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Genome Characteristics of the Cyclophragma Undans Nucleopolyhedrovirus: A Distinct Species in Group Ⅰ of Alphabaculovirus

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Virologica Sinica 2018年第4期33卷 359-368页

作者： Zheng Zhu Jun Wang Qianran Wang Feifei Yin Xiaoping Liu Dianhai Hou Lei Zhang Haizhou Liu Jiang Li Basil M. Arif Hualin Wang Fei Deng Zhihong Hu Manli Wang State Key laboratory of Virology and China Center for virus Culture Collection Wuhan Institute of Virology Chinese Academy of Sciences Wuhan 430071 China Canadian Forest Service Great Lakes Forestry Centre Sault Ste Marie ON P6A 2E5 Canada

The Cyclophragma undans nucleopolyhedrovirus(Cyun NPV), a potential pest control agent, was isolated from Cyclophragma undans(Lepidoptera: Lasiocampidae), an important forest pest. In the present study, we performed detailed genome analysis of Cyun NPV and compared its genome to those of other Group Ⅰ alphabaculoviruses. Sequencing of the Cyun NPV genome using the Roche 454 sequencing system generated 142,900 bp with a G + C content of 45%. Genome analysis predicted a total of 147 hypothetical open reading frames comprising 38 baculoviral core genes, 24 lepidopteran baculovirus conserved genes, nine Group Ⅰ Alphabaculovirus conserved genes, 71 common genes, and five genes that are unique to Cyun NPV. In addition, the genome contains 13 homologous repeated sequences(hrs). Phylogenetic analysis groups Cyun NPV under a distinct branch within clade ‘‘a'' of Group Ⅰ in the genus Alphabaculovirus. Unlike other members of Group Ⅰ, Cyun NPV harbors only nine of the 11 genes previously determined to be specific to Group Ⅰ viruses.Furthermore, the Cyun NPV lacks the tyrosine phosphatase gene and the ac30 gene. The Cyun NPV F-like protein contains two insertions of continuous polar amino acids, one at the conventional fusion peptide and a second insertion at the pretransmembrane domain. The insertions are likely to affect the fusion function and suggest an evolutionary process that led to inactivation of the F-like protein. The above findings imply that Cyun NPV is a distinct species under Group Ⅰ Alphabaculovirus.

关键词：染色体分析核心基因特征害虫控制森林害虫重复序列种系发生进化过程

Pitfalls and optimal approaches to diagnose melioidosis

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Asian Pacific Journal of Tropical Medicine 2016年第6期9卷 501-510页

作者： Paul Vijay Kingsley Govindakarnavar Arunkumar Meghan Tipre Mark Leader Nalini Sathiakumar Sultan Ismail Hospital Manipal Center for virus Research Manipal University School of Public Health University of Alabama at Birmingham

Melioidosis is a severe and fatal infectious disease in the tropics and subtropics. It presents as a febrile illness with protean manifestation ranging from chronic localized infection to acute fulminant septicemia with dissemination of infection to multiple organs characterized by abscesses. Pneumonia is the most common clinical presentation. Because of the wide range of clinical presentations, physicians may often misdiagnose and mistreat the disease for tuberculosis, pneumonia or other pyogenic infections. The purpose of this paper is to present common pitfalls in diagnosis and provide optimal approaches to enable early diagnosis and prompt treatment of melidoidosis. Melioidosis may occur beyond the boundaries of endemic areas. There is no pathognomonic feature specific to a diagnosis of melioidosis. In endemic areas, physicians need to expand the diagnostic work-up to include melioidosis when confronted with clinical scenarios of pyrexia of unknown origin, progressive pneumonia or sepsis. Radiological imaging is an integral part of the diagnostic workup. Knowledge of the modes of transmission and risk factors will add support in clinically suspected cases to initiate therapy. In situations of clinically highly probable or possible cases where laboratory bacteriological confirmation is not possible, applying evidence-based criteria and empirical treatment with antimicrobials is recommended. It is of prime importance that patients undergo the full course of antimicrobial therapy to avoid relapse and recurrence. Early diagnosis and appropriate management is crucial in reducing serious complications leading to high mortality, and in preventing recurrences of the disease. Thus, there is a crucial need for promoting awareness among physicians at all levels and for improved diagnostic microbiology services. Further, the need for making the disease notifiable and/or initiating melioidosis registries in endemic countries appears to be compelling.

