virology exam 3

7-10

history of retroviruses

• chicken leukemia virus and Rous sarcoma viruses were discovered, and it was known that they could cause tumors, but didn’t know how since they were RNA viruses

  • bc in order to induce tumors, virus must cause permanent changes to the cell, which can only happen through DNA integration

• Howard Tenin discovered that a DNA copy of the RNA genome was integrated into the host DNA, and became a permanent part of the host chromosome

• Tenin also first used the term “provirus” to describe viral DNA that had been incorporated into a host genome

  • these ideas led to the discovery of reverse transcriptase, which is the enzyme that is used by retroviruses to convert their RNA into DNA so that it can be incorporated into the host genome

retrovirus structure

• all are enveloped and have a lipid membrane that surrounds the viral nucleocapsid

• all have matrix proteins underneath the envelope that help provide the envelope with stability and help contribute to the structure

• have glycoproteins that are protruding out of the envelope like all enveloped viruses

  • there is a surface portion of the glycoprotein, and a transmembrane part that is embedded in the envelope

• most retroviruses have nucleocapsids with icosahedral symmetry, but the HIV capsid is shaped like a cone

• within the capsid is ss(+) RNA, but differ from other viruses with this genome

  • they have two copies of the RNA genome, which are an essential part of the replication process (could be bc there’s a greater probability of making function viral genomes by having two strands)

  • molecules of RNA are coded with a nucleocapsid protein, and this coat is crucial for successful replication of the virus

• package three distinct proteins within the viral particle: reverse transcriptase, integrase, and protease (many copies of these enzymes packaged within the particle)

lentivirus structure and replication

• have LTR (long terminal repeats) regions on the 5’ end and 3’ end of the genome, which are involved in the integration process

• in between the LTRs is the viral coding region, which is the region that contains all the viral genes and proteins that will be transcribed and translated

• proviral DNA genome is after the RNA has be converted to DNA and then inserted into the host chromosome

  • integrated DNA is going to be transcribed by the host cell DNA pol to make mRNA, then mRNA is made into a full-length copy of mRNA

  • this is the RNA that is transcribed and translated, but also packaged inside of the virus particles

• once the viral mRNA is made by the host, the process of expressing the genes into proteins is different from what occurs with other ss(+) RNA viruses

gene expression of lentiviruses

• instead of generating one long polyprotein, the virus generates several polyproteins that eventually are cleaved by viral proteases

  • production of these polyproteins occurs in several stages

• first, there is the translation of the gag proteins (first polyprotein that is made), which is then cleaved by viral proteases into various structural proteins

• after the gag protein sequence, there is a stop codon that causes the ribosome to fall off the RNA, so in order for the other genes on the mRNA to be expressed, the stop codon has to be suppressed or inhibited

• when the stop codon is suppressed, the ribosome can continue to read through and translate farther down the RNA and make all the proteins encoded in the message, which leads to the formation of a longer polyprotein called the gag pol precursor, which is also cleaved by viral protease

  • gag pol precursor has the proteins for the reverse transcriptase

  • suppression doesn’t happen all the time (only about 10% of the time), but without it viral enzymes would never be made

• in addition to the full-length mRNA, there is a separate spliced mRNA that is made by the cell, and this is translated to produce the envelope proteins

• there’s another stop codon after the pol sequence, but there is no suppression of that one (don’t know why), so the only way that these envelope glycoproteins can be made is through this splicing mechanism

• there is a portion of the coding sequence on the 5’ and 3’ ends and an intervening sequence, which gets spliced out in order to join the RNA sequences and allow for complete translation of the envelope proteins

gene expression of HIV

• the genome for HIV is organized in a similar fashion as other retroviruses, and encodes all the same proteins

• but it also encodes additional proteins: the tat, rev, and nef proteins

• these proteins are involved in crucial parts of viral replication and survival of the virus; they aid in transporting spliced RNAs out of the nucleus

• they also help in dampening the host immune response

• HIV can encode for these proteins bc it has additional splicing mechanisms for these various mRNAs

• HIV has evolved ways of modifying the host transcription process and the host process to generate these additional proteins

why is splicing important

• unique to certain retroviruses that encode more complex genomes and proteins

• allows for coding and expression of different mRNAs and proteins all from the same region of the virus

