Posts Tagged ‘Virology’
Principles of Molecular Virology, Chapter 6, discusses RNA interference and virus infection.
RNA interference (RNAi) is an important set of pathways that are used to regulate gene expression. RNAi is a blanket term which can refer to both small interfering RNAs (siRNAs) and microRNAs (miRNAs). There are important differences between siRNAs and miRNAs but I’ll get to those later…
I’m interested in Middle East Respiratory Syndrome Coronavirus (MERS-CoV) for a number of reasons, and as a result I have a student currently doing a final year project with me on this topic – not chucking buckets of MERS-CoV around in the laboratory, but trying to figure out where this virus came from and what it is likely to do next. Both of these are interesting questions.
There has been a lot published about the origins of MERS-CoV recently. Only this week came the news that a camel in Saudi Arabia has tested positive for the virus. But which came first – the virus or the camel? Almost certainly the camel – there’s no reason to suppose that camels are the original source of the outbreak. MERS is almost certainly a zoonotic infection – arising in animals and transmitted to humans – but which animals? The closest relatives to MERS-CoV have been found in bats, and those viruses are pretty similar to the virus currently causing human deaths. However, these bat viruses have only been identified by nucleotide sequences and have never been isolated as live viruses from either bats or the environment, so the animal reservoir of MERS-CoV has still not been identified (Emergence of the Middle East Respiratory Syndrome Coronavirus. (2013) PLoS Pathog 9(9): e1003595. doi:10.1371/journal.ppat.1003595).
If we don’t know where MERS came from, we should all be interested in the question of what it is likely to do next. Since September 2012, there have been over 150 laboratory-confirmed cases of infection with MERS-CoV – not that many on a global scale. That’s because the virus is only weakly infectious in humans. As long as this remains the case we are OK, but if at some point it decides it likes being in humans and wants more of the same, then we’re in trouble. What are the odds of that happening? Right now, we simply don’t know. And that’s why I’m interested in MERS.
To answer the question of what MERS will do next, we need a lot more knowledge than we have right now. One of the key pieces of information is exactly how MERS-CoV gets inside a host cell, and specifically, why it finds it difficult to infect human cells. It was recently shown that the receptor MERS-CoV needs to infect cells is dipeptidyl peptidase 4, a cell surface protein which cleaves dipeptides from hormones and chemokines after a proline amino acid residue, regulating their bioactivity (Dipeptidyl peptidase 4 is a functional receptor for the emerging human coronavirus-EMC. (2013) Nature 495, 251-254). Dipeptidyl peptidase 4 is similar to other known coronavirus receptors, but the use of these peptidases as receptors by coronaviruses could be more related to their abundance on epithelial and endothelial tissues – the primary tissues involved in coronavirus infection – rather than any inherent properties of the protein.
That’s where a new paper in the Journal of General Virology comes in. It’s difficult to study lethal viruses in humans, so like it or not animal models of infection still have their place in these life-threatening outbreaks. The study of SARS-CoV pathogenesis progressed rapidly due to the development of a mouse adapted variant of SARS-CoV that produced lethal lung disease in mice similar to SARS in humans. But MERS-CoV doesn’t like growing in mice and it turns out that this is because mice have low levels of dipeptidyl peptidase 4 mRNA in their lungs (Wild type and innate immune deficient mice are not susceptible to the Middle East Respiratory Syndrome Coronavirus. J Gen Virol. 06 Nov 2013 doi: 10.1099/vir.0.060640-0). Good news for the mice, but also of great interest when thinking about how the pathogenesis of MERS is shaped in humans. Most viruses are not able to switch from one receptro to another easily, so drugs which interfere with the binding of the virus to this protein or antibodies which block attachment could be the best way to treat MERS until we have a vaccine which is able to stop people becoming infected. And the search for those drugs and antibodies is going on right now.
In a discussion on Twitter earlier this week I made an off the cuff remark which turned out to be unexpectedly telling. Discussing online science writing, I said:
We need sense-making, not more coverage.
