12

There is a "anti-virus," although many call it a virophage.In 2008, a paper in Nature was published about the observations of a new strain of a virus known as Acanthamoeba polyphaga mimivirus. This virus mainly attacks amoeba. It was discovered in 1992. It was one of the biggest viruses ever found.Later, a related virus called the mamavirus was discovered. ...


10

There are many other things inside the HIV capsid besides RNA. The ssRNA is bound to the p7 nucleocapsid protein, the p6 late assembly protein, as well as integrase and reverse transcriptase, both of which are vital for infectivity. Also enclosed within the virion are Vif (Viral Infectivity Factor), protease, Nef (Negative Regulatory Factor), Tat (HIV ...


9

There is no anti-virus to all viruses and there is no such anti-virus against a single virus yet, but there is immune response to virus. How efficient the immune response is then depends on many things. There is no perfect immune response. To develop such an antivirus that decreases viral load requires cooperation with the immune response. To develop such ...


9

The Yohn et. al. (2005) paper (from Evan Eichler's lab) is describing a single type of endogenous retroviral element (loosely think of it as a 'species'), called PTERV1. They show that there were multiple independent infection events that resulted in permanent integrations in the ancestors of modern species (~3-4 MYA in the ancestors of gorillas and chimps, ~...


8

Retroviruses depend on being able to convert their RNA genome into a DNA copy, and have a reverse transcriptase enzyme to do that. This unique activity is not found in human cells, allowing for potential antiviral therapy if a drug can be used to inhibit the reverse transcriptase while not affecting the human enzymes. AZT is one such drug, by mimicking the ...


8

As you point out human beings (and other organisms) have hundreds of retroviruses and many can be seen in the human genome, some of which appear to be the remains of deactivated viruses, others which may be active. Most retroviruses are not pathogenic - they don't cause disease. This is because many retroviruses replicate slowly, budding and secreting ...


7

In Latin, lente means slow, so lentiviruses are retroviruses that are characterized by long periods of latency. lentivirus A group of retroviruses that include human immunodeficiency virus, HIV-1. They cause disease after a long incubation period. latency A state in which a virus infects a cell but does not replicate. -Janeway's Immunobiolgy, 8th ...


6

There is viral DNA within our genomes. Embedded in the genomes of all vertebrates are the proviral remnants of previous retroviral infections. It is possible that some have conferred biological benefits. Human endogenous retroviruses (HERVs) represent the proviral phase of exogenous retroviruses that have integrated into the germ line of their host. They ...


5

But is there something like an anti-virus? A single celled entity that does the opposite: spreads around 'kills' other viruses and/or cures diseases. Has anybody discovered something like it or is there any research group working on synthesizing one? Actually there is, it is called immune system. :-) Most of the cells in your body have proteasomes, ...


4

Retroviruses, such as HIV, have a genome that is composed of RNA. Once inside the host cell, that RNA is reverse-transcribed into DNA; it is that DNA which is inserted into the host genome. All retroviral genomes are integrated through insertion; there is never any replacement. Some retroviruses do, however, disrupt normal gene function. Mouse mammary ...


4

Others have already touched the important points. Consider this as a summary. What gives HIV the ability to mutate? All organisms mutate by two mechanisms: Replication errors Mutagenesis by physical/chemical agents that cause a chemical change (lesion) on DNA The main enzyme responsible for HIV replication is reverse transcriptase which makes a DNA ...


3

In short, yes. Breast milk can contain virions which can be transferred from Mother-to-Child. These are the guidelines from the National Institute of Health in the United States regarding the Prevention for Mother-to-Child Transmission of HIV and how the prevent Mother-to-Child Transmission of HIV After Birth While the guidelines in the US are geared ...


3

First, your idea that "efficiency" has some relation to "genome size" divided by "diameter" is odd. You end up with arbitrary numbers that are not any kind of measure of "efficiency". Second, HIV is an enveloped virus, while lambda phage is not; the internal viral core, less than half the size, is a better comparison. Other enveloped viruses like influenza ...


3

The high mutation rate is only a small part of the reason it's hard to make vaccines against those RNA viruses. The real problem is not that they mutate rapidly, but that they can tolerate high levels of variation in their antigenic regions without losing fitness. Viruses like polio and measles, as you say, have mutation rates easily on a par with ...


