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本课件为英文版病毒学章节，介绍病毒的形体大小、基本形态与核酸类型，解析衣壳与囊膜等结构及蛋白功能，说明噬菌体的复制周期与溶原性，并延伸到亚病毒因子及病毒的致癌机制。
Chapter 4 Viruses
The concept of virusesVirusesareauniquegroupoftinyinfectiousparticlesthatareobligateparasitesofcells,arenotcellsbutresemblecomplexmoleculescomposedofDNAorRNA.Mostofthemaresosmall(0.02-0.3µm)thatanelectronmicroscopeisnecessarytodetectthem.
Classification of the viruses：VirusesSubviral agentsViroids PrionsSatellites and DeltavirusNon-cell organism
Characteristicsofvirions(virusparticles)：1）aretinyparticlesthatareultramicroscopicsize,cangothroughthebacteriafilter.2）arenotcellbutcomposedofproteinandnucleicacid3）NucleicacidcanbeeitherDNAorRNAbutnotboth.4）usethemselvesnucleicacidtoreplicateandapplytheassemblingofviralproteinandnucleicacidtomultiplymassively.5）areobligateintracellularparasitesandlackenzymesformostmetabolicprocessesandsynthesizingprotein,multiplybytakingcontrolofhostcell’smetabolismandsyntheticmachinery.6）areabioticmacromolecularandcontaintheinfectivityforalongtimeoutsideofthehostcell.7）arenotsensitivetoantibioticbutsensitivetointerferon.8）Someofthemcanbeintegratedintothehostcell’sgenomeinprovirus.
Significanceofvirusresearch：1)Controlandeliminatetheaversiveviruses,whichdoharmtothehumanhealthandthedomesticanimals.Thenationaleconomyisseverelyaffectedbythevirusdiseases.Infermentationindustry,contaminationofphageswillhavebadinfluenceinthefermentationproduction.2)Bystudyofthevirus,wecanupgradethespecies,cultivatelivevirusvaccinestrain,protecttheecologicalenvironment,applyvirusasinsecticidaandusethemasvectorsforgeneengineering.
Section 1.The General structure and Chemical Composition of Viruses1.SizeofthevirusparticleMostofthemaresosmallandvarywidely（0.02-0.3µm）thatanelectronmicroscopeisnecessarytodetectthem,theirsizerelegatesthemtotherealmoftheultramicroscopic.Thetiniestcircoviridae,17nmindiameter，isalittlebiggerthanribosome,whilethemaximumPoxviruses,200nmindiameter，isasbigastheminimumbacteria,eventobedetectedbylightmicroscope.
VirusparticleNucleocapsid(BasicUnit)EnvelopewithSpike(nonbasicUnit）CentrelcoreCapsidDNA/RNAGenome:Double/singlestrandsectile/unsectile多肽（结构亚单位）CapsomerComponent of virus particle
3. Morphology and symmetry of viruses3.1 Morphologyof Virus
3.2 Architecturetype of Virushelical symmetryicosahedral symmetrycomplex symmetryNaked envelopehabditiform：TMV etcsilkiness：Bacterium coli M13phage etccoiling：Influenza virus etcbullet：Wut virus etcEnvelopeNaked envelopeEnvelope:herper virussmall：Poliovirus big：adenovirus Envelope：poxvirus（Brick shape）Naked envelope：Bacterium coli T phage (tadpole shape)Architecturetype of Virus
1.HelicalsymmetryAtypicalvirushelicalsymmetryisthetobaccomosaicvirus(TMV).ThisisaRNAvirusinwhichthe2130proteinsubunits(each158aminoacidsinlength)arearrangedinhelix.InTMV,thehelixhas16½subunitsperturnandtheoveralldimensionsofthevirusparticlesare18*300nm.Thelengthsofhelicalvirusesaredeterminedbythelengthsofthenucleicacid,butthewidthofthehelicalvirusesparticlesisdeterminedbythesizeandpackingoftheproteinsubunits.
