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Complex positive selection pressures drive the evolution of HIV-1 with different co-receptor tropisms

Science China(Life Sciences) 2010年第10期53卷 1204-1214页

作者： zhang chiyu DING Na CHEN KePing YANG RongGe Institute of Life Sciences Jiangsu UniversityZhenjiang 212013China HIV Molecular Epidemiology and Virology Research Group State Key Laboratory of VirologyWuhan Institute of VirologyChinese Academy of SciencesWuhan 430071China

HIV-1 co-receptor tropism is central for understanding the transmission and pathogenesis of HIV-1 infection. We performed a genome-wide comparison between the adaptive evolution of R5 and X4 variants from HIV-1 subtypes B and C. The results showed that R5 and X4 variants experienced differential evolutionary patterns and different HIV-1 genes encountered various positive selection pressures, suggesting that complex selection pressures are driving HIV-1 evolution. Compared with other hypervariable regions of Gp120, significantly more positively selected sites were detected in the V3 region of subtype B X4 variants, V2 region of subtype B R5 variants, and V1 and V4 regions of subtype C X4 variants, indicating an association of positive selection with co-receptor recognition/binding. Intriguingly, a significantly higher proportion (33.3% and 55.6%, P<0.05) of positively selected sites were identified in the C3 region than other conserved regions of Gp120 in all the analyzed HIV-1 variants, indicating that the C3 region might be more important to HIV-1 adaptation than previously thought. Approximately half of the positively selected sites identified in the env gene were identical between R5 and X4 variants. There were three common positively selected sites (96, 113 and 281) identified in Gp41 of all X4 and R5 variants from subtypes B and C. These sites might not only suggest a functional importance in viral survival and adaptation, but also imply a potential cross-immunogenicity between HIV-1 R5 and X4 variants, which has important implications for AIDS vaccine development.

关键词： HIV-1 co-receptor tropism adaptive evolution positively selected site R5 and X4 Gp120 epitopes

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Laos is Affected by HIV CRF01_AE and the Newly Identified CRF97_01B

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Virologica Sinica 2020年第5期35卷 538-547页

作者： Xin Chen Mei Ye Yu Wang chiyu zhang Yong-Tang Zheng Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province National Kunming High Level Biosafety Research Center for Non-human PrimateKunming Institute of ZoologyChinese Academy of SciencesKunming 650223China Department of Pathogenic Biology School of Basic Medical SciencesGannan Medical UniversityGanzhou 341000China KIZ-SU Joint Laboratory of Animal Models and Drug Development College of Pharmaceutical SciencesSoochow UniversitySuzhou 215006China Pathogen Discovery and Evolution Unit Pathogen Discovery and Big Data CenterInstitut Pasteur of ShanghaiChinese Academy of SciencesShanghai 200031China

Laos is the only landlocked country in Southeast Asia and borders Thailand,Myanmar and Cambodia,the three countries in this region that have been hardest hit by human immunodeficiency virus(HIV).Laos has been regarded as a low-HIVprevalence country for *** understand the status of HIV in Laos in recent years,a retrospective study was performed among 2851 patients visiting a hospital in Vientiane,the capital of Laos,from November 2011 to May *** blood samples were obtained from the patients,and DNA was *** status was determined by HIV gag fragment-specific PCR ***-nine samples were detected as HIV proviral DNA positive with a positive rate of 2.4%(69/2851).Sixty-one near full-length genomic sequences were obtained from the positive *** results of phylogenetic analysis showed that the vast majority(91.8%)of the HIV strains belonged to CRF01AE,and the other five(8.2%)strains were identified as a new HIV circulating recombinant form CRF9701B,which had a CRF01AE backbone with an insertion of subtype B in the gag-pol *** analysis revealed that HIV CRF01AE circulating in Laos were multiply introduced from *** results indicated that Laos might be suffering a considerably more serious impact of HIV than previously *** keep this country from undergoing the same increase in HIV prevalence observed in its neighbors,immediate intervention measures and sufficient epidemiological research are urgently needed.

