introduction
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Lentivirus
Saturday, January 31, 2009/ 11:47 PM
Lentiviruses
The Lentiviruses are complex Retroviruses whose core is cone shaped in the mature virion. The most important are the Human Immunodeficiency Viruses, HIV-1 and HIV-2. Other members of the genus include Simian Immunodeficiency Virus (SIV), Feline Immunodeficiency Virus (FIV), Bovine Ficiency Virus (BIV), Visna virus (which causes disease in sheep), Equine Infectious Anemia virus (EIAV), and Caprine Arthritis-Encephalitis Virus (CAEV). As described above, the regulation of Lentivirus replication is complex because Lentiviruses encode three to six accessory genes, depending on the virus, to regulate the replication cycle and aid in the assembly of progeny viruses.
All Lentiviruses have a specific tropism for macrophages, which comprise the major reservoir of infected cells in an animal. Other cells can also be infected and this can be important in the disease process (e.g., CD4+ T cells in HIV infection). Lentiviruses establish a lifelong, chronic infection which elicits a vigorous immune response that is still unable to clear the infection. Most known Lentiviruses cause serious disease in their native host after a long latent period. However, SIV produces a asymptomatic, lifelong infection of its natural host, African monkeys. Intriguingly, SIV causes AIDS when transmitted to Asian monkeys.
Labels: Natasya
Integration
Integration (Retrovirus)
After the appearance of the full-length dsDNA genome in the nucleus, the viral integrase catalyzes it insertion into a host cell chromosome by means of a single recombinational event. Insertion is essentially random within the host genome. The first event in integration is the removal of two nucleotides from the 3’ end of both strands of the viral DNA. The next two nucleotides are always AC, from 3’ to 5’. The 3’ OH of the now 3’-terminal A residue is used to attack an internucleotide phosphate in the host DNA. Attack is coordinated so that both ends of the viral DNA are inserted at once. The spacing between the two insertion points depends on the viral integrase and is 4, 5, or 6 nucleotides in different viruses. The ends of the inserted structure are then cleaned up, probably by host enzymes. Insertion results in the loss of the two terminal nucleotides of the viral DNA. In addition, a duplication of the 4, 5, or 6 nucleotides of the host that lie between the two insertion points is produced, and these duplicated nucleotides flank the two ends of the viral genome.
The integrated form of the virus, the provirus, is stable. No mechanism for precise excision of the provirus is known, and integration is essentially irreversible. Most Retroviruses do not kill the host cell, and the provirus behaves as a simple Mendelian gene that is transmitted to all daughter cells. It is obvious that insertion of such a provirus into the germ line would lead to its transfer to progeny organisms, which appears to have occurred many times in the past.
After the appearance of the full-length dsDNA genome in the nucleus, the viral integrase catalyzes it insertion into a host cell chromosome by means of a single recombinational event. Insertion is essentially random within the host genome. The first event in integration is the removal of two nucleotides from the 3’ end of both strands of the viral DNA. The next two nucleotides are always AC, from 3’ to 5’. The 3’ OH of the now 3’-terminal A residue is used to attack an internucleotide phosphate in the host DNA. Attack is coordinated so that both ends of the viral DNA are inserted at once. The spacing between the two insertion points depends on the viral integrase and is 4, 5, or 6 nucleotides in different viruses. The ends of the inserted structure are then cleaned up, probably by host enzymes. Insertion results in the loss of the two terminal nucleotides of the viral DNA. In addition, a duplication of the 4, 5, or 6 nucleotides of the host that lie between the two insertion points is produced, and these duplicated nucleotides flank the two ends of the viral genome.
The integrated form of the virus, the provirus, is stable. No mechanism for precise excision of the provirus is known, and integration is essentially irreversible. Most Retroviruses do not kill the host cell, and the provirus behaves as a simple Mendelian gene that is transmitted to all daughter cells. It is obvious that insertion of such a provirus into the germ line would lead to its transfer to progeny organisms, which appears to have occurred many times in the past.