2. Icosahedral symmetryTakeadenovirusforexample.Theicosahedralcapsid(70to100nm)ismadeupof252capsomeres:240hexonsformingthefacesand12pentonsatthevertices.Eachpentonbearsaslenderfiberandiscomposedofapentamer(Ⅲ)andatrimerfibrin(Ⅳ)buteachhexamereisnothexamerbuttrimerconstitutedbythree110KpolypeptideⅡ.
Sense and antisense single strand ：sense（+）：identical to the mRNA base sequence.antisense（-）：complementary to the mRNA base sequence.Sense/antisence（±）：complementary double strands.+RNA：as mRNA template for translation to protein.-RNA：complementary to +RNA, can not as mRNA template for translation to protein.+DNA：complementary to-DNA, not as template for transcription to mRNA. -DNA：as template for transcription to mRNA。
Segmentation and amerism：Some RNA viruses are not strictly ‘antisense' but ambisense, since they are part (-)sense & part (+)sense.
4. Proteins of viruses1.Constitutiveprotein:constitutethemorphologicalmaturityandinfectiousvirusparticle,includingcapsid,peplosandenzymesaccountingfor30-70%perparticle.（1）capsidprotein:theproteincoveringofavirus’snucleicacidcore,exhibitsymmetryduetothesubunitscalledcapsomers.Functionsofcapsidprotein：constitutestheviruscapsidtoshieldthenucleicacid;nakedvirus’scapsidparticipatestheabsorption,penetration,determinationthehosttropsimandsurfaceantigen.
(2）peplomereprotein:arecomposedofpeplosglycoproteinandmatrixprotein,locatedinpeplossurface.Peplosglycoprotein:arethechiefsurfaceantigen(SA)ofvirus;mostofthemarevirusattachmentproteinbyinteractionwithcellreceptortoswitchtotheinfection.Someofthemmaymediatethepenetrationofvirus,agglutinatevertebrateanimalakaryocyte,cellfusionandenzymeactivity.Matrixprotein:isthesubmembranestructurebetweenlipidbilayerandnucleocapsidforsupportingthepeplosandvirusstructure.Itcanalsomediatetherecognitionbetweennucleocapsidandpeplosglycoproteinandisveryimportantinvirusbuddingoff.
(3)Virionenzyme:existinvirocapsomer,categorizedasfollowbyfunction.Onekindismediatepenetrationandreleaseofvirus,suchasT4phagelysozyme,fluvirusneuramidinase.Anotherisinvolvedinvirusmacromoleculesynthesis,suchasretrovirus,hepadnavirus,thedsRNAvirus,antisenseRNAvirus.Asforsomecomplicateviruses,forinstancethepoxvirusduplicatedincytoplasmhavemanyenzymesinvolvedinDNAduplicationandRNAtranscriptfabrication.
2.Non-structureprotein(NSprotein):itmeansproteinsencodedbyvirusgenomehavefunctionbutdonotbindthevirusparticlesinduplicateprocess.Thequantitiesandqualityofthemaredependentonthevirusspecies,complexofvirusgenomeandtheperiodsofvirusduplication.MostlyNSproteinshaveenzymeactivitiesandinvolvedinregulatingvirusreplicationandtranscription.Recentlydatashowthatpartofviruseshavetheabilitytoantiapoptosisandinhibitionantigenpresentation.Forexample,the3ABCproteininfootandmouthdiseasevirusisusedtoclassifythewildvirusandattentuatedvaccineimmune.
3.Viruslipoid:viruslipoidisformedfromthehostcellduringthereleaseofvirus,mainlyresidesinviruspeplos.Thelipoidaccountsfor20-35%inthestructuralcomposition,thepoxviruslipoidis5%andtherabiesvirusisupto50%.4.ViralcarbohydrateSomeofvirusescontainafewcarbohydrate.Itispresentinviruscarbohydrateandglucolipidebyoligosacharidelateralchainormucopolysaccharides.Exceptfortheenvelopedviruses’glucoproteinecphyma,someofcomplexvirusparticleshaveinternalglucoproteinorglycosylatedcapsidprotein.Glucoproteinissignificantimmunigen,forinstance,anti-influenzavirushemagglutininserumhaveconspicuousvirusneutralization.5.OthercompositionTherearesomepositiveioniccompounds(suchastetramethylenediamine,apermidine,spermine)insomeanimalviruses,plantvirusesandphageviruses.Itisreportedthatthereismetalpositiveioninseveralplantviruses.Theseminimalorganicpositiveionorinorganicpositiveionbindrandomlywithvirusnucleicacidandaffecttheconformationofnucleicacid.Thecombiningweightofthemisrelevanttothecorrelatedionconcentrationinenvironmentandacquiretheunconstantingredientfromenvironmentwhenvirusassembly.
