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Origin and molecular characterization of the human-infecting H6N1 infl uenza virus in Taiwan

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Protein & Cell 2013年第11期4卷 846-853页

作者： weifeng shi Yi shi Ying Wu Di Liu George F.Gao School of Medical Sciences Taishan Medical CollegeTaian 271016China CAS Key Laboratory of Pathogenic Microbiology and Immunology Institute of MicrobiologyChinese Academy of SciencesBeijing 100101China Beijing Institutes of Life Sciences Chinese Academy of SciencesBeijing 100101China Network Information Center Institute of MicrobiologyChinese Academy of SciencesBeijing 100101China Offi ce of Director-General Chinese Center for Disease Control and Prevention(China CDC)Beijing 102206China

In June 2013,the fi rst human H6N1 infl uenza virus infec-tion was confirmed in ***,the origin and molecular characterization of this virus,A/Taiwan/2/2013(H6N1),have not been well studied thus *** the present report,we performed phylogenetic and coalescent analy-ses of this virus and compared its molecular profi le/char-acteristics with other closely related *** characterization of H6N1 revealed that it is a typical avian infl uenza virus of low pathogenicity,which might not rep-licate and propagate well in the upper airway in *** analysis revealed that the virus clusters with A/chicken/Taiwan/A2837/2013(H6N1)in seven genes,except *** the PB1 gene,A/Taiwan/2/2013 was clus-tered with a different H6N1 lineage from A/chicken/Taiwan/A2837/*** a previous study demonstrated that the PB2,PA,and M genes of A/Taiwan/2/2013 might be derived from the H5N2 viruses,coalescent analyses revealed that these H5N2 viruses were derived from more recent strains than that of the ancestor of A/Taiwan/2/***,we propose that A/Taiwan/2/2013 is a reassor-tant from different H6N1 lineages circulating in chickens in ***,compared to avian isolates,a sin-gle P186L(H3 numbering)substitution in the hemaggluti-nin H6 of the human isolate might increase the mammali-an receptor binding and,hence,this strain’s pathogenicity in ***,human infection with this virus seems an accidental event and is unlikely to cause an infl uenza ***,its co-circulation and potential reas-sortment with other infl uenza subtypes are still worthy of attention.

关键词： molecular characterization phylogenetic analysis coalescent analysis H6N1 infl uenza virus Taiwan

Pathogen genomic surveillance elucidates the origins, transmission and evolution of emerging viral agents in China

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Science China(Life Sciences) 2017年第12期60卷 1317-1330页

作者： weifeng shi Juan Li Hong Zhou George F.Gao Key Laboratory of Etiology and Epidemiology of Emerging Infectious Diseases in Universities of Shandong (Taishan Medical College) Taishan Medical College National Institute for Viral Disease Control and Prevention Chinese Center for Disease Control and Prevention (China CDC) CAS Key Laboratory of Pathogenic Microbiology and Immunology Institute of Microbiology Chinese Academy of Sciences

In the past twenty years, numerous novel zoonotic viral agents with pandemic potential have emerged in China, such as the severe acute respiratory syndrome(SARS) coronavirus and, more recently, the avian-origin influenza A/H7N9 virus, which have caused outbreaks among humans with high morbidity and mortality. In addition, several emerging and re-emerging viral pathogens have also been imported into China from travelers, e.g. the Middle East respiratory syndrome(MERS) coronavirus and Zika virus(ZIKV). Herein, we review these emerging viral pathogens in China and focus on how surveillance by pathogen genomics has been employed to discover and annotate novel pathogenic agents, identify natural reservoirs, monitor the transmission events and delineate their evolution and adaption to the human host. We also highlight the application of genomic sequencing in the recent Ebola epidemics in Western Africa. In summary, genomic sequencing has become a standard research tool in the field of emerging infectious diseases which has been proven invaluable in containing these viral infections and reducing burden of disease in humans and animals. Genomic surveillance of pathogenic agents will serve as a key epidemiological and research tool in the modern era of precision infectious diseases and in the future studies of virosphere.

关键词： emerging infectious diseases SARS-CoV MERS-CoV genomic surveillance H7N9 Zika Ebola

The Asian Lineage of Zika Virus: Transmission and Evolution in Asia and the Americas

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Virologica Sinica 2019年第1期34卷 1-8页

作者： Tao Hu Juan Li Michael J.Carr Sebastián Duchêne weifeng shi Key Laboratory of Etiology and Epidemiology of Emerging Infectious Diseases in Universities of Shandong Taishan Medical College Global Station for Zoonosis Control Global Institution for Collaborative Research and Education (GI-CoRE)Hokkaido University National Virus Reference Laboratory School of MedicineUniversity College Dublin Department of Biochemistry and Molecular Biology Bio21 Molecular Science and Biotechnology InstituteUniversity of Melbourne

Since first isolation in 1947 from the Zika forest in Uganda, Zika virus(ZIKV) has been principally known as a benign agent associated with sporadic human infections in a restricted number of African countries. However, during 2015–2016,an Asian lineage of ZIKV caused an unprecedentedly large outbreak in the Americas and sizeable numbers of exported cases across the globe. In this review, we critically appraise the recent advances in molecular epidemiological studies of ZIKV performed to date, and we highlight the pivotal role played by genomic surveillance in elucidating the origins,dissemination and evolution of the Asian lineage of ZIKV in Asia and in the Americas.

