Virology question of the week: why a segmented viral genome?

22 April 2014

influenza-reassortmentThis week’s virology question comes from Eric, who writes:

I’m working on an MPH and in one of my classes we are currently studying the influenza virus. I’d forgotten that the genome is in 8 separate parts. Curious, I’ve been searching but can’t find any information as to why that is?

What evolutionary advantage is conferred by having a segmented genome?

Terrific question! Here is my reply:

It’s always hard to have answers to ‘why’ questions such as yours. We answer these questions from a human-centric view of what viruses ‘need’. We might not be right. But I’d guess there are at least two important advantages of having a segmented RNA genome.

Mutation is an important source of RNA virus diversity that is made possible by the error-prone nature of RNA synthesis. Viruses with segmented genome have another mechanism for generating diversity: reassortment (illustrated).

An example of the evolutionary importance of reassortment is the exchange of RNA segments between mammalian and avian influenza viruses that give rise to pandemic influenza. The 2009 H1N1 pandemic strain is a reassortant of avian, human, and swine influenza viruses.

Having a segmented genome is another way to get around the limitation that eukaryotic mRNAs can only encode one protein. Viruses with segmented RNA genomes can produce at least one protein per segment, sometimes more. There are other ways to overcome this limitation – for example by encoding a polyprotein (picornaviruses), or producing subgenomic RNAs (paramyxoviruses).

Other segmented viral genomes include those of reoviruses, arenaviruses, and bunyaviruses.

There are various ways to achieve genetic variation and gene expression, and viruses explore all aspects of this space.

    7 comments

    TWiV 281: The Salk legacy with Peter L. Salk

    20 April 2014

    On episode #281 of the science show This Week in Virology, Vincent meets up with Peter L. Salk to talk about development of the first poliovaccine, eradication of poliomyelitis, and Jonas Salk’s 100th birth anniversary.

    You can find TWiV #281 at www.twiv.tv.

      TWiV 280: Post viral

      13 April 2014

      On episode #280 of the science show This Week in Virology, the TWiVmeisters answer listener email about the NEIDL, negative results, patenting MERS-coronavirus, human papillomavirus transmission, canine distemper virus, and much, much more.

      You can find TWiV #280 at www.twiv.tv.

        Unraveling the NEIDL

        11 April 2014

        Threading the NEIDLThe NEIDL (National Emerging Infectious Diseases Laboratory) at Boston University is a newly constructed biosafety level 4 facility which can be used to study the most dangerous human pathogens. The facility is amazingly safe, as we documented in our film about the facility, Threading the NEIDL. Some members of the Boston City Council think otherwise and have moved to stop the facility from opening.

        In January 2014 a draft ordinance was introduced to the Boston City Council that would prohibit BSL-4 research within the city limits. The first public hearing on the proposed ordinance is scheduled for Wednesday, April 16, 2014 at Boston City Hall. Members of the public are invited to attend and testify. I encourage you to read the proposed ordinance which is available online. If you live in the Boston area and have a view on this ordinance, you might consider attending the public hearing. The Boston City Council Calendar of Meetings should be consulted for scheduling changes.

        The American Society for Microbiology has provided this statement on the ordinance:

        As background information you should be aware that In 2007, the ASM filed an Amicus brief with the Supreme Court of Massachusetts on a case involving a BSL-4 laboratory affirming the importance and safety of BSL-4 research laboratories. That same year, the Society also provided similar testimony before the U.S. House of Representatives.

        We believe that scientists should be aware of events that can impact science in their region and have the opportunity to voice their opinions on actions that could affect them, directly or indirectly. We urge any members who are inclined to attend.

        The Boston City Council Ordinance seems ill-advised, especially since the NEIDL has gone through a supplemental risk assessment process, and has been blessed by two independent scientific groups (the National Research Council and the NIH Blue Ribbon Panel), and prevailed in Federal Court.

        While it might seem frightening to have a BSL-4 facility within a major city, after having toured the NEIDL I can say with confidence that the precautions taken to prevent release of pathogens, both physical and operational, are second to none. As Elke Muhlberger noted during our tour, it is the safest place to work on Earth. I strongly recommend that the Boston City Council members view Threading the NEIDL to learn why it does not make sense to prevent opening of this facility.

          3 comments

          Virology question of the week

          9 April 2014

          HIV binding CD4 and ccrOn the science show This Week in Virology we receive many questions and comments, which are read every week. I also get many questions here on virology blog, which I tend to answer by email. However I think that everyone could benefit from these questions, so I’ve decided to post one here each week along with my answer.

          This week’s question is from Joseph, who wrote:

          I’m relatively new to virology or anything biology-related. Hell, I’m studying computer science as an undergrad at the moment; however, there’s something about virology that fascinates me – the simplistic fact that we can’t cure viruses, which are less complex than bacterium (in which we can treat, and they’ll eventually pack their bags and leave).