Section 3 Reproduction and taxnomy of viruses
1.Principle groups and classification systemNumbercharacter1Nature of host（animal、plant、bacteria、insect、mycetes）2Nature of nucleic acid（DNA or RNA；single or double strands；molecular mass；segmentation or not，how many
International Committee on the Taxonomy of Viruses( ICTV) is the "international court" of experts that rules on names and relationships of all viruses ,but only to the level of species,. The ICTV virus classification system apply order, family, subfamily, genus and species as categorization units, Below this level, the nomenclature of serovar, genotype, toxicity, variant, isolation are determined by received international experts. It is reported that all the recoganized viruses are categorized into 233 families, 1550 species and 204 families are belonged to 64 orders. Since the sixth report, the viruses are categorized into DNA viruses, DNA and RNA retroviruses and RNA viruses. On the basis of virus evolution genetics, ICTV set up 3 orders based on part families in the 7th report, which are Caudovirales,Mononegavirales, Nidovirales. The classification of different genera in a subfamily is based on the virus’s immunology properties and host specificity. But the viral specie is a kind of uncertain taxonomical unit.In 1990, ICTV make a definition that the species is a group of viruses with generation relation and occupancy of some niche. It also means that , under the preconditions having same family and genus features,the virus having some similar secondory features but not same are classified into the same kind if viruses.
Virus Nomenclature:The principal style changes are that the virus family, subfamily, and genus names should be capitalized and printed in italics. When such a name is used formally, the term for the taxon should precede the term for the taxonomic unit, for example,“the family Bunyaviridae” and “the genus Tospovirus”. When used formally, a virus species name should also be printed in italics, with the first word of any subsequent proper noun capitalized, for example, Avian leukosis virus, Lucerne Australian latent virus, Queensland Kashmir bee virus. Generally, the designation of the taxonomic unit “species” need not precede the species name, for example, Rous sarcoma virus need not be written as “the species Rous sarcoma virus”. The first use of a virus species name in a paper should usually be treated formally and therefore should appear in italics with the first word capitalized. Subsequent reference to the same virus should be an accepted acronym, which is not italicized,for example, AMV for Alfalfa mosaic virus.Virus names presented in tables should be written formally. The name of a tentative species whose taxonomic status is uncertain should not be written in italics, but its first word (and any proper nouns) should be capitalized.
2.BacteriophagePhagesareakindofvirusthatinfectprotocaryonmicroorganism(bacteria,rayfungusandcyanobacteriaetal)anddistributeswidespread.TheyaredividedintodsRNAvirus,ssDNAvirus,dsRNAvirusandssRNAviruswithoutenvelope.Theyareintheshapeoftadpole,microballoonsandsilk(Fig4-19).Thequantitiesandqualitiesoffermentationbadlycontaminatedbyphageswillresultinheavyloss.Itisextensivelyusedinmolecularbiologyresearch,suchasthecolibacillaryλphageasgeneengineeringvector;colibacillaryM13phageasphagedisplaytechniqueforexpressionofpolypeptideandproteinaswellasprotein-proteininteraction.
Bateriaphage pantomorphia（source from Richard ）
1.VirulentbacteriaphageandreproductivemodeThiskindofphagesmakescellreleasevirionbylysiscellwhentheypenetratehostcell.Therefortheyarecalledvirulentphage,suchasT4phage.The cycle of virus mutiplication:The cycle is separated into adsorption, penetration, duplication, assembly , maturation and release. This process iscalled lytic cycle.
