Viruses are boring! I mean, what’s the point to viruses? All they do is make us sick, right? You just have to look at the past year to know that, and you can’t turn on the TV without seeing some product that “kills all known germs… including the coronavirus… dead!” Shouldn’t we be trying to eliminate all viruses, wouldn’t the World be better if there were no viruses?
 
But some say not all viruses are bad for us!? More importantly, some say there would be no humans if there were no viruses!! How stupid is that?!
 
Well to look at this question, let’s first consider what we are, mammals.

​What is a mammal?
According to the Oxford dictionary a mammal is “any animal that gives birth to live young, not eggs, and feeds its young on milk”. The first important part of the definition is the feeding with milk which is from a mammary gland or breast and hence where the name mammal comes from (“mamma” means breast).
 
Another important part of being a mammal is that the young are born alive and not in eggs. When you think about it this is truly remarkable. Half of the foetal genetics are from the father so as far as the mother’s immune system is concerned this foetus is a foreign object. So why is the foetus allowed to grow inside a mother and thrive? After all, if you took any other organ from a father and implanted it in the mother it would be rejected within a few days! Hence the need for a cocktail of anti-rejection drugs after transplant surgery.
 
Hold on! This is supposed to be a micro-biology blog not a macro-biology blog. Bear with me, I’m getting there.
 
Okay, here we go…
 
The organ that allows the foetus to survive is the placenta [yes, yes we all know this!!!, ECIC]; it’s where the foetus gets oxygen, nutrition and also where waste products are removed. And it exists because of microbiology… or more specifically, virology! WHAT, I hear you cry!!
 
Evolution of the placenta
About 400 million years ago placentas started to appear in fish. Although fish placentas are still relatively uncommon, and most fish still lay eggs, some fish do have a placenta and give birth to live young e.g. blue sharks, rose fish and red banded rockfish (they’re still not mammals though as they don’t feed their young with milk!). Other animals keep their eggs internally until the young hatch e.g. adders, insects and other types of sharks; they do not have a placenta even though they appear to give birth to live young.
 
About 130 million or so years ago mammals developed placentas and started to give birth to live young, but this required a major change in reproductive physiology in order to lead to the formation of the placenta.
 
The placenta evolved due to the action of retroviruses that changed the genetic makeup of cells in early pregnancy back 130 million years ago (and probably ever since!)

Retroviruses
Retroviruses are RNA viruses that convert to DNA inside infected cells which is then incorporated into the cell’s chromosome. If that cell is a germ cell, an early foetal cell giving rise to all of the future baby’s cells, then the retroviral DNA becomes a permanent part of that baby; natural genetic manipulation if you like.
 
The best-known retrovirus is Human Immunodeficiency Virus (HIV) which causes the clinical condition Acquired Immune Deficiency Syndrome (AIDS). But it turns out not all retroviruses are bad.
 
The most important aspect of placental evolution is the ability to produce a protein called “syncytin”. Syncytin is a viral protein that is used by mammals to help form a layer of the placenta called the “syncytiotrophoblast”. The syncytiotrophoblast is the layer of the placenta that invades the uterine wall fixing the placenta in place and allowing the transfer of nutrients and waste across the placental surface. It is also the only part of the placenta that is NOT recognised as abnormal by the mother’s immune system.
 
The gene that now exists in human cells and is responsible for the ability to produce syncytin originated from the envelope gene of Human Endogenous defective RetroVirus known as HERV-W.
 
Over time the placenta has been “improved” by further retroviral “infection” and incorporation of more effective and efficient viral versions, and no doubt it will be further improved in the future. The evidence that the placenta can be improved by further infections does make me wonder if the opposite can happen, and that perhaps infection with a less effective or outright damaging retrovirus could be the reason for some early foetal losses… I’m not sure if anyone has ever looked at that?
 