• allows the virus to make more proteins from relatively little genetic space, which ultimately makes them much more efficient pathogens

HIV infection

• directly infects T helper cells with its outer envelope protein by coming up the cell surface and using receptors on the T helper cells, which are CD4 molecule (surface receptor that binds to the envelope protein)

  • CD4 molecules can also be expressed at times on macrophages and dendritic cells, which can also be infected by HIV (T cells primary target)

• the binding causes a conformational change and allows a second receptor to grab hold of the envelope, which is the chemokine co-receptor (aka CCR5)

• the stalk (fusion protein) of the envelope protein then pierces through the virus into the host cell and starts to draw the two cell membranes together, fusing the membranes

• the viral genetic material is injected into the cell, and the envelope protein is left at the cell surface

• the virus has a matrix and a capsid protein, that are digested when it enters the cell, this then releases viral enzyme and the viral RNA

• reverse transcriptase then takes the viral RNA and uses host nucleotides to convert it into a single strand of DNA

  • makes some errors as reverse transcriptase has poor proofreading activity

• the single stranded DNA is reverse transcribed again into ds DNA, and the RNA is degraded

• integrase then comes in and grabs the dsDNA and carries it through a nuclear pore into the nucleus of the cell where it finds the host chromosome

• the integrase makes a nick in the host DNA and allows for HIV to insert itself into the host chromosome, and establishes lifelong infection

• now host RNA pol comes along and makes mRNA (doesn’t use RDRP)

envelope proteins of HIV

• mRNAs encode for different viral proteins that associate with ribosomes at the surface of the rough ER

• shuttled through the ER and taken to the cell surface, where it becomes embedded in the cellular membrane

• at this point, coalescing with other envelope proteins that have been produced, there is a cluster of envelope proteins now on the surface of this infected cell

• at the same time, other mRNAs are being produced allow for the translation of other viral proteins, so there are additional viral proteins being made which are going to be used to make up the key components that the virus will need

• these are transported again to the cell surface to the area where these envelope proteins are, and a strand of RNA and some enzymes are a part of that complex

• this then buds off at the cell surface, but its not a mature virion bc the polyprotein chain needs to be digested into its component parts by protease

• protease breaks up the polyprotein and allows for them to coalesce and form the mature structures that make up the final virion

• HIV gets its envelope form the external membrane of the host cell, instead of internal like from the ER

infection cycle of retroviruses

• first bind to the cellular receptor, and the envelope fuses with the cellular membrane

  • not all enter through membrane fusion, but most do

• after fusion, the core (or nucleocapsid) gets into the cytoplasm, and then the reverse transcriptase begins to work

• contents are not simply released into cytoplasm, instead they remain in the subviral structure, and within this structure is where reverse transcriptase converts viral RNA to DNA

  • maintenance of subviral particle is an important feature of retrovirus replication because it ensures that the viral genome isn’t transcribed when the virus is released into the cytoplasm

• the permeable nature of the structure allows DNTPs to flow inside of it so DNA can be made, but it still prevents ribosomes from accessing the RNA genome

• the DNA is made in the cytoplasm within the subviral structure and then the newly-made DNA gets transported into the nucleus, where it then integrates with the host genome

• the job of transport and integration into the nucleus is carried out by another of the packaged viral enzymes, which is the integrase enzyme

integrase enzyme

• finds the chromosomal DNA and then cat. the integration of the viral DNA into the host chromosome

• once the viral DNA is integrated into the genome, its genes will get transcribed by the host DNA pol in the normal cellular replication process to make mRNA

two types of mRNA made

• unspliced, full-length mRNA that results in translation of the gag and pol proteins

• spliced RNA, which results in the translation of the envelope proteins

infection cycle cont.

