welcome back today's lecture is on viruses and here you see a beautiful electron micrograph of a bacteriophage we talked a little bit about these bacteriophage when we talked about transduction which is one of the three different types of horizontal gene transfer so let's go ahead and get started now quick little introduction to viruses okay here we go they are considered to be obligate intracellular parasites remember at the beginning of the semester we talked about how viruses are classified as non living because they require a host in order for them to be to be able to replicate right so they're considered to be obligate intracellular parasites they have very simple viral structures and we're gonna type in a little bit into the viral structure in the next couple of slides but basically they consist of a capsid they have a genome and they may have an envelope for comparison purposes here you see the size of a red blood cell looks pretty large when you compare it to any coli the Accola and looks pretty large when you compare it to a smallpox virus or even this bacteriophage here that we talked about so and so on and so forth they have different types of shapes they can be helical polyhedral envelope complex etc okay most of them are going to be smaller than point 2 microns therefore we cannot see these viruses with our compound microscope that we use in the lab even at a thousand magnification so they do require a specialized microscope called an electron microscope a very on is what's referred to as a fully formed virus ready and able to establish infection so let's continue again talking more about their viral structure these viruses will have the genetic material that will code for various enzymes and various virulence factor although they're simple they have the basic components that they need in order for them to be able to assemble themselves and establish infection so they will contain nucleic acid one of the interesting things about viruses however is that viruses can consist of DNA or RNA but not both that DNA and RNA can be single-stranded or it can be double-stranded even the army so that's very very interesting so as we talked about the viral structure and the various things about the viruses what's on our minds and everybody's mind right now is this whole corona virus specifically Kovan 19 right so I'm going to tell you a little bit about corona virus as we progress in this lecture so as far as a nucleic acid what's a nucleic acid of this copán 19 or corona virus it's going to be a single-stranded RNA more specifically it's positive strand positive-sense single-stranded RNA another component for the viral structure of viruses is that they will have a capsid these are protein coats these protein coats are made of individual protein units called caps Amir's okay so let's take a look at what these caps and years look like okay see if I can get this to work so these viruses have these little individual caps Amir's like this so this is a capsule yeah and they come together essentially to form a capsid okay now what is the purpose of this capsid something like this the purpose of that capsid is going to be to basically control not control but basically it's going to house or protect the nucleic acid so this is the nucleic acid and this nucleic acid remember can be DNA or RNA but not both together the caps Amir and the nucleic acid is referred to as a nucleo capsid okay let's move on alright now another thing that some of these viruses can have not all of them is an envelope so let's take a look at what that looks like surrounding this nucleo capsid some viruses can have an envelope this envelope is a lipid envelope and some viruses can additionally have some spike proteins that will be surrounding the virus or surrounding this envelope okay covet 19 is considered an envelope virus it has an RNA for nucleic acid single-stranded RNA it has an envelope and it has these spike proteins the spike protease for corona virus is called s Spyke proteins are not found in all viruses some of them do some of them don't influenza is another one of those viruses that has a couple of slight different spike proteins and they have different purposes for coronavirus even for influenza attachment is one of the purposes of these spike proteins so let's continue general structure of a virus I just illustrated to you on the whiteboard that they have there consists of a capsid okay they consist of a capsid all viruses do have these protein capsids that enclose and protect their nucleic acid remember that in clayey Cassatt is going to be either DNA or RNA double stranded or single stranded but not both this is why they require a host right so each capsid is going to be constructed by these identical little cap some years of little things that I drew here you see the little capsule years okay and together the capsid what the nucleic acid is referred to as a nucleic acid and some viruses are going to have an external cult covering those are referred to as envelope viruses so if I go back to my figure that I drew on the whiteboard I'll show you really quick so this virus here that has the envelope the lipid envelope and the spike protease that's referred to as an envelope to virus okay so that's referred to as an envelope virus the viruses that do not have an envelope like here this is referred to as a naked virus so if it has an envelope it's called or referred to as an envelope virus if it doesn't have this lipid envelope this this lipid envelope right there then it's referred to as a naked virus and here we see naked virus no sorry this is an envelope virus and you see the little different spike proteins and here we see a naked virus Omega virus just consists of the nucleic acid if you will it has the cap Samir's that make up the capsid that basically are going to enclose and protect the nucleic acid of the virus so here we see another picture of the viral structure of an envelope virus you can see the electron micrograph of influenza very pretty and you can almost make out the spike proteins there on the envelope virus very pretty there are other shapes of course - viruses here you see Ebola we know Ebola causes highly liter lethal