Labels: Natasya
Why is Genome Diploid?
Why Is the Genome Diploid?
Why the retroviral genome is not clear. In other instances where reverse transcription occurs, such as in the Hepadnaviruses and the Retrotransposons, the RNA to be copied is not diploid. Furthermore, in vitro studies have shown that retroviral RT can use a single copy of the RNA genome to produce a full-length dsDNA. Thus, two copies of the genome are not essential. However, it is possible that during infection the process is more efficient if the RT can go back and forth between the two copies, and this resulted in selection for a diploid genome in Retroviruses. The process of reverse transcription to produce the viral dsDNA is complex with the multiple jumps more efficient. Other possible advantages of a diploid genome that could have resulted in selective pressure for diploid are the possibility of overcoming at least some damage in the RNA by switching templates, and the fact that switching templates result in recombination. Recombination does occur frequently in Retroviruses, and it is clear from many studies of virus evolution that recombination is important in their evolution.
Labels: Natasya
Synthesis of 2nd DNA Strand (RETROVIRUS)
Synthesis of the Second DNA Strand
The first-strand DNA produced in this way is the template for second-strand (plus-strand) DNA synthesis. The primer for second-strand is an RNA oligonucleotide, called the polypurine tract or PPT, positioned immediately 5’ of U3, PPT survives RNase H degradation and its 3’ terminus is exact; that is, the cleavages to produce it are precise. In addition to this precise primer for plus-strand synthesis, which defines the boundary of U3 and thus of the LTR, additional priming sites are used in some Retroviruses, such as HIV.
The PPT plus-strand primer is extended through U3, R, U5, and into the region of the primer tRNA, which is still attached to the first-strand DNA. The 18 nucleotides of the tRNA primer that are complementary to the PBS are copied, but further copying is thought to be blocked by a modified nucleotide in the tRNA that cannot be copied. The tRNA primer is then removed by RNase H and a second jump occurs. In the second jump, the nascent second-strand DNA is transferred to the other end of the template, using the PBS sequence, which is now present at the 3’ ends of both strands. Synthesis of both strands of DNA resumes and it becomes full length and double stranded. The resulting dsDNA is cleaned up, probably by cellular enzymes. In the full-length, linear ds copy of the genome, the LTR sequence U3-R-U5 has been formed at both ends of the DNA genome.
It is of interest that RT, like DNA polymerases, requires a primer to synthesize DNA, but unlike most DNA polymerases it can copy either DNA or RNA, given the appropriate primers. Thus, the enzyme differs from the RNA replicases of RNA viruses, which use other mechanisms for the initiation of RNA replication.
The first-strand DNA produced in this way is the template for second-strand (plus-strand) DNA synthesis. The primer for second-strand is an RNA oligonucleotide, called the polypurine tract or PPT, positioned immediately 5’ of U3, PPT survives RNase H degradation and its 3’ terminus is exact; that is, the cleavages to produce it are precise. In addition to this precise primer for plus-strand synthesis, which defines the boundary of U3 and thus of the LTR, additional priming sites are used in some Retroviruses, such as HIV.
The PPT plus-strand primer is extended through U3, R, U5, and into the region of the primer tRNA, which is still attached to the first-strand DNA. The 18 nucleotides of the tRNA primer that are complementary to the PBS are copied, but further copying is thought to be blocked by a modified nucleotide in the tRNA that cannot be copied. The tRNA primer is then removed by RNase H and a second jump occurs. In the second jump, the nascent second-strand DNA is transferred to the other end of the template, using the PBS sequence, which is now present at the 3’ ends of both strands. Synthesis of both strands of DNA resumes and it becomes full length and double stranded. The resulting dsDNA is cleaned up, probably by cellular enzymes. In the full-length, linear ds copy of the genome, the LTR sequence U3-R-U5 has been formed at both ends of the DNA genome.