Later that day I came across this post by Nathalia Holt - The Goldilocks Approach to Vaccines. I was already considering featuring this story in MicrobiologyBytes this week. Now, I feel I don’t need to (as long as you promise to go and read the full story on her blog):
“On Tuesday, Louis Picker began his talk to a packed room at the AIDS Vaccine meeting in Barcelona, Spain with the line, “The trick to making a vaccine is to be humble and accept the fact that viruses are smarter than we are.” He wasn’t referring just to HIV. Instead he was talking about CMV, or cytomegalovirus. CMV is very clever. A member of the herpes virus family, it’s over 200 million years old. This long evolution means that the virus has become adept in surviving within mammals. While the virus is found in roughly 45% of people, it rarely causes disease. Given its benign nature, Picker calls it “a parasite not a pathogen.” With these characteristics, perhaps it’s surprising that no one has attempted to use CMV in vaccines before now. What makes Picker’s approach unique is not how it manipulates HIV. In fact, the parts of HIV used in his vaccine are far from exceptionable. The vaccine uses pieces of an HIV protein called gag, a group of proteins that make up the basic structure of the virus. The gag protein has been a component of many failed vaccine attempts. What makes this vaccine different is not the innards of HIV it contains but instead how these pieces are delivered.”
This is exactly the sort of approach to science writing I had in mind when I mentioned sense-making on Twitter. Nathalia is not an average blogger. She is a talented and very experienced author for who her blog is merely a sideline. I have plenty of academic colleagues who would cringe and quibble at some of the terms Nathalia uses in this post, and the way in which she puts across some of the ideas. In spite of that, this is exactly the sort of approach I was thinking of when I tweeted. And it is exactly what I am trying to do when I write MicrobiologyBytes.
I honour of Nathalia, and all the other great science writers online, you’ll notice that I have changed the tagline at the top of MicrobiologyBytes. No longer does it say “The latest news about microbiology”, although that’s what you’ll get if you follow MicrobiologyBytes on Twitter, Facebook or Google+. The new tagline on the site better reflects what MicrobiologyBytes is about.
MicrobiologyBytes Weekly – timebombs, smarter antibiotic use and bacteriophages you’ve never even heard ofThursday, October 24th, 2013
In this week’s edition:
- Today is World Polio Day
- Antibiotics – have we got it all wrong?
- Unexploded device? The vCJD timebomb
- How science works
- The wonderful world of archaeal viruses
|Today (October 24th) is World Polio Day
In support of this event the UK Society for General Microbiology has published a useful document describing the fight against this disease – past, present and future – and the lessons it hold for other infections (free, and very useful for teachers and students).
|When the Most Potent Combination of Antibiotics Selects for the Greatest Bacterial Load
Cancer is a difficult disease to treat, but great advances have been made in the past few decades, mostly coming from using drugs in combination rather than one at a time. Exactly the same drug combination approach works for HIV infection, although sadly it doesn’t provide a cure. As it becomes harder and harder to treat bacterial infections with the few remaining antibiotics which are still effective, we need similarly imaginative approaches to therapy. A new paper in PLOS Biology looks at combinations of different drugs that are purposefully used to produce potent therapies. Textbook orthodoxy in medicine and pharmacology states one should hit the pathogen hard with the drug and then prolong the treatment to be certain of clearing it from the host. If the textbooks are correct, a combination of two antibiotics that prevents bacterial growth more than if just one drug were used should provide a better treatment strategy. Testing alternatives like these, however, is difficult to do in vivo or in the clinic, so the authors examined these ideas in laboratory conditions where treatments can be carefully controlled and the optimal combination therapy easily determined by measuring bacterial densities at every moment for each treatment trialled. Studying drug concentrations where antibiotic synergy can be guaranteed, they found that treatment duration was crucial. The most potent combination therapy on day 1 turned out to be the worst of all the therapies we tested by the middle of day 2, and by day 5 it barely inhibited bacterial growth; by contrast, the drugs did continue to impair growth if administered individually.
