非洲猪瘟病毒研究进展:组学视角Advances in African Swine Fever Virus Research:An Omics View
潘力;罗瑞;王涛;罗玉子;孙元;仇华吉;
摘要(Abstract):
非洲猪瘟(African swine fever,ASF)是由非洲猪瘟病毒(African swine fever virus,ASFV)引起的一种致死率可高达100%的猪烈性传染病。ASF的传播方式复杂多样,目前无商品化疫苗可用,仅能依靠检疫结合扑杀进行防控,严重威胁全球养猪及相关行业的健康发展。阻碍ASF疫苗研发的主要因素是ASFV的基因型众多、结构复杂,以及对ASFV致病和免疫逃逸机制的认识不足。本文从基因组学、转录组学、蛋白质组学和代谢组学等层面多角度综述ASFV的生物学特性及其致病和免疫逃逸机制,以期揭开ASF这个"杀手"的神秘面纱,为ASFV的致病机制研究和ASF的防控提供参考。
关键词(KeyWords): 非洲猪瘟病毒;基因组学;转录组学;蛋白质组学;代谢组学
基金项目(Foundation): 国家自然科学基金项目(项目号:U20A2060),题目:辽宁省非洲猪瘟流行关键风险因素识别、病毒演化与毒力变化的分子机制;国家自然科学基金项目(项目号:32072854),题目:非洲猪瘟病毒毒力相关新基因的鉴定及其调控病毒毒力的机制~~
作者(Authors): 潘力;罗瑞;王涛;罗玉子;孙元;仇华吉;
DOI: 10.13242/j.cnki.bingduxuebao.004055
参考文献(References):
- [1]罗玉子,孙元,王涛,仇华吉.非洲猪瘟——我国养猪业的重大威胁[J].中国农业科学,2018,51(21):4177-4187.
- [2] Alonso C,Borca M,Dixon L,Revilla Y,Rodriguez F,Escribano J M. ICTV virus taxonomy profile:Asfarviridae[J]. J Gen Virol,2018,99(5):613-614.
- [3]王涛,孙元,罗玉子,仇华吉.非洲猪瘟防控及疫苗研发:挑战与对策[J].生物工程学报,2018,34(12):1931-1942.
- [4] Sánchez-Cordón P J,Montoya M,Reis A L,Dixon L K. African swine fever:a re-emerging viral disease threatening the global pig industry[J]. Vet J,2018,233(5):41-48.
- [5] Teklue T,Sun Y,Abid M,Luo Y,Qiu H J. Current status and evolving approaches to African swine fever vaccine development[J]. Transbound Emerg Dis,2020,67(2):529-542.
- [6] Liu S,Luo Y,Wang Y,Li S,Zhao Z,Bi Y,Sun J,Peng R,Song H,Zhu D,Sun Y,Li S,Zhang L,Wang W,Sun Y,Qi J,Yan J,Shi Y,Zhang X,Wang P,Qiu H J,Gao G F. Cryo-EM structure of the African swine fever virus[J/OL]. Cell Host Microbe,2019,26(6):836-843 e833.
- [7] Tian W M,Zhang N,Jin R H,Feng Y M,Wang S Y,Gao S X,Gao R Q,Wu G Z,Tian D,Tan W J,Chen Y,Gao G F,Wong C C L. Immune suppression in the early stage of COVID-19 disease[J]. Nat Commun,2020,11(1):5859.
- [8] Simon R. A viral ecogenomics framework to uncover the secrets of nature's"microbe whisperers"[J/OL].MSystems,2019,4(3):e00111-19.
- [9]张立兴,王丽娜,康广博,黄鹤.多组学分析在炎症性肠病中的应用与研究进展[J].生物技术通报,2020,37(1):155-167.
- [10]Pikalo J, Zani L, Hühr J, Beer M, Blome S.Pathogenesis of African swine fever in domestic pigs and European wild boar–Lessons learned from recent animal trials[J]. Virus Res,2019,27(11):197614.
- [11]Whisnant A W,Jürges C S,Hennig T,Wyler E,Prusty B,Rutkowski A J,Hainault A,Djakovic L,G?bel M, D?ring K, Menegatti J, Antrobus R,Matheson N J,Künzig F W H,Mastrobuoni G,Bielow C, Kempa S, Liang C, Dandekar T, Zimmer R,Landthaler M,Gr?sser F,Lehner P J,Friedel C C,Erhard F,D?lken L. Integrative functional genomics decodes herpes simplex virus 1[J]. Nat Commun,2020,11(1):2038.
