Biosafety and Health最新文献_第8页

Epidemiology and genetic characteristics of coxsackievirus A16 associated with hand-foot-and-mouth disease in Yantai city, China in 2018–2021 烟台市2018-2021年与手足口病相关的柯萨奇病毒A16流行病学及遗传特征

Biosafety and Health Pub Date : 2023-06-01 DOI: 10.1016/j.bsheal.2023.05.001

Zhenlu Sun , Ji Wang , Xin Chi , Peihua Niu , Ruiqing Zhang , Qiao Gao , Yong Zhang , Xuejun Ma

{"title":"Epidemiology and genetic characteristics of coxsackievirus A16 associated with hand-foot-and-mouth disease in Yantai city, China in 2018–2021","authors":"Zhenlu Sun , Ji Wang , Xin Chi , Peihua Niu , Ruiqing Zhang , Qiao Gao , Yong Zhang , Xuejun Ma","doi":"10.1016/j.bsheal.2023.05.001","DOIUrl":"10.1016/j.bsheal.2023.05.001","url":null,"abstract":"<div><p>In 2008, China launched a national surveillance system for hand-foot-and-mouth disease (HFMD). Several million cases of HFMD are reported every year, coxsackievirus A16 (CVA16) was the leading cause of HFMD epidemic in Yantai city, China in recent years, but the information of epidemiology and molecular characterization of CVA16 in Yantai is limited. The aim of this study is to investigate the epidemiological characteristics and pathogenic spectrum of HFMD, and most importantly, the molecular characterization of CVA16 in Yantai from 2018 to 2021. A total of 2,000 clinical samples were collected in Yantai city from 2018 to 2021 and the enterovirus typing was performed using real-time reverse transcriptase–polymerase chain reaction (qRT-PCR). <em>VP1</em> coding regions of 41 CVA16 isolates were amplified and Sanger sequenced, and phylogenetic analysis was performed. During the study period, HFMD became prevalent from May to August each year. It peaked in June and declined in September. The incidence was highest in children aged 1 to 5 years, while more common in males than females. 1,617 out of 2,000 clinical collection of samples were tested positive for enterovirus. Among them, 614 were identified as CVA16, 45 were enterovirus A71 (EV A17), and 958 were other enterovirus serotypes. All 41 CVA16 strains belonged to the Bla and B1b genotypes. Homology analysis showed that 41 CVA16 isolates shared 83.2%–100% nucleotide and 93.7%–100% amino acid similarity among themselves. The results of this study update molecular epidemiology of CVA16 and provide a reference for HFMD prevention and control.</p></div>","PeriodicalId":36178,"journal":{"name":"Biosafety and Health","volume":"5 3","pages":"Pages 181-186"},"PeriodicalIF":0.0,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46190803","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}

引用次数: 0

Mosquito CYP4C21 knockout reduces dengue virus and Zika virus replication in Aedes aegypti cells 敲除蚊子CYP4C21可减少埃及伊蚊细胞中的登革热病毒和寨卡病毒复制

Biosafety and Health Pub Date : 2023-06-01 DOI: 10.1016/j.bsheal.2023.04.005

Xiaoxue Xie , Di Wang , Bo Li , Manjin Li , Dan Xing , Teng Zhao , Xinyu Zhou , Chunxiao Li

引用次数: 0

mNGS-based dynamic pathogen monitoring for accurate diagnosis and treatment of severe pneumonia caused by fungal infections 基于mngs的重症肺炎真菌感染动态病原体监测准确诊治

Biosafety and Health Pub Date : 2023-06-01 DOI: 10.1016/j.bsheal.2023.04.004

Zhen Li , Changcheng Wu , Li-An Tang , Yinjie Liang , Ruhan A , Debin Huang , Chuanyi Ning , Wenling Wang , Wenjie Tan