          I’ll get to my question … since most, if not all, cells in the body replicate and reproduce and none of them merge, why do our cells let virions in? You would think after years of viral/immune system encounters, our bodies would have adapted to repelling these viruses off. I understand it’s probably much more complicated than that, but I would love to hear your answer. Does it have anything to do with virions’ size being so small?

          This is a great question. In fact, I had a similar question on a midterm examination in my virology course. I phrased it this way: Could cells evolve to not have receptors for binding viruses?

          I sent this answer to Joseph:

          Viruses get into cells by binding to proteins on the cell surface – viruses have evolved to do this: they are safecrackers.

          You would think that the cells would evolve to change these proteins – and you would be right. Over thousands of years, the cell proteins change, so the viruses can’t bind anymore.

          But guess what? The viruses change right back so that they can bind to the cell protein once more.

          Now you might ask: why doesn’t the cell get rid of that surface protein? The answer there is that they are needed for the cell, so they can’t be removed.

          There seems to be one exception to the last statement: about 4-16% of people of Northern European descent don’t make one of the receptors for HIV. They are resistant to infection. But this doesn’t happen for most other viruses.

          Joseph wrote back:

          Hmm. I thought by definition virions weren’t living organisms, yet they “adapt” to bind to living cells. Sounds like those emotional virions just can’t deal with rejection – that and our cells just aren’t as smart as we need them to be. I’m not sure if you are a Trekkie; however, it reminds me of the Borg and The Enterprise’s encounter – The Enterprise adapting to The Borg’s every frequency of their phasers, bypassing their bruteforce.

          That does make sense that our cells do need that protein surface for energy; however, I never thought it would actually be the surface itself. Interesting.

          I did read about that somewhere – because of the Bubonic Plague causing some genetic mutation, if I’m not mistaken.

          To which I responded:

          Virus particles are not alive – but once they infect a living cell they can evolve.

          Both cells and viruses are smart – they both have managed to be around for a long time. We have great immune systems; virus infected cells can evolve very quickly. It’s an arms race.

          Correct, one idea is that the mutation conferring resistance to HIV was acquired in the Plague, but that’s hard to prove.

          The mutation we are discussing is of course ccr5delta32, which confers resistance to infection with HIV-1 (the illustration shows the HIV-1 glycoprotein binding CD4 and ccr, a chemokine receptor). You can read more about ccr5delta32 here or listen to us discuss it on TWiV #278. We also talked about virus-receptor arms races on TWiV #242, and I wrote about it here.

            3 comments

            TWiV 279: The missing LNC

            6 April 2014

            On episode #279 of the science show This Week in Virology, Vincent, Alan, and Kathy reveal how a retrovirus in the human genome keeps embryonic stem cells in a pluripotent state, from where they can differentiate into all cells of the body.

            You can find TWiV #279 at www.twiv.tv.

              Retroviruses R us

              3 April 2014

              HERV-HAbout eight percent of human DNA is viral – remnants of ancestral infections with retroviruses. These endogenous retroviral sequences do not produce infectious viruses, and most are considered to be junk DNA. But some of them provide important functions. The protein called syncytin, which is essential for formation of the placenta, originally came to the genome of our ancestors, and those of other mammals, via a retrovirus infection. Another amazing role of endogenous retroviruses is that they regulate the stem cells that are the precursors of all the cells in our body.

              The genetic material of retroviruses is RNA, but during infection it is converted to DNA which then integrates into the chromosome of the cell.  If the infected cell happens to be a germ cell, then the viral DNA, now called called an endogenous retrovirus, becomes a permanent part of the animal and its offspring. One of our endogenous retroviruses, called HERV-H, infected human ancestors about 25 million years ago. HERV-H has been found to be important for the properties of human embryonic stem cells.

              Embryonic stem cells (ES cells), which are derived from the inner cell mass of a blastocyst (which forms 4-5 days after implantation), are pluripotent – they can differentiate into every cell type in the human body. Being pluripotent means expressing a very different set of genes compared with somatic cells – the cells of skin, muscle, organs, to name a few. The genes that are expressed in ES cells are controlled by a small number of key proteins that regulate mRNA synthesis. If these proteins – just four – are produced in a differentiated cell, it will turn into an ES cell – an induced, pluripotent embryonic stem cell, or iPSC. This observation garnered Shinya Yamanaka the Nobel Prize in 2012.

              The first clue that HERV-H might be important for the pluripotency of ES cells was the finding that this DNA is preferentially expressed in human ES cells (the figure [credit] shows the expression of HERV-H in ES and two other cell types). When the levels of HERV-H RNAs are reduced (by RNA interference) in ES cells, the morphology of the cells changes – they become fibroblast-like, a sign of differentiation. In contrast, when fibroblasts are reprogrammed to become iPSCs, the levels of HERV-H RNAs rise. These findings suggest that HERV-H is essential for keeping ES cells pluripotent, and for making somatic cells pluripotent.

