical relevance.</p><p><strong>Conclusion: </strong>In CHB patients without significant liver fibrosis who receive antiviral therapy, concurrent MASLD enhances HBsAg response, particularly in HBeAg-negative patients. Factors like younger age, NAs with PEG IFNα therapy, lower initial HBsAg levels, and MASLD presence predict treatment success. Further investigations are required to elucidate the impact of diverse metabolic disorders on the advancement of liver fibrosis.</p><p><strong>Trial registration: </strong>Registry and the registration No. Of the study/trial: ChiCTR23000 74064(2023-07-28).</p>","PeriodicalId":23616,"journal":{"name":"Virology Journal","volume":"22 1","pages":"30"},"PeriodicalIF":4.0,"publicationDate":"2025-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11804069/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143371301","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":"Association between cadherin-related family member 3 rs6967330-A and human rhinovirus-C induced wheezing in children.","authors":"Hanhaoyu Fu, Ri De, Yu Sun, Yao Yao, Runan Zhu, Dongmei Chen, Yutong Zhou, Qi Guo, Linqing Zhao","doi":"10.1186/s12985-025-02644-7","DOIUrl":"10.1186/s12985-025-02644-7","url":null,"abstract":"<p><strong>Background: </strong>The heterogeneity of childhood wheezing illnesses is associated with viral and host factors. Human rhinoviruses (HRV) are the major pathogens in severe wheezing in young children. The single nucleotide polymorphism (SNP) rs6967330 G > A proved to heighten the risk of wheezing. However, the relation between rs6967330 variants of cadherin-related family member 3 (CDHR3) and wheezing induced by human rhinovirus (HRV)-C has not been determined.</p><p><strong>Methods: </strong>A total of 11,756 respiratory specimens collected from hospitalized children with acute respiratory infections (ARIs) between September 2017 and March 2023 were screened for enterovirus (EV)/HRVs by the capillary electrophoresis-based multiplex PCR (CEMP) assay, and those positive only for HRVs were amplified and sequenced for HRV and CDHR3 genotyping. The clinical data of the enrolled patients were obtained and analyzed.</p><p><strong>Results: </strong>EV/HRVs (15.2%; 1,616/10,608) were the more common viruses detected in inpatients with ARIs. Among the enrolled samples, 148 were positive for HRV-A (49.83%; 148/297), 129 for HRV-C (43.4%; 129/297), and 20 for HRV-B (6.7%; 20/297). More patients infected with HRV-C had history of allergy (P = 0.004), family history of asthma (P = 0.001), wheezing (P = 0.005) and asthma (P = 0.001) than those infected with HRV-A or HRV-B, while patients infected with HRV-C were less likely to have older siblings compared to those infected with HRV-A (P = 0.014). The rs6967330-A variant was related to a high incidence of the three concave signs (P = 0.047), asthma exacerbation (P = 0.025), a higher risk of HRV-C infection determined by the dominant model (OR 1.91, 95% confidence interval 1.05-3.48; P = 0.033), and a high proportion of wheezing (56.67%) in patients infected with HRV-C.</p><p><strong>Conclusions: </strong>HRV-C is the dominant species responsible for HRV-induced wheezing. The rs6967330-A variant is a risk factor for HRV-C infection, and was associated with the high rate of wheezing induced by HRV-C.</p>","PeriodicalId":23616,"journal":{"name":"Virology Journal","volume":"22 1","pages":"29"},"PeriodicalIF":4.0,"publicationDate":"2025-02-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11804036/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143366096","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 ribodepletion and tagging protocol to multiplex samples for RNA-seq based virus detection: application to the cassava virome.","authors":"Daniel H Otron, Justin S Pita, Murielle Hoareau, Fidèle Tiendrébéogo, Jean-Michel Lett, Pierre Lefeuvre","doi":"10.1186/s12985-025-02634-9","DOIUrl":"10.1186/s12985-025-02634-9","url":null,"abstract":"<p><strong>Background: </strong>Cassava (Manihot esculenta, Crantz), is a staple food and the main source of calories for many populations in Africa, but the plant is beset by several damaging viruses. So far, eight families of virus infecting cassava have been identified; the Geminiviridae (ssDNA viruses responsible for cassava mosaic disease, CMD) and Potyviridae (ssRNA + viruses responsible for cassava brown streak disease, CBSD) families being the most damaging to cassava in Africa. In