1. Adsorption2. Penetration
NucleicacidTypeNucleicAcidStructureVirusExamplesSingle-StrandedDouble-strandedLinear,singlestranded,positivestrandLinear,singlestranded,negativestrandLinear,singlestranded,segmented,positivestrandLinear,singlestranded,segmented,diploid(twoidenticalsinglestrands),positivestrandLinear,singlestranded,segmented,negativestrandLinear,doublestranded,segmentedPicornaviruses(polio,rhinoviruses),togaviruses,RNAbacteriophages,TMV,andmostplantvirusesRhabdoviruses(rabies),paramyxov-iruses(mumps,measles)Bromemosaicvirus(individualsegmentsinseparatevirions)Retroviruses(Roussarcomavirus,humanimmunodeficiencyvirus)Paramyxoviruses,orthomyxoviruses(influenza)Retroviruses,wound-tumorvirusofplants,cytoplasmicpolyhdrosisvirusofinsects,phageФ6,manymycovirusesTypes of Viral Nucleic Acids(RNA)
3. Biosynthesis±DNA+mRNATranslationProteinsNewvirionsTranscriptionReplication（a）The Reproduction of Double-Stranded DNA（T4 Bacteriophages）
+DNABacterialDNApolymerase±DNA(Replicativeform)+DNA+mRNATranslationTranscriptionReplicationNewvirionsProteins（b）The Reproduction of ФX174,a +Strand DNA
＋RNA±RNA(replicativeform)RNAreplicase＋RNAgenomesReplicationTranslation＋RNANewvirionsVirusProteinsmRNAactivity（c）The Reproduction of Single-Stranded RNA Bacteriophages
ViralreplicaseNewvirions+RNAProteins(afterprocessingbyhostandvirus-codedproteinases±RNAReplicativeform+RNA（a）positive single-stranded RNA viruses(picornaviruses)RNA Animal virus Reproductive Strategies:
RNA-dependentRNApolymerases*(Transcriptases)＋mRNANewvirions±RNAProteinsRNA-dependentRNApolymerase(Replicase)±RNA(b) Double-stranded RNA viruses (reoviruses)
－RNA＋mRNAproteinsRNN-dependentRNApolymerase(viralreplicase)±RNAReplicativeform－RNARNA-dependentRNApolymerase+(Transcriptase)Newvirions（c）Negative single-stranded RNA viruses (paramyxoviruses-mumps and measles;orthomyxoviruses-influenza
＋mRNANewvirionsRNA-dependentDNApolymeraseReversetranscriptase+Proteins+RNARibonuclease HComponent of RTReversetranscriptase++RNA/-DNAProviralDNA±DNA-DNA+RNA（virion）Transcription(d )Retroviruses (Rous sarcoma virus,HIV)
4. Assembly and maturation
5.Release(lysis)
（1）Eclipseperiod：itistheperiodfromtheviruspenetratinghostcelltothereleasingofvirion.Latentprophaseorcalledaseclipsephasemeanstheperiodduringwhichvirusnucleicacidpenetrateshostcellandassemblythefirstvirion.Atthattimetherearenotcomplete,infectiousmaturevirion.Latencyanaphase:Duringthisperiod,thetiterofactivevirusparticlesinsidecellrisesdramatically,butarenotreleasefromhostcell,whichmarkstheendoflatency.（2）Burstphase：Duringthisperiod,thenumberofvirionincreasesrapidlywithlysisofhostcell.（3）Platformphage：Itistheperiodthatallofthehostcellsarelysatedandthevalenceofvirusreachestheapogee.
Two characteristic dataEclipse period:：it is the minimum course from the penetration of virus to virion release. It is different from different viruses, such as phage’s eclipse period is counted by minute, animal and plant viruses are by hour or day.Burst size: it is the average number of released virion, which is equal to the number of all the released virion divided by infected cell numbers in eclipse period and is also equal to the ratio between viral valence in stable phage and viral valence in eclipse period. Determined by one step growth curve, the phage’s burst size is generously from a few to a few hundred and plant and animal viruses’ burst size are up to a few hundred even to ten thousand.