{"title":"mNGS-based dynamic pathogen monitoring for accurate diagnosis and treatment of severe pneumonia caused by fungal infections","authors":"Zhen Li , Changcheng Wu , Li-An Tang , Yinjie Liang , Ruhan A , Debin Huang , Chuanyi Ning , Wenling Wang , Wenjie Tan","doi":"10.1016/j.bsheal.2023.04.004","DOIUrl":"10.1016/j.bsheal.2023.04.004","url":null,"abstract":"<div><p>Metagenomic next-generation sequencing (mNGS) has been widely applied to identify pathogens associated with infectious diseases. However, limited studies have explored the use of mNGS-based dynamic pathogen monitoring in intensive care unit patients with severe pneumonia. Here, we present a clinical case of an 86-year-old male patient with severe pneumonia caused by a fungal infection. During the clinical treatment, four mNGS analyses were performed within two consecutive weeks. Various respiratory fungal pathogens, including <em>Candida orthopsilosis</em>, <em>Candida albicans,</em> and <em>Aspergillus fumigatus</em> were detected by mNGS of bronchoalveolar lavage fluid (BALF). Based on conventional pathogen identification and clinical symptoms, the patient was diagnosed with severe pneumonia caused by a fungal infection. The abundance of fungal species decreased gradually in response to antifungal and empirical therapies, and the fungal infections were effectively controlled. In summary, our results demonstrated that mNGS could effectively identify pathogens in patients with severe pneumonia. Additionally, dynamic pathogen monitoring based on mNGS could assist in the precise diagnosis of complex infections and may facilitate rapid induction of the most appropriate therapy.</p></div>","PeriodicalId":36178,"journal":{"name":"Biosafety and Health","volume":"5 3","pages":"Pages 138-143"},"PeriodicalIF":0.0,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47282466","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}

引用次数: 0

Emvirus: An embedding-based neural framework for human-virus protein-protein interactions prediction Emvirus:一个基于嵌入的神经框架，用于预测人-病毒蛋白-蛋白相互作用

Biosafety and Health Pub Date : 2023-06-01 DOI: 10.1016/j.bsheal.2023.04.003

Pengfei Xie , Jujuan Zhuang , Geng Tian , Jialiang Yang

{"title":"Emvirus: An embedding-based neural framework for human-virus protein-protein interactions prediction","authors":"Pengfei Xie , Jujuan Zhuang , Geng Tian , Jialiang Yang","doi":"10.1016/j.bsheal.2023.04.003","DOIUrl":"10.1016/j.bsheal.2023.04.003","url":null,"abstract":"<div><p>Human-virus protein-protein interactions (PPIs) play critical roles in viral infection. For example, the spike protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) binds primarily to human angiotensin-converting enzyme 2 (ACE2) protein to infect human cells. Thus, identifying and blocking these PPIs contribute to controlling and preventing viruses. However, wet-lab experiment-based identification of human-virus PPIs is usually expensive, labor-intensive, and time-consuming, which presents the need for computational methods. Many machine-learning methods have been proposed recently and achieved good results in predicting human-virus PPIs. However, most methods are based on protein sequence features and apply manually extracted features, such as statistical characteristics, phylogenetic profiles, and physicochemical properties. In this work, we present an embedding-based neural framework with convolutional neural network (CNN) and bi-directional long short-term memory unit (Bi-LSTM) architecture, named Emvirus, to predict human-virus PPIs (including human–SARS-CoV-2 PPIs). In addition, we conduct cross-viral experiments to explore the generalization ability of Emvirus. Compared to other feature extraction methods, Emvirus achieves better prediction accuracy.</p></div>","PeriodicalId":36178,"journal":{"name":"Biosafety and Health","volume":"5 3","pages":"Pages 152-158"},"PeriodicalIF":0.0,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10166638/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9717247","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Seroprevalence of human enterovirus A71 in Guangzhou, China, 2019–2021 2019-2021年广州地区人肠道病毒A71血清阳性率分析