• after the mRNA are made, translation of the viral proteins can occur

• the envelope proteins are made in the ER, where they get embedded in the membrane

• then enter the cell’s natural secretory pathway and go to the cell surface, where they come together with capsid proteins and nucleic acid and a new viral particle is formed, and they bud off of the host cell, ending the infectious cycle

• after integration of the viral chromosome, the rest of replication is carried out by the host cell without any involvement of viral proteins, which is unique to retroviruses

integration process

• begins after the viral genome has been converted into DNA

• two characteristic features that happen when retroviral DNA gets inserted into the host genome

• first is that some of the bases on the end of the LTRs are lost from the viral DNA

  • four bases on the either side of the LTR, then integrase activity chops off the bases at the end of the viral DNA, so that only two bases remain and get integrated

• this first step is necessary for the process to happen bc the way in which integrase degrades the DNA exposes free hydroxyl groups at the end of the DNA molecule, and then the enzyme an use these free hydroxyls to cat. the cleavage of the host DNA

• once cleavage occurs, the viral DNA will then bind to the cleaved host NDA, and the integrase has completed its job so host repair enzymes will come in and fill the areas where the viral DNA has joined up with the host DNA

• second is the duplication of the host DNA at the insertion site; duplication is made by host enzymes, which have come in to repair the genome at the viral DNA insertion site

• integration can happen almost anywhere in the host chromosome and in any chromosome; it is not sequence-specific, but it is permanent

  • this characteristic has to do with the tumor formation ability of some retroviruses

assembly of the viral particle and egress from the cell

• when the virus replicates and when its mRNA is made, you get two forms: full-length and spliced

• full-length is translated into viral proteins, but it can also be packaged as a genome for when new viral particles are made

• viral RNA is made in the nucleus, goes into cytoplasm, some of it will be translated into proteins, but other portions will come together and bind to the gag protein

• the gag protein contains a portion of matrix proteins and also contains nucleocapsid proteins, which are the proteins that specifically bind to the viral RNA, which is what helps pull the genome into the new viral particle

• all of these proteins come together to form a complex, which binds to that mRNA that is made by the cell

• they will then be directed to the cellular membrane areas where the viral glycoproteins have been embedded, forming the capsid underneath the cellular membrane

• in addition to transcribing the gag complex, the cells will also transcribe the gag-pol complex, which is only translated when the stop codon on the mRNA is suppressed

  • contains the same structural gag proteins that are in the gag complex (matrix and nucleocapsid) and some additional proteins (reverse transcriptase, integrase, protease)

• this complex is directed to the cellular surface, and will sometimes get incorporated into the viral particle

• as the viral particle forms underneath the cellular membrane, the matrix and capsid proteins drive this budding process of the virus, and as the virus builds, it begins to bud off the host cell

• as it buds off, the interior of the virus structure begins to change, and this is the maturation process for retroviruses; a result of the protease activity that occurs, the cleavage of the gag proteins, maturing the particle, allowing the formation of the final capsid structure within the viral particle

  • all happens after the virus has budded off from the host cell

• now there is a fully-formed retrovirus that can infect new cells and begin the infectious cycle again

HIV (human immunodeficiency virus)

• targets cells in the immune system; CD4+ cells, which are cells that have this specific CD4 molecule on their membrane

  • macrophages, t-helper cells, and dendritic cells all have this molecule

• over time, the immune system begins to fail, which is called immunodeficiency, and this increases the risk of infections and tumors that a healthy immune system would usually be able to fend off

  • these complications are referred to as AIDS (acquired immunodeficiency syndrome)

two types of HIV

• HIV-1: commonly associated with AIDS in the US and worldwide

• HIV-2: more rare and typically restricted to areas in Western Africa and Southern Asia

  • so uncommon that HIV almost always refers to HIV-1

CD4 molecule and co-receptors

• helps these cells attach to and communicate with other immune cells, which is particularly important when the cells are launching attacks against foreign pathogens

• HIV targets and attaches to the CD4 molecule via protein called gp120 found on its envelope

• HIV then uses gp120 to attach to another receptor called a co-receptor; HIV needs to bind to both the CD4 molecule and co-receptor to get inside the cell

• the most common co-receptor that uses are the CXCR4 co-receptor, which is found primarily on t cells, or the CCR5 co-receptor, which is found on T cells, macrophages, monocytes, and dendritic cells

• these co-receptors are so important for HIV that some people with homogeneous genetic mutations in their CCR5 actually have resistance or immunity to HIV since it can’t attach

  • even heterozygous mutations, which lead to a fewer co-receptor on the cells, can make it harder for the virus to spread and results in a slower disease progression

HIV viral tropism

• HIV is known to make a lot of errors when replicating, and during infection it can mutate to create slightly different strains of viruses