When the Most Potent Combination of Antibiotics Selects for the Greatest Bacterial Load: The Smile-Frown Transition. (2013) PLoS Biol 11(4): e1001540.
|Unexploded device? The vCJD timebomb
Over at the Principles of Molecular Virology blog, I’m publishing the updated content for the next edition of the book as I research it. Chapter 8 of Principles of Molecular Virology discusses subviral agents – viroids and prions responsible for diseases such as scrapie, BSE and CJD. So many facts about human prion disease remain unknown, but what is clear is that decades after it started, mad cow disease has not gone away – the effects of the outbreak will rumble on for decades to come. New data from the UK show that the previous estimate of the number of vCJD carriers was an underestimate, but what does the future hold for those exposed to BSE-infected food in the 1980s and 1990s?
|Molecular structure of the HIV-1 envelope protein
A group of researchers publishes a structure for the HIV-1 envelope protein complex – the crucial membrane-fusing molecular machine responsible for virus attachment and entry into host cells and which is the sole virus-specific target for neutralizing antibodies (Molecular architecture of the uncleaved HIV-1 envelope glycoprotein trimer. (2013) PNAS USA 110 (30): 12438-12443). You’d think people would be happy. But not everyone is. “You got it wrong” they say, or “Oh no it isn’t“. “We took you comments into account and we still believe we are right” say the original authors. “Look at this picture of Einstein” says the world’s leading expert in the field. This saga is a great illustration of how science really works and a warning for students and journalists who want to believe that there are simple right/wrong answers to complex questions and that we either know something or we don’t. A great example of how sciences inches closer to the truth one step at a time.
|The wonderful world of archaeal viruses
Think you know about bacteriophages? You might be shocked at how much you have to learn. Most microbiologists are obsessed with “true bacteria”, to the virtual exclusion of the Archaea. That prejudice carries over to their viruses. This review [sorry this one requires a subscription - I try to avoid this whenever I can] presents a personal account of research on archaeal viruses and describes many new virus species and families, demonstrating that viruses of Archaea constitute a distinctive part of the virosphere and display structures that are not associated with the other two domains of life, Bacteria and Eukarya. Studies of archaeal viruses provide new perspectives concerning the nature, diversity, and evolution of virus-host interactions. Broaden your outlook – this one is well worth reading.
The wonderful world of archaeal viruses. (2013) Ann Rev Microbiol. 67: 565-585.
Got any comments or questions about any of these items? Just let me know.
University of Leicester researchers use phages to fight Clostridium difficile
Since the discovery of the first antibiotic – penicillin – antibiotics have been heralded as the ‘silver bullets’ of medicine. They have saved countless lives and impacted on the well-being of humanity. This was beautifully illustrated in Michel Mosley’s TV series Pain Pus and Poison this week. But less than a century following their discovery, the future impact of antibiotics is dwindling at a pace that no one anticipated, with more and more bacteria out-smarting and ‘out-evolving’ these miracle drugs. This has re-energised the search for new treatments, such as phages. The key advantage of using phages over antibiotics lies in their specificity. A phage will infect and kill only a specific strain/species of bacteria. This is particularly important when treating conditions like C. difficile infections:
It began routinely enough. A patient with severe respiratory disease at the Dr. Soliman Fakeeh Hospital in Jeddah, Saudi Arabia was getting worse and no one knew why. A sample of sputum was sent to Dr. Ali Mohamed Zaki to identify the culprit, as he had identified these diseases many times before. However, this time would be different. The sample showed no positive hits on any of the virus assays he normally used. He contacted Dr. Ron Fouchier, at Erasmus Medical College in Rotterdam, Netherlands, to see if he could be of help. Dr. Zaki’s initial idea was that the virus was a paramyxovirus, and Dr Fouchier had recently published a Pan-paramyxovirus polymerase chain reaction (PCR) assay. In Dr. Fouchier’s lab, the virus was identified as a novel coronavirus, one that had never been seen before…
They may not know it, but up to half a million people in Britain today may carry a particular form of herpesvirus 6 inherited from a parent in their genetic material. Recent research led by Nicola Royle at the University of Leicester has identified a mechanism by which the inherited herpesvirus 6 can escape from the chromosome and may be able to reactivate under certain conditions.
