Pub Date : 2025-08-01DOI: 10.1016/j.bsheal.2025.07.005
Xindi Wang , Junyu Luo , Xiyang Cai , Ruibin Liu , Yixue Li , Chitin Hon
Understanding human-virus protein-protein interactions is critical for studying molecular mechanisms driving viral infection, immune evasion, and propagation, thereby informing strategies for public health. Here, we introduce a novel multimodal deep learning framework that integrates high-confidence experimental datasets to systematically predict putative interactions between human and viral proteins. Our approach incorporates two complementary tasks: binary classification for interaction prediction and conditional sequence generation to identify interacting protein partners. By leveraging protein language models and multimodal fusion, the framework demonstrates improved accuracy in identifying biologically relevant interactions. For empirical validation, we applied this method to predict severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-human interactions, identifying candidate proteins absent from training data, several of which were corroborated by independent studies. These predictions offer critical insights into potential therapeutic targets, facilitating the design of antiviral drugs and vaccines. By enabling rapid, cost-effective discovery pipelines, our study contributes to pandemic preparedness and public health interventions, underscoring its value in combating emerging infectious diseases.
{"title":"DeepHVI: A multimodal deep learning framework for predicting human-virus protein-protein interactions using protein language models","authors":"Xindi Wang , Junyu Luo , Xiyang Cai , Ruibin Liu , Yixue Li , Chitin Hon","doi":"10.1016/j.bsheal.2025.07.005","DOIUrl":"10.1016/j.bsheal.2025.07.005","url":null,"abstract":"<div><div>Understanding human-virus protein-protein interactions is critical for studying molecular mechanisms driving viral infection, immune evasion, and propagation, thereby informing strategies for public health. Here, we introduce a novel multimodal deep learning framework that integrates high-confidence experimental datasets to systematically predict putative interactions between human and viral proteins. Our approach incorporates two complementary tasks: binary classification for interaction prediction and conditional sequence generation to identify interacting protein partners. By leveraging protein language models and multimodal fusion, the framework demonstrates improved accuracy in identifying biologically relevant interactions. For empirical validation, we applied this method to predict severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-human interactions, identifying candidate proteins absent from training data, several of which were corroborated by independent studies. These predictions offer critical insights into potential therapeutic targets, facilitating the design of antiviral drugs and vaccines. By enabling rapid, cost-effective discovery pipelines, our study contributes to pandemic preparedness and public health interventions, underscoring its value in combating emerging infectious diseases.</div></div>","PeriodicalId":36178,"journal":{"name":"Biosafety and Health","volume":"7 4","pages":"Pages 257-266"},"PeriodicalIF":3.0,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144896486","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Healthcare-associated infections are linked with the contamination of inanimate surfaces and the air in occupied hospital areas by recognized pathogens. However, there is limited information about the presence of these microorganisms or other potential pathogens in critical areas prior to their clinical operation. Here, we determined the microbial community in critical areas prior to their validation for hospital care and reviewed the background for the potential pathogenic role of this microbiota for populations susceptible to opportunistic infections. We evaluated environmental samples from operating theatres (OTs) and bone marrow transplant rooms (BMTRs) at the Peruvian National Cancer Center. A total of 164 samples (58 air samples and 106 surface samples) were collected for bacterial and fungal culture. In the OTs, the air conditioning sample yielded the highest microbial isolation from air, with a predominance of the genera Bacillus (5/12 isolates; 41.7%) and Aspergillus (5/8 isolates; 62.5%), including Nigri (2/5) and Flavi (2/5) sections and Aspergillus sp. (1/5). Meanwhile, the surface sample with the highest bacterial isolation came from the shelf in the stock area, where there was a predominance of non-glucose-fermenting Gram-negative bacilli (NF-GNB) (8/15 isolates; 53.3%), including the genera Pseudomonas (4/8), Acinetobacter (2/8) and Stenotrophomonas (2/8). In BMTRs, the only microorganisms isolated from the air were coagulase-negative Staphylococcus species and Penicillium sp. In conclusion, the microbial community composition of the critical areas prior to their reopening was consistent with their unoccupied status, consisting of nosocomial saprophytic microorganisms. Furthermore, the predominant species of the basal microbiota included uncommon hospital pathogens for people susceptible to opportunistic infections, such as cancer patients.