• these viruses are still considered HIV but they behave slightly differently from each other and target different cells in the host

• this host cell preference is called viral tropism

HIV entering through sexual intercourse

• enters the body through sex (how it typically spreads), and at this early point (acute infection), the R5 strain of HIV, which binds to the CCR5 co-receptor, will get into macrophages, dendritic cells, and T cells

• usually dendritic cells are in the epithelial or mucosal tissue where the virus enter the body, captures the virus and migrates to the lymph nodes, where a lot of immune cells live

• the R5 strain of HIV infects T cells, macrophages, and more dendritic cells, which leads to a big spike in HIV replication and the amount of virus found in the patient’s blood

phases of HIV infection

• during the acute phase, patients usually experience flu-like or mononucleosis-like symptoms

• in response, the immune system mounts a counterattack and starts to control the amount of viral replication

  • the amount of virus in the blood declines to lower but still detectable levels by 12 weeks

• after this point, the patient enters into the chronic or clinically latent phase, which can last 2-10 years

  • during this phase, T cell counts usually remain above 500 cells per cubic mm, and patients can still fight infections fairly well, although some infections like TB become more common and severe

• during chronic phase on infection, some patients develop an X4 strain of HIV, which targets the CXCR4 co-receptor (essentially only T cells); these strains lay low in the lymphoid tissue and steadily destroy CD4 T cells

  • not all patients develop this strain, and it is unclear what the presence of this strain implies about the disease course

• when the body’s T cells drop low enough (205-100 cells per cubic mm), patients start experiencing symptoms like swollen lymph nodes (lymphadenopathy), and minor infections like oral hairy leukoplakia (a hairy looking white patch on the side of the tongue caused by the same EPV that causes mono and oral candidiasis)

• as more T cells are lost and levels fall below 200, the immune system becomes severely compromised, and the condition has progressed from HIV to AIDS

symptoms of AIDS

• people will begin to experience persistent fever, fatigue, weight loss, and diarrhea; HIV count in the blood might increase significantly

• other conditions will start to develop that are said to be AIDS-defining, like recurrent bacterial pneumonia, pneumocystis pneumonia, and fungal infections like candidiasis of the esophagus

• other conditions are tumors and malignancies like kaposi sarcoma, which causes lesions on the skin and other soft tissue, and primary lymphoma of the brain

• many people with AIDS die from infections that a healthy immune system would typically be able to fend off, like pneumocystis, cytomegalovirus, or mycobacterium avium complex

transmission of HIV/AIDS

• male to male is the most common mode of transmission in the US, and male to female is the most common mode in resource limited-settings

• although less common female to male transmissions occur as well since HIV is present in the vaginal and cervical fluids of infected women

• over 75% of all cases of HIV are contracted from sexual intercourse

• the next most common means of transmission is intravenous drug abuse and mother-to-child transmission, which can be via the placenta during delivery or via breast milk

• must less common modes of transmission are accidental needle sticks, and use of blood products like blood transfusions

diagnosis of HIV

• antibody tests: look for antibodies that the body’s made against HIV

• antibody/antigen tests: antigen tests look for the virus directly, so antigen/antibody tests detect both antibodies to the virus, and the virus itself

• RNA/DNA tests: RNA tests screen for viral RNA, and can detect the virus directly; DNA tests look for copies of the viral RNA (since its a retrovirus so it copies its genetic material into DNA)

• for screening purposes, antigen/antibody tests are recommended, bc they are better at identifying early infection

• also recommended that if the first test is positive, to follow it with a confirmatory test that looks for antibody or nucleic acids

treatment for AIDS

• currently no cure

• treatment can help someone with AIDS live longer, healthier lives and help reduce the risk of transmission

• the primary method is to use antiretroviral therapy (ART); not a single medicine, but a combination of medicines that’s known as an HIV regimen

  • help to slow down HIV replication, which gives the immune system a chance to recover and help fight off other infections more effectively

hepatitis B virus structure

• a hepadnavirus that infects the liver

• has a gapped dsDNA genome; these genomes are only partially ds, and always circular

• also have small pieces of RNA bound to one end and a packaged pol bound to the other end