关键词： Zika virus(ZIKV) Asian lineage Transmission Evolution Re

Non-coding regions of the Ebola virus genome contain indispensable phylogenetic and evolutionary information

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Science China(Life Sciences) 2015年第7期58卷 682-686页

作者： JIANG XinQuan ZHANG ZhenJie ZHUANG DongMing CARR Michael J. ZHANG RuiLing LV Qiang shi weifeng School of Public Health Taishan Medical College Institute of Pathogen Biology Taishan Medical College National Virus Reference Laboratory University College Dublin

We compared the numbers of nucleotide substitutions occurring in the non-coding regions and coding regions of Ebola virus genomes and found that non-coding regions contain indispensable phylogenetic and evolutionary information. The omission of genetic data from non-coding regions can lead to unreliable phylogenies and inaccurate estimates of evolutionary parameters.

关键词： EBOV Ebola non-coding region phylogenetic analysis evolutionary information

Phylogenetics of varied subtypes of avian influenza viruses in China： potential threat to humans

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Protein & Cell 2014年第4期5卷 253-257页

作者： weifeng shi Wei Li Xianbin Li Joel Haywood Juncai Ma George F.Gao Di Liu School of Basic Medical Sciences Taishan Medical CollegeTaian 271016China Network Information Center Institute of MicrobiologyChinese Academy of SciencesBeijing 100101China Shenzhen Institute of Advanced Technology Chinese Academy of ScienceShenzhen 518055China University of Chinese Academy of Sciences Beijing 100049China CAS Key Laboratory of Pathogenic Microbiology and Immunology Institute of MicrobiologyChinese Academy of SciencesBeijing 100101China Beijing Institutes of Life Science Chinese Academy of SciencesBeijing 100101China Office of Director-General Chinese Center for Disease Control and Prevention(China CDC)Beijing 102206China

Dear Editor, Since February 2013, infections with several novel avian- origin influenza viruses have occurred in Taiwan and the Mainland of China. The H7N9 influenza virus has caused 136 human infections with 44 deaths in the first influenza season, and has continued to cause infections during the current influenza season （Li et al., 2014）. As of February 11th, 2014, a total of 331 human infections with 101 deaths in China have been reported （http：//***）. During the outbreak of H7N9 in the Mainland of China, Tai- wan reported the first human infection of avian H6N1 influ- enza virus, which again hit the public （shi et al., 2013a; Wei et al., 2013）. In November 2013, the first infection of H10N8 influenza virus was reported by Nanchang Center for Dis- ease Control and Prevention （Chen et al., 2014）.

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Ubiquitin-specific protease 24 promotes EV71 infection by restricting K63-linked polyubiquitination of TBK1

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Virologica Sinica 2023年第1期38卷 75-83页

作者： Lichao Zang Jin Gu Xinyu Yang Yukang Yuan Hui Guo Wei Zhou Jinhong Ma Yan Chen Yumin Wu Hui Zheng weifeng shi Department of Laboratory Medicine The Third Affiliated Hospital of Soochow UniversityChangzhou213003China International Institute of Infection and Immunity Institutes of Biology and Medical SciencesSoochow UniversitySuzhou215123China Jiangsu Key Laboratory of Infection and Immunity Soochow UniversitySuzhou215123China Hubei Hospital of Integrated Chinese and Western Medicine Wuhan430015China

TANK-binding kinase 1(TBK1)is an essential protein kinase for activation of interferon regulatory factor 3(IRF3)and induction of the type I interferons(IFN-I).Although the biochemical regulation of TBK1 activation has been studied,little is known about how enterovirus 71(EV71)employs the deubiquitinases(DUBs)to regulate TBK1 activation for viral immune ***,we found that EV71 infection upregulated the expression of ubiquitinspecific protease 24(USP24).Further studies revealed that USP24 physically interacted with TBK1,and can reduce K63-linked polyubiquitination of *** of USP24 upregulated TBK1 K63-linked polyubiquitination,promoted the phosphorylation and nuclear translocation of IRF3,and in turn improved IFN-I production during EV71 *** a consequence,USP24 knockdown dramatically inhibited EV71 *** study revealed USP24 as a novel regulator of TBK1 activation,which promotes the understanding of immune evasion mechanisms of EV71 and could provide a potential strategy for treatment of EV71 infection.