{"title":"Microbiota of critical areas prior to reopening in an oncology center: Potential uncommon nosocomial pathogens for vulnerable populations","authors":"Freddy Villanueva-Cotrina , Fiorella Quiroz , Kathya L. Mimbela , Katia Quispe","doi":"10.1016/j.bsheal.2025.07.002","DOIUrl":"10.1016/j.bsheal.2025.07.002","url":null,"abstract":"<div><div>Healthcare-associated infections are linked with the contamination of inanimate surfaces and the air in occupied hospital areas by recognized pathogens. However, there is limited information about the presence of these microorganisms or other potential pathogens in critical areas prior to their clinical operation. Here, we determined the microbial community in critical areas prior to their validation for hospital care and reviewed the background for the potential pathogenic role of this microbiota for populations susceptible to opportunistic infections. We evaluated environmental samples from operating theatres (OTs) and bone marrow transplant rooms (BMTRs) at the Peruvian National Cancer Center. A total of 164 samples (58 air samples and 106 surface samples) were collected for bacterial and fungal culture. In the OTs, the air conditioning sample yielded the highest microbial isolation from air, with a predominance of the genera <em>Bacillus</em> (5/12 isolates; 41.7%) and <em>Aspergillus</em> (5/8 isolates; 62.5%), including <em>Nigri</em> (2/5) and <em>Flavi</em> (2/5) sections and <em>Aspergillus</em> sp. (1/5). Meanwhile, the surface sample with the highest bacterial isolation came from the shelf in the stock area, where there was a predominance of non-glucose-fermenting Gram-negative bacilli (NF-GNB) (8/15 isolates; 53.3%), including the genera <em>Pseudomonas</em> (4/8), <em>Acinetobacter</em> (2/8) and <em>Stenotrophomonas</em> (2/8). In BMTRs, the only microorganisms isolated from the air were coagulase-negative <em>Staphylococcus</em> species and <em>Penicillium</em> sp. In conclusion, the microbial community composition of the critical areas prior to their reopening was consistent with their unoccupied status, consisting of nosocomial saprophytic microorganisms. Furthermore, the predominant species of the basal microbiota included uncommon hospital pathogens for people susceptible to opportunistic infections, such as cancer patients.</div></div>","PeriodicalId":36178,"journal":{"name":"Biosafety and Health","volume":"7 4","pages":"Pages 218-223"},"PeriodicalIF":3.0,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144896484","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-08-01DOI: 10.1016/j.bsheal.2025.07.003
Wanying Gao , Zongzhen Wu , Kunlan Zuo , Qiangyu Xiang , Xiaoya Chen , Lu Zhang , Huan Liu
Biosafety is essential to ensuring the safe and effective conduct of biological research by minimizing risks associated with laboratory work and biological materials. This paper traces the historical and conceptual development of biosafety, from its origins in pathogen containment to its expansion into broader domains. In the modern context, biosafety also involves the regulation of genetically modified organisms and the strengthening of laboratory oversight mechanisms. Biosafety and biosecurity are closely related in origin. Biosafety focuses on biological risks within laboratory environments, while biosecurity addresses biological risks associated with non-laboratory environments. The article summarizes the development of biosafety, extracting the evolution of its conceptual framework from a historical perspective, condenses and compares its scientific characteristics with those of biosecurity, and applies the methodology of science history to define its conceptual framework.
{"title":"Biosafety concept: Origins, Evolution, and Prospects","authors":"Wanying Gao , Zongzhen Wu , Kunlan Zuo , Qiangyu Xiang , Xiaoya Chen , Lu Zhang , Huan Liu","doi":"10.1016/j.bsheal.2025.07.003","DOIUrl":"10.1016/j.bsheal.2025.07.003","url":null,"abstract":"<div><div>Biosafety is essential to ensuring the safe and effective conduct of biological research by minimizing risks associated with laboratory work and biological materials. This paper traces the historical and conceptual development of biosafety, from its origins in pathogen containment to its expansion into broader domains. In the modern context, biosafety also involves the regulation of genetically modified organisms and the strengthening of laboratory oversight mechanisms. Biosafety and biosecurity are closely related in origin. Biosafety focuses on biological risks within laboratory environments, while biosecurity addresses biological risks associated with non-laboratory environments. The article summarizes the development of biosafety, extracting the evolution of its conceptual framework from a historical perspective, condenses and compares its scientific characteristics with those of biosecurity, and applies the methodology of science history to define its conceptual framework.</div></div>","PeriodicalId":36178,"journal":{"name":"Biosafety and Health","volume":"7 4","pages":"Pages 209-217"},"PeriodicalIF":3.0,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144896483","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-06-01DOI: 10.1016/j.bsheal.2025.05.001
Defu Yuan , Fei Zhao , Shanshan Liu , Li Li , Hongxia Yan , Lifeng Liu , Tong Zhang , Christiane Moog , Bei Wang , Bin Su
Prior research indicated low genotypic resistance testing (GRT) for human immunodeficiency virus (HIV) utilization in China due to partial cost coverage under national antiretroviral therapy policies, limited testing accessibility, and financial barriers. Temporal and spatial data on GRT trends were also scarce. We analyzed GRT patterns among 6,895 untreated individuals at a tertiary hospital using Joinpoint regression, multivariable logistic modeling, and spatial analysis (GeoDa/SatScan). GRT rates showed a significant two-phase upward trend, increasing from 5.36 % in 2014 to 74.17 % in 2023, with an average annual percentage change of 31.30 % (P < 0.001). Beijing residency (adjusted odds ratio [aOR] = 2.596, 95 % confidence interval [CI]: 2.307–2.921) and older age were associated with higher GRT uptake. Specifically, ages 35–44 years (aOR = 1.207, 95 % CI: 1.026–1.420), 45–54 years (aOR = 1.335, 95 % CI: 1.104–1.613), and ≥ 55 years (aOR = 1.424, 95 % CI: 1.126–1.802) had significantly higher odds of testing. Lower testing rates were observed in individuals with lower education attainment (high school or technical secondary: aOR = 0.827; junior high school: aOR = 0.835; primary school: aOR = 0.695), unknown sexually transmitted diseases (STDs) history (aOR = 0.415), and non-heterosexual transmission routes (homosexual: aOR = 0.834). Spatial analysis identified GRT clustering across Beijing until 2021, with two space–time clusters identified in 2019–2023 and 2018–2022. This study demonstrates substantial increase in GRT uptake achieving more balanced district-level distribution since 2021. Age, educational attainment, STDs history, and transmission route influence GRT utilization. Improving access, reducing costs, and implementing targeted interventions are critical for optimizing testing and guiding antiretroviral therapy decisions.