  • pol is an RDRP, which is also known as a reverse transcriptase

• only DNA virus that uses a reverse transcriptase in the replication scheme

• genome is packaged in an icosahedron viral capsid, and the genome and capsid make up the nucleocapsid (sometimes referred to as the viral core)

• core particle is then covered with an envelope

two types of RNA made by hepatitis B

• pre-genomic RNA: the longest piece of RNA generated by the host cellular pol (about 3.4 kb in length)

  • begins at 5’ cap

  • longer than the DNA genome of the virus

• mRNAs: generated by the host cellular pols (host pols are responsible for generating all the RNA for this virus)

  • have a variety of lengths

  • several frame shifts in the genome that allow for the production of the various overlapping RNAs that can be made by hep B

hep B entry and replication

• infects hepatocytes by binding to its receptor, the NTCP protein

• once bound, the virus enters the cell through caveolin-mediated endocytosis

• once inside the cell, the virus is transported via microtubules all the way to the nucleus

• the core particle binds to the proteins within the nuclear pore, and the virus releases its genome into the nucleus

• once inside, the host cell enzymes then complete the gap to close the circle of the viral dsDNA, then once closed, the viral DNA is called CCC DNA (covalently closed circular DNA)

• cellular pols then act on the DNA circle to form the pre-genomic RNA and mRNAs

• for hep B, only the RNA is made in the nucleus, not DNA (contrast to other DNA viruses); it is able to do this bc it brings in its own enzymes to do the work

• after the pre-genomic and mRNAs are made, they go into the cytoplasm where the mRNAs are translated (some by free ribosomes and some by ribosomes along the ER)

  • those translated by ribosomes on ER are usually viral glycoproteins that are going to be embedded in the envelope

• in the cytoplasm, capsid protein and the P protein (the reverse transcriptase), join with the pre-genomic RNA by the reverse transcriptase binding to the end of the RNA, and the capsid forms around the complex

  • within this forming capsid, production of the DNA genome takes place, ultimately becoming the gapped, circular dsDNA

• bc the conversion to DNA by reverse transcriptase occurs in the cytoplasm, there is no chance for the genome to be integrated into the host genome (differs from retroviruses, which is the other type of virus that encodes reverse transcriptase)

synthesizing the viral genome from pre-genomic RNA

• viral pol has three functional activities: priming, reverse transcription, and DNA synthesis

• the principle function is to convert pre-genomic viral RNA into viral DNA for incorporation into the next generation of hep B virions

• three sequential steps must be completed:

  1. priming step initiates the process of negative strand DNA synthesis

     • in this step, the newly formed HPV pol recognizes a section of the pre-genomic RNA composed of a stem loop that has a bulge and loop at the top; a molecule of deoxyguanosine triphosphate becomes covalently bound to the pol and base pairs with the cytosine within the RNA stem loop

     • two molecules of deoxyadenosine triphosphate are added to the guanosine to form a short, three base DNA priming sequence

     • this priming sequence is essential; this primer base pairs with the other end of the pre-genomic RNA and serves as the initiation point for the synthesis of negative strand viral DNA by reverse transcriptase

  2. the negative strand of DNA is generated by reverse transcription with degradation of pre-genomic RNA

     • picking up from priming step, DNA synthesis proceeds, the RNA template is removed from the growing strand by the RNAs H activity of the pol

     • DNA synthesis continues until the end of the pre-genomic RAN template is reached

     • a short segment of degraded RNA remains associated with the end of the new negative DNA strand, and transfers to the beginning of the DNA strand near its point of attachment to the pol

  3. the complementary (positive) strand of DNA is synthesized to result in an infectious DNA genome

     • RNA segment then serves as a primer for the third and final stage of replication, positive DNA strand synthesis

     • as positive strand DNA synthesis proceeds, it jumps back across the end of the negative strand of DNA, thus circularizing the partially dsDNA structure

viral formation and escape

• once the genome has formed within the core particle, this particle is going to migrate to the ER where it joins with the envelope proteins

• buds into ER, and then comes out of the ER inside and moves into another structure that forms during viral replication, called a multivesicular body

• this body then fuses with the outer membrane of the host cell

• unique mechanism of escape; takes envelope from the ER and uses the multivesicular body to exit the infected cell