关键词： Human immunodeficiency virus(HIV) Subtype CRF01_AE CRF9701B Epidemiology Laos

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National Epidemiology and Evolutionary History of Four Hand, Foot and Mouth Disease-Related Enteroviruses in China from 2008 to 2016

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Virologica Sinica 2020年第1期35卷 21-33页

作者： Xuemin Fu Zhenzhou Wan Yanpeng Li Yihong Hu Xia Jin chiyu zhang Pathogen Discovery and Big Data Center CAS Key Laboratory of Molecular Virology and ImmunologyInstitut Pasteur of ShanghaiChinese Academy of SciencesUniversity of Chinese Academy of SciencesShanghai 200031China Medical Laboratory of Taizhou Fourth People’s Hospital Taizhou 225300China Viral Disease and Vaccine Translational Research Unit CAS Key Laboratory of Molecular Virology and ImmunologyInstitut Pasteur of ShanghaiChinese Academy of SciencesShanghai 200031China

Hand, foot and mouth disease(HFMD) is a major public health concern in China. The most predominant enteroviruses that cause HFMD have traditionally been attributed to enterovirus A71(EVA71) and coxsackievirus A16(CVA16). Since its first large outbreak in 2008, the dominant HFMD pathogens are constantly changing. In 2013 and 2015, CVA6 exceeded both EVA71 and CVA16 to become the leading cause of HFMD in some provinces. However, there still lacks a comprehensive overview on the molecular epidemiology and evolution of HFMD-related enteroviruses at the national level. In this study, we performed systematic epidemiological analyses of HFMD-related enteroviruses using the data of 64 published papers that met the inclusion criteria, and conducted phylogenetic analyses based on 12,080 partial VP1 sequences identified in China before 31 st June 2018. We found that EVA71 prevalence has decreased sharply but other enteroviruses have increased rapidly from 2008 to 2016 and that one subtype of each enterovirus is represented during the epidemic. In addition, four genotypes EVA71_C4, CVA16_B1, CVA6_D and CVA10_C are the most predominant enterovirus strains and collectively they cause over 90% of all HFMD cases in China according to the phylogenetic trees using representative partial VP1 sequences. These four major enterovirus genotypes have different geographical distributions, and they may cocirculate with other genotypes and serotypes. These results suggest that more molecular epidemiological studies should be performed on several enteroviruses simultaneously, and such information should have implications for virological surveillance, disease management, vaccine development and policy-making on the prevention and control of HFMD.

关键词： Enterovirus Hand,foot and mouth disease(HFMD) Molecular epidemiology Evolution Genotype

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Non-Chinese Immigrants： Challenge Faced by Yunnan of China to Achieve the 90–90–90 Goals

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Virologica Sinica 2018年第3期33卷 291-293页

作者： Xin Chen Lin Duo Mei Ye chiyu zhang Yong-Tang Zheng Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province Kunming Institute of Zoology Chinese Academy of Sciences Kunming 650223 China Pathogen Discovery and Big Data Center CAS Key Laboratory of Molecular Virology and Immunology Institut Pasteur of Shanghai Chinese Academy of SciencesShanghai 200031 China Yunnan Fuwai Cardiovascular Hospital Kunming 650032China

China’s AIDS epidemic started among people who inject drugs(PWID)in Ruili county-level city,a China–Myanmar border city of Yunnan Province,in 1989(Fig.1).Since then HIV has spread rapidly across the country(He and D... 详细信息

关键词：中国云南移民流行病爱滋病注射药 HIV 城市

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Altered vaginal eukaryotic virome is associated with different cervical disease status

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Virologica Sinica 2023年第2期38卷 184-197页

作者： Yanpeng Li Le Cao Xiao Han Yingying Ma Yanmei Liu Shujun Gao chiyu zhang Shanghai Public Health Clinical Center Fudan UniversityShanghai201508China Center of Diagnosis and Treatment for Cervical Diseases Obstetrics and Gynecology Hospital of Fudan UniversityShanghai200080China Shanghai Key Laboratory of Female Reproductive Endocrine-Related Disease Fudan UniversityShanghai200080China