{"title":"Spatiotemporal patterns and influencing factors of genotypic resistance testing utilization among people living with HIV: A 10-year retrospective analysis at a tertiary care hospital in Beijing, China (2014–2023)","authors":"Defu Yuan , Fei Zhao , Shanshan Liu , Li Li , Hongxia Yan , Lifeng Liu , Tong Zhang , Christiane Moog , Bei Wang , Bin Su","doi":"10.1016/j.bsheal.2025.05.001","DOIUrl":"10.1016/j.bsheal.2025.05.001","url":null,"abstract":"<div><div>Prior research indicated low genotypic resistance testing (GRT) for human immunodeficiency virus (HIV) utilization in China due to partial cost coverage under national antiretroviral therapy policies, limited testing accessibility, and financial barriers. Temporal and spatial data on GRT trends were also scarce. We analyzed GRT patterns among 6,895 untreated individuals at a tertiary hospital using Joinpoint regression, multivariable logistic modeling, and spatial analysis (GeoDa/SatScan). GRT rates showed a significant two-phase upward trend, increasing from 5.36 % in 2014 to 74.17 % in 2023, with an average annual percentage change of 31.30 % (<em>P</em> < 0.001). Beijing residency (adjusted odds ratio [aOR] = 2.596, 95 % confidence interval [CI]: 2.307–2.921) and older age were associated with higher GRT uptake. Specifically, ages 35–44 years (aOR = 1.207, 95 % CI: 1.026–1.420), 45–54 years (aOR = 1.335, 95 % CI: 1.104–1.613), and ≥ 55 years (aOR = 1.424, 95 % CI: 1.126–1.802) had significantly higher odds of testing. Lower testing rates were observed in individuals with lower education attainment (high school or technical secondary: aOR = 0.827; junior high school: aOR = 0.835; primary school: aOR = 0.695), unknown sexually transmitted diseases (STDs) history (aOR = 0.415), and non-heterosexual transmission routes (homosexual: aOR = 0.834). Spatial analysis identified GRT clustering across Beijing until 2021, with two space–time clusters identified in 2019–2023 and 2018–2022. This study demonstrates substantial increase in GRT uptake achieving more balanced district-level distribution since 2021. Age, educational attainment, STDs history, and transmission route influence GRT utilization. Improving access, reducing costs, and implementing targeted interventions are critical for optimizing testing and guiding antiretroviral therapy decisions.</div></div>","PeriodicalId":36178,"journal":{"name":"Biosafety and Health","volume":"7 3","pages":"Pages 192-198"},"PeriodicalIF":3.5,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144480218","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-06-01DOI: 10.1016/j.bsheal.2025.05.007
Min Li , Yalan Wang , Peiwen Qiao , Yaxin Guo , Peipei Guo , Tian Ma , Shaobo Dong , Jianbo Zhan , Jun Liu , Guizhen Wu
Acute viral infections may lead to long-term adverse health effects. Investigating the hematological and biochemical profiles during recovery can provide valuable insights into the prognosis of severe fever with thrombocytopenia syndrome (SFTS) virus infection. Herein, we performed a cross-sectional analysis of 24 hematological parameters and 12 liver and kidney function-related indicators in 143 naturally infected SFTS patients from the acute phase to 10 years post-recovery. Statistical analyses were performed using the Chi-square test (χ2), Fisher’s exact test, or the ANOVA with Bonferroni correction to assess group differences. Most indicators gradually recovered over time during the recovery period. The decrease in platelet (PLT), white blood cell, neutrophil (NEU), and lymphocyte counts in the acute phase showed a gradual recovery trend from 1–8 months to 6–10 years post-recovery. PLT count levels positively correlated significantly with recovery duration (P = 0.0149). NEU % and thrombocytocrit continued to improve with the recovery time. In addition, some indicators, including platelet distribution width, mean platelet volume, and mean corpuscular hemoglobin concentration, continued to show abnormalities in a certain proportion (12.9 %–69.8 %) of individuals post-recovery. For liver and kidney function-related indicators, acute-phase elevations in aspartate aminotransferase and alanine aminotransferase resolved progressively. Direct bilirubin showed a gradual upward trend over time. Additionally, persistent reductions in total protein and albumin were observed in a subset of recovered individuals. These findings highlight the need for long-term monitoring of SFTS survivors and inform clinical management strategies.