hemorrhagic fever him hemorrhagic fever syndrome in humans and as well as non-human primates actually and costs many deaths here right in Africa it was first discovered in near the Ebola River Valley in Sierre in the mid-1970s and on the right side here we have our basic characteristic of a bacteriophage this is a special type of virus that infects bacteria and that's the one that we're gonna focus on in this lecture and in this class here you see that this bacteria thought has DNA as its genome but it has a very interesting structure so we'll talk a little bit more about this anatomy taxonomy of viruses I'm not sure what the cue is doing there the main criteria for how do we mean viruses right well they look at the structure they look at the chemical composition that genetic makeup there are no attacks so there's no families or Kingdom or phylum like we have in bacteria there are orders there are families and usually the names of viruses and in verde or just in virus and there are some subspecies even a virus actually there are some species such hope it stars Coby one SARS Kobe - which is actually cope at 19 isn't that subcategory so classification of taxonomy in coronavirus and what we know right now is we know it asked Colvin 19 they called it or named it Koba 19 for coronavirus disease 2019 because it was first reported to the w-h-o in China on December 31st of 2019 but you know upon further studies they realize that it has many similarities to Tsarskoe v1 and so they are also calling it Co V SARS Kobe - one of the interesting things about corona virus is that when they looked at its nucleotide they saw that 89% of the nucleotide of this strain that's coming around that is circulating right now is identical to the bat SARS like Cole V okay so it's eighty eighty nine percent identical to that one and it is 82% identical to the human SARS Cole V and so therefore they called this virus Tsarskoe v2 but we know it as cold vid 19 viral replication so we know what viruses have viruses have genetic information I already mentioned that to you that they will have either DNA or RNA but not both they have the genes necessary for replication and infection basically they have the genes for them synthesizing themselves and they may have a few enzymes as well with as it pertains to corona virus and I'm not going to examine you on corona virus for the test but I know that many students are interested in they want to know coronavirus actually has four main proteins it consists of four proteins there are very simple viruses but they're capable of causing harm right so they have their s protein which is a spike protein that I told you about that exists on the outside of the envelope so if you think about this this is not a corona virus this is actually not even an envelope virus this is an ink Advisors but if you can pretend that this blue is the envelope that's housing or protecting the nucleic acid right here you see the genetic material let's pretend that this is RNA and the white and here I see my spike proteins you see that these are my spike proteins they look like little clubs there this would be my s protein in the corona virus and it's believed that this is what's used to gain access into the cell maybe fuse in the membrane even have access to the endoplasmic reticulum of the cells so s protein is one of the proteins that's found in coronavirus another protein that's found is called M protein and this is going to be the most abundant protein in the virus that basically helps with a viral shape of the organism of the virus rather then there is a protein and a protein is found in small quantities and it basically allows the virus to assemble itself and may be required for pathogenesis in some of the corona viruses I've worked with corona viruses in the past in research not mirroring one is what the one that I worked with that I used to use it to infect my mice and have induce induce demyelination in my mice when I used to do research the last Prout so I know a little bit about corona viruses the last protein that we find in corona viruses is going to be in an protein and this is a only protein that's found in the nucleocapsid and it binds to the RNA so remember the nucleo capsid what is the nuclear capsid it is the capsid and the nucleic acid combined so that's what viruses can have for as an example but what don't they have viruses don't have any cellular components they don't have mitochondria and they don't have ribosomes so even though this virus coronavirus for example is you know an RNA virus it doesn't have any ribosomes it doesn't have mitochondria it doesn't have any other cellular components so what do you do what do you do with that RNA how do you translate that RNA into the actual proteins to synthesize more of this virus right okay so growing viruses in the laboratory can be very tricky actually it is very tricky because remember that viruses are going to require a host they don't grow on auger plates like bacteria grow well we do kind of grow them on auger plates but we have to give them a host if we're working with viruses right so we have two different types of viruses we have the animal viruses those are the ones that can infect us we grow those in tissue culture what does that mean it means that we use cells in the lab when I used to do research what we would often do is I would use cancer cells and infect those cells they continue to replicate and the virus keeps infecting those cells and spits out the virus as they either lyse the cells or they bud out okay and they what is also used in order to grow animal viruses is bird embryos right in fact that is what's used for the production of the flu vaccine so we'll talk more about that when we talk about vaccines the incubating egg is an ideal system for the virus to be injected through the shell and the virus will replicate in the chick so let's see live animal inoculations it's not usually used but it can be used if needed well the one that we use in microbiology here is going to be bacteriophage the ones the the ones that we've talked about and these are viruses that infect bacteria and in order for us to be able to see that we have to grow something called a lawn