关键词： Melioidosis pseudomallei Review Diagnosis Treatment Pitfalls Approaches route of infection

Occurrence and molecular characterization of Potato spindle tuber viroid(PSTVd) isolates from potato plants in North China

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Journal of Integrative Agriculture 2016年第2期15卷 349-363页

作者： QIU Cai-ling ZHANG Zhi-xiang LI Shi-fang BAI Yan-ju LIU Shang-wu FAN Guo-quan GAO Yan-ling ZHANG Wei ZHANG Shu Lü Wen-he Lü Dian-qiu Northeast Agricultural University Harbin 150030 P.R. China virus-free Seedling Research Institute Heilongjiang Academy of Agricultural Sciences Harbin 150086 PR China State Key laboratory of Biology of Plant Diseases and Insect Pests Institute of Plant Protection Chinese Academy of Agricultural Sciences Beijing 100193 P.R. China

China is the largest potato producing country worldwide,with this crop representing the fourth largest staple food crop in China.However,the steady presence of Potato spindle tuber viroid（PSTVd） over the past five decades has a significant economic impact on potato production.To determine why PSTVd control measures have been ineffective in China,more than 1 000 seed potatoes collected between 2009 and 2014 were subjected to PSTVd detection at the Supervision and Testing Center for virus-free Seed Potatoes Quality,Ministry of Agriculture,China.A high PSTVd infection rate（6.5%） was detected among these commercial seed potatoes.Some breeding lines of potato collected from 2012 to 2015 were also tested for PSTVd infection,revealing a high rate of PSTVd contamination in these potato propagation materials.Furthermore,comparison of the full-length sequences of 71 different Chinese PSTVd isolates revealed a total of 74 predominant PSTVd variants,which represented 42 different sequence variants of PSTVd.Comparative sequence analysis revealed 30 novel PSTVd sequence variants specific to China.Comprehensive phylogenetic analysis uncovered a close relationship between the Chinese PSTVd sequence variants and those isolated from Russia.It is worth noting that three intermediate strains and six mild strains were identified among these variants.These results have important implications for explaining the ineffective control of PSTVd in China and thus could serve as a basic reference for designing more effective measures to eliminate PSTVd from China in the future.

关键词： certification germplasm phylogenetic analysis quarantine seed potato viroid

The E3 ligase RNF5 restricts SARS-CoV-2 replication by targeting its envelope protein for degradation

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Signal Transduction and Targeted Therapy 2023年第3期8卷 1175-1185页

作者： Zhaolong Li Pengfei Hao Zhilei Zhao Wenying Gao Chen Huan Letian Li Xiang Chen Hong Wang Ningyi Jin Zhao-Qing Luo Chang Li Wenyan Zhang Departement of Infectious Diseases Infectious Diseases and Pathogen Biology CenterInstitute of Virology and AIDS ResearchKey Laboratory of Organ Regeneration and Transplantation of The Ministry of EducationThe First Hospital of Jilin UniversityChangchunChina Research Unit of Key Technologies for Prevention and Control of virus Zoonoses Chinese Academy of Medical SciencesChangchun Veterinary Research InstituteChinese Academy of Agricultural SciencesChangchun 130000 JilinChina

The coronavirus disease 2019(COVID-19)pandemic caused by severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)has caused a severe global health crisis;its structural protein envelope(E)is critical for viral entry,budding,production,and induction of pathology which makes it a potential target for therapeutics against COVID-19.Here,we find that the E3 ligase RNF5 interacts with and catalyzes ubiquitination of E on the 63rd lysine,leading to its degradation by the ubiquitin-proteasome system(UPS).Importantly,RNF5-induced degradation of E inhibits SARS-CoV-2 replication and the RNF5 pharmacological activator Analog-1 alleviates disease development in a mouse infection model.We also found that RNF5 is distinctively expressed in different age groups and in patients displaying different disease severity,which may be exploited as a prognostic marker for COVID-19.Furthermore,RNF5 recognized the E protein from various SARS-CoV-2 strains and SARS-CoV,suggesting that targeting RNF5 is a broad-spectrum antiviral strategy.Our findings provide novel insights into the role of UPS in antagonizing SARS-CoV-2 replication,which opens new avenues for therapeutic intervention to combat the COVID-19 pandemic.