{"title":"The holistic rehabilitation from acute severe fever with thrombocytopenia syndrome virus infection to 10 years after recovery: A cross-sectional study","authors":"Min Li , Yalan Wang , Peiwen Qiao , Yaxin Guo , Peipei Guo , Tian Ma , Shaobo Dong , Jianbo Zhan , Jun Liu , Guizhen Wu","doi":"10.1016/j.bsheal.2025.05.007","DOIUrl":"10.1016/j.bsheal.2025.05.007","url":null,"abstract":"<div><div>Acute viral infections may lead to long-term adverse health effects. Investigating the hematological and biochemical profiles during recovery can provide valuable insights into the prognosis of severe fever with thrombocytopenia syndrome (SFTS) virus infection. Herein, we performed a cross-sectional analysis of 24 hematological parameters and 12 liver and kidney function-related indicators in 143 naturally infected SFTS patients from the acute phase to 10 years post-recovery. Statistical analyses were performed using the Chi-square test (<em>χ<sup>2</sup></em>), Fisher’s exact test, or the ANOVA with Bonferroni correction to assess group differences. Most indicators gradually recovered over time during the recovery period. The decrease in platelet (PLT), white blood cell, neutrophil (NEU), and lymphocyte counts in the acute phase showed a gradual recovery trend from 1–8 months to 6–10 years post-recovery. PLT count levels positively correlated significantly with recovery duration (<em>P</em> = 0.0149). NEU % and thrombocytocrit continued to improve with the recovery time. In addition, some indicators, including platelet distribution width, mean platelet volume, and mean corpuscular hemoglobin concentration, continued to show abnormalities in a certain proportion (12.9 %–69.8 %) of individuals post-recovery. For liver and kidney function-related indicators, acute-phase elevations in aspartate aminotransferase and alanine aminotransferase resolved progressively. Direct bilirubin showed a gradual upward trend over time. Additionally, persistent reductions in total protein and albumin were observed in a subset of recovered individuals. These findings highlight the need for long-term monitoring of SFTS survivors and inform clinical management strategies.</div></div>","PeriodicalId":36178,"journal":{"name":"Biosafety and Health","volume":"7 3","pages":"Pages 183-191"},"PeriodicalIF":3.5,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144480217","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-06-01DOI: 10.1016/j.bsheal.2025.05.003
Xinxin Li , Yuanjiao Gao , Ziyu Zhang , Wen Deng , Weihua Cao , Xin Wei , Zixuan Gao , Linmei Yao , Shuojie Wang , Yao Xie , Minghui Li
Since the discovery of the double helix structure of deoxyribonucleic acid (DNA), significant progress has been made in engineering technologies such as gene analysis and editing, greatly promoting the development of biomedical research and clinical applications. In recent years, the rapid development of genome-editing technologies, especially the clustered regularly interspaced short palindromic repeats-associated protein 9 (CRISPR-Cas9) system, have brought unprecedented opportunities for biomedical research and clinical applications. However, with the widespread application of genome-editing technologies, biosafety issues have gradually attracted the attention of the scientific community and the public. Potential risks such as off-target effects, genomic instability, and ethical and legal issues need to be taken seriously, and their safety and effectiveness in clinical applications still require further verification. This review summarizes the current status and potential risks of gene editing technologies in the medical field and discusses how to ensure its safe application through policies, regulations, and technical means. Through in-depth exploration of these issues, we hope to provide a comprehensive perspective for the scientific community, policy makers, and the public to promote the safe and responsible application of genome-editing technologies.