3.Template phage and lysogenySomeofphagesintegratetheirgenomeintothehostgenomeandduplicatealongwithhostmaterialatthetimeofcelldivisionbutdonotinducehostcelllysisaftertheypenetratingthehostcell.Therefore，theyarecalledtemperatephage.Theconcurrentstateiscalledlysogeny，theinfectedcellscalledlysogen，thevirusintegratedintocellgenomecalledasprophage.
细胞反复分裂溶原途径裂解途径The mode of λphage lysis and lysogenic pathway 诱导
Thecharactersofoflysogeny：（1）lysogenicconversion：Theprophagewillresultinthephenotypicalternationofhostcell,whichisnotdirectlyrelatedtothecompletionoflifecycleandareknownaslysogenicconversion.（2）Immunity：Althoughalysogenicbacteriummaybesusceptibletootherviruses,itcannotbeinfectedbyvirusparticlesofthetypeforwhichitislysogenic.Theλrepressorproteinexpressedbyprophagegenecaninhibitstheduplicationofvirusinhostcell.
3.Pathogenicityconversion：Someofprophagesresultinpathogenicityconversion.Forinstance,CorynebecteriumdiphtheriaeandClostridiumbotulinumarenottoxictohuman.Onceinfectedbytemplatephages,theyareconvertedintotoxogenicstrains,resultingindamagetoinfectedtissueanddiphthereaandbotulismtoxicsymtom.4.Lysogenyisreversible：Theprophagescanbereactivatedspontaneouslyofunderoutsidestimulus，andenterlyticcyclewithlysisofhostcells.Theprobabilityofthisprocessisverylow(1/10000-1/100000orso）.
3.VertebrateanimalvirusTheremanyvirusparasitizeinallkindsofvertebrateanimals，butonlythoseassociatedwithhumanhealthyanddomesticelivestockpoultryareinvestigatedmuchmore.Therearemorethan300kindofvirusesassociatedwithhumanhealthandmorethan900withothervertebrateanimals.70-80%ofhumancontagiousdiseasesarecausedbyviruses.ThevertebrateanimalsvirusesarecategorizedintodsRNA,ssDNA,daDNA,dsRNAandssRNA.Someofthemhaveenvelopeornot;Someofthemhavespikeproteinoutsideenvelopeornot.
1.Vertebrate animal Viruses multiplication1.Adsorption.The virus attaches to its host cell by specific binding of its spikes to cell receptors.2.Penetration. The virus is engulfed into a vesicle and its envelope is uncoated, thereby freeing the viral RNA into cell cytoplasm.Duplication. Under the control of viral genes, the cell synthesizes the basic components of new viruses: RNA molecule, capsomers, spikes.4.Assembly.Viralspikeproteinsareinsertedintothecellmembraneforviralenvelope;nucleocapsididformedformRNAandcapsomers.5. Release. Enveloped viruses bud off of the membrane , carrying away an envelope with spikes. This complete virus of virion id ready to infect another cell.
The mode by which animal viruses adsorb to the host cell membrane.
1）Naked virus direct penetration.2）Virus with envelope penetrates by endocytosis.3）Virus with envelope penetrate by fusion of cell membraneThe mode by whichanimal viruses penetrate
The mode by which animal viruses bud off and release:
2.Vertebrate animal virus persistenceSomeofvirusdonotkillhostcellnutintegrateditsDNAintohostgenomeorexistinhostcellasplasmidsafterinfectingthehost.Thiskindofviralnucleicacidiscalledasprotovirus.