              The HERV-H DNA in our genome is flanked by viral sequences called long terminal repeats, or LTRs. These provide initiation sites for the synthesis of viral mRNAs. In human ES cells the HERV-H LTRs appear to be enhancing the transcription of nearby human genes that are important for maintaing pluripotency. In an interesting twist, the HERV-H viral RNA is important for this activity: it appears to bind proteins involved in the regulation of mRNAs important for pluripotency. This observation explains why reducing HERV-H viral RNA leads to loss of pluripotency.

              The HERV-H RNA made in human ES cells is not translated into protein because it contains many mutations that have accumulated over the past 25 million years. Therefore HERV-H is a long, non-coding RNA (lncRNA), a relatively recently discovered class of regulatory RNAs. There are about 35,000 lncRNAs in human cells that are involved in controlling a variety of processes such as splicing, translation and epigenetic modifications. Now we know that endogenous retroviruses can also produce lncRNAs.

              Without endogenous retroviruses, humans might not be recognizable as the Homo sapiens that today walk the Earth. They might also be egg-layers – but the eggs would be white. Viruses don’t just make us sick.

                4 comments

                TWiV 278: Flushing HIV down the zinc

                30 March 2014

                On episode #278 of the science show This Week in Virology, Vincent, Dickson, Alan, and Kathy discuss disruption of the ccr5 gene in lymphocytes of patients infected with HIV-1.

                You can find TWiV #278 at www.twiv.tv.

                  Cross-stitched viruses

                  29 March 2014

                  The latest addition to the Microbe Art gallery here at virology blog is Watty’s Wall Stuff, where you will find beautiful cross-stitched viruses such as influenza virus, rabies virus, human immunodeficiency virus, herpesvirus and more. Here are some examples of Alicia Watkin’s delicate and creative work.

                  influenza virus

                   

                  bacteriophage T4

                  There are even bacteria, fungi, and parasites:

                  E. coli

                  Aspergillus

                  Naegleria

                  And one of my favorite cells of the immune system, dendritic cells:

                  Dendritic cell

                  You can even ask Alicia to make a cross-stitch of your favorite microbe. Mine, of course, is poliovirus. You can also purchase the patterns if you’d like to engage in some synthetic virology.

                  Thanks to Stephen and Jon for making Watty’s Wall Stuff a Listener Pick of the Week on TWiV #278.

                    1 comment

                    Heartland virus disease

                    28 March 2014

                    Amblyomma americanum

                    Six new cases of Heartland virus disease have been identified in residents of Missouri and Tennessee. The cause of this disease appears to be a member of the Phlebovirus genus in the Bunyaviridae family that was first identified in 2009 and appears to be transmitted by the Lone Star tick (Amblyomma americanum, pictured).

                    Heartland virus was first identified in two Missouri farmers who were hospitalized with fever, leukopenia (low numbers of white blood cells), and thrombocytopenia (low numbers of platelets). Both were males over 55 years old who reported being bitten by ticks in the week before disease onset. The novel virus was identified by electron microscopy, viral culture, and genome sequencing. For a complete discussion of this case, listen to This Week in Virology #199.

                    The tick A. americanum was implicated in transmission of Heartland virus because this species is extremely abundant in central and southern Missouri. However, virus was not isolated from ticks.

                    Since the description of the first two cases of Heartland virus disease, the Centers for Disease Control and Prevention have worked with state and local partners to develop diagnostic tests and identify additional cases. The six new cases were identified in 2012-13 in men over 50 years of age with fever, leukopenia, and thrombocytopenia. Presence of Heartland virus was determined by polymerase chain reaction using blood or tissue specimens, and by detecting a rise in antibodies against the virus in serum samples taken during and after illness. All six patients spent hours outdoors each day, and five reported tick bites in the two weeks preceding illness onset.

                    These studies strongly suggest but do not prove that Heartland virus was transmitted by ticks to these patients. One important piece of information will be finding Heartland virus in ticks. A first step is the identification of viral RNA sequences by polymerase chain reaction from ticks captured on the farms of the first two Missouri patients.

                    These findings raise several interesting questions. Why have the 8 patients with Heartland virus disease all been elderly males? Has this virus been present in the US for some time, and we have just detected it, or was it introduced from elsewhere? Does the virus circulate only in Missouri and Tennessee, and might it be found in other species of tick? Is there an animal reservoir as has been suggested? And what is the relationship of Heartland virus with the phlebovirus that causes severe fever with thrombocytopenia syndrome (SFTSV), an emerging disease in China that has also been detected in Japan and South Korea? Nucleotide sequence analysis reveals that Heartland viruses and SFTSV are highly related.

                      1 comment

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