full of cells and then we can infect the bacteria so let me show you what that looks like okay so let's say that I have my auger plate okay and I'm going to dip it in e.coli use bacteriophage often times they like to infective coli and what I'm going to do is I'm going to swab my coli on my auger plate in one direction then in another direction right and then yet again in another direction so at the end of it all when I grow it and incubate it at 37 degrees what I've created is what's referred to as a lawn full of cells my entire plate is going to be full with the bacteria right okay so that's what that's the way that it would look completely yellowing I did a terrible job at this okay maybe if I do this there we go it would be completely yellow right with complete bacterial growth but this is what I would do instead so I would streak my plate so as to grow a lawn full of cells after inoculation and incubation right but before I actually incubate my plate after swabbing it three times the way that I showed you that I would do it I would then at my bacteriophage I would add my bacteriophage onto the auger plate I would spread it throughout the auger plate and then I would incubate it okay so remember that the bacteriophage what does it do it infects bacteria so what we look for then after inoculation and incubation and the addition of the virus we're going to look for areas where there is clearing that occurs like this see that now why do I have these areas that are clear within my auger plate these areas or these little plaques are referred to whoa that was not good these plaques are referred to as PFU for plaque forming units okay what that means is that wherever there is a plaque the bacteriophage infected the cell and lysed it it lysed it so wherever you see yellow is where the bacteria grew because remember that I swab the entire plate so the entire place should be full of bacteria except in those sites where the virus infected the bacteria and therefore there is that clearing so here you see an agar plate and you can take a look at the plaques that we that were as a result of the bacteria podge infecting the bacterial infection of cell culture is obvious due to cytopathic of fact basically what happens the cells will deteriorate and they we can count them same as plaques and on the left side and a we see a picture of uninfected male cells they're nice mono layer nice mono layer as opposed to be where the cells are rounded up they're piled up because they're infected this is after 24 hours of infection so this is what it would should look like this is what it looks like after infection okay now let's talk about the bacteriophage lytic lifecycle so I wanted to use these models that we have to depict viral replication bacteriophage how it replicates and so what you see here is a bacterial cell okay so here we have our bacteria now through a random collision this bacteriophage is going to land on a bacteria and bacteria have actually they have these receptor sites and so the bacteria have receptors under cell wall that are going to attach to the virus this step is called attachment or adsorption that is going to be the first step once attachment has occurred the next thing that needs to happen is that that viral genome must enter the bacterial cell so what the virus does it releases some lytic enzymes lysozyme that will basically dissolve some of the peptidoglycan to allow for the penetration of its viral genome doesn't matter if it's DNA or RNA single-stranded or double-stranded the viral genome must enter the bacterial cell right so after penetration or entry of the viral genome we move on to the next step which is going to be essentially it's going to be replication so or synthesis of the assembly of the various viral components and so what you see here is that the viral DNA is taking advantage of the host cell machinery to basically synthesize the various parts that are going to make these viruses so after synthesis or after yeah after synthesis of the various parts there's going to be assembly of the viral components so it's like making a bike right you have the various parts to make a bike you assemble them and you have your little bacteriophage that are now inside of the cell so how are these bacteriophage that are newly synthesized taking use or making use of the host cell machinery right so it's taking advantage of the host cell its DNA to allow for the synthesis of more of these bacteria Foggia to being to be a synthesized and assembled so how are they going to exit the cell how are they going to exit the cell look at that they lyse the host cell in this case see here we see the lytic lifecycle of a bacteriophage in which what it's going to do in order for it to get out and infect other cells is it's going to lyse the host so let's continue on with a PowerPoint to outline these steps that I just basically outlined with you you've seen the models that I had from the lab the first thing that's going to happen is the random collision the bacteriophage is going to basically land on the bacterial cell it's going to bind to the receptors that are found on the cell wall of the bacteria following attachment there's going to be entry of the viral genomic makeup of the virus whether its DNA or RNA the bacterial DNA is going to basically be used to synthesize the various viral components and then it's going to be degraded okay after synthesis of the various viral components and here you see the various parts that were individually made they're going to be assembled kind of like assembling a bike and then what you're gonna end up with is your mature very own your mature very honest referred to as a very own because now it's able and capable of going on and infecting other cells how can this bacteriophage leave the host cell to go on and infect other cells so here we see that it is going to the viral genomic material enters the cell right it's going to synthesize the various parts assemble them and the way that it exits is through lysis so it kills the whole cell this is referred to as lytic replication or the lytic lifecycle of a bacterial fudge hmm I wonder if there's another way that this happens let's see okay so