Biosafety and Health Pub Date : 2023-06-01 DOI: 10.1016/j.bsheal.2023.05.002

Huimin Lian , Huimin Jiang , Lina Yi , Jing Sun , Huaping Xie , Ming Qiu , Limei Sun , Huifang Lin , Mingda Yang , Lin Qu , Haiyi Yang , Jing Lu , Hanri Zeng

{"title":"Seroprevalence of human enterovirus A71 in Guangzhou, China, 2019–2021","authors":"Huimin Lian , Huimin Jiang , Lina Yi , Jing Sun , Huaping Xie , Ming Qiu , Limei Sun , Huifang Lin , Mingda Yang , Lin Qu , Haiyi Yang , Jing Lu , Hanri Zeng","doi":"10.1016/j.bsheal.2023.05.002","DOIUrl":"10.1016/j.bsheal.2023.05.002","url":null,"abstract":"<div><p>Enterovirus A71 (EV-A71) is a significant hand-foot-mouth disease (HFMD) etiology. The inactivated EV-A71 vaccines were approved in China in 2016. However, the seroprevalence of EV-A71 after the vaccine application and its potential association with the EV-A71 epidemic in the population are rarely studied. In this study, we analyzed the incidence of EV-A71 infection and seroepidemiology in Guangzhou City, China. From 2019 to 2021, 167,920 clinically confirmed HFMD cases were reported in Guangzhou. In 6,868 enterovirus-positive samples, Coxsackievirus A6 and Coxsackievirus A16 were dominant genotypes, and only 3 EV-A71-positive samples were detected, highlighting the deficient epidemic activity of EV-A71. Microneutralization assay was performed on 1,000 representative serum samples. Notably, the seroprevalence and geometric mean titer (GMT) decreased significantly in 2020, and that in the < 3-year age group were increased and even higher than that in 3–5-year age group in 2019 and 2021, which was contrary to our previous surveillance result and other studies in Guangzhou. Furthermore, a moderate decline of GMT level was observed following the vaccination, but the seropositive serums were still detected for 49 months after second immunization, suggesting the long-term persistence of the immunity. Our seroepidemiology study revealed relatively higher neutralizing antibody activity in the susceptible population after the EV-A71 vaccine was adopted in 2016 in Guangzhou. It may be one of the reasons for the lower epidemic activity of EV-A71 in Guangzhou from 2019 to 2021.</p></div>","PeriodicalId":36178,"journal":{"name":"Biosafety and Health","volume":"5 3","pages":"Pages 168-173"},"PeriodicalIF":0.0,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48904263","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}

引用次数: 0

Risk and countermeasure of laboratory-acquired infection based on pathogen transmission routes 基于病原体传播途径的实验室获得性感染风险及对策

Biosafety and Health Pub Date : 2023-06-01 DOI: 10.1016/j.bsheal.2023.04.006

Kunlan Zuo , Zongzhen Wu , Chihong Zhao , Huan Liu

引用次数: 0

Biosafety and mental health: Virus induced cognitive decline 生物安全和心理健康:病毒引起的认知能力下降

Biosafety and Health Pub Date : 2023-06-01 DOI: 10.1016/j.bsheal.2023.04.002

Chunxiao Du, Ge Li, Gencheng Han

引用次数: 0

A one-step reverse-transcription recombinase aided PCR assay for the rapid and sensitive detection of human enteroviruses 一步逆转录重组酶辅助聚合酶链式反应快速灵敏检测人肠道病毒

Biosafety and Health Pub Date : 2023-04-01 DOI: 10.1016/j.bsheal.2023.03.002

Xiuli Sun , Huanhuan Lu , Yanqing Tie , Mengchuan Zhao , Ruiqing Zhang , Zhenlu Sun , Guohao Fan , Fengyu Li , Fengyu Tian , Yaxin Hu , Mengyi Zhang , Xinxin Shen , Xuejun Ma , Zhishan Feng