several cassava-growing regions, the co-existence of species and strains from these two families results in a complex epidemiological situation making it difficult to correctly identify the viruses in circulation and delaying the implementation of disease management schemes. Nevertheless, the development of next generation sequencing (NGS) methods has revolutionized plant virus detection and identification. One NGS method that has been successfully used in virus detection and identification is ribodepleted RNA sequencing. Unfortunately, the relatively high cost makes it difficult to upscale this method to large epidemiological surveys and limits its adoption as a diagnostic tool.</p><p><strong>Results: </strong>Here, we develop a high-throughput sequencing protocol, named Ribo-M-Seq, that combines plant rRNA ribodepletion, cDNA synthesis, tagging with a 96 multiplexing scheme and Illumina sequencing. We evaluated the protocol on a series of cassava samples with a known assemblage of viruses. After confirming that the protocol was suitable for ribodepletion, we demonstrated it was possible to detect RNA and DNA viruses via identification of near full-size genomes. Additional phylogenetic analyses confirmed the presence of begomoviruses and ipomoviruses responsible for CMD and CBSD, respectively. We also detected a recently described ampelovirus (Manihot esculenta-associated virus) that was not detected in previous analyses.</p><p><strong>Conclusions: </strong>The use of the Ribo-M-Seq protocol will pave the way for large-scale sample analyses of collections with potentially complex viromes, such as those collected in the West African cassava integrated pest management program.</p>","PeriodicalId":23616,"journal":{"name":"Virology Journal","volume":"22 1","pages":"27"},"PeriodicalIF":4.0,"publicationDate":"2025-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11796006/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143256883","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":"First detection and molecular characterization of porcine epidemic diarrhea virus (PEDV) in India: evidence of a new variant in Karnataka.","authors":"Jagadish B Hiremath, M Swathi, R Ramamoorthy, M Shijili, Damini Sharma, Divakar Hemadri, H B Chethankumar, K P Suresh, Sharanagouda S Patil, Shivasharanappa Nayakvadi, S P Satheesha, B R Shome, Baldev Raj Gulati","doi":"10.1186/s12985-024-02606-5","DOIUrl":"10.1186/s12985-024-02606-5","url":null,"abstract":"<p><strong>Background: </strong>Porcine epidemic diarrhea (PED) is a significant pig disease causing high mortality in suckling pigs and high morbidity across all age groups. It is highly prevalent in Southeast Asia, posing a threat of transboundary transmission to India. Although antibodies were detected as early as 2003 in Assam, there was no evidence of viral detection or molecular characterization until this study. This study reports the first clinical outbreak of PED in India, followed by the detection and genetic characterization of PED virus (PEDV) during 2022-23.</p><p><strong>Methods: </strong>The outbreak was characterized, and fecal samples (n = 21) were collected from affected pigs. These samples were screened for PEDV using RT-PCR, targeting the N, S, and M genes. Serosurveillance was conducted in eight districts, and serum samples (n = 339) were tested for PEDV antibodies using ELISA. Partial N, S, and M gene sequencing, followed by phylogenetic analysis using MEGA v11.0.13, was performed to identify the prevailing genotype and variations in the coding region.</p><p><strong>Results: </strong>This study identified the first clinical outbreak of PEDV in India, with morbidity rates of 55-57.1% and symptoms including yellow watery diarrhea, vomiting, and abdominal pain. PEDV was confirmed in 17 of 21 fecal samples by amplifying the N, S, and M genes. Serosurveys showed seropositivity in Mandya (2.8%), Bengaluru Rural (6.6%), and Kolar (21.6%), districts indicating PEDV circulation in the state of Karnataka, India. The phylogenetic analysis of the S and M genes placed our study sequences within the Genotype 2a (G2a) clade, aligning with other known G2a strains. In contrast, the phylogenetic tree of the N gene clustered our sequences within the Genotype 1a (G1a) clade suggesting potential recombination. The Indian PEDV strains clustered with strains of China, with unique amino acid substitutions in the S gene, particularly in the receptor binding region.