{"title":"Biosafety considerations triggered by genome-editing technologies","authors":"Xinxin Li , Yuanjiao Gao , Ziyu Zhang , Wen Deng , Weihua Cao , Xin Wei , Zixuan Gao , Linmei Yao , Shuojie Wang , Yao Xie , Minghui Li","doi":"10.1016/j.bsheal.2025.05.003","DOIUrl":"10.1016/j.bsheal.2025.05.003","url":null,"abstract":"<div><div>Since the discovery of the double helix structure of deoxyribonucleic acid (DNA), significant progress has been made in engineering technologies such as gene analysis and editing, greatly promoting the development of biomedical research and clinical applications. In recent years, the rapid development of genome-editing technologies, especially the clustered regularly interspaced short palindromic repeats-associated protein 9 (CRISPR-Cas9) system, have brought unprecedented opportunities for biomedical research and clinical applications. However, with the widespread application of genome-editing technologies, biosafety issues have gradually attracted the attention of the scientific community and the public. Potential risks such as off-target effects, genomic instability, and ethical and legal issues need to be taken seriously, and their safety and effectiveness in clinical applications still require further verification. This review summarizes the current status and potential risks of gene editing technologies in the medical field and discusses how to ensure its safe application through policies, regulations, and technical means. Through in-depth exploration of these issues, we hope to provide a comprehensive perspective for the scientific community, policy makers, and the public to promote the safe and responsible application of genome-editing technologies.</div></div>","PeriodicalId":36178,"journal":{"name":"Biosafety and Health","volume":"7 3","pages":"Pages 141-151"},"PeriodicalIF":3.5,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144480329","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-06-01DOI: 10.1016/j.bsheal.2025.05.002
Haoran Jiang , Baicheng Xia , Xujing Chi , Liwei Sun , Hongmei Xu , Wenhui Wang , Min Mu , Pengbo Yu , Xingyu Xiang , Feng Zhang , Hui Zhang , Caixiao Jiang , Linqing Zhao , Zhenguo Gao , Kongxin Hu , Yan Zhang , Aili Cui
Human bocavirus (HBoV) is a common respiratory virus among patients with acute respiratory infection (ARI). To investigate the prevalence and genetic characteristics of HBoV, clinical specimens from 13,109 ARI patients were collected through active surveillance from 12 provinces of China during 2012–2021. Extracted nucleic acid was screened and the viral protein 1 (VP1) gene was directly amplified and sequenced in HBoV-positive specimens. 3.51 % of patients were HBoV-positive, with children under 5 years old accounting for 93.48 % of cases. HBoV detection rate increased from 2.35 % in 2012–2019 to 5.38 % in 2020 and 7.68 % in 2021, with a pronounced increase in children aged 2–4 years and in Southern China. The age group with the highest detection rate shifted from infants under 2 years in 2012–2019 to children aged 2–4 years in 2020–2021. The proportion of HBoV co-detections increased significantly in 2020–2021, from 43.98 % to over 60.00 %. All HBoV cases were identified as HBoV-1 with 165 full length sequences of VP1 gene obtained. No temporal or geographic clustering was observed. The VP1 gene evolved at a rate of 7.99 × 10−5 substitutions/site per year, with ω-value less than 1, indicating that the VP1 protein was under negative selection pressure. Multiple antigen-associated amino acid mutations and positive selection sites were found in the VP1 protein. In conclusion, HBoV1 remains a major cause of pediatric ARI in China, but its epidemic pattern exhibited dynamic shifts during the coronavirus disease 2019 pandemic, while the viral genetic evolution remained relatively stable.
{"title":"The prevalence and genetic characteristics of human bocavirus in patients with acute respiratory infection in China during 2012–2021","authors":"Haoran Jiang , Baicheng Xia , Xujing Chi , Liwei Sun , Hongmei Xu , Wenhui Wang , Min Mu , Pengbo Yu , Xingyu Xiang , Feng Zhang , Hui Zhang , Caixiao Jiang , Linqing Zhao , Zhenguo Gao , Kongxin Hu , Yan Zhang , Aili Cui","doi":"10.1016/j.bsheal.2025.05.002","DOIUrl":"10.1016/j.bsheal.2025.05.002","url":null,"abstract":"<div><div>Human bocavirus (HBoV) is a common respiratory virus among patients with acute respiratory infection (ARI). To investigate the prevalence and genetic characteristics of HBoV, clinical specimens from 13,109 ARI patients were collected through active surveillance from 12 provinces of China during 2012–2021. Extracted nucleic acid was screened and the viral protein 1 (VP1) gene was directly amplified and sequenced in HBoV-positive specimens. 