Thecharactersofpersistence：1）Thepersistentinfectedanimalcellscankeepnormalfunctionformanyyears.2)Thevirusdosenotduplicateandstayinpersistencestatebefoereactivated.3）Theexpressionofintegratedprotovirusgenesometimesassignhostcellnewfeatures.4）ProtovirusesareactivatedbyenvironmentalagentssuchasUV,thentheyareduplicated,maturedandreleased,departingfromthechrosome.5)Someherperviruscan“turnoff/on”multiplicationofvirion.Understimulussuchascold,heat,pressorimmunesuppression,herpervirusstayinginorganismcellallthelifetimewillbereactivatedtoduplicationandlysisofhostcell,resultingindeasees,thencomebacktopersistencestate.Thereby,thiskindofpersistenceosalsocelledaslatency.6）Somevirusesleadtoslowvirusinfections.Measlesviruscanhiddeninbraincellsformangyears,causingprogressivedamageandlossoffunction.
3. Virus and tumorgenesisTumor :An abnormal mass of tissue that results from excessive cell division .Tumors perform no useful body function. They may be either begin or malignat. Benign tumors: do not invade neighboring tissues and do not seed metastases, but may locally grow to great size. They usually do not return after surgical removal. Malignant tumors are called cancer:. Cancer has the potential to invade and destroy neighboring tissues and create mtastases. There many complex factors, such as physical, chemical and biological factors , causing the human and vertebrate animal tumorgenesis.Some animal viruses enter their host cell and permanently alter its genetic material, leading to cancer. These viruses are termed oncovirus those are mainly dsRNA viruses and retroviruses. Their effect on the cell is called transformation.
It is estimated that 15 % of human cancers are caused by virus infection.Some human cancers which may be caused by virusesOncovirus cancer typeEpstein-Barr(EB) Burkitt leucoma（epstein-barr virus）hepatitis b virus hepatomahepatitis c virus hepatomaretrovirusmany animals leucemiahtlvhuaman adenolymphoma papovaviruseach animal tumors; huamnuterninecervix cancer
Conspicuouscharacterofoncovirus：canintegrateditsnucleicacidintohostcellgenomelikelysogenicphage.Thetransformedcells’growthrateincreasesuickly.Thechromosomeandcellsurfacemoleculesarechanged.Thecellcaninfinitedivisionandlostthecontact
Themechanismofcelltransformationbyoncovirus（1）Theintegrationofprotovirus.（2）Theexpressionofspecificgenerelatedwithtransformation.Thesespecialtransformation-relatedgeneistermedViraloncogenes，whichishomologueofhumanandvertebrateanimalsproto-oncogeneandismutationofnormalcellproto-oncogene.Itisconsideredthattheproto-oncogenesinnormalhostcellareveryimportantregulatinggenes,whichencodingproteinsareveryimportantinregulatingcellproliferationandmultiplication.Themutationproteinsencodedbymutantproto-oncogeneswillleadtocellaggressivegrowth.Someofhumancancersareinducedbyseveralproto-oncogenesmutatingatthesametime,suchascoloncarcinima.Virusesmayalsoinducecellabnormalgrowth.Forexample,thetumorvirusesaltertheproto-oncogenesactivitiesorabnormalexpression,thereforresultingincelltransformationandtumorgenesis.
4.EmergingvirusEmergingvirusesarethevirusesthoseareregionallowleverofinfectionandhaveinterspeciesbarrierenlargetheirhosttootherspecies,resultinginwide-ranginghumaninfectiousdiseases.Suchasebolavirus,lassavirus,AIDSvirus.RecentlyemergingSARSvirusandbirdsinfluenzavirusarebelongedtothiskindofvirus.Weshouldpaymuchattentiontothesedefectiondiseasescausedbythem.
The causes of emerging virus：1）The environment are destroyed by human activity. 。2）The modern transportation, development of tourism and large scale population migration.3）The mutation of virus gene change the host range . 4）The intimate contact between human and animals.
ReferencesPrescottLM,HarleyJP,andKleinDA.,Microbiology(5thed.),HighereducationpressandMcGraw-HillCompanies,Inc.2002MichaelTM,JohnMM,JackP.Brock.,BiologyofMicoorganisms，Internationaledition,PearsonEducation,Inc.2003TalaroK.P.FoundationsinMicrobiology(FifthEdition),HighereducationpressandMcGraw-HillCompanies,Inc.2005ZhouDe-qing，Microbiologytextbook，secondedition，higheducationpublishinghouse，2002
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