</p><p><strong>Conclusion: </strong>This study reports the first clinical outbreak of PED in India and identifies the circulating genotype of PEDV. The study emphasizes the need for large-scale surveillance studies to understand the disease's status. Understanding PEDV's genetic diversity and evolution is essential to develop area-specific vaccines to mitigate the disease impact on India's pig population.</p>","PeriodicalId":23616,"journal":{"name":"Virology Journal","volume":"22 1","pages":"28"},"PeriodicalIF":4.0,"publicationDate":"2025-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11800441/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143256884","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":"Advances in antiviral strategies targeting mosquito-borne viruses: cellular, viral, and immune-related approaches.","authors":"Ayyaz Khan, Zakirullah, Shahid Wahab, Seong-Tshool Hong","doi":"10.1186/s12985-025-02622-z","DOIUrl":"10.1186/s12985-025-02622-z","url":null,"abstract":"<p><p>Mosquito-borne viruses (MBVs) are a major global health threat, causing significant morbidity and mortality. MBVs belong to several distinct viral families, each with unique characteristics. The primary families include Flaviviridae (e.g., Dengue, Zika, West Nile, Yellow Fever, Japanese Encephalitis), transmitted predominantly by Aedes and Culex mosquitoes; Togaviridae, which consists of the genus Alphavirus (e.g., Chikungunya, Eastern and Western Equine Encephalitis viruses), also transmitted by Aedes and Culex; Bunyaviridae (recently reorganized), containing viruses like Rift Valley Fever and Oropouche virus, transmitted by mosquitoes and sometimes sandflies; and Reoviridae, which includes the genus Orbivirus (e.g., West Nile and Bluetongue viruses), primarily affecting animals and transmitted by mosquitoes and sandflies. Despite extensive research, effective antiviral treatments for MBVs remain scarce, and current therapies mainly provide symptomatic relief and supportive care. This review examines the viral components and cellular and immune factors involved in the life cycle of MBVs. It also highlights recent advances in antiviral strategies targeting host factors such as lipid metabolism, ion channels, and proteasomes, as well as viral targets like NS2B-NS3 proteases and nonstructural proteins. Additionally, it explores immunomodulatory therapies to enhance antiviral responses and emphasizes the potential of drug repurposing, bioinformatics, artificial intelligence, and deep learning in identifying novel antiviral candidates. Continued research is crucial in mitigating MBVs' impact and preventing future outbreaks.</p>","PeriodicalId":23616,"journal":{"name":"Virology Journal","volume":"22 1","pages":"26"},"PeriodicalIF":4.0,"publicationDate":"2025-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11792744/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143189977","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":"The immunogenicity of PRV ΔgE/TK/UL49.5 three-gene-deleted vaccine in mice.","authors":"Chenmeng Ding, Yawei Sun, Xianfeng Zhang, Mengmeng Shi, Han Yang, Xin Zhou, Shuangshuang Li, Yongtao Li, Xia Yang, Linyang Yu, Lu Chen","doi":"10.1186/s12985-025-02641-w","DOIUrl":"10.1186/s12985-025-02641-w","url":null,"abstract":"<p><strong>Background: </strong>Pseudorabies (PR) caused by the re-emerging of pseudorabies virus (PRV) variant has outbroken among PRV vaccine immunized swine in many pig farms, which has caused serious social and economic consequences since the end of 2011. The PRV UL49.5 protein can inactivate the transporter associated with antigen processing (TAP), thereby downregulating the cell surface expression of swine leukocyte antigen class I (SLA-I) to evade host immune surveillance.</p><p><strong>Methods: </strong>In this study, based on the PRV ΔgE/TK strain, PRV ΔgE/TK/UL49.5 triple gene deletion strain was constructed through homologous recombination and deletion of the PRV UL49.5 gene by the Cre-LoxP system. Its growth curve and effect on SLA-I transcription level were determined. Preliminary studies were carried out on serum neutralizing antibody levels, IFN-γ and IL-4 cytokines levels in mice immunized with PRV ΔgE/TK/UL49.5, and the viral load and challenge protection in mice tissues after challenge.