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| 1 | Viral Metagenomics Analysis of Planktonic Viruses in East Lake,Wuhan,China显示文摘East Lake(Lake Donghu),located in Wuhan,China,is a typical city freshwater lake that has been experiencing eutrophic conditions and algal blooming during recent years.Marine and fresh water are considered to contain a large number of viruses.However,little is known about their genetic diversity because of the limited techniques for culturing viruses.In this study,we conducted a viral metagenomic analysis using a high-throughput sequencing technique with samples collected from East Lake in Spring,Summer,Autumn,and Winter.The libraries from four samples each generated 234,669,71,837,12,820,and 34,236 contigs(>90 bp each),respectively.The genetic structure of the viral community revealed a high genetic diversity covering 23 viral families,with the majority of contigs homologous to DNA viruses,including members of Myoviridae,Podoviridae,Siphoviridae,Phycodnaviridae,and Microviridae,which infect bacteria or algae,and members of Circoviridae,which infect invertebrates and vertebrates.The highest viral genetic diversity occurred in samples collected in August,then December and June,and the least diversity in March.Most contigs have low-sequence identities with known viruses.PCR detection targeting the conserved sequences of genes(g20,psbA,psbD,and DNApol)of cyanophages further confirmed that there are novel cyanophages in the East Lake.Our viral metagenomic data provide the first preliminary understanding of the virome in one freshwater lake in China and would be helpful for novel virus discovery and the control of algal blooming in the future. | Xingyi Ge Yongquan Wu Meiniang Wang Jun Wang Lijun Wu Xinglou Yang Yuji Zhang Zhengli Shi | 2013 | Virologica Sinica2013，28，5： | 8 |
| 2 | Study of the Dynamics of Microcystis aeruginosa and its Cyanophage in East Lake using quantitative PCR显示文摘Dear Editor,East Lake,located in the middle and lower reaches of the Yangtze River,is a major source of drinking water for local residents.However,the large increase of population density and the rapid development of industry has resulted in heavy eutrophication of East Lake over the past few decades.Microcystis aeruginosa is a well-known | Han Xia Meiniang Wang Xingyi Ge Yongquan Wu Xinglou Yang Yuji Zhang Tianxian Li Zhengli Shi | 2013 | Virologica Sinica2013，28，5： | 2 |
| 3 | The taxonomy, host range and pathogenicity of coronaviruses and other viruses in the Nidovirales order显示文摘The frequent emergence of coronavirus(CoV)epidemics has seriously threatened public health and stock farming.The major hosts for CoVs are birds and mammals.Although most CoVs inhabit their specific natural hosts,some may occasionally cross the host barrier to infect livestock and even people,causing a variety of diseases.Since the beginning of the new century,increasing attention has been given to research on CoVs due to the emergence of highly pathogenic and genetically diverse CoVs that have caused several epidemics,including the recent COVID-19 pandemic.CoVs belong to the Coronaviridae family of the Nidovirales order.Recently,advanced techniques for viral detection and viral genome analyses have enabled characterization of many new nidoviruses than ever and have greatly expanded the Nidovirales order with new classification and nomenclature.Here,we first provide an overview of the latest research progress in the classification of the Nidovirales order and then introduce the host range,genetic variation,genomic pattern and pathogenic features of epidemic CoVs and other epidemic viruses.This information will promote understanding of the phylogenetic relationship and infectious transmission of various pathogenic nidoviruses,including epidemic CoVs,which will benefit virological research and viral disease control. | Zhijian Zhou Ye Qiu Xingyi Ge | 2021 | Animal Diseases2021，1，1： | 2 |
| 4 | Expression Profile and Function Analysis of Long Non-coding RNAs in the Infection of Coxsackievirus B3显示文摘The roles of IncRNAs in the infection of enteroviruses have been barely demonstrated.In this study,we used coxsackievirus B3(CVB3),a typical enterovirus,as a model to investigate the expression profiles and functional roles of IncRNAs in enterovirus infection.We profiled IncRNAs and mRNA expression in CVB3-infected HeLa cells by IncRNA-mRNA integrated microarrays.As a result,700 differentially expressed IncRNAs(431 up-regulated and 269 down-regulated)and 665 differentially expressed mRNAs(299 up-regulated and 366 down-regulated)were identified in CVB3 infection.Then we performed IncRNA-mRNA integrated pathway analysis to identify potential functional impacts of the differentially expressed mRNAs,in which IncRNA-mRNA correlation network was built.According to IncRNA-mRNA correlation,we found that XLOC-001188,an IncRNA