Monthly Archives: December 2012

This winter’s viral scare: hCoV-EMC

Every couple of years or so it seems the world is gripped by a new epidemiological scare: CJD, SARS, Avian flu, Swine flu… This year’s new panic seems to be over coronavirus, one of the many viruses that can be responsible for the common cold (or even SARS). The coronaviruses are RNA viruses with a massive genome (26-32kb: which is frankly ridiculous) and a protective envelope, covered in viral spike peplomers which lead to their name. The particular strain of interest right now presents as pneumonia, with renal failure in some patients, and is referrred to as hCoV-EMC.

The key ingredients for a global pandemic are that it occurs across a wide area and that it is able to spread from person to person. Various zoonotic diseases are able to be passed from animals to humans (see rabies, swine flu and bird flu), but this only becomes a global risk when individual humans are seen to pass the disease to one another. In the last two months there have been nine reported infections with a novel strain of coronavirus, in Qatar, Saudi Arabia and Jordan, five of which were fatal. Because three patients in Qatar and two patients in Jordan were closely associated, there is a very real chance that human-to-human transmission has occurred (although they may have simply been exposed to the same source). This, combined with the currently-reported very high death rate (i.e. more than 50%) is really very concerning.

SARS (severe acute respiratory syndrome) is also caused by a coronavirus, and there has been some concern that we could be facing a pandemic of similar size and severity. It was this fear that led to a recent paper in mBio investigating the receptor sites of the virions. The particular receptor utilised by the SARS-causing coronavirus (angiotensis-converting enzyme 2, or ACE2) is limited to humans, meaning that zoonotic transfer was unlikely. It has previously been shown that SARS-CoV infection can be blocked with an anti-ACE2 antibody. What Muller et al have demonstrated in this paper is that the anti-ACE2 antibody works in kidney cells from monkeys, humans and swine to block infection with SARS-CoV, but that the same is not true of the new coronavirus currently making the headlines. This is apparently because the ACE2 enzyme isn’t actually involved in CoV-EMC replication, as it is in the SARS-responsible CoV.  

This is actually slightly worrying and depressing news. While it’s interesting that the two viruses are unlikely to utilise the same receptor, and therefore have similar epidemiology, from the point of view of fighting the disease, this makes it an unknown quantity. Given that the Müller et al suggest it may utilise a broadly conserved receptor present across the animal kingdom. From the point of view of preventing repeated infection, or multiple posts, this could be very serious indeed.

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Müller, MA et al (2012) mBio 3 (6):e00515-12
doi: 10.1128/​mBio.00515-1211 

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The Ramen Diaries, Part 6: Where I work on a Sunday

When I started Grad School, two of my best undergraduate friends and plenty of acquaintances were already at the end of their first years of a PhD. I think just about everyone from my circle of friends who went directly to PhD without going via a Masters stayed at our alma mater (which, I suppose makes sense: somebody who already knows you and your work is more likely to take a chance on you, and somebody who has already found a lab they want to work in is more likely to take time out of studying for finals to apply). Continue reading

The Ramen Diaries, Part 5: Where I throw a tantrum

When I was in my teens, the thing that I loved more about science was the opportunity to learn something new every day. I loved that what I thought I knew was never exactly true, and hated it at the same time. I wanted to know what we’d be told in our GCSE classes, or our A-level classes, or our undergraduate lectures long before I was old enough for it to be on the syllabus. I had this idea that if I kept studying science for long enough, eventually it would make sense.

It will never make sense.  Continue reading

Round Up #5

Today has been a very bitty lab day. At lunchtime I was carolling, and I spent the afternoon lying in an MRI scanner in the name of science. I haven’t achieved much since I got back, though whether I’m actually reacting to magnetic waves, or just being stuck in a box with my head pinned down for 90 minutes remains to be seen.

Nevertheless I’m determined to get one more qPCR run on before the week is out… except I foolishly put everything back in the freezer. While I wait for it to defrost, here are a few things that have caught my eye this week, but that I haven’t yet had a chance to write about:

PhD 2 Published have released a snazzy little app to keep track of how writing is going.

Prof Serious has some tough love advice for people about quitting their PhD (*gulp*)

PubMed have announced a new science writing competition (primarily aimed at biomedical researchers, but I can’t see anything to stop me entering provided I can write about biomedicine…)

The new edition of DSM-5 has been published, and along the way a whole bunch of non-neurotypical conditions have been reclassified (including autism). Long post on that probably coming over the weekend or early next week.

Molecular Biology 101: A map from here to there (and the barley genome)

Barley and Wheat are pretty similar. After all they’re sisters… No really. In a flash of food-security related brilliance I named my guinea pigs Wheat and Barley. Let it never be said that I don’t take my PhD seriously…

But seriously: wheat and barley are both cereals; important food crops, important feed crops, vital for producing my two favourite beverages (20% of the worldwide narley yield goes for malting), not to mention bread… Wheat tends to get a lot more coverage though: the world grows around a quarter of the amount of barley that it does of wheat and the amount spent on barley-related science is therefore always likely to be a bit lower.  Continue reading

The Ramen Diaries, Part 4: Oh god, it worked?!

This afternoon as I walked back over to the post-PCR lab (after more ramen – today’s was pork) I thought sadly to myself about how far I have come. When I started Grad school, full of enthusiasm and confidence, if something like a PCR reaction didn’t work I would instantly start looking for what might be wrong: what could I do differently next time. The idea that ‘it just didn’t work’ was completely alien to me. Now I know better. Primers that look perfect could easily correspond to a repeated sequence. Reaction conditions that are completely contrary to everything I know about PCR design can produce much cleaner results than a perfectly designed reaction. I’ve learned to loathe PCR, and along with it, expect that any ‘completely new’ reaction just won’t work.

Continue reading

The Ramen Diaries, Part 3: A cunning plan

On today’s postgrad menu, Tom Yum ramen. Why are all of my noodles so spicy?!

Supervisor has suggested a cunning plan to solve my qPCR woes: put DNA into a regular PCR for 5 cycles first, then transfer to qPCR afterwards. While this doesn’t really solve the problem that after X number of PCR cycles we expect an artefact to appear anyway, it does have the advantage that the machine will actually call the Ct value. (Anything over 35 cycles, even if it’s ‘real’ isn’t called by my software, and is just 35+).

So far, so unsuccessful: but I tried using the qPCR primers with a high fidelity Taq that I haven’t tried them out with, so it’s entirely possible that the reaction just wouldn’t work like that. Tomorrow I’ll repeat it with my regular everyday Taq.

Annoyingly, somebody from another department keeps calling up wanting to use our qPCR machine, since theirs is bust, and then never turning up. I have to plan my labwork around somebody else, but then lose big chunks of every day when the machine is “full” and by the time I know it’s not it’s usually too late! GRRR.