3.51 % of patients were HBoV-positive, with children under 5 years old accounting for 93.48 % of cases. HBoV detection rate increased from 2.35 % in 2012–2019 to 5.38 % in 2020 and 7.68 % in 2021, with a pronounced increase in children aged 2–4 years and in Southern China. The age group with the highest detection rate shifted from infants under 2 years in 2012–2019 to children aged 2–4 years in 2020–2021. The proportion of HBoV co-detections increased significantly in 2020–2021, from 43.98 % to over 60.00 %. All HBoV cases were identified as HBoV-1 with 165 full length sequences of VP1 gene obtained. No temporal or geographic clustering was observed. The VP1 gene evolved at a rate of 7.99 × 10<sup>−5</sup> substitutions/site per year, with ω-value less than 1, indicating that the VP1 protein was under negative selection pressure. Multiple antigen-associated amino acid mutations and positive selection sites were found in the VP1 protein. In conclusion, HBoV1 remains a major cause of pediatric ARI in China, but its epidemic pattern exhibited dynamic shifts during the coronavirus disease 2019 pandemic, while the viral genetic evolution remained relatively stable.</div></div>","PeriodicalId":36178,"journal":{"name":"Biosafety and Health","volume":"7 3","pages":"Pages 166-172"},"PeriodicalIF":3.5,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144480331","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-06-01DOI: 10.1016/j.bsheal.2025.05.005
Tingting Sun , Shumin Chen , Rui Zhou , Saisai Guo , Yilu Ye , Jingyi Qiu , Xiaoyu Li , Shan Cen , Jing Wang
The productive infection of influenza A virus (IAV) requires the functional involvement of host long noncoding ribonucleic acids (lncRNAs). Identification of key cellular lncRNAs and elucidation of their molecular mechanisms in IAV replication are expected to expand our understanding of virus-host interactions and develop antiviral therapeutics. Our previous work has identified that influenza virus polymerase basic protein 1 (PB1)-associated long noncoding RNA (IPAN) associates with and stabilizes viral RNA-dependent RNA polymerase PB1 of IAV, warranting efficient viral RNA synthesis. This provides a unique viral strategy of co-opting host lncRNA for replication, whereas the molecular pathways exploited by the virus are unknown. Here, we aim to further investigate the detailed mechanisms underlying IPAN-mediated PB1 stabilization. We employed cellular-level molecular interaction techniques to demonstrate that both retinoic acid-inducible gene I (RIG-I) and tripartite motif-containing protein 25 (TRIM25) interacted with PB1 and co-operated to induce its degradation triggered by viral RNA synthesis. The experimental data obtained from RIG-I knockout cell lines and mutational analyses demonstrated RIG-I promoted PB1 degradation independently of its canonical signaling pathway, suggesting an “effector-like” antiviral activity of RIG-I. Furthermore, IPAN knockdown enhanced the association of PB1 with both RIG-I and TRIM25 to restore PB1 stability. These results collectively demonstrated that IAV hijacked host IPAN to protect PB1 from RIG-I/TRIM25-mediated antiviral degradation. Thus, our data reveal a mechanism of RIG-I and TRIM25 against IAV infection by degrading PB1 and highlight how IAV exploits host lncRNAs to evade immune surveillance.
{"title":"IncRNA IPAN antagonizes RIG-I/TRIM25-mediated degradation of influenza A virus PB1 to promote viral replication","authors":"Tingting Sun , Shumin Chen , Rui Zhou , Saisai Guo , Yilu Ye , Jingyi Qiu , Xiaoyu Li , Shan Cen , Jing Wang","doi":"10.1016/j.bsheal.2025.05.005","DOIUrl":"10.1016/j.bsheal.2025.05.005","url":null,"abstract":"<div><div>The productive infection of influenza A virus (IAV) requires the functional involvement of host long noncoding ribonucleic acids (lncRNAs). Identification of key cellular lncRNAs and elucidation of their molecular mechanisms in IAV replication are expected to expand our understanding of virus-host interactions and develop antiviral therapeutics. Our previous work has identified that influenza virus polymerase basic protein 1 (PB1)-associated long noncoding RNA (IPAN) associates with and stabilizes viral RNA-dependent RNA polymerase PB1 of IAV, warranting efficient viral RNA synthesis. This provides a unique viral strategy of co-opting host lncRNA for replication, whereas the molecular pathways exploited by the virus are unknown. Here, we aim to further investigate the detailed mechanisms underlying IPAN-mediated PB1 stabilization. We employed cellular-level molecular interaction techniques to demonstrate that both retinoic acid-inducible gene I (RIG-I) and tripartite motif-containing protein 25 (TRIM25) interacted with PB1 and co-operated to induce its degradation triggered by viral RNA synthesis. The experimental data obtained from RIG-I knockout cell lines and mutational analyses demonstrated RIG-I promoted PB1 degradation independently of its canonical signaling pathway, suggesting an “effector-like” antiviral activity of RIG-I. Furthermore, IPAN knockdown enhanced the association of PB1 with both RIG-I and TRIM25 to restore PB1 stability. These results collectively demonstrated that IAV hijacked host IPAN to protect PB1 from RIG-I/TRIM25-mediated antiviral degradation. Thus, our data reveal a mechanism of RIG-I and TRIM25 against IAV infection by degrading PB1 and highlight how IAV exploits host lncRNAs to evade immune surveillance.</div></div>","PeriodicalId":36178,"journal":{"name":"Biosafety and Health","volume":"7 3","pages":"Pages 199-208"},"PeriodicalIF":3.5,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144480219","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-06-01DOI: 10.1016/j.bsheal.2025.05.006