关键词： envelope acute respiratory

Fusarivirus accessory helicases present an evolutionary link for viruses infecting plants and fungi

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Virologica Sinica 2022年第3期37卷 427-436页

作者： Assane Hamidou Abdoulaye Jichun Jia Aqleem Abbas Du Hai Jiasen Cheng Yanping Fu Yang Lin Daohong Jiang Jiatao Xie State Key laboratory of Agricultural Microbiology Huazhong Agricultural UniversityWuhan430070China Hubei Key laboratory of Plant Pathology College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhan430070China Hubei Hongshan laboratory Wuhan430070China

A significant number of mycoviruses have been identified that are related to plant viruses,but their evolutionary relationships are largely unexplored.A fusarivirus,Rhizoctonia solani fusarivirus 4(RsFV4),was identified in phytopathogenic fungus Rhizoctonia solani(R.solani)strain XY74 co-infected by an alphaendornavirus.RsFV4 had a genome of 10,833 nt(excluding the poly-A tail),and consisted of four non-overlapping open reading frames(ORFs).ORF1 encodes an 825 aa protein containing a conserved helicase domain(Hel1).ORF3 encodes 1550 aa protein with two conserved domains,namely an RNA-dependent RNA polymerase(RdRp)and another helicase(Hel2).The ORF2 and ORF4 likely encode two hypothetical proteins(520 and 542 aa)with unknown functions.The phylogenetic analysis based on Hel2 and RdRp suggest that RsFV4 was positioned within the fusarivirus group,but formed an independent branch with three previously reported fusariviruses of R.solani.Notably,the Hel1 and its relatives were phylogenetically closer to helicases of potyviruses and hypoviruses than fusariviruses,suggesting fusarivirus Hel1 formed an evolutionary link between these three virus groups.This finding provides evidence of the occurrence of a horizontal gene transfer or recombination event between mycoviruses and plant viruses or between mycoviruses.Our findings are likely to enhance the understanding of virus evolution and diversity.

关键词： Fusarivirus Potyvirus Hypovirus Helicase Horizontal gene transfer(HGT)

Partial recovery of disturbed V-J pairing profiles of T-cell receptor in people living with HIV receiving long-term antiretroviral therapy

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Science China(Life Sciences) 2021年第1期64卷 152-161页

作者： Guoli Li Jiarui Li Henghui Zhang Yu Zhang Di Liu Yu Hao Junyan Han Juan Du Liuluan Zhu Yongqin Zeng Bei Li Rui Li Chuan Song Fujie Zhang Chen Chen Hongxin Zhao Hui Zeng Institute of Infectious Diseases Beijing Ditan HospitalCapital Medical UniversityBeijing100015China Beijing Key laboratory of Emerging Infectious Diseases Beijing100015China Clinical and Research Center of Infectious Diseases Beijing Ditan HospitalCapital Medical UniversityBeijing100015China Computational Virology Group Center for Bacteria and Virus Resources and ApplicationWuhan Institute of VirologyChinese Academy of SciencesWuhan430071China University of Chinese Academy of Sciences Beijing101408China

Chronic human immunodeficiency virus(HIV) infection not only causes a gradual loss of CD4~+T cells but also leads to a disturbance of the T cell receptor(TCR) repertoire. In people living with HIV(PLWH), monitoring TCR repertoire is challenged by the inconsistency of complementarity determining region 3(CDR3) and limited cell numbers in clinical samples. Thus, a quantitative method is necessary for monitoring the TCR repertoire in PLWH.We characterized the TCR V-J pairing profile of na?ve and memory CD4~+T cells in healthy donors, HIV-infected antiretroviral therapy(ART)-na?ve patients and long-term(over5 years) ART-experienced patients by performing TCR sequencing. We developed a V-J index with 18 parameters which were subdivided into five categories(expression coverage, cumulative percentage of the top tenth percentile, diversity, intra-individual similarity and inter-individual similarity). In ART-na?ve patients, 14 of the 18 parameters were significantly altered.Long-term ART recovered ten parameters. The four unrecovered parameters were related to inter-individual similarity.Therefore, these findings indicate that long-term ART could only partially recover TCR V-J pairs and introduce newly impacted V-J pairs. Moreover, these results provide new insights into the V-J pairing of the TCR and into the disturbance of TCR repertoire in HIV infection.