• once the virus has left, it can go on and infect new hepatocytes nearby

RNA molecule used to make a packaged DNA genome

• to make the partially dsDNA genome, the virus first starts with the pre-genomic RNA that was made in the nucleus and is now inside that forming viral capsid along with the reverse transcriptase

  • transcriptase also has another protein attached to it called the terminal protein

• this pol is bound to the 5’ end of the RNA as a template to make a strand of negative-sense DNA

• after this piece of DNA is made, an event called strand exchange occurs where the DNA essentially jumps, and binds to a complementary strand of RNA that’s right above it

• the RNA pol is going to move with it and eventually makes a complete copy of the negative strand of the viral genome

• most of the original pre-genomic RNA that served as the template is going to get chewed up by the RNAs H activity of the pol (the reverse transcriptase), but a portion of this RNA is going to remain bound to the negative strand of DNA

  • the RNA will serve as a primer for the synthesis of positive strand of DNA, and will also be the RNA that remains with the viral genome and gets packaged into new viral particles

• begins next step with the newly-made strand of negative sense DNA that has the RNA primer bound to it, and we get a second template exchange where that piece of RNA jumps to a complementary sequence of DNA

• picked up by reverse transcriptase and it begins synthesizing a new strand of positive DNA, but the synthesis will remain incomplete

• will end up with a packaged genome that has a full length copy of negative NDA but only a partial copy of that positive strand

infection of hepatocytes

• most commonly targets the cells in the liver

• when the virus gets in and infects the cells, they tend to cause them to present weird and abnormal proteins via their MHC class I molecules

• at the same time, immune cells are infiltrating the liver and trying to fix the issue

  • the CD8+ T cells recognize the abnormal proteins as a sign that the cells are in danger, and then the hepatocytes go through cytotoxic killing by the T cells and apoptosis

• hepatocytes undergoing apoptosis are sometimes referred to as councilman bodies, and typically takes place in the portal tracks and the globules of the liver

• the cytotoxic killing of the hepatocytes is the main mechanism behind inflammation of the liver, and eventually, liver damage in viral hepatitis

signs and symptoms of hepatitis

• symptoms relating to the immune system mounting an attack like fever, malaise, and nausea

• patients might have hepatomegaly where their liver is abnormally large from inflammation, which can cause pain

• as more damage is done to the liver, the amount of transaminase in their blood will increase; bc the liver has transaminase enzymes that break down various amino acids

• elevated levels of atypical lymphocytes (atypical lymphocytosis) are common, which are usually large due to stimulation from antigens

• patients often develop jaundice with a mix of conjugated bilirubin and unconjugated bilirubin

  • leaks out when bile duct jewels are damaged or destroyed when the hepatocytes die bc they make up some of its lining

  • and since they are dying they start to lose the ability to conjugate bilirubin and make it water-soluble, that’s why there is some unconjugated too

stages of infection

• if symptoms persist or the virus is present for more than six months, viral hepatitis goes from being acute to being chronic

• at this point, inflammation mostly happens in the portal tract, and if the inflammation and fibrosis keep happening, it could be progressing to post-necrotic cirrhosis

5 different types of hepatitis

• hep A

• hep E

• hep C

• hep B

• hep D (not talked about)

hepatitis A

• transmitted through ingestion of contaminated food or water

• transmitted through ingestion of contaminated food or water

• the fecal-oral route and is known to be acquired by travelers

• almost always acute; essentially no chronic HAV

• HAV IgM antibody indicated an active infection

• HAV IgG antibody is a protective antibody that indicates recovery from HAV or vaccination in the past

• has the option for immunization

hepatitis E

• similar to HAV with the same route of transmission and is most commonly acquired through under-cooked seafood or contaminated water

• doesn’t have much of a chronic state, and HEV IgM antibodies tell us that there’s an active infection

• HEV IgG antibodies are protective and signal recovery; no immunization

• HEV infection for pregnant women can be very serious and can lead to acute liver failure, also called fulminant hepatitis

hepatitis C

• transmitted via blood; could be from childbirth, intravenous drug abuse, or unprotected sex

• usually moves on to chronic hepatitis

• a couple of tests to help diagnose HCV, one being by enzyme immunoassay

  • screen for HCV IgG antibody, and if present, it doesn’t necessarily confirm acute, chronic, or even resolved infection bc it isn’t regarded as a protective antibody like in HAV and HEV