</p><p><strong>Results: </strong>The growth characteristics of PRV ΔgE/TK/UL49.5 strain were similar to those of PRV ΔgE/TK strain. The level of SLA-I was returned to normal after the deletion of PRV UL49.5 gene. The immunization of PRV ΔgE/TK/UL49.5 did not affect the weight gain of mice. Immunized mice could induce high levels of serum neutralization antibodies and immune cytokines, including IFN-γ and IL-4, which could provide complete protection against virulent PRV challenge. No obvious pathological damage was observed in lung, brain and trigeminal ganglion of mice immunized with PRV ΔgE/TK/UL49.5, and the tissue viral load was the lowest.</p><p><strong>Conclusions: </strong>PRV ΔgE/TK/UL49.5 strain can induce enhanced immunogenicity and had the potential to be used as a candidate strain.</p>","PeriodicalId":23616,"journal":{"name":"Virology Journal","volume":"22 1","pages":"25"},"PeriodicalIF":4.0,"publicationDate":"2025-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11792629/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143190169","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":"Development of a duplex real-time recombinase aided amplification assay for the simultaneous and rapid detection of PCV3 and PCV4.","authors":"Renjie Sun, Hanze Liu, Siqi Sun, Yating Wang, Ying Shan, Xiaoliang Li, Weihuan Fang, Yongle Yang, Ronghui Xie, Lingyan Zhao","doi":"10.1186/s12985-025-02625-w","DOIUrl":"10.1186/s12985-025-02625-w","url":null,"abstract":"<p><strong>Background: </strong>Porcine circoviruses 3 (PCV3) and 4 (PCV4) are emerging pathogens with global implications for swine industry, disturbing the diagnosis of PCVs associated diseases due to a range of similar clinical symptoms and increasingly coinfections. A rapid and accurate method for detection of PCV3 and PCV4 is critical for controlling the transmission of associated disease.</p><p><strong>Methods: </strong>We developed a duplex real-time recombinase aided amplification (RAA) assay for detection of both PCV3 and PCV4 simultaneously. The assay was completed within 20 min at 39℃ with the designed optimal primers and probes.</p><p><strong>Results: </strong>The established assay was more convenient and simpler operation compared with conventional molecular biological assays. The assay achieved a detection limit of 73.67 copies/reaction for each circovirus (at 95% probability by probit regression analysis) and showed high specificity and no cross-reactivity with other important porcine viruses (including PCV2). The intra- and inter-group coefficients of variation (CV) were ranged from 2.08 to 4.97%, indicating high stability and reliability. Comparative analysis with PCV3 and PCV4 qPCR on 60 clinical samples and artificially spiked samples indicated high congruence (the kappa value was 0.966 and 1, respectively, with p < 0.001), with only minor discrepancies, validating effectiveness of the duplex RAA assay in detecting co-infections and its suitability for preliminary clinical diagnosis of PCV3 and PCV4.</p><p><strong>Conclusions: </strong>This study provides a robust basis for multiplex detection of veterinary pathogens using RAA technique, enhancing the field's capacity to control PCV3 and PCV4, and supporting reliable aid for epidemiological understanding of emerging circoviruses.</p>","PeriodicalId":23616,"journal":{"name":"Virology Journal","volume":"22 1","pages":"23"},"PeriodicalIF":4.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11786481/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143075793","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 comparative analysis of sequence composition in different lots of a phage display peptide library during amplification.","authors":"Anders Wilgaard Sinkjaer, Ane Beth Sloth, Amanda Oester Andersen, Malte Jensen, Babak Bakhshinejad, Andreas Kjaer","doi":"10.1186/s12985-024-02600-x","DOIUrl":"10.1186/s12985-024-02600-x","url":null,"abstract":"<p><strong>Background: </strong>To develop efficient selection strategies and improve the discovery of promising ligands, it is highly desirable to analyze the sequence composition of naïve phage display libraries and monitor the evolution of their peptide content during successive rounds of amplification. In the current study, we performed a comparative analysis of the compositional features in different lots of the same naïve phage display library and monitored alterations in their peptide compositions during three rounds of amplification.</p><p><strong>Methods: </strong>We conducted three rounds of duplicate serial amplification of two different lots of the Ph.D.