It is of interest that RT, like DNA polymerases, requires a primer to synthesize DNA, but unlike most DNA polymerases it can copy either DNA or RNA, given the appropriate primers. Thus, the enzyme differs from the RNA replicases of RNA viruses, which use other mechanisms for the initiation of RNA replication.
Labels: Natasya
Orthomyxoviridae (1)
www.flickr.comIntroduction:
For this family of viruses, we'll be focusing on the Influenza virus (type A and B). The influenza virus is a single stranded negative RNA (ss(-) RNA) virus. An influenza virus particle is typically spherical, has an envelope, could be pleomorphic,has spikes on the envelope called haemagglutinin and neuraminidase,the ratio of HA:NA is 5:1.
As mentioned earlier, the virus is a ss(-) RNA in 8 segments. It has 3 polymerase polypeptides with each segment and the 5' and 3' end of the segments are all highly conserved.
Reproductive cycle of the Influenza virus:
There are basically 6 phases for virus replication. They are:
- Attachment
- Penetration
- Uncoating
- Replication
- Assembly
- Release
It takes about 6 hours for the complete replication of the Influenza virus. The reproduction of the virus kills the host cell in process. The virus attaches to the glycolipids or glycoproteins of the cell membrane of the host cell via its haemugglutinin subunit on the virion envelope. Then, the virus is engulfed into the endosomes. The acidic environment of the endosome causes the virus envelope to fuse with the endosome's plasma membrane, and in the process, uncoating the nucleocapsid which is released into the cytoplasm. A transmembrane protein help forms an ion channel for protons to enter the virion and destabilize protein binding. This allows the transport of the nucleocaspid to the nucleus, where the genome is transcribed by important enzymes to get viral mRNA. The nucleocaspid is then assembled in the nucleus. As the virions bud through the host cell membranes, they acquire envelopes and undergo maturation. The viral envelope haemagglutinin may be subjected to degradation(digestion). This process helps the virions to be infectious. Virions that are newly synthesized have surface glycoproteins that contain a N-acetylneuraminic acid as a part of their carbohydrate structure.This factor makes them susceptible to self-agglutination by the hemagglutinin. One of the functions of the viral neuraminidase is to remove these residues, to avoid self-agglutination.
Pathogenesis:
The influenza virus is transmitted from person to person in droplets mostly by sneezing and coughing. The inhaled droplets then land on the lower espiratory tract and the virus starts to invade and infect the mucosal cells. The influenza virus affects the human respiratory tract because of its haemagglutinin's (HA) affinity for receptors in the epithelium of the tract. In an attempt to fight off the virus, the epithelium of the tract produces mucus to trap the virus particles. The virus may extensively infect the alveoli, especially pateints who have lung and heart problems. Some of the compounds that help to fight off these virus are:
- existing antibodies
- Macrophages
- IgA, IgG
- Anti-HA Ab
- Cytokines www.humpath.com
- Natural killer cells
Labels: Shu Juan
Synthesis of 1st DNA Strand (RETROVIRUS)
Synthesis of First DNA Strand
At the ends of the viral RNA are domains that are essential for production of the dsDNA copy of the RNA genome. A direct repeat element called R, 15-230 nt in length depending on the virus, is present at the two ends of the RNA genome. At the 5’ end of the genome, a unique sequence element called U5 (70-220 nt long) is present immediately downstream of R, and at the 3’ end of the genome a unique element called U3 (230-1200 nt) is present immediately upstream of R. On completion of DNA synthesis, these elements give rise to direct repeats present at the ends of the viral DNA, called the long terminal repeats or LTRs, which have the sequence U3—U5.
Immediately 3’ of U5 is a primer binding site (PBS), where 18 nucleotides are exactly complementary to the 3’ end of a specific cellular tRNA. Each genomic RNA molecule has bound to it at PBS one molecule of the appropriate tRNA, which is used as a primer for DNA synthesis. The tRNA used depends on the virus, and several different tRNAs are known to be used by different viruses.