This research may have important implications for transplantation, as those seeking transplants are often immunosuppressed, and are more susceptible to viral reactivation. The implications of the study suggested screening donors for this inherited form of HHV-6 could help doctors make more informed decisions about which donors to use.
Human telomeres that carry an integrated copy of human herpesvirus 6 are often short and unstable, facilitating release of the viral genome from the chromosome. Nucleic Acids Research, September 2013 doi: 10.1093/nar/gkt840
Linear chromosomes are stabilized by telomeres, but the presence of short dysfunctional telomeres triggers cellular senescence in human somatic tissues, thus contributing to ageing. Approximately 1% of the population inherits a chromosomally integrated copy of human herpesvirus 6 (CI-HHV-6), but the consequences of integration for the virus and for the telomere with the insertion are unknown. Here we show that the telomere on the distal end of the integrated virus is frequently the shortest measured in somatic cells but not the germline. The telomere carrying the CI-HHV-6 is also prone to truncations that result in the formation of a short telomere at a novel location within the viral genome. We detected extra-chromosomal circular HHV-6 molecules, some surprisingly comprising the entire viral genome with a single fully reconstituted direct repeat region (DR) with both terminal cleavage and packaging elements (PAC1 and PAC2). Truncated CI-HHV-6 and extra-chromosomal circular molecules are likely reciprocal products that arise through excision of a telomere-loop (t-loop) formed within the CI-HHV-6 genome. In summary, we show that the CI-HHV-6 genome disrupts stability of the associated telomere and this facilitates the release of viral sequences as circular molecules, some of which have the potential to become fully functioning viruses.
Dengue virus (DV) infections cause undisputedly the most important arthropod-borne viral disease in terms of worldwide prevalence, human suffering, and cost. Worldwide DV infection prevalence in 2010 was between 284 to 528 million cases. Approximately 84% of these cases come from Asia and the Americas, where the cost for emerging economies can be as high as 580 million dollars per year. The need for an efficient vaccine against DV is extreme.
Vaccination has been the most desired strategy for controlling the spread of DV. Neutralizing antibodies directed against mosquito-borne flavivirus envelopes can prevent the development of infectious disease. This has been beautifully illustrated by the development of successful vaccines against other related mosquito-borne flaviviruses with similar structure, specifically the attenuated strain 17D vaccine against yellow fever virus (YFV) and the attenuated strain 14-14-2 against Japanese encephalitis virus (JEV), both obtained by serial passage in cell culture.
Why then has the development of a DV vaccine proven so challenging? Natural DV infection triggers a robust, neutralizing immunity that provides an apparently life-long protection against the infecting DV serotype and a short-lived (months) cross-protection against heterologous DV serotypes. Interestingly, the humoral response to DV not only mediates protection though viral neutralization, but also seems to play a major role in the development of more severe forms of dengue disease. Dengue hemorrhagic fever and dengue shock syndrome (DHF/DSS) cases are often associated with secondary DV infections with a heterologous DV serotype.
There are two main windows of opportunity to build upon toward realizing efficient vaccination for DV. First, a clinically relevant animal model for dengue infection and vaccine development is lacking. Rhesus monkeys do not show clinical signs of infection after a wild-type DV challenge; instead the intensity and length of viremia serves as a proxy to infer protection. Second, rigorous correlates of protection have not been established for DV. The best available indicator of immunogenicity is the titration of neutralizing antibodies, however titration of plaque reduction neutralization antibodies has not been promoted to a bona fide correlate of protection because of ambiguous results pertaining to the protective titer. Testing the protection efficiency of tetravalent vaccine candidates in volunteers may answer both questions. Results from the first human DV challenge experiments have been recently published and demonstrate the viability of this approach.