What about other animals?
Now we all know that lizards are reptiles, right? [Here he goes again with weird facts, ECIC!!] But what about a reptile with a placenta? About 25 million years ago a reptile called the Mabuya lizard, from the Caribbean, evolved a placenta and now gives birth to live young. Wow! I never knew there were so many “non-mammals” which gave birth to live young.
 
Are retroviruses involved in other body organs?
It turns out that retroviruses are involved in the evolution of other body organs as well. In particular the brains of land animals appear to be affected by a retroviral gene known as “Arc” which has led to more effective and efficient neuronal signalling as well as plasticity (where the brain tissue can adapt to change).
 
In fact it is now estimated that 8% of the human genome is actually made up of retroviral genes… that means we are at least 8% viral! However, a lot of that genetic material is actually redundant or “fossilised” having no “apparent purpose” anymore, but these fragments may have been important in the past and then been replaced by new improved “features”, who knows?
 
It does make me wonder if apparent jumps in evolution are more than just natural selection? My understanding has been that if a single member of a species has a particular trait that gives it a survival advantage then it is more likely to reproduce and therefore it’s characteristic will be increasingly represented within future generations. This is the basis to Darwin’s work on evolution, but apparently Darwin didn't know about viruses. However, mutations in genes occurring at random are usually small and slow to occur, and therefore would be unlikely to give much of an advantage or “quick change”. A retrovirus incorporating a lot of new genes though could cause a big shift in genetic make up of an organism which in turn could give a more significant “jump” in evolution and a major selective advantage… Wow, that makes my brain hurt!
 
Golly. Time to go and lie down somewhere quiet and let my brain recover… maybe there’s a virus that can help with that….
 
References

• Viruses and the placenta: the essential virus first view
• Identification of an ancient endogenous retrovirus, predating the divergence of placental mammals
• The placenta goes viral: Retroviruses control gene expression in pregnancy

P.S. Who thought of looking for a virus that "created" the placenta anyway, and how do these researchers get funding for that!?!

One thing lockdown has taught me is that being outdoors in whatever weather the UK can throw at me is something to be embraced as much as possible. I’ve been fortunate. By being a healthcare worker, I’ve been able to leave the house and get a change of scenery even if it’s just a hospital building. On top of that the ECIC and I have a nice garden we can use at home to relax in the fresh air (sometimes more fresh than is comfortable!).
 
The ECIC and I are now even more lucky. We have recently been able to buy a bit of land to turn into our own little growing space for fruit and vegetables… okay, this may not be your idea of fun, but we like it…. Whilst we’re busy digging out the brambles and nettles we have been chewing over ideas about how to look after our crops, and one of our problems to solve is water.
 
The land we have has no mains water. We can collect a lot of water from the roof of our shed and greenhouses (planning permission pending!), but if we need more then we’ll have to look somewhere else. One option is the small stream nearby, so we wandered over to have a look at what it’s like… and it’s ORANGE!

Back in the blog in August called “My pandemic is worse than your pandemic” I mentioned I might do a future blog on the ancient disease called Cocoliztli, which I had never heard of before… well for once I’ve remembered I said I would do a particular topic and here it is!
 
So I’ve delve into my historical medical books (and Google!) to look further into the unknown pandemic of Cocoliztli.
 
It is well known that imported infections from Europe with the Spanish Conquistadors caused many deaths; Smallpox for example was imported in about 1520 and killed about 8 million people. In fact during the 16th Century about 90% of the native population of Mexico was wiped out by disease. But as if Smallpox wasn’t enough, this was followed in 1545 by the first Cocoliztli epidemic which killed a further 15 million people. Local people called this disease Cocoliztli or “pest” and as pandemics go this one seems pretty bad! A further Cocoliztli epidemic in 1576 killed another 50% of the population, so by this time more than 90% of the natives had been killed in just over 50 years!

Did you know that guinea pigs cough? I didn’t… but then I’ve never had a pet guinea pig… In fact I’ve discovered that all mammals cough, who knew?! Guinea pigs apparently have a cough pathway (from something stimulating a cough through neural networks and chemical signals to the actual cough) that is the same as humans so they are a great animal model for studying coughs in humans…??