Reverse transcription begins by extending the primer tRNA through U5 and R, and stops when the end of the RNA genome is reached. The cDNA product, called the first strong stop DNA, is then transferred while still attached to the primer, from the 5’ end of the RNA to the 3’. It is unknown whether transfer is usually to the 3’ end of the same molecule, to the 3’ end of the second copy of the genome, or randomly to either copy of the RNA in the virus. This transfer uses the repeat element R at the 5’ end 3’ ends – the DNA copy detaches from R at the 5’ end and anneals to R at the 3’ end, so that only one copy of R is present in the DNA transcript. RNase H is presumably important for this. During reverse transcription, the RNA strand is destroyed by RNase H about 18 nt behind the transcription point. The degradation of the RNA strand during transcription of the DNA copy may encourage the jump to the other end. Other components of the particle may also be involved in the jump.
After the jump, reverse transcription resumes until the 5’ end of the RNA template is reached. Note that the RNA strand now at PBS because RNase H has degraded the RNA strand of the DNA/RNA hybrid (but not the RNA in PBS because this is an RNA-RNA duplex). This process results in the formation of what is called first-strand DNA or minus-strand DNA, because it is the antimessage sense.
At the ends of the viral RNA are domains that are essential for production of the dsDNA copy of the RNA genome. A direct repeat element called R, 15-230 nt in length depending on the virus, is present at the two ends of the RNA genome. At the 5’ end of the genome, a unique sequence element called U5 (70-220 nt long) is present immediately downstream of R, and at the 3’ end of the genome a unique element called U3 (230-1200 nt) is present immediately upstream of R. On completion of DNA synthesis, these elements give rise to direct repeats present at the ends of the viral DNA, called the long terminal repeats or LTRs, which have the sequence U3—U5.
Immediately 3’ of U5 is a primer binding site (PBS), where 18 nucleotides are exactly complementary to the 3’ end of a specific cellular tRNA. Each genomic RNA molecule has bound to it at PBS one molecule of the appropriate tRNA, which is used as a primer for DNA synthesis. The tRNA used depends on the virus, and several different tRNAs are known to be used by different viruses.
Reverse transcription begins by extending the primer tRNA through U5 and R, and stops when the end of the RNA genome is reached. The cDNA product, called the first strong stop DNA, is then transferred while still attached to the primer, from the 5’ end of the RNA to the 3’. It is unknown whether transfer is usually to the 3’ end of the same molecule, to the 3’ end of the second copy of the genome, or randomly to either copy of the RNA in the virus. This transfer uses the repeat element R at the 5’ end 3’ ends – the DNA copy detaches from R at the 5’ end and anneals to R at the 3’ end, so that only one copy of R is present in the DNA transcript. RNase H is presumably important for this. During reverse transcription, the RNA strand is destroyed by RNase H about 18 nt behind the transcription point. The degradation of the RNA strand during transcription of the DNA copy may encourage the jump to the other end. Other components of the particle may also be involved in the jump.
After the jump, reverse transcription resumes until the 5’ end of the RNA template is reached. Note that the RNA strand now at PBS because RNase H has degraded the RNA strand of the DNA/RNA hybrid (but not the RNA in PBS because this is an RNA-RNA duplex). This process results in the formation of what is called first-strand DNA or minus-strand DNA, because it is the antimessage sense.
Labels: Natasya
Reverse Transcription of Viral RNA
Most Retroviruses penetrate into a cell by fusion with the plasma membrane, but some use the endosomal pathway. Once inside the cell, reverse transcription takes place in a subviral particle to produce a full-length, linear dsDNA copy of the RNA. The composition of this subviral particle is not well defined. It certainly contains RT and its associated activities as well as components derived from Gag, but which Gag components are present and whether cellular proteins form part of this particle are not known.