关键词： Ubiquitin-specific protease 24(USP24) Enterovirus 71(EV71) TANK-binding kinase 1(TBK1) Type I interferons(IFN-I) Innate immunity

Co-existence and co-infection of influenza A viruses and coronaviruses: Public health challenges

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The Innovation 2022年第5期3卷 38-47页

作者： Jing Yang Yuhuan Gong Chunge Zhang Ju Sun Gary Wong weifeng shi Wenjun Liu George FGao Yuhai Bi CAS Key Laboratory of Pathogenic Microbiology and Immunology Institute of MicrobiologyCenter for Influenza Research and Early-warning(CASCIRE)CAS-TWAS Center of Excellence for Emerging Infectious Diseases(CEEID)Chinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China Institut Pasteur of Shanghai Chinese Academy of SciencesShanghai 200031China Key Laboratory of Etiology and Epidemiology of Emerging Infectious Diseases in Universities of Shandong Shandong First Medical University&Shandong Academy of Medical SciencesTaian 271016China

Since the 20th century,humans have lived through five pandemics caused by influenza A viruses(IAVs)(H1N1/1918,H2N2/1957,H3N2/1968,and H1N1/2009)and the coronavirus(CoV)severe acute respiratory syndrome coronavirus 2(SARS-CoV-2).IAVs and CoVs both have broad host ranges and share multiple *** co-circulation and even co-infections facilitate genetic reassortment among IAVs and recombination among CoVs,further altering virus evolution dynamics and generating novel variants with increased cross-species transmission ***,SARS-CoV-2 may maintain longterm circulation in humans as seasonal ***-existence and co-infection of both viruses in humans could alter disease transmission patterns and aggravate disease ***,we demonstrate how virus-host ecology correlates with the co-existence and co-infection of IAVs and/or CoVs,further affecting virus evolution and disease dynamics and burden,calling for active virus surveillance and countermeasures for future public health challenges.

关键词： infection maintain generating

Identification of bovine coronavirus in a Daurian ground squirrel expands the host range of Betacoronavirus 1

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Virologica Sinica 2023年第2期38卷 321-323页

作者： Lin Xu Wei Liu Mengyu Bie Tao Hu Dong Yan Zhishu Xiao Edward C.Holmes weifeng shi School of Public Health Shandong First Medical University&Shandong Academy of Medical SciencesJi'nan250117China Key Laboratory of Emerging Infectious Diseases in Universities of Shandong Shandong First Medical University&Shandong Academy of Medical SciencesTai'an271000China State Key Laboratory of Integrated Management of Pest Insects and Rodents Institute of ZoologyChinese Academy of SciencesBeijing100101China University of Chinese Academy of Sciences Beijing100049China Anti-plague Institute of Hebei Province Zhangjiakou075000China Sydney Institute for Infectious Diseases School of Medical SciencesThe University of SydneySydneyNSW 2006Australia

Dear Editor,Bovine coronavirus(BCoV)is a member of the species Betacoronavirus 1 in the genus Betacoronavirus,subgenus *** members of the species Betacoronavirus 1 comprise porcine hemagglutinating encephalomyelitis virus(PHEV),human coronavirus OC43(HCoVOC43),equine coronavirus(ECoV),and rabbit coronavirus HKU14(RbCoV HKU14)(Corman et al.,2018).BCoV is known to infect a wide range of mammals including domestic and wild ruminants,causing enteritis and pneumonia(Saif,2010).BCoV is ubiquitous in cattle worldwide,even in the respiratory and intestinal samples of healthy individuals,causing major economic losses to the beef and dairy cattle industries(Vlasova and Saif,2021).Importantly,it has been suggested that HCoV-OC43 originated in rodents,and that the major host of BCoV–cattle–acts as intermediate host(Kin et al.,2016;Forni et al.,2017;Corman et al.,2018;Cui et al.,2019).

关键词： U14 rabbit

Characterization of Avian-like Influenza A (H4N6)Virus Isolated from Caspian Seal in 2012

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Virologica Sinica 2018年第5期33卷 449-452页

作者： Marina Gulyaeva Ivan Sobolev Kirill Sharshov Olga Kurskaya Alexander Alekseev Lidia Shestopalova Anna Kovner Yuhai Bi weifeng shi Michael Shchelkanov Alexander Shestopalov Novosibirsk State University NovosibirskRussia 630090 Federal State Budget Scientific Institution "Federal Research Center of Fundamental and Translational Medicine" NovosibirskRussia 630117 School of Biomedicine Far Eastern Federal UniversityVladvostokRussia 690090 Federal Scientific Center of East Asia Terrestrial Biodiverslty Far Eastern Branch of Russian Academy of SciencesVladivostokRussia 690022 CAS Key Laboratory of Pathogenic Microbiology and Immunology Institute of MicrobiologyCenter for Influenza Research and Early-warning (CASCIRE)Chinese Academy of SciencesBeijing 100101China Key Laboratory of Etiology and Epidermology of Emerging Infectious Diseases in Universiues of Shandong Taishan Medical CollegeTaian 271000China

Dear Editor Marine mammals are widely distributed and can be found almost in all coastal waters and coastlines around the *** interface areas between marine and terrestrial environments provide natural habitats for aquatic and semiaquatic mammals as well as for reservoir species of avian influenza viruses (AIV)(Runstadler et al.2013).

关键词： Caspian Seal Avian-like Influenza