Viruses are important components of the human *** evidence suggests that they are engaged in the physiology and disease status of the *** though the vaginal microbiome is involved in human papillomavirus(HPV)infection and cervical cancer(CC)progression,little is known about the role of the vaginal *** this pilot exploratory study,using unbiased viral metagenomics,we aim to investigate the vaginal eukaryotic virome in women with different levels of cervical lesions,and examine their associations with different cervical disease *** altered eukaryotic virome was observed in women with different levels of lesions and Lactobacillus *** and papillomaviruses are the most commonly detected eukaryotic viruses of the vaginal *** abundance and richness of anelloviruses and papillomaviruses were associated with lowgrade squamous intraepithelial lesion(LSIL)and ***,higher anellovirus abundance was also associated with lactobacillus-depleted microbiome profiles and bacterial community state(CST)type ***,increased correlations between Anelloviridae and Papillomaviridae occurred in the women with increased cervical disease severity level from LSIL to *** data suggest underlying interactions between different microbes as well as the host *** abundance and diversity of both anelloviruses and papillomaviruses shared by LSIL and CC suggest that anellovirus may be used as a potential adjunct biomarker to predict the risk of HPV persistent infection and/or *** studies need to focus on the clinical relevance of anellovirus abundance with cervical disease status,and the evaluation of their potential as a new adjunct biomarker for the prediction and prognoses of CC.

关键词： Vaginal virome Cervical cancer Anellovirus Papillomavirus

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Progressive deterioration of the upper respiratory tract and the gut microbiomes in children during the early infection stages of COVID-19

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Journal of Genetics and Genomics 2021年第9期48卷 803-814页

作者： Rong Xu Pengcheng Liu Tao zhang Qunfu Wu Mei Zeng Yingying Ma Xia Jin Jin Xu Zhigang zhang chiyu zhang Shanghai Public Health Clinical Center Fudan UniversityShanghai 201508China Pathogen Discovery and Evolution Unit Institut Pasteur of ShanghaiChinese Academy of SciencesShanghai 200031China Children's Hospital of Fudan University Shanghai 201102China State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan School of Life SciencesYunnan UniversityKunmingYunnan 650091China

Children are less susceptible to coronavirus disease 2019 (COVID-19), and they have manifested lower morbidity and mortality after infection, for which a multitude of mechanisms may be considered. Whether the normal development of the gut-airway microbiome in children is affected by COVID-19 has not been evaluated. Here, we demonstrate that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)infection alters the upper respiratory tract and the gut microbiomes in nine children. The alteration of the microbiome is dominated by the genus Pseudomonas, and it sustains for up to 25e58 days in different individuals. Moreover, the patterns of alternation are different between the upper respiratory tract and the gut. Longitudinal investigation shows that the upper respiratory tract and the gut microbiomes are extremely variable among children during the course of COVID-19. The dysbiosis of microbiome persists in7 of 8 children for at least 19e24 days after discharge from the hospital. Disturbed development of both the gut and the upper respiratory microbiomes and prolonged dysbiosis in these nine children imply possible long-term complications after clinical recovery from COVID-19, such as predisposition to the increased health risk in the post-COVID-19 era.

关键词： SARS-CoV-2/COVID-19 Upper respiratory microbiome Gut microbiota Dysbiosis Children

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A Novel 2-dimensional Multiplex qPCR Assay for Single-Tube Detection of Nine Human Herpesviruses

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Virologica Sinica 2021年第4期36卷 746-754页

作者： Yingxue Li Zhenzhou Wan Lulu Zuo Shenwei Li Honglian Liu Yingying Ma Lianqun Zhou Xia Jin Yuye Li chiyu zhang Shanghai Public Health Clinical Center Fudan UniversityShanghai201508China CAS Key Laboratory of Bio-Medical Diagnostics Suzhou Institute of Biomedical Engineering and TechnologyChinese Academy of SciencesSuzhou215163China School of Biomedical Engineering University of Science and Technology of ChinaHefei260026China Medical Laboratory of Taizhou Fourth People's Hospital Taizhou225300China Viral Hemorrhagic Fevers Research Unit Institut Pasteur of ShanghaiChinese Academy of SciencesShanghai200031China Shanghai International Travel Healthcare Center Shanghai200335China Department of Dermatology and Venereology First Affiliated Hospital of Kunming Medical UniversityKunming650032China

Human herpesviruses are double-stranded DNA viruses that are classified into nine *** than 90%of adults are ever infected with one or more *** symptoms of infection with different herpesviruses are diverse ranging from mild or asymptomatic infections to deadly diseases such as aggressive lymphomas and *** and accurate detection of herpesvirus infection is critical for clinical management and *** this study,we established a single-tube nonuple qPCR assay for detection of all nine herpesviruses using a 2-D multiplex qPCR method with a house-keeping gene as the internal *** novel assay can detect and distinguish different herpesviruses with 30 to 300 copies per 25µL single-tube reaction,and does not cross-react with 20 other human viruses,including DNA and RNA *** robustness of the novel assay was evaluated using 170 clinical *** novel assay showed a high consistency(100%)with the single qPCR assay for HHVs *** features of simple,rapid,high sensitivity,specificity,and low cost make this assay a high potential to be widely used in clinical diagnosis and patient treatment.