- [12]魏若瑾,李济彤,常静,杨璐,潘一帆,王会利,朱莉飞.多组学技术应用于化学品风险评估的研究进展[J].生态毒理学报,2020,15(10)1-12.
- [13]Yang T L,Shen H,Liu A,Dong S S,Zhang L,Deng F Y, Zhao Q, Deng H W. A road map for understanding molecular and genetic determinants of osteoporosis[J]. Nat Rev Endocrinol,2020,16(2):91-103.
- [14]Kwok A J,Mentzer A,Knight J C. Host genetics and infectious disease:new tools,insights and translational opportunities[J]. Nat Rev Genet,2020,22(3):137-153.
- [15]Sung A Y, Floyd B J, Pagliarini D J. Systems biochemistry approaches to defining mitochondrial protein function[J]. Cell Metab,2020,31(4):669-678.
- [16]Fan Y,Pedersen O. Gut microbiota in human metabolic health and disease[J]. Nat Rev Microbiol,2020 19(1):55-71.
- [17]González-Pe?a D,Brennan L. Recent advances in the application of metabolomics for nutrition and health[J].Annu Rev Food Sci Technol,2019,10(7):479-519.
- [18]Montaner J,Ramiro L,Simats A,Tiedt S,Makris K,Jickling G C,Debette S,Sanchez J C,Bustamante A.Multilevel omics for the discovery of biomarkers and therapeutic targets for stroke[J]. Nat Rev Neurol,2020,16(5):247-264.
- [19]Moreno L F,Vicente V A,de Hoog S. Black yeasts in the omics era:Achievements and challenges[J]. Med Mycol,2018,56(suppl-1)32-41.
- [20]McShane L M,Cavenagh M M,Lively T G,Eberhard D A,Bigbee W L,Williams P M,Mesirov J P,Polley M Y,Kim K Y,Tricoli J V,Taylor J M,Shuman D J,Simon R M,Doroshow J H,Conley B A. Criteria for the use of omics-based predictors in clinical trials[J].Nature,2013,502(7471):317-320.
- [21]Kim D Y, Scalf M, Smith L M, Vierstra R D.Advanced proteomic analyses yield a deep catalog of ubiquitylation targets in Arabidopsis[J]. Plant Cell,2013,25(5):1523-1540.
- [22]李伟,印莉萍.基因组学相关概念及其研究进展[J].生物学通报,2000,(11):1-3.
- [23]Velculescu V E,Zhang L,Zhou W,Vogelstein J,Basrai M A,Bassett D E,Jr.,Hieter P,Vogelstein B,Kinzler K W. Characterization of the yeast transcriptome[J]. Cell,1997,88(2):243-251.
- [24]Martyniuk C J,Feswick A,Munkittrick K R,Dreier D A,Denslow N D. Twenty years of transcriptomics,17alpha-ethinylestradiol, and fish[J]. Gen Comp Endocrinol,2020,286(10):113325.
- [25]Costa V, Angelini C, De Feis I, Ciccodicola A.Uncovering the complexity of transcriptomes with RNASeq[J]. J Biomed Biotechnol,2010,18(7):853916.
- [26]Wasinger V C,Cordwell S J,Cerpa-Poljak A,Yan J X,Gooley A A,Wilkins M R,Duncan M W,Harris R,Williams K L,Humphery-Smith I. Progress with gene-product mapping of the Mollicutes:Mycoplasma genitalium[J]. Electrophoresis,1995,16(7):1090-1094.
- [27]尹稳,伏旭,李平.蛋白质组学的应用研究进展[J].生物技术通报,2014,(1):32-38.
- [28]Graves P R,Haystead T A J. Molecular biologist's guide to proteomics[J]. Microbiol Mol Biol Rev,2002,66(1):39-48.
- [29]席晓敏,张和平.微生物代谢组学研究及应用进展[J].食品科学,2016,37(11):283-289.
- [30]马丽华,杨宏静,徐晓艳,石中全.代谢组学研究进展[J].现代医药卫生,2017,33(17):2636-2639.
- [31]Nicholson J K, Lindon J C. Systems biology:Metabonomics[J]. Nature,2008,455(7216):1054-1056.
- [32]Zhang H P,Wang L,Hou Z C,Ma H,Mamtimin B,Hasim A,Sheyhidin I. Metabolomic profiling reveals potential biomarkers in esophageal cancer progression using liquid chromatography-mass spectrometry platform[J]. Biochem Biophys Res Commun,2017,491(1):119-125.