bacteriophage this is the lysogenic lifecycle there are actually two life cycles within the bacteria budget okay the one that I outlined with you is referred to as a little life cycle it goes through the steps that I outlined with you attachment of the bacterial watch to the bacterial cell entry of the genomic material and then we have basically assembly and synthesis and then the way that it is going to be released to infect other cells is via lysis but there is another life cycle that this bacteriophage can take and the second option does not kill the host cell this is referred to as the latent life cycle now the first steps are the same we have attachment we have entry of the viral genome but then what happens is that the viral genome does not take advantage of the host cell machinery to assemble and synthesize or synthesize and assemble itself instead the viral genome is going to integrate into the DNA of the host when that happens where you call this a pro phage the bacteria can go on and replicate normally every 20 minutes the bacteria will separate etc etc right like you learned well is this a bad thing for the bacteria well not necessarily because this virus may have genes that can aid in its survival it can grant the bacteria some virulence factors it can actually be a pretty good thing for the bacteria because now even though it has this extra piece of DNA that's been inserted into a host chromosome it can take advantage of the genes that that virus brings with it so may not be a bad thing this is referred to as lysogeny the silent virus infection not all phages are going to complete the lytic cycle like I mentioned to you and so what I'm going to go over with you is that other life cycle so let's start up here in the front at the top left here we see that the phage through random collision is going to bind to a bacterial cell we have entry of the viral in this case viral DNA is going to enter the cell at this point here we see the viral DNA and the host DNA right the host chromosome there is a choice the phage DNA can go ahead and enter the lytic cycle by using the whole cell machinery to synthesize the various parts that make it and then assemble and then be released via lysis okay or what can happen is that the phage DNA can actually integrate within the bacterial chromosome and become a pro Futch or prophase well I really want to say it when it's inside the host chromosome the bacteria can continue on with replication it's gonna be happy he just continued to live on generation after generation after generation for reasons we don't quite understand there are times that the bacterial cell will actually excise the prophase from its host chromosome maybe it's under stress it could be UV radiation it could be chemicals not really sure what can cause that but occasionally the pro fetch can actually be quote-unquote popped out okay at that point we're back to this stage if the phage if the profile is excised from the host chromosome at that point it's going to enter into the lytic cycle okay so there's two life cycles there is the lytic cycle right here where the virus is going to replicate and it's gonna kill the cell or there's the lysogenic life cycle where the virus the viral the phage DNA rather will integrate into the host chromosome now it's referred to as a pro phage and can continue to divide okay excision from host chromosome as I mentioned to you that can happen and this can occur by different stresses that the cell can undergo at that point remember what I said if that phage DNA gets popped out of the host chromosome at that point it's gonna go into the lytic life cycle so what are the results of lysogeny right of a cell being infected with the virus well the cell cannot be infected by the same phage so it doesn't have to worry about it actually forcing it to go into the lytic life cycle another advantage is phage conversion and this is where the cell can actually take advantage of the toxins for example toxin production rather which was gained by having those extra viral genes that it did not before so he can take advantage of those genes that were afforded to it if they granted the ability to produce toxins and there are some microorganisms that if they were not infected with the phage they wouldn't be capable of doing what they do so I'll give you some examples in just a second and then number three specialized transduction and this refers to the fact that if the virus is able to remove itself from the chromosome and it removes itself incorrectly it can actually leave part of its viral DNA in the chromosome and so then that becomes basically part of its chromosome and if that little piece codes for for genes that have some variants factor then it can take advantage of that as well okay so phage conversion what is that that is basically when the phage integrates into the bacterial chromosome and as I mentioned to you it brings new genes to the bacteria and those genes that it brings to the bacteria can code for toxins and we see this an example in Clostridium botulinum Clostridium botulinum is a gram positive rod that is anaerobic and it causes botulism we're going to talk more about this when we get to the disease portion of this class and part of its ability to form or to produce these terrible toxins is because it was actually afforded the ability to produce those toxins by a bacteria ponch interesting Leanna corynebacterium diphtheria is another organism as well as Vibrio cholera they're both encoded by Pro phages and these organisms will only make their toxins when they are carrying these lysogenic wages so if they don't carry that phage then they don't have the ability to produce those toxins that are very bad and Vibrio is another one Vibrio cholera is another one that we're going to talk about and it's ability to basically reverse water absorption and that's one of the reasons why individuals that are infected with Vibrio cholera die from dehydration because they're losing so much fluid and the ability of the virus and not the virus cuz it's a bacteria the ability of the bacteria to do this was it's it's very lens factor was supported to it by of age okay and so that concludes today's lecture