Posts Tagged ‘SARS’

A Very Intriguing Theory about Possible Artificial Origins of COVID-19

April 26, 2020 28 comments

A couple of days ago, I came across a rather long medium post about how COVID-19 aka SARS-2 might have been created in a laboratory rather than through natural selection. While I considered posting a link to it yesterday, it was prudent to do some due diligence first. See.. part of my job and training involves using software tools similar to the ones used in that post, so I decided to first independently verify a few of the main sequence alignments, structural models of proteins and publications etc before promoting it. Well.. while I have not re-verified every single point of data in this post, whatever I have done to date suggests that its main conclusions are correct.

Here is the post: SARS-CoV-2 Genealogy Through the Lens of Gain-of-Function Research

Since this post is very long and technical, let me summarize it- very briefly. The author starts by pointing out the unusual coincidence of an absolutely minimal furin cleavage site evolving at the junction of S1 and S2 subunits of the Spike protein in SARS-2. This is suspicious since gain of function by natural mutations usually tend to first create less than optimal sequences for new functions before being optimized via evolutionary selection. But this virus is too new for such an optimization to have occurred naturally- at least, that is not the most likely explanation.

He then points out that the two viruses which SARS-2 is most similar to ones discovered a few years ago (2014 and 2017/2019) in two different parts of the China. The Bat virus (RaTG13 with 96% similarity) came from a faecal swab from bat droppings from some cave in a part of China that is over 1,000 km from Wuhan, while the Pangolin virus (MP789 – 70% something similarity) came from autopsy of a bunch of smuggled sick pangolins from Malaysia in 2017. He then compares their sequences and while the Bat virus (RaTG13) is very similar to SARS-2, the Pangolin Virus has considerable dissimilarity with SARS-2 in first quarter of sequence for Spike Protein. Homologous recombination in a host infected with two viruses of same “species” without a segmented genome requires them to be very similar to each other.

More curiously, the new furin cleavage site in SARS-2 is a “gain of function” mutation, which means that it allows the virus to be more pathogenic (more infectious or capable of infecting a wider range of hosts/ cell types). It should be noted that more than a couple western research groups tried to insert similar enzymatic cleavage sites into other Coronaviruses such as SARS, MERS etc in the past. So it is not unreasonable to assume that the Chinese group in that Wuhan lab might have also tried it. In fact, we know that multiple research groups in Beijing tried that same gain of function mutation in a chicken Coronavirus. Oh ya.. and they also showed that putting that site into the S protein of another bat Coronavirus allowed it to infect human cells.

He then goes on talk about the whole field of Coronavirus research including many publications by a prominent researcher named Ralph Baric, who pioneered many of these techniques used for creating “gain of function” mutations in Coronaviruses. And yes.. he collaborated with the head of that Wuhan Coronavirus lab over the years, so it is makes perfect sense that you would see some his techniques are used in the later’s lab. Long story short, they looked at many “gain of function” mutations which made the resultant viruses deadlier. Also, Baric’s work seems to be have been “inspirational” to the lab in Wuhan since they kept trying out his ideas on Bat Coronaviruses.

The author then goes on to point out that accidental “leaks” of viruses from secure labs are far more common than most people realize, and are almost always due to poorly or hastily trained staff. So the idea that a poorly trained or careless researcher getting infected, but not developing serious illness and going on to spread it outside the lab is far more plausible than many would like to believe. He also points out the restriction enzyme map of nucleotide sequence, necessary for many types of genetic engineering, is rather similar for SARS-2, Bat and Pangolin coronvirus. And there are some other unusual similarities between the nucleotide codons used for certain amino acids- The explanation for which is a bit technical and complicated.

To summarize, the likelihood that this virus was created (along with others) to study effect of various “gain of function” mutations in Coronaviruses but then accidentally released into community through the actions of a poorly trained junior researcher is much more likely than it evolving naturally from a bat Coronavirus found in some remote part of the Yunnan province in China somehow magically recombining with a Pangolin Coronavirus from Malaysia and gaining just the right fragment of the Spike protein from it.

What do you think? Comments?

An Unusual Observation about Ongoing Coronavirus Outbreak in China

February 8, 2020 18 comments

As mentioned in the previous post on this topic, it is my opinion that the coronavirus outbreak in China is far more hype than reality. To be clear, I am not denying that a bit over 700 people are dead from this particular outbreak at the time of writing this post. Then again, a few thousand people die from influenza and its many complications in USA every single year- in a ‘good’ year. