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Current research status of immunology in the genomic era

science china(life sciences) 2009年第1期52卷 43-49页

作者： li haowen1,li jinzhi1,zhao guoping2 & wang ying1,2 1 shanghai institute of immunology,institute of medical science,shanghai jiaotong university school of medicine,shanghai 200025,china 2 shanghai-MOST Key Laboratory of Health and Disease Genomics,Chinese National Human Genome Center,shanghai 201203,china 1. shanghai institute of immunology Institute of Medical Science Shanghai Jiaotong University School of Medicine Shanghai 200025 China 2. shanghai-MOST Key Laboratory of Health and Disease Genomics Chinese National Human Genome Center Shanghai 201203 China

This review updates the current status of immunology research under the influence of genomics,both conceptually and *** particularly highlights the advantages of employing the high-throughput and large-scale technology,the large genomic database,and bioinformatic power in the immunology *** fast development in the fields of basic immunology,clinical immunology(tumor and infectious immunology) and vaccine designing is illustrated with respect to the successful usage of genomic *** also speculate the future research directions of immunology in the era of genomics and post-genomics.

关键词： genomics immunology clinical immunology vaccine design

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Reduced clinical severity during 2022 shanghai Spring epidemic of SARS-CoV-2 omicron BA.2 variant infection——an integrated account of virus pathogenicity and vaccination effectiveness

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National science Review 2024年第4期11卷 24-27页

作者： Xingyue Wu Yao Chen Kangli Cao Yao Shen Xueling Wu Yilin Yang Zhongshu Kuang Qingrun li Zhenzhen Lu Yichen Jia Mian Shao Guorong Gu Xiangwei wang Ye Yao ying wang Shaodie Chen Zhigao Yu Wei Wei Longfei Ding Lulu Lan Tianwen Gu Xiangyu Long Jian Sun lingyu Xing Jiayuan Shen Yi Han Yue Luo Sucheng Mu Mengna lin Xiaoyan Zhang Rong Zeng Jianqing Xu guoping zhao lihong Huang Zhenju Song Department of Emergency medicine Clinical Center for Bio-Therapy Department of Biostatistics and Department of UrologyShanghai Key Laboratory of Lung Inflammation and Injury Zhongshan Hospital Fudan University Department of Respiratory and Critical Care medicine Shanghai Pudong Hospital Fudan University Department of Pulmonology Renji Hospital Shanghai Jiao Tong University School of Medicine Key Laboratory of Systems Biology Center for Excellence in Molecular Cell Science Shanghai Institute of Biochemistry and Cell Biology Chinese Academy of Sciences shanghai Public Health Clinical Center Fudan University Department of Biostatistics School of Public Health Key Laboratory of Public Health Safety of Ministry of Education and Shanghai Institute of Infectious Disease and Biosecurity School of Public Health Fudan University shanghai institute of immunology Department of Immunology and Microbiology Shanghai Institute of Virology Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of EducationSchool of Medicine Shanghai Jiao Tong University State Key Laboratory of Genetic Engineering Fudan Microbiome CenterSchool of Life Sciences Fudan University Bio-Med Big Data Center Shanghai Institute of Nutrition and Health Chinese Academy of Sciences

The emergence of SARS-Co V-2 variant of concern omicron BA.2 led to high infection incidence rates as well as reduced severity of COVID-19 during the shanghai Spring epidemic of 2022 [1]. We assessed the role of viral pathogenicity and the effectiveness of inactivated vaccines in a retrospective observational study including 10 258 confirmed COVID-19cases identified between April and June of 2022, from four COVID-19 designated hospitals located in two areas of shanghai, namely the West Bund and the East Bund, where the populations’ demographic characteristics varied significantly (Table S1, Fig. S1).

关键词： REPliCATION

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Evolutionary analysis and lineage designation of SARS-CoV-2 genomes

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science Bulletin 2021年第22期66卷 2297-2311,M0004页

作者： Xiaolu Tang Ruochen ying Xinmin Yao Guanghao li Changcheng Wu Yiyuli Tang Zhida li Bishan Kuang Feng Wu Changsheng Chi Xiaoman Du Yi Qin Shenghan Gao Songnian Hu Juncai Ma Tiangang liu Xinghuo Pang Jianwei wang guoping zhao Wenjie Tan Yaping Zhang Xuemei Lu Jian Lu State Key Laboratory of Protein and Plant Gene Research Center for BioinformaticsSchool of Life SciencesPeking UniversityBeijing 100871China State Key Laboratory of Genetic Resources and Evolution Kunming Institute of ZoologyCenter for Excellence in Animal Evolution and GeneticsChinese Academy of SciencesKunming 650223China Beijing institute of Genomics Chinese Academy of SciencesBeijing 100101China Yuxi Rongjian Information Technology Co. Ltd.Yuxi 653100China State Key Laboratory of Microbial Resources(SKLMR) The Institute of MicrobiologyChinese Academy of SciencesBeijing 100101China The Microresource and Big Data Center The Institute of MicrobiologyChinese Academy of SciencesBeijing 100101China Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education and Wuhan University School of Pharmaceutical SciencesWuhan 430071China Beijing Center for Disease Prevention and Control(CDC)&Research Center for Preventive medicine of Beijing Beijing 100013China NHC Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory Institute of Pathogen BiologyChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing 100730China Key Laboratory of Respiratory Disease Pathogenomics Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing 100730China Key Laboratory of Synthetic Biology Institute of Plant Physiology and EcologyShanghai Institutes for Biological SciencesChinese Academy of SciencesShanghai 200032China NHC Key Laboratory of Biosafety National Institute for Viral Disease Control and PreventionChinese Center for Disease Control and PreventionBeijing 102206China

The pandemic due to the severe acute respiratory syndrome coronavirus 2(SARS-CoV-2),the etiological agent of coronavirus disease 2019(COVID-19),has caused immense global *** the rapid accumulation of SARS-CoV-2 genome sequences,however,thousands of genomic variants of SARSCoV-2 are now publicly *** improve the tracing of the viral genomes’evolution during the development of the pandemic,we analyzed single nucleotide variants(SNVs)in 121,618 high-quality SARS-CoV-2 *** divided these viral genomes into two major lineages(L and S)based on variants at sites 8782 and 28144,and further divided the L lineage into two major sublineages(L1 and L2)using SNVs at sites 3037,14408,and ***,we categorized them into 130 sublineages(37 in S,35 in L1,and 58 in L2)based on marker SNVs at 201 additional genomic *** lineage/sublineage designation system has a hierarchical structure and reflects the relatedness among the subclades of the major *** also provide a companion website(***)that allows users to visualize sublineage information and upload their own SARS-CoV-2 genomes for sublineage ***,we discussed the possible roles of compensatory mutations and natural selection during SARS-CoV-2’s *** efforts will improve our understanding of the temporal and spatial dynamics of SARS-CoV-2’s genome evolution.

关键词： COVID-19 Evolutionary analysis Compensatory advantageous mutation Adaptive evolution lineage designation

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