- [33]Wesdorp N J, Hellingman T, Jansma E P, van Waesberghe J T M, Boellaard R, Punt C J A,Huiskens J, Kazemier G. Advanced analytics and artificial intelligence in gastrointestinal cancer:a systematic review of radiomics predicting response to treatment[J]. Eur J Nucl Med Mol Imaging,2020,49(3):14-27.
- [34]Aguayo-Orozco A,Taboureau O,Brunak S. The use of systems biology in chemical risk assessment[J]. Curr Opin Toxicol,2019,15(5):11-15.
- [35]Hader M,Frey B,Fietkau R,Hecht M,Gaipl U S.Immune biological rationales for the design of combined radio and immunotherapies[J]. Cancer Immunol Immunother,2020,69(6):33-41.
- [36]Eren A M,Kiefl E,Shaiber A,Veseli I,Miller S E,Schechter M S,Fink I,Pan J N,Yousef M,Fogarty E C,Trigodet F,Watson A R,Delmont T O,Willis A D. Community-led, integrated, reproducible multiomics with anvi'o[J]. Nat Microbiol,2021,6(1):3-6.
- [37]Lambin P,Rios-Velazquez E,Leijenaar R,Carvalho S,van Stiphout R G P M,Granton P,Zegers C M L,Gillies R, Boellard R, Dekker A, Aerts H J,Consortium Q C. Radiomics:Extracting more information from medical images using advanced feature analysis[J]. Eur J Cancer,2012,48(4):441-446.
- [38]Sette A,Fleri W,Peters B,Sathiamurthy M,Bui H H, Wilson S. A roadmap for the immunomics of category A-C pathogens[J]. Immunity,2005,22(2):155-161.
- [39]Zhou X T,Li N,Luo Y Z,Liu Y,Miao F M,Chen T,Zhang S F,Cao P L,Li X D,Tian K G,Qiu H J,Hu R L. Emergence of African swine fever in China,2018[J]. Transbound Emerg Dis,2018,65(6):1482-1484.
- [40]Hakizimana J N,Nyabongo L,Ntirandekura J B,Yona C, Ntakirutimana D, Kamana O, Nauwynck H,Misinzo G. Genetic analysis of African swine fever virus from the 2018 outbreak in South-Eastern Burundi[J].Front Vet Sci,2020,7(12):1-10.
- [41]Dixon L K,Abrams C C,Chapman D D,Goatley L C,Netherton C L,Taylor G,Takamatsu H H. Prospects for development of African swine fever virus vaccines[J]. Dev Biol(Basel),2013,135:147-157.
- [42]Zhao Y X,Zuo X L,Li Q,Chen F,Chen Y R,Yang H H,Tan W H,Fan C H. Nucleic acids analysis[J].Sci China Chem,2020,2(11):1-33.
- [43]Malogolovkin A, Kolbasov D. Genetic and antigenic diversity of African swine fever virus[J]. Virus Res,2019,271(8):93-106.
- [44]Bastos A D,Penrith M L,Crucière C,Edrich J L,Hutchings G,Roger F,Couacy-Hymann E,Thomson G R. Genotyping field strains of African swine fever virus by partial p72 gene characterisation[J]. Arch Virol,2003,148(4):693-706.
- [45]Malogolovkin A,Burmakina G,Titov I,Sereda A,Gogin A,Baryshnikova E,Kolbasov D. Comparative analysis of African swine fever virus genotypes and serogroups[J]. Emerging Infect Dis,2015,21(2):312-315.
- [46]Gallardo C,Mwaengo D M,Macharia J M,Arias M,Taracha E A,Soler A,Okoth E,Martin E,Kasiti J,Bishop R P. Enhanced discrimination of African swine fever virus isolates through nucleotide sequencing of the p54, p72, and pB602L(CVR)genes[J]. Virus Genes,2009,38(1):85-95.
- [47]Redrejo-Rodriguez M,Rodriguez J M,Suarez C,Salas J, Salas M L. Involvement of the Reparative DNA polymerase Pol X of African swine fever virus in the maintenance of viral genome stability in vivo[J]. J Virol,2013,87(17):9780-9787.
- [48]Quembo C J,Jori F,Vosloo W,Heath L. Genetic characterization of African swine fever virus isolates from soft ticks at the wildlife/domestic interface in Mozambique and identification of a novel genotype[J].Transbound Emerg Dis,2018,65(2):420-431.