关键词： Human herpesviruses(HHVs) 2-D multiplex qPCR Melting temperature(Tm) Fluorescence probe Melting curve

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Development of a Novel Reverse Transcription Loop-Mediated Isothermal Amplification Method for Rapid Detection of SARS-CoV-2

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Virologica Sinica 2020年第3期35卷 344-347页

作者： Renfei Lu Xiuming Wu Zhenzhou Wan Yingxue Li Lulu Zuo Jianru Qin Xia Jin chiyu zhang Clinical Laboratory Nantong Third Hospital Affiliated to Nantong UniversityNantong 226006China Pathogen Discovery and Evolution Unit Institut Pasteur of ShanghaiChinese Academy of SciencesShanghai 200031China Medical Laboratory of Taizhou Fourth People’s Hospital Taizhou 225300China College of Life Sciences Henan Normal UniversityXinxiang 453007China Shanghai Public Health Clinical Center Fudan UniversityJinshan DistrictShanghai 201508China

Dear Editor,Since early December 2019, a large outbreak of pneumonia caused by a novel coronavirus(COVID-19) had emerged in Wuhan, China(Wu et al. 2020 a, b;Zhou et al. 2020;Zhu et al. 2020;Jiang and Shi 2020). Similar to severe acute respiratory syndrome coronavirus(SARS-CoV) and Middle East respiratory syndrome coronavirus(MERS-CoV),the new coronavirus also belongs to Betacoronavirus。

关键词： al. respiratory acute

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基于分类回归树算法的专利价值评估指标体系研究

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厦门大学学报（自然科学版） 2017年第2期56卷 244-251页

作者：邱一卉张驰雨陈水宣厦门理工学院经济与管理学院厦门理工学院机械与汽车工程学院福建厦门361024

我国专利数据来源众多、指标关系复杂,针对现有专利价值评估过程依赖人为主观判断,缺乏客观、合理评估方法等问题,提出了一种基于分类回归树(classification and regression tree,CART)模型的属性选择方法,用于构建专利价值评估的指标体... 详细信息

我国专利数据来源众多、指标关系复杂,针对现有专利价值评估过程依赖人为主观判断,缺乏客观、合理评估方法等问题,提出了一种基于分类回归树(classification and regression tree,CART)模型的属性选择方法,用于构建专利价值评估的指标体系.实验结果表明相较于基于随机森林的属性选择方法,该方法不仅能有效地降低指标体系的规模,并且能提高评估建模的效率,在兼顾评估模型可解释性的基础上更好地提高专利价值评估的准确性.进一步通过枚举遍历的方法,约减指标集大小,构建出规模更小的指标体系,结合专家知识和实证研究,有效地验证了该指标体系的可解释性和现实意义.

关键词：专利价值评估指标体系属性选择决策树算法

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新疆乌鲁木齐冰上运动中心人工冰场施工技术

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施工技术 2015年第15期44卷 26-28页

作者：刘加华张赤宇江苏工程职业技术学院建筑工程学院江苏南通226007 南通四建集团有限公司江苏南通226300

结合新疆乌鲁木齐冰上运动中心人工冰场大型冰场项目实践,从冰场地层结构施工、F200级抗冻混凝土配制、浇筑和场地平整精度控制等环节进行设计和优化,保证工程各项指标满足现行的国际标准及国家规范的要求,降低了运行成本和维护费用、... 详细信息

结合新疆乌鲁木齐冰上运动中心人工冰场大型冰场项目实践,从冰场地层结构施工、F200级抗冻混凝土配制、浇筑和场地平整精度控制等环节进行设计和优化,保证工程各项指标满足现行的国际标准及国家规范的要求,降低了运行成本和维护费用、节能环保。

关键词：混凝土人工冰场抗冻混凝土平整精度环保

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