Reverse transcription begins in the cytoplasm. In most viruses, the full-length dsDNA is produced in the cytoplasm, but in some the finishing touches occur after transfer to the nucleus. After transfer to the nucleus, the viral DNA is integrated into the host chromosome, essentially t random, in a process that requires the activity of IN. In the simple viruses, transfer to the nucleus occurs during cell division, when the nuclear envelope is disassembled. At least some of the complex retroviruses, however, such as HIV, encode proteins that allow the DNA-containing complex to traverse the nuclear membrane. Thus, the simple Retroviruses can only productively infect dividing cells, whereas HIV can infect non-dividing cells.
Labels: Natasya
Retroviral Genome
The RNA genome in the retrovirion is diploid, consisting of two copies of a 7- to 10-kb single-stranded (ss) RNA that is capped and polyadenylated. The two copies of the genome are normally identical, but during mixed infection hybrid genomes can result. They are joined near their 5’ ends, and perhaps in other regions as well, by hydrogen bonds.
All Retroviruses encode the four genes called gag, pro, pol, and env, which are always found in his order in the genome. The name gag comes from group-specific antigen, because the proteins encoded in this gene are more highly conserved, and therefore more widely cross reactive immunologically, than are the envelope proteins of the virion. The peptides derived from the Gag polyprotein, the precursor polyprotein encoded in the gag gene, form the capsid of the retrovirion. The pro gene encodes a protease (PR) that is required for the processing of Gag, and pol encodes three activities, RT,RNase H, and integrase (IN). RNase H forms a separate domain in the RT-RNase H protein, but functions as an integral component of RT. IN is required for the integration of the dsDNA copy of the retroviral genome into the host chromosome. The fourth gene, env, encodes the envelope glycoprotein at the surface of the envelope retrovirion. The primary product is Env, which is processed by cleavage to form an N-terminal external protein called SU (for surface) and a C-terminal protein that spans the membrane called TM (for transmembrane). The order of genes in the provirus is the same as in the viral genome.
As described above, the genomes of complex Retroviruses contain a number of regulatory genes in addition to these four basic genes present in all Retroviruses genes will be described later on the next post.
Labels: Natasya
FAMILY RETROVIRIDAE
The retroviruses are a very large group of viruses that infect invertebrates as well as vertebrates. Most of what we know about this group of viruses comes from studies of viruses that higher vertebrates. Hundreds have been studied and, although considerable divergences exist, they form a well-defined taxon. All are sufficiently similar to be classified as belonging to a single family, the Retroviridae. The family gets it name from the concept that these viruses use retrograde flow of information, from RNA to DNA, whereas the conventional flow of information in living organisms is from DNA to RNA.
The RTs of Retroviruses are the most highly conserved elements of these viruses and have been used to study the relationships among them. Lineage of fish viruses, now classified as members of the genus Epsilonretrovirus. Based on these sequence relationships, the Retroviruses that infect birds and mammals are classified into six genera. Of these, members of three genera are characterized as simple retroviruses, which encode only the genes gag, pro, pol, and env (and sometimes dut). The other three genera retroviruses of higher vertebrates, as well as the fish viruses, encode, in addition, regulatory genes that control their life cycle, and they are called complex Retroviruses. Notice that these regulatory genes independently entered the four different lineages of complex Retroviruses represented by the four different genera. Thus, recombination to acquire new functions has been an ongoing process in the Retroviruses. Also notice that the complex Retroviruses do not group together.
The Epsilonretroviruses are more closely related to the Gammaretroviruses, which are simple viruses, than they are to other complex Retroviruses, and the Deltaretroviruses, Lentiviruses, and Spumaviruses are not particularly closely related.
Members of the different genera differ in their structure as visualized in the electron microscope. The simple viruses were formerly classified on the basis of morphology into groups A, B, C, and D. The nucleocapsids of C-type viruses, now classified as Alpharetrovirus and Gammaretroviruses, assemble during budding, and the nucleocapsid is centrally located in the mature virion. The nucleocapsids of B-type and D-type viruses, now classified as Betaretroviruses, assemble before budding and the nucleocapsid is eccentrically located (type B) or bar shaped (type D) in the mature virion.