Qinghong Fan , Guofang Tang , Mengling Jiang , Yujuan Xu , Nenglang Pan , Zhiwei Liang , Chuyu Zhang , Pinghong Li , Feilong Xu , Zhimin Chen , Bo Liu , Lingzhen Chen , Youxia Li , Chuo Li , Fengyu Hu , Feng Li
Opportunistic infections caused by viruses, bacteria, fungi, and parasites, are commonly reported in hospitalized human immunodeficiency virus (HIV)-positive patients, but their detrimental contribution to disease severity remains under explored. In this study, we examined the coinfection profiles of 126 HIV-positive patients with suspected respiratory, bloodstream, or neurological infections. Lower respiratory tract (LRT) samples, cerebrospinal fluid, and blood samples collected within the first seven days of admission were subjected to metagenomic next-generation sequencing (mNGS). Additionally, a multiplex polymerase chain reaction (PCR) detection kit to identify ten commonly known respiratory pathogens was applied to the LRT samples. Of 126 HIV-positive patients, 111 (88.1 %) were coinfected with at least one known virus. Epstein-Barr virus (EBV) (71/111, 64.0 %), human cytomegalovirus (HCMV) (64/111, 57.7 %), and torque teno virus (TTV) (63/111, 56.8 %) were the three most prevalent coinfected viruses. Fungal coinfections (58/126, 46.0 %) and bacterial coinfections (47/126, 37.3 %) were less frequent than viral coinfections. Higher viral loads of coinfection were associated with fungal coinfections (odds ratio [OR] = 2.573, 95 % confidence interval [CI]: 1.150–5.757, P = 0.0214) and lower CD4+/CD8+ T cell ratios (OR = 0.048, 95 % CI: 0.005–0.429, P = 0.0067). Importantly, patients with higher loads of HCMV and TTV, but not EBV, exhibited worse clinical outcomes. Specifically, patients with HCMV reads per million (RPM) > 0 and TTV RPM > 5 exhibited significantly higher risks of poor prognosis and intensive care unit (ICU) admission. In contrast, EBV RPM showed no association with clinical outcomes in this context. In conclusion, HCMV and TTV may serve as prognostic biomarkers linked to poorer outcomes in HIV-positive patients. Detection of HCMV and TTV could predict clinical outcomes and improve patient management strategies.
{"title":"Clinical prognostic value of TTV and HCMV but not EBV for outcomes in hospitalized HIV-positive patients","authors":"Qinghong Fan , Guofang Tang , Mengling Jiang , Yujuan Xu , Nenglang Pan , Zhiwei Liang , Chuyu Zhang , Pinghong Li , Feilong Xu , Zhimin Chen , Bo Liu , Lingzhen Chen , Youxia Li , Chuo Li , Fengyu Hu , Feng Li","doi":"10.1016/j.bsheal.2025.05.006","DOIUrl":"10.1016/j.bsheal.2025.05.006","url":null,"abstract":"<div><div>Opportunistic infections caused by viruses, bacteria, fungi, and parasites, are commonly reported in hospitalized human immunodeficiency virus (HIV)-positive patients, but their detrimental contribution to disease severity remains under explored. In this study, we examined the coinfection profiles of 126 HIV-positive patients with suspected respiratory, bloodstream, or neurological infections. Lower respiratory tract (LRT) samples, cerebrospinal fluid, and blood samples collected within the first seven days of admission were subjected to metagenomic next-generation sequencing (mNGS). Additionally, a multiplex polymerase chain reaction (PCR) detection kit to identify ten commonly known respiratory pathogens was applied to the LRT samples. Of 126 HIV-positive patients, 111 (88.1 %) were coinfected with at least one known virus. Epstein-Barr virus (EBV) (71/111, 64.0 %), human cytomegalovirus (HCMV) (64/111, 57.7 %), and torque teno virus (TTV) (63/111, 56.8 %) were the three most prevalent coinfected viruses. Fungal coinfections (58/126, 46.0 %) and bacterial coinfections (47/126, 37.3 %) were less frequent than viral coinfections. Higher viral loads of coinfection were associated with fungal coinfections (odds ratio [OR] = 2.573, 95 % confidence interval [CI]: 1.150–5.757, <em>P</em> = 0.0214) and lower CD4<sup>+</sup>/CD8<sup>+</sup> T cell ratios (OR = 0.048, 95 % CI: 0.005–0.429, <em>P</em> = 0.0067). Importantly, patients with higher loads of HCMV and TTV, but not EBV, exhibited worse clinical outcomes. Specifically, patients with HCMV reads per million (RPM) > 0 and TTV RPM > 5 exhibited significantly higher risks of poor prognosis and intensive care unit (ICU) admission. In contrast, EBV RPM showed no association with clinical outcomes in this context. In conclusion, HCMV and TTV may serve as prognostic biomarkers linked to poorer outcomes in HIV-positive patients. Detection of HCMV and TTV could predict clinical outcomes and improve patient management strategies.</div></div>","PeriodicalId":36178,"journal":{"name":"Biosafety and Health","volume":"7 3","pages":"Pages 173-182"},"PeriodicalIF":3.5,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144480216","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-06-01DOI: 10.1016/j.bsheal.2025.05.004