- [49]Krug P W,Holinka L G,O'Donnell V,Reese B,Sanford B,Fernandez-Sainz I,Gladue D P,Arzt J,Rodriguez L,Risatti G R,Borca M V. The Progressive adaptation of a Georgian isolate of African swine fever virus to Vero cells leads to a gradual attenuation of virulence in swine corresponding to major modifications of the viral genome[J]. J Virol,2015,89(4):2324-2332.
- [50]Goller K V,Malogolovkin A S,Katorkin S,Kolbasov D,Titov I,Hoper D,Beer M,Keil G M,Portugal R,Blome S. Tandem repeat insertion in African swine fever virus,Russia,2012[J]. Emerging Infect Dis,2015,21(4):731-732.
- [51]Forth J H,Tignon M,Cay A B,Forth L F,Hoper D,Blome S, Beer M. Comparative analysis of wholegenome sequence of African swine fever virus Belgium2018/1[J]. Emerging Infect Dis,2019,25(6):1249-1252.
- [52]Forth J H,Forth L F,Lycett S,Bell-Sakyi L,Keil G M, Blome S, Calvignac-Spencer S, Wissgott A,Krause J,Hoper D,Kampen H,Beer M. Identification of African swine fever virus-like elements in the soft tick genome provides insights into the virus'evolution[J].BMC Biol,2020,18(1):33-42.
- [53]Mazur-Panasiuk N,Wozniakowski G,Niemczuk K.The first complete genomic sequences of African swine fever virus isolated in Poland[J]. Sci Rep,2019,9(1):4556.
- [54]Farlow J,Donduashvili M,Kokhreidze M,Kotorashvili A,Vepkhvadze N G,Kotaria N,Gulbani A. Intraepidemic genome variation in highly pathogenic African swine fever virus(ASFV)from the country of Georgia[J]. Virol J,2018,15(1):190.
- [55]Forth J H,Forth L F,King J,Groza O,Hubner A,Olesen A S,Hoper D,Dixon L K,Netherton C L,Rasmussen T B,Blome S,Pohlmann A,Beer M. A deep-sequencing workflow for the fast and efficient generation of high-quality African swine fever virus whole-genome sequences[J]. Viruses,2019,11(9):35-43.
- [56]O'Donnell V K,Grau F R,Mayr G A,Samayoa T L S,Dodd K A,Barrette R W. Rapid sequence-based characterization of African swine fever virus by use of the Oxford Nanopore MinION Sequence Sensing Device and a companion analysis software tool[J]. J Clin Microbiol,2020,58(1):1104-1119.
- [57]Wang L,Luo Y Z,Zhao Y H,Gao G F,Bi Y H,Qiu H J. Comparative genomic analysis reveals an'open'pangenome of African swine fever virus[J]. Transbound Emerg Dis,2020,67(4):1553-1562.
- [58]Wen X X,He X J,Zhang X,Zhang X F,Liu L L,Guan Y T, Zhang Y, Bu Z G. Genome sequences derived from pig and dried blood pig feed samples provide important insights into the transmission of African swine fever virus in China in 2018[J]. Emerg Microbes Infect,2019,8(1):303-306.
- [59]Masembe C,Phan M V T,Robertson D L,Cotten M.Increased resolution of African swine fever virus genome patterns based on profile HMMs of protein domains[J].Virus Evol,2020,6(2):veaa044.
- [60]Kuhn J H,Wolf Y I,Krupovic M,Zhang Y Z,Maes P,Dolja V V,Koonin E V. Classify viruses-the gain is worth the pain[J]. Nature,2019,566(7744):318-320.
- [61]Coradini A L V,Hull C B,Ehrenreich I M. Building genomes to understand biology[J]. Nat Commun,2020,11(1):61-77.
- [62]Gavier-Widen D,Stahl K,Dixon L. No hasty solutions for African swine fever[J]. Science,2020,367(6478):622-624.
- [63]Cackett G,Sykora M,Werner F. Transcriptome view of a killer:African swine fever virus[J]. Biochem Soc Trans,2020,48(4):1569-1581.
- [64]Netherton C L,Connell S,Benfield C T O,Dixon L K. The genetics of life and death:virus-host interactions underpinning resistance to African swine fever,a viral hemorrhagic disease[J]. Front Genet, 2019, 10(10):402.
- [65]Zhu J J,Ramanathan P,Bishop E A,O'Donnell V,Gladue D P,Borca M V. Mechanisms of African swine fever virus pathogenesis and immune evasion inferred from gene expression changes in infected swine macrophages[J]. PLoS One,2019,14(11):e0223955.