3

What gives HIV the ability to mutate? HIV is a single standed RNA virus. DNA is much more stable than RNA as it has a stronger backbone and it is typically double stranded. But HIV mutates at a rate far higher than just being a RNA virus. That's because it uses an enzyme called reverse transcriptase (RT) to build it's RNA genome from RNA bases. RT is meant ...


3

RNA has Uracil instead of thymine and DNA has thymine instead of uracil. So, how can RNA be converted into DNA? I think you may want to ask a more basic question. DNA and RNA are extremely similar, with only an oxygen being the difference. This has vast consequences for organisms, and life as we know it uses DNA and RNA for very separate purposes. DNA ...


3

Really interesting question. I am not sure, if the mutation rate is something "actively done" by the virus. I think its more a byproduct of vast replication after taking over the host cell. Mutations with a negative effect are deleted, those with neutral effects will be there, and those with positive mutations will be selected for. This paper looks ...


2

Both things are not exclusive of each other. Retroviruses are RNA-based viruses which need to reverse transcribe their RNA genome into DNA before they can multiply. This is done by the reverse transcriptase enzyme, which is part of the virus and is incorporated into the cell. Once the reverse transcriptase has been active and made the DNA, this DNA can also ...


2

I think it might be of use to show you the difference between uracil and thymine They are very similar structures. The part that is involved in base pairing is actually the Nitrogen and the oxygen furthest from the sugar. See below: So having an extra methyl group on the other side of the molecule does not interrupt basepairing. And remember, with DNA/RNA ...


2

Just to give a simpler example of what Amory has explained. Viruses can overwrite existing information, just not the way you would think if coming from the world of computers. As already mentioned, viruses have the ability to insert their genetic information into the host's genome. They do this by essentially cutting the host DNA open and inserting ...


2

Since most answers have already covered multicellular immune systems, I will try to explore the concept of unicellular immune systems. The now famous CRISPR-CAS system originally evolved as a bacterial immune system to protect itself against phages. Much like computer-based antivirus solutions, CRISPR CAS relies on a "signature" system. Known targets ...


2

Viral recombination produces genetic variation that contributes mostly to the evolution of the HIV-1 virus. HIV being an RNA Virus utilizes an enzyme called reverse transcriptase, which produces DNA from RNA. HIV also has two RNA genomes. After infection and then replication, which is catalyzed by reverse transcriptase, recombination between the two ...


2

In my experience, transduction efficiencies skyrocketed when I applied a spin-infection procedure. A 30 min low speed centrifuge with the virus changed a lot. Here is the TRC protocol for this: http://www.broadinstitute.org/rnai/public/dir/download?dirpath=protocols/production&filename=TRC%20viral%20infection%20200909.pdf


2

You are right, they should have written "all currently known PERVs". Although the structure of ERVs is generally well understood (https://www.ncbi.nlm.nih.gov/pubmed/26104559; https://www.ncbi.nlm.nih.gov/pubmed/26818261) there may be some complex cases that have been missed. Also, the map of the porcine genome is not fully complete yet (nor the human one) ...


2

I am going to focus the answer on mainly "why HIV virus has evolved such mechanisms to go from RNA to DNA and back to RNA when it could simply use the first RNA to make its copies". While others have already discussed the broad point, I will discuss more about the details. There are a few points which might support this, all of which basically come down to ...


2

Interpreting the question Initially I interpreted the question as little more than “Why one type of virus rather than another?” (dsDNA. ssDNA, ssRNA [+ve v. –ve] etc.), and this (which would be unanswerable) was the way @Taimur seems to have understood it. And I also felt that the poster’s reference to ‘complexity’ reflected more his familiarity with other ...


2

One of the reasons we don't have an HIV vaccine yet is we've only been trying to make one for a little over 30 years. It can take a long time to develop a vaccine. Beyond that, there are a number of specific challenges. One of them is that, yes as your teacher said, the virus is highly variable. Specifically, the parts of the viral proteins involved in ...


1

Viruses are one of the particles whose evolutionary origin is still a mystery to scientists. Various hypotheses have been presented but none of them have been proven so far. However, as one of our commenters has said, "What works, works and what doesn't, doesn't." This is the basic concept of the evolutionary theory. All organisms which can survive in an ...


1

I don't know what your application is, but RepBase has a curated set of ERV loci in a BED file that you can use to retrieve sequence/define regions of interest et cetera. Of course, generally speaking repetitive regions may be harder to map in terms of genomic location, and in my lab, where we regularly study ERVs in cancer, we usually map RNAseq data to ...


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