{"title":"A one-step reverse-transcription recombinase aided PCR assay for the rapid and sensitive detection of human enteroviruses","authors":"Xiuli Sun , Huanhuan Lu , Yanqing Tie , Mengchuan Zhao , Ruiqing Zhang , Zhenlu Sun , Guohao Fan , Fengyu Li , Fengyu Tian , Yaxin Hu , Mengyi Zhang , Xinxin Shen , Xuejun Ma , Zhishan Feng","doi":"10.1016/j.bsheal.2023.03.002","DOIUrl":"10.1016/j.bsheal.2023.03.002","url":null,"abstract":"<div><p>Human enteroviruses (HEVs) include many different types that cause a wide range of diseases, and an effective method of genus-level identification has therefore significant clinical implications. However, quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR), the gold-standard method, still has shortfalls in diagnostic sensitivity and timeliness. Here we established a one-step real-time reverse-transcription recombinase-aided PCR assay (RT-RAP) to detect HEV fragment within an hour. The RT-RAP assay showed a detection limit of 5 copies/μL using recombinant plasmids and was extensively verified using 15 HEV strains. Among 15 types of HEV (species A-C), the sensitivity of RT-RAP was approximately 2–8 folds lower than that of the qRT-PCR in 9 types, and no-cross reaction with other viruses was observed. RT-RAP was further applied to analyze CSF and fecal specimens; the clinical performance demonstrated that the RT-RAP and the commercial qRT-PCR kit provided consistent results. These results indicated that RT-RAP assay may be a promising approach for rapid and sensitive detection of HEV.</p></div>","PeriodicalId":36178,"journal":{"name":"Biosafety and Health","volume":"5 2","pages":"Pages 126-131"},"PeriodicalIF":0.0,"publicationDate":"2023-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47816143","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}

引用次数: 0

A multiplex method for detection of SARS-CoV-2 variants based on MALDI-TOF mass spectrometry 基于MALDI-TOF质谱法的多重检测SARS-CoV-2变异体方法

Biosafety and Health Pub Date : 2023-04-01 DOI: 10.1016/j.bsheal.2023.02.003

Ziyuan Zhao , Liying Sun , Liqin Wang , Xiaodong Li , Junping Peng

{"title":"A multiplex method for detection of SARS-CoV-2 variants based on MALDI-TOF mass spectrometry","authors":"Ziyuan Zhao , Liying Sun , Liqin Wang , Xiaodong Li , Junping Peng","doi":"10.1016/j.bsheal.2023.02.003","DOIUrl":"10.1016/j.bsheal.2023.02.003","url":null,"abstract":"<div><p>The recent outbreak of the coronavirus disease 2019 (COVID-19) pandemic and the continuous evolution of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have highlighted the significance of new detection methods for global monitoring and prevention. Although quantitative reverse transcription PCR (RT-qPCR), the current gold standard for diagnosis, performs excellently in genetic testing, its multiplexing capability is limited because of the signal crosstalk of various fluorophores. Herein, we present a highly efficient platform which combines 17-plex assays with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), enabling the targeting of 14 different mutation sites of the spike gene. Diagnosis using a set of 324 nasopharyngeal swabs or sputum clinical samples with SARS-CoV-2 MS method was identical to that with the RT-qPCR. The detection consistency of mutation sites was 97.9% (47/48) compared to Sanger sequencing without cross-reaction with other respiratory-related pathogens. Therefore, the MS method is highly potent to track and assess SARS-CoV-2 changes in a timely manner, thereby aiding the continuous response to viral variation and prevention of further transmission.</p></div>","PeriodicalId":36178,"journal":{"name":"Biosafety and Health","volume":"5 2","pages":"Pages 101-107"},"PeriodicalIF":0.0,"publicationDate":"2023-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9977071/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9392325","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Towards precision medicine: Omics approach for COVID-19 迈向精准医学:治疗COVID-19的组学方法

Biosafety and Health Pub Date : 2023-04-01 DOI: 10.1016/j.bsheal.2023.01.002

Xiaoping Cen , Fengao Wang , Xinhe Huang , Dragomirka Jovic , Fred Dubee , Huanming Yang , Yixue Li

引用次数: 4