- [66]Rodriguez J M,Salas M L. African swine fever virus transcription[J]. Virus Res,2013,173(1):15-28.
- [67]Salas M L, Kuznar J, Vinuela E. Polyadenylation,methylation,and capping of the RNA synthesized in vitro by African swine fever virus[J]. Virology,1981,113(2):484-491.
- [68]Broyles S S. Vaccinia virus transcription[J]. J Gen Virol,2003,84(2):2293-2303.
- [69]Jaing C,Rowland R R R,Allen J E,Certoma A,Thissen J B,Bingham J,Rowe B,White J R,Wynne J W,Johnson D,Gaudreault N N,Williams D T. Gene expression analysis of whole blood RNA from pigs infected with low and high pathogenic African swine fever viruses[J]. Sci Rep,2017,7(1):10115.
- [70]Cackett G, Matelska D, Sykora M, Portugal R,Malecki M,Bahler J,Dixon L,Werner F. The African swine fever virus transcriptome[J]. J Virol,2020,94(9):e00119-00120.
- [71]Alejo A, Matamoros T, Guerra M, Andres G. A proteomic atlas of the African swine fever virus particle[J]. J Virol,2018,92(23):e01293-18.
- [72]Salas M L, Andres G. African swine fever virus morphogenesis[J]. Virus Res,2013,173(1):29-41.
- [73]Chen Y Q,Liu H H,Yang C,Gao Y Q,Yu X,Chen X,Cui R X,Zheng L N,Li S H,Li X H,Ma J B,Huang Z,Li J X,Gan J H. Structure of the error-prone DNA ligase of African swine fever virus identifies critical active site residues[J]. Nat Commun, 2019, 10(1):387.
- [74]Penades J R,Donderis J,Garcia-Caballer M,TormoMas M A,Marina A. dUTPases,the unexplored family of signalling molecules[J]. Curr Opin Microbiol,2013,16(2):163-170.
- [75]Li C,Chai Y,Song H,Weng C,Qi J,Sun Y,Gao G F. Crystal structure of African swine fever virus dUTPase reveals a potential drug target[J]. mBio,2019,10(5):2483-24819.
- [76]Lacasta A,Ballester M,Monteagudo P L,Rodriguez J M,Salas M L,Accensi F,Pina-Pedrero S,Bensaid A,Argilaguet J,Lopez-Soria S,Hutet E,Le Potier M F,Rodriguez F. Expression library immunization can confer protection against lethal challenge with African swine fever virus[J]. J Virol,2014,88(22):13322-13332.
- [77]Zakaryan H, Karalova E, Voskanyan H, TerPogossyan Z,Nersisyan N,Hakobyan A,Saroyan D,Karalyan Z. Evaluation of hemostaseological status of pigs experimentally infected with African swine fever virus[J]. Vet Microbiol,2014,174(1-2):223-228.
- [78]Karalyan N Y, Tatoyan M R, Semerjyan A B,Nersisyan N H, Semerjyan Z B, Hakobyan L H,Karalyan Z A. Association of hemophagocytic lymphohistiocytosis with kidney lesions in acute African swine fever virus infection[J]. Ann Parasitol,2018,64(4):343-350.
- [79]Cuesta-Geijo M A,Chiappi M,Galindo I,Barrado-Gil L, Munoz-Moreno R, Carrascosa J L, Alonso C.Cholesterol flux is required for endosomal progression of African swine fever virions during the initial establishment of infection[J]. J Virol,2016,90(3):1534-1543.
- [80]Sanchez E G,Quintas A,Perez-Nunez D,Nogal M,Barroso S,Carrascosa A L,Revilla Y. African swine fever virus uses macropinocytosis to enter host cells[J].PLoS Pathog,2012,8(6):234-251.
- [81]Herrera-Uribe J, Jimenez-Marin A, Lacasta A,Monteagudo P L, Pina-Pedrero S, Rodriguez F,Moreno A,Garrido J J. Comparative proteomic analysis reveals different responses in porcine lymph nodes to virulent and attenuated homologous African swine fever virus strains[J]. Vet Res,2018,49(1):90.
- [82]Wang T,Sun Y,Huang S J,Qiu H J. Multifaceted immune responses to African swine fever virus:implications for vaccine development[J]. Vet Microbiol,2020,249(8):108832.
- [83]Baker M. Synthetic genomes:The next step for the synthetic genome[J]. Nature,2011,473(7347):403,405-408.