™-12 phage display library. DNA from the samples was subjected to Next-Generation Sequencing (NGS) using an Illumina platform. The NGS datasets underwent a variety of bioinformatic analyses using Python and MATLAB scripts.</p><p><strong>Results: </strong>We observed substantial heterogeneity in the sequence composition of the two lots indicated by differences in the enhanced percentage of wildtype clones, reduced diversity (number of unique sequences), and increased enrichment factors (EFs) during amplification as well as by observing no common sequence between lots and decreased number of common sequences between the naïve library and the consecutive rounds of amplification for each lot. We also found potential propagation-related target-unrelated peptides (TUPs) with the highest EFs in the two lots, which were displayed by the fastest-propagating phage clones. Furthermore, motif analysis of the most enriched subpopulation of amplified libraries led to the identification of some motifs hypothesized to contribute to the increased amplification rates of the respective phage clones.</p><p><strong>Conclusion: </strong>Our results highlight tremendous heterogeneity in the peptide composition of different lots of the same type of naïve phage display library, and the divergent evolution of their compositional features during amplification rounds at the amino acid, peptide, and motif levels. Our findings can be instrumental for phage display researchers by bringing fundamental insights into the vast extent of non-uniformity between phage display libraries and by providing a clear picture of how these discrepancies can lead to different evolutionary fates for the peptide composition of phage pools, which can have profound impacts on the outcome of phage display selections through biopanning.</p>","PeriodicalId":23616,"journal":{"name":"Virology Journal","volume":"22 1","pages":"24"},"PeriodicalIF":4.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11786364/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143075791","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":"Advances in bioinformatics and multi-omics integration: transforming viral infectious disease research in veterinary medicine.","authors":"Alyaa Elrashedy, Walid Mousa, Mohamed Nayel, Akram Salama, Ahmed Zaghawa, Ahmed Elsify, Mohamed E Hasan","doi":"10.1186/s12985-025-02640-x","DOIUrl":"10.1186/s12985-025-02640-x","url":null,"abstract":"<p><p>The world is changing due to factors like bioterrorism, massive environmental changes, globalization of trade and commerce, growing urbanization, changing climate, and pollution. Numerous diseases have emerged because of these factors, especially in companion and food-producing animals. Numerous pathogens have established themselves in naïve populations, harming reproduction, productivity, and health. Bioinformatics is considered a valuable tool in infectious disease research, as it provides a comprehensive overview of the identification of pathogens, their genetic makeup, and their evolutionary relationship. Therefore, there is an urgent need for a novel bioinformatics approach to help decipher and model viral epidemiology and informatics on domestic animals and livestock. With significant advancements in bioinformatics and NGS, researchers can now identify contigs, which are contiguous sequences of DNA that are assembled from overlapping fragments, assemble a complete genome, perform phylogenetic analysis to diagnose, investigate the risk of viral diseases in animals, handle and share large biological datasets across various species. Additionally, multi-omics data integration further deepens our understanding of homology, divergence, mutations, and evolutionary relationships, providing a comprehensive perspective on the molecular mechanisms driving animal pathogens infections. This review aims to reveal the importance of utilizing the multidisciplinary areas of bioinformatics, genomics, proteomics, transcriptomics, metabolomics, and metagenomics and their roles in studying viral infectious diseases in veterinary medicine that will eventually improve the health of animals.</p>","PeriodicalId":23616,"journal":{"name":"Virology Journal","volume":"22 1","pages":"22"},"PeriodicalIF":4.0,"publicationDate":"2025-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11783962/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143075792","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}