One of life’s unsolved mysteries is “how did life on Earth begin?” Did it start here spontaneously as “God created us” or did Darwin get it right with his “evolution theory”? And are we alone in our universe? Let’s skip the God versus Darwin bit and jump straight to the question “did life arrive from outer space” and “can life survive in space?”
 
When times get “trying” here on planet Earth ECIC wishes she was on Pluto with her cats, her rules and no people! But she may not be alone!! The newest research suggests that bacteria can survive in the hostile environment of space; maybe the dream of living on Pluto with remote “homeworking” for a Consultant Microbiologist might be a reality (our hospital computer system is called Enterprise after all!)
 
No, No, No, stick with me!!! It’s true, those pesky microorganisms have been found to survive on the outside of the ISS (International Space Station). There’s even a named theory… the theory that living organisms can survive and transfer through space is known as “panspermia”. 

Editor Chief in Charge and I have spent the weekend trying to work out what we’re going to do if/when we can’t go on holiday later this year because of a certain unmentionable pesky virus. The basic answer is that we might not be going somewhere exotic! But why might not being able to go on holiday somewhere exotic be a good idea?!?
 
I know… pufferfish!
 
Pufferfish are tropical fish found especially in Asia. They are called pufferfish because they have a rather unusual defence strategy; they can fill their stomachs with water so that they balloon up into a ball shooting numerous spiky spines outwards. Any predator stupid enough to try and eat a pufferfish gets a mouth or stomach full of spines and probably chokes… nasty. Bloat, from the Disney film “Finding Nemo” was a pufferfish; he blows up like a beach ball every time something startles him… he’s my favourite character and he’s hilarious!

The Editor-Chief-in-Charge is a curd nerd… she not only loves to eat cheese BUT she also makes her own cheese. There is nothing quite as tasty as homemade cheese but it’s certainly not fast food. In fact it’s a very, very, very slow food. It takes a day to make, a couple of days to press, and months or years to mature…. But it is great fun and it might surprise you to know that it is also a lesson in microbiology. [I wonder if the ECIC will still be a curd nerd after reading this?!]

The government are allowing us to visit the beach but are advising us to stay out of the water as there are no lifeguards on duty and do not want additional casualties in hospital. But there might be another reason for us to consider staying out too! Viruses!!! Really!!? Can you actually find viruses in the sea? It’s a simple question but not one many of us have considered before… including me, but then why would we?
 
You might think that seawater is too salty for viruses and that they would never survive in such a hostile environment. Alternatively you might think that if viruses can survive on surfaces like plastic, metal and cardboard then why not also in the sea. But do we know?
 
Well back in 1990 Scientists confirmed that viruses can indeed be found in seawater; while looking at seawater with transmission electron microscopes (TEM) they saw “something unusual” but they didn’t actually know at that time what it was… however they could see them! So they started to study them. Remember, TEMs can “see” much smaller objects than normal light microscopes; the limit of magnification of a light microscope is about 1,000x, not enough to see a virus, whereas TEMs can magnify 10,000,000x! OK I know you youngsters think 1990 seems a long time ago but in scientific terms it’s not that long, it’s only since these discoveries in the 1990s that they actually confirmed viruses were there, even though “infection” from contaminated seawater was suspected.
 
Further studies have shown that in fact there are lots and lots and lots of viruses in seawater….

There seems to be huge amount of confusion about what tests are available for Covid-19. It doesn’t help that politicians and the media keep using the wrong terms and don’t understand what the different tests tell us. The squabbles seem to surround the numbers delivered rather than correct testing!
 
There are 3 main tests that are currently being discussed:

1. Polymerase Chain Reaction (PCR) commonly referred to as a “molecular test”
2. Antigen (Ag)
3. Antibody (IgM and IgG)

 
In order to understand the value of these tests it is important to understand the basic structure of a virus.
 
The structure of a virus