Eukaryotic genomes contain a very large number of genetic elements that are related to retroviral genomes. Retrotransposons encode RT and can move around within the genome by a process that uses reverse transcription and insertion, similar to what happens with Retroviruses. They are related to retroviruses but have no independent lives as viruses. Other elements in the eukaryotic genome contain additional Retrovirus-like genes and appear to have arisen by insertion of retroviral into the germ line at some time in the past. Some of these are still active, capable of giving rise to infectious Retroviruses, whereas others are defective. It is clear that this class of elements has been coevolving with the eukaryotes for a long period of time. The integrated copies of Retroviruses in the germline constitute a form of fossil record that allows us to trace the lineage of at least some retroviruses for 100 million years or longer. For other viruses, whether RNA or DNA, we can only trace ancestry for much shorter periods of time.
Labels: Natasya
INTRODUCTION
Two families of animal viruses utilize reverse transcriptase (RT) in the replication of their genome, the Retroviridae and the Hepadnaviridae.
The retroviruses have been intensively studied for years because researchers discovered early that avian Retroviruses have the ability to induce leukaemia and sarcomas in chickens. The study of these viruses led to the discovery of cellular oncogenes, of RT, and of mechanisms that regulate cycling of the animal cell, and several Nobel prizes have been awarded for work with the avian retroviruses.
Although clearly important for our understanding of biology, for many years after their discovery Retroviruses were in some ways biological curiosities because no human disease was known to be associated with Retroviral infection. This changed with the discovery of human T-cell leukemia viruses, now known as primate T-lymphotropic viruses (PTLV), which cause leukemia in man. More recently, the appearance of Human Immunodeficiency Virus (HIV) and of acquired Immunodeficiency Syndrome (AIDS) in the human population has dramatically altered our understanding of the disease-causing potential of retroviruses.
Labels: Natasya
Poxviridae ( History of smallpox and its eradication)
Tuesday, January 27, 2009/ 2:02 AM
Unique featues
Poxviridae is the largest family of viruses, which can be seen under a light microscope. It has linear dsDNA covalently cross linked at ends. Important characteristic of poxvirus is that it is remains stable for hours in air.
Poxvirus can be split into 2 major groups and they are
Bioterrorism
(watch the video on the how pox virus is used as bioterrorism)
Poxviridae is the largest family of viruses, which can be seen under a light microscope. It has linear dsDNA covalently cross linked at ends. Important characteristic of poxvirus is that it is remains stable for hours in air.
Poxvirus can be split into 2 major groups and they are
- Chordopoxviriniae(poxvirus of vertebrates) and
- Entomopoxvirinae( poxvirus of insects)
Clinical features
- human is the only host
- causes respiratory secretions
- causes skin lesions
- 12-7 days of incubation
- there are nine types of poxvirus that causes the disease
- variola (infects human) and vacinnia (infects cow)
- show inflenza like sympotoms
- form pustules which scars the skin
- if not treated it causes blindness or even
(watch the video on the features of small pox)
Vaccination
- Edward jenner was the first person came out the first vaccination for small pox
- used cow pox(vaccinia which is used as vector) from milkmaids
- to vaccinate james phipps
- and cured him
Eradication
- no reservoir for vaccinia or variola except man
- causes acute infection where the patients dies or obtains life long immunity
- is also an efficient immunogen.
Lab diagnosis, epidemology, control
- it was eradicated in 1980
- it was found to be infectious during symptoms and not during incubation.
- best defence against small pox was vaccination
- last outbreak in happened in yugoslavia in 1972
- after the outbreak the infectious materials was incinerated
- now the vaccination have stopped
Bioterrorism
(watch the video on the how pox virus is used as bioterrorism)
Labels: selvi