The origins of viruses

The origin of viruses is mysterious:

The origins of viruses are even more obscure than the origins of cellular forms of life. Since viruses are obligate cellular parasites, we can only assume that they evolved later than cells, either as degenerate cells or as renegade cellular genes that learned to manipulate the replication machinery of the cells in which they arose. Viral genomes evolve more rapidly than the genomes of cellular organisms. This rapid genetic change has obscured or erased any relationships that may have existed between various types of viruses and might have been used to illuminate their ancient roots.

The coronavirus is scary. Many experts are certain it will result in a pandemic!

If viruses are ultimately of cellular origin, then there is a persistent risk new ones, and even harmful ones will keep entering the biosphere. I can’t imagine this is a good thing for humanity.

Sal, can I recommend this book, which is the most gripping I have read in the past few years.

From the blurp
Epidemiologist Steffanie Strathdee and her husband, psychologist Tom Patterson, were vacationing in Egypt when Tom came down with a stomach bug. What at first seemed like a case of food poisoning quickly turned critical, and by the time Tom had been transferred via emergency medevac to the world-class medical center at UC San Diego, where both he and Steffanie worked, blood work revealed why modern medicine was failing: Tom was fighting one of the most dangerous, antibiotic- resistant bacteria in the world.

Frantic, Steffanie combed through research old and new and came across phage therapy: the idea that the right virus, aka “the perfect predator,” can kill even the most lethal bacteria. Phage treatment had fallen out of favor almost 100 years ago, after antibiotic use went mainstream. Now, with time running out, Steffanie appealed to phage researchers all over the world for help. She found allies at the FDA, researchers from Texas A&M, and a clandestine Navy biomedical center-and together they resurrected a forgotten cure.

Not a science book, per se, but written by a scientist. Why I suggest it is that much of the discussion around here revolves around distant topics such as what happened millions of year back, population genetics, and personally remote and abstract elements of evolution and adaptation. I found it fascinating to follow this story where a life, nearly spent, hangs in the balance while a pitched three way battle between a person’s immune system, bacteria, and viruses literally gleaned from effluent plants, waxes and wanes with microbial measure, counter measures, and regrouping, not over epochs but in the course of weeks and months. A true page turner, it give a feel for evolution in a microcosm.


From a dispassionate objective point of view, the human race isn’t threatened by coronavirus. The last pandemic flu strain form 1918 killed less than 3% of the world population. Our species will be just fine. We will gain herd immunity to this new strain, and it will quickly lose its ability to sicken and kill large portions of the population.

From the human point of view, it could be “pretty bad”, at least from our privileged position in the West. Ten million dying from the flu in the modern 1st world is something our society hasn’t seen, but it isn’t even close to the suffering that 3rd World countries have endured over the last 100 years. In the last 10 years, malaria has killed approximately 5 million people in poorer countries. Diseases like measles used to have pretty high death tolls, and it still kills 100,000 people a year in poorer countries. I happened to be at a presentation given by an ID doctor in which he reported that the WHO estimates that the measles vaccine has saved 20 million lives in the last 20 years. That vaccine didn’t exist until the 1960’s, so think about how bad it was before that.

Yes, a flu pandemic would be bad. However, we should also recognize how good we have it too.


From the human point of view, it could be “pretty bad”, at least from our privileged position in the West. Ten million dying from the flu in the modern 1st world is something our society hasn’t seen,


From the CDC

Disease Burden of Flu | CDC

CDC estimates that influenza has resulted in between 9 million – 45 million illnesses, between 140,000 – 810,000 hospitalizations and between 12,000 – 61,000 deaths annually since 2010.

The problem with Corona is that it is easily transmitted, like the flu! It’s not like SARS or other viruses.

I guess we can only hope that we can contain it long enough to make a vaccine, and that’s assuming a vaccine is possible.

The last pandemic flu strain form 1918 killed less than 3% of the world population.

If we assume 8 billion people, 2% would be 160 million souls in addition to hospitalization and sickness. That could be enough to disrupt a very delicate economic/financial situation and might induce a serious global recession. Much like health, economies can get sick from little things even though there is lots of technology and adequate natural resources. Financial markets are driven by psychology and panic can create problems that don’t need to happen otherwise.