down-regulated in CVB3 infection,was negatively correlated with NFAT5 mRNA,an anti-CVB3 gene reported previously.This interaction was supported by qPCR detection following siRNA-mediated knockdown of XLOC-001188,which showed an increase of NFAT5 mRNA and a reduction of CVB3 genomic RNA.In addition,we observed that four most significantly altered IncRNAs,SNHG11,RP11-145F16.2,RP11-1023L17.1 and RP11-1021N1.2 share several common correlated genes critical for CVB3 infection,such as BRE and IRF2BP1.In all,our studies reveal the alteration of IncRNA expression in CVB3 infection and its potential influence on CVB3 replication,providing useful information for future studies of enterovirus infection. | Lei Tong Ye Qiu Hui Wang Yunyue Qu Yuanbo Zhao Lexun Lin Yan Wang Weizhen Xu Wenran Zhao Hongyan He Guangze Zhao Mary HZhang Decheng Yang Xingyi Ge Zhaohua Zhong | 2019 | Virologica Sinica2019，34，6： | 2 |
| 5 | Prediction of coronavirus 3C-like protease cleavage sites using machine-learning algorithms显示文摘The coronavirus 3C-like(3CL)protease,a cysteine protease,plays an important role in viral infection and immune escape.However,there is still a lack of effective tools for determining the cleavage sites of the 3CL protease.This study systematically investigated the diversity of the cleavage sites of the coronavirus 3CL protease on the viral polyprotein,and found that the cleavage motif were highly conserved for viruses in the genera of Alphacoronavirus,Betacoronavirus and Gammacoronavirus.Strong residue preferences were observed at the neighboring positions of the cleavage sites.A random forest(RF)model was built to predict the cleavage sites of the coronavirus 3CL protease based on the representation of residues in cleavage motifs by amino acid indexes,and the model achieved an AUC of 0.96 in cross-validations.The RF model was further tested on an independent test dataset which were composed of cleavage sites on 99 proteins from multiple coronavirus hosts.It achieved an AUC of 0.95 and predicted correctly 80%of the cleavage sites.Then,1,352 human proteins were predicted to be cleaved by the 3CL protease by the RF model.These proteins were enriched in several GO terms related to the cytoskeleton,such as the microtubule,actin and tubulin.Finally,a webserver named 3CLP was built to predict the cleavage sites of the coronavirus 3CL protease based on the RF model.Overall,the study provides an effective tool for identifying cleavage sites of the 3CL protease and provides insights into the molecular mechanism underlying the pathogenicity of coronaviruses. | Huiting Chen Zhaozhong Zhu Ye Qiu Xingyi Ge Heping Zheng Yousong Peng | 2022 | Virologica Sinica2022，37，3： | 1 |
| 6 | RNA barcode segments for SARS-CoV-2 identification from HCoVs and SARSr-CoV-2 lineages显示文摘Severe acute respiratory syndrome coronavirus 2(SARS-CoV-2),the pathogen responsible for coronavirus disease 2019(COVID-19),continues to evolve,giving rise to more variants and global reinfections.Previous research has demonstrated that barcode segments can effectively and cost-efficiently identify specific species within closely related populations.In this study,we designed and tested RNA barcode segments based on genetic evolutionary relationships to facilitate the efficient and accurate identification of SARS-CoV-2 from extensive virus samples,including human coronaviruses(HCoVs)and SARSr-CoV-2 lineages.Nucleotide sequences sourced from NCBI and GISAID were meticulously selected and curated to construct training sets,encompassing 1733 complete genome sequences of HCoVs and SARSr-CoV-2 lineages.Through genetic-level species testing,we validated the accuracy and reliability of the barcode segments for identifying SARS-CoV-2.Subsequently,75 main and subordinate species-specific barcode segments for SARS-CoV-2,located in ORF1ab,S,E,ORF7a,and N coding sequences,were intercepted and screened based on single-nucleotide polymorphism sites and weighted scores.Post-testing,these segments exhibited high recall rates(nearly 100%),specificity(almost 30%at the nucleotide level),and precision(100%)performance on identification.They were eventually visualized using one and two-dimensional combined barcodes and deposited in an online database(http://gffzz5c123ad9140e4e5fhu6b9x556qbvo6fb0.ffgz.tsg.suse.edu.cn/).The successful integration of barcoding technology in SARS-CoV-2 identification provides valuable insights for future studies involving complete genome sequence polymorphism analysis.Moreover,this cost-effective and efficient identification approach also provides valuable reference for future research endeavors related to virus surveillance. | Changqiao You Shuai Jiang Yunyun Ding Shunxing Ye Xiaoxiao Zou Hongming Zhang Zeqi Li Fenglin Chen Yongliang Li Xingyi Ge Xinhong Guo | 2024 | Virologica Sinica2024，39，1： | 0 |
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