• more specific confirmation is done by recombinant immunoblot assay; more specific, but less sensitive than immunoassay

  • doesn’t provide much usefulness and needs an additional supplemental test if its positive

• best way to diagnose is by using an HCV RNA test using PCR, which can detect the virus very early on (1-2 weeks after infection)

  • detects levels of viral RAN in the blood, which tells the level of virus circulating

  • if RNA levels begin to decrease, the patient is recovering; if RNA remains the same, patient probably has chronic HCV

hepatitis B

• contracted via the blood; same routes as HCV

• only moves on to chronic hepatitis in 2-% of cases overall

  • also depends on age that someone gets infected

  • children less than 6 years old are most likely to get chronic infections

  • about 50% (percentage increases), the younger they are

• chronic HBV is known to be linked to liver cancer

• uses a variety of testing methods like PCR to look for certain markers, especially the HBV antigens

  • the presence or absence of each of these at different time points can tell different things

• key marker for HBV infection is the HBV surface antigen (HBsAg), which lives on the surface of the virus

• another marker is the core antigen (HBcAg), which come from the core of the virus

  • work alongside the surface antigen

• the E antigen is secreted by infected cells, so it serves as a marker for infection

• at the onset of infection during the acute phase, the surface antigen will be present and come up positive, and its factory will pump out viral DNA and E antigen

how to fight hepatitis B infection

• the immune system produces IgM antibodies against the core antigens

• in order to defeat it, must target the surface antigen

• the IgG antibody attacks the surface antigen

• at this point, the host enters a phase called the window, where neither the surface antigen or IgG can be detected cause levels are both so low (can last several weeks to months)

  • the only thing you can detect during this stage is the IgM core antibodies

• two options: IgG antibodies beat the surface antigen, or surface antigens are still detected and infection has not been fought

  • if surface antigens are still present, there could also be a presence of HBV DNA and E antigen bc its replicating

• regardless of which wins, the IgM antibodies will be promoted to IgG by about six months time, but it does not mean that the host is protected

  • can have IgG antibodies and still not win against the infection

• if the infection persists, the host transitions into chronic viral hepatitis, defined by continuing after six months

• when chronic, the host could present as healthy and will likely have the presence of surface antigen, core antibody, and no DNA or E antigen

  • no replication; host is contagious but there’s lower risk

• fighting antibodies can also be ineffective, which increases the risk for post-necrotic cirrhosis and hepatocellular carcinoma

• immunization can skip these steps and get you to the right IgB antibody for surface antigen ration

MODULE 8

MODULE 9

herpes virus symptoms

• usually, herpes (HSV) infects a person and causes no symptoms, even moving between people without symptoms

  • can move through a population silently

• once in a while, it can cause symptoms which are usually in the form of skin and mucous membrane lesions

  • can be divided into infections above the waist (mostly involving mouth and tongue) and below the waist (involving genitals)

types of simplex herpes viruses

• HSV1 and HSV2

• both are part of a larger family of enveloped ds DNA viruses, the herpesviridae family

• HSV1 tends to cause infections above the waist and HSV2 tends to cause infections below the waist

  • there is crossover, bc both viruses can cause both types of infections

herpes infection

• herpes is most contagious when there are virus filled lesions present

• can also spread by asymptomatic shedding, meaning that herpes viruses can be in saliva or genital secretions even when there are no signs of a cold sore or genital lesion

• typically, when herpes virus lands on a new host (never been infected) it dives into small cracks in the skin or mucosa and binds to epithelial cell receptors, triggering those cells to internalize the virus

• once inside, the virus starts up the lytic cycle, which is where its DNA gets transcribed and translated by cellular enzymes which help to form viral proteins, which are packaged into new herpes viruses which can leave to go and infect neighboring epithelial cells

herpes infection of neurons

• HSV1 and HSV2 can also infect nearby sensory neurons and travel up their axon to the neuron cell body to start the latent cycle

• the sensory neurons of the face have their cell bodies in the trigeminal ganglia, and those on the genitalia are located in the sacral ganglia

• these sensory neurons aren’t destroyed, they become a permanent home for the herpes virus

• from time to time, the virus makes a few viral copies of itself and sends those virus particles back down the axon so they can get released and infect epithelial cells