关键词： acquired immune deficiency syndrome human immunodeficiency virus antiretroviral therapy T cell receptor V-J pairing

Small animal model for HIV-1 Disease

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中国实验动物学报 2005年第S1期13卷 9-页

作者： Yoshio Koyanagi laboratory of Viral Pathogenesis Institute for Virus ResearchKyoto University Kyoto 606-8507 Japan

Structural and functional insights into MCR-2 mediated colistin resistance

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Science China(Life Sciences) 2018年第11期61卷 1432-1436页

作者： Xudong Wang Qiong Lu Jianxun Qi Yan Chai Youchun Wang George Fu Gao CAS Key laboratory of Pathogenic Microbiology and Immunology Institute of Microbiology Chinese Academy of Sciences College of Life Sciences University of Chinese Academy of Sciences Key laboratory of the Ministry of Health for Research on Quality and Standardization of Biotech Products Division of HIV/AIDS and Sexually Transmitted Virus Vaccines National Institutes for Food and Drug Control National Institute for Viral Disease Control and Prevention Chinese Center for Disease Control and Prevention (China CDC) Research Network of Immunity and Health (RNIH) Beijing Institutes of Life Science Chinese Academy of Sciences

Dear Editor,The spread of antibiotic resistance genes among bacteria is a serious and growing threat to global health (Peleg and Hoopet,2010).One emerging case is transferable genes found in bacteria-encoding enzymes resistant to colistin.Colistin is a cationic polypeptide antibiotic with broadspectrum activity against Gram-negative bacteria through interactions with the lipid A moiety of bacterial lipopoly-saccharide(LPS),subsequently destroying the cell envelope.During late 2015,a plasmid-mediated gene,mcr-1,was first reported from Escherichia coli(E.coli)in China to confer resistance to colistin(Liu et a1.,2016),and detected world-wide soon afterwards(Gao et a1.,2016;Hu et a1.,2016).

关键词： colistin resistance genes bacteria

The prevalence of deleterious mutations during the domestication and improvement of soybean

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The Crop Journal 2023年第2期11卷 523-530页

作者： Shichao Sun Yumin Wang He Wei David E.Hufnagel Ya Wang Shiyu Guo Yinghui Li Li Wang Li-juan Qiu Shenzhen Branch Guangdong laboratory for Lingnan Modern Agriculture/Genome Analysis laboratory of the Ministry of Agriculture/Agricultural Genomics Institute at Shenzhen Chinese Academy of Agricultural SciencesShenzhen 518000GuangdongChina Soybean Research Institute Jilin Academy of Agricultural SciencesChangchun 130033JilinChina Henan Academy of Crops Molecular Breeding Henan Academy of Agricultural Sciences/National Centre for Plant BreedingZhengzhou 450002HenanChina virus and Prion Research Unit National Animal Disease CenterThe Agricultural Research Service(ARS)of the United States Department of Agriculture(USDA)AmesIA 50010USA The National Key Facility for Crop Gene Resources and Genetic Improvement(NFCRI)/Key laboratory of Crop Gene Resource and Germplasm Enhancement(MOA)/Key laboratory of Soybean Biology(Beijing)(MOA) Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijing 100081China Kunpeng Institute of Modern Agriculture at Foshan Foshan 528200GuangdongChina

Soybean(Glycine max L.)is a protein and oil crop grown worldwide.Its fitness may be reduced by deleterious mutations,whose identification and purging is desirable for crop breeding.In the published whole-genome re-sequenced data of 2214 soybean accessions,including 221 wild soybean,1132 landrace cultivars and 861 improved soybean lines,we identified 115,275 deleterious single-nucleotide polymorphisms(SNPs).Numbers of deleterious alleles increased from wild soybeans to landraces and decreased from landraces to modern improved lines.Genes in selective-sweep regions showed fewer deleterious mutations than the remaining genes.Deleterious mutations explained 4.3%-48%more phenotypic variation than randomly selected SNPs for resistance to soybean cyst nematode race 2(SCN2),soybean cyst nematode race 3(SCN3)and soybean mosaic virus race 3(SMV3).These findings illustrate how mutation load has shifted during soybean domestication,expansion and improvement and provide candidate sites for breeding out deleterious mutations in soybean by genome editing and/or conventional breeding focused on the selection of progeny with fewer deleterious alleles.

关键词： Deleterious mutations Domestication cost Expansion load BAD_Mutations Soybean cyst nematode