Anyway, thanks for your observations. I hope we can survive this without too much pain.

Hundreds more Americans evacuated from China as coronavirus death toll rises

You’ve been infected by many coronaviruses already. P.S. The name is not capitalized.

I predict that it will evolve to become less pathogenic and more extensively disseminated.

But what do I know? [Eddie] I have a PhD in virology! [/Eddie]


The reason the Corona Virus is catching my eye is the financial markets are reacting to it. This shows a serious level of concern:

Coronavirus Fears See $400 Billion Wiped Off China’s Stock Market

I don’t think so. It was an 8% loss–a heavy loss certainly, but not really unusual–and there’s been a recovery today. Concern, sure, but I don’t think it’s any kind of major indicator in its own right. Clearly the economy is going to take a hit from this kind of disruption, and the market is responding to that primarily. If you had a string of days like that, it could be another story.

The stock market has a history of overreacting to not just news but also fake news, political views, elections and other upcoming events that haven’t yet happened, spoofs, rumours and ridiculous stories; as well as having been shown to be readily manipulable by speculators and fake buying requests.

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Measles is particularly pernicious, since besides killing directly it greatly increases the mortality from other infectious diseases. It does so by killing memory B cells that provide protection against pathogens the patient has already survived. I recently heard an estimate that, prior to widespread measles vaccination, half of all childhood mortality from infectious disease could be blamed on measles (and historically, that was a lot of mortality).

I think at this point that 2019nCoV is more likely than not to cause a pandemic, but the case fatality rate (CFR) is likely to be much lower than 2%, and the total mortality rate for the population will be a lot lower than the CFR. The reported CFR for Hubei province (home to Wuhan) has been around 3.5%, while the CFR for the rest of China, which has 7000 confirmed cases, has been around 0.2%. Some of the difference is likely due to lag, but it can’t be that much, especially since the 0.2% is dropping, not increasing. It’s possible that the virus mutated very early in the outbreak to be less virulent (and presumably more transmissible), but it would take an awfully large change in virulence to explain the discrepancy. I suspect the biggest factor is that only the sickest people in Wuhan have been tested, and they’re the ones most likely to die. So I think the actual CFR is a lot closer to 0.2% than 3.5% – but also that a lot more people have been infected in Wuhan than the number of confirmed cases.

Note: the CFR from Hubei is also trending down, and is now just above 3%.


That’s what I have learned as well. Pneumonia caused by secondary bacterial infections is also a risk factor with measles as the viral infection can cause an acute reduction in many different populations of white blood cells in addition to memory B cells. It’s a nasty little virus which causes medical professionals pull their hair out when faced with propaganda from anti-vaxxers.

Thanks for the reply. I should hope the CFR is ultimately low as you suggested, that 3.5% CFR figure from Hubei/Wuhan was scary. Thanks for weighing in.

One reason the article from that MIT website on the origin of viruses caught my attention was that it said that viruses can’t live long outside the host.

This is the reason packages from Wuhan china, even if contaminated by the Coronavirus, if there isn’t a host on the package, it can’t live long, or more correctly won’t be viable to infect a human.

Some frozen viruses, like in frozen fecal matter, have been speculated to be viable to infect after 700 years.

The fact that viruses are thought to come from cellular creatures suggests to me that the RNA world was not the path toward cellular life since RNAs that sit out in the open would degrade. Unfortunately, I haven’t gotten good data on the persistence and half life of RNA ribozymes in plausible prebiotic conditions. There is plenty of data on mRNA half-lives in the cellular context however, but it wasn’t exactly what I was looking for.

Viroids are naked RNAs that cause diseases in plants and can be transmitted by contaminated machinery and the like. This means that naked RNAs can conceivably persist for some time in the wild, outside of cells.

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It is also worth mentioning that modern organisms produce tons of RNases that can quickly breakdown naked RNA in the environment.

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It’s enveloped.

Some viruses are not enveloped.

That’s fascinating, as RNase secreted by existing organisms is the main reason for that degradation. The stability of RNase makes perfect sense as competition in going beyond the RNA world.

Thanks Art.