Lizhe Hong , Lijun Suo , Kang Chang , Hongyun Cao , Jiahui Luan , Fuxin Zhang , Xiaofeng Yu , Xiaohui Zou , Bo Liu , Bin Cao , CAP-China Network
Community-acquired pneumonia (CAP) is a major global health concern, with limited understanding of longitudinal changes in host gene expression and respiratory microbiome throughout disease progression and recovery. To address this gap, we longitudinally collected CAP patients’ peripheral blood for transcriptome and oropharyngeal swabs for microbiome analysis from admission to 4 months post infection. Age- and sex-matched volunteers were recruited as controls. We observed CAP patients mounted rapid, effective, and moderate immune responses against infection. Coagulation activation and mitochondrial dysfunction were the striking pathways showing distinct difference in CAP patients compared to controls, and the latter was validated by lower adenosine triphosphate (ATP) levels in the peripheral blood mononuclear cells (PBMCs) of CAP patients. Although transcriptional perturbations gradually decreased, they did not fully recover during the follow-up period. Similarly, persisting oropharyngeal microbiome dysbiosis was observed, characterized by significantly lower alpha diversity and altered taxonomy distribution (P < 0.05). CAP increased the relative abundance of Streptococcus, Veillonella, and Peptostreptococcus, while decreasing that of Haemophilus, Neisseria, and Porphyromonas. Integrated analysis of host response and oropharyngeal microbiome revealed that the relative abundance of Haemophilus, Neisseria, Porphyromonas, and Stomatobaculum were positively related to mitochondrial structure and function pathways, whereas the relative abundance of Prevotella declined over time in patients and positively correlated with anti-pathogen and interferon signaling pathways. These results underscore the persistent impact of CAP on both host immunity and oropharyngeal microbiome, even months after infection, emphasizing the need for long-term follow-up and targeted strategies to facilitate full recovery and restore homeostasis.
{"title":"Longitudinal profiling of host response and oropharyngeal respiratory microbiome reveals dynamic alterations during recovery from community-acquired pneumonia","authors":"Lizhe Hong , Lijun Suo , Kang Chang , Hongyun Cao , Jiahui Luan , Fuxin Zhang , Xiaofeng Yu , Xiaohui Zou , Bo Liu , Bin Cao , CAP-China Network","doi":"10.1016/j.bsheal.2025.05.004","DOIUrl":"10.1016/j.bsheal.2025.05.004","url":null,"abstract":"<div><div>Community-acquired pneumonia (CAP) is a major global health concern, with limited understanding of longitudinal changes in host gene expression and respiratory microbiome throughout disease progression and recovery. To address this gap, we longitudinally collected CAP patients’ peripheral blood for transcriptome and oropharyngeal swabs for microbiome analysis from admission to 4 months post infection. Age- and sex-matched volunteers were recruited as controls. We observed CAP patients mounted rapid, effective, and moderate immune responses against infection. Coagulation activation and mitochondrial dysfunction were the striking pathways showing distinct difference in CAP patients compared to controls, and the latter was validated by lower adenosine triphosphate (ATP) levels in the peripheral blood mononuclear cells (PBMCs) of CAP patients. Although transcriptional perturbations gradually decreased, they did not fully recover during the follow-up period. Similarly, persisting oropharyngeal microbiome dysbiosis was observed, characterized by significantly lower alpha diversity and altered taxonomy distribution (<em>P</em> < 0.05). CAP increased the relative abundance of <em>Streptococcus, Veillonella</em>, and <em>Peptostreptococcus</em>, while decreasing that of <em>Haemophilus</em>, <em>Neisseria</em>, and <em>Porphyromonas</em>. Integrated analysis of host response and oropharyngeal microbiome revealed that the relative abundance of <em>Haemophilus</em>, <em>Neisseria</em>, <em>Porphyromonas</em>, and <em>Stomatobaculum</em> were positively related to mitochondrial structure and function pathways, whereas the relative abundance of <em>Prevotella</em> declined over time in patients and positively correlated with anti-pathogen and interferon signaling pathways. These results underscore the persistent impact of CAP on both host immunity and oropharyngeal microbiome, even months after infection, emphasizing the need for long-term follow-up and targeted strategies to facilitate full recovery and restore homeostasis.</div></div>","PeriodicalId":36178,"journal":{"name":"Biosafety and Health","volume":"7 3","pages":"Pages 152-165"},"PeriodicalIF":3.5,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144480330","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
扫码关注我们
求助内容：
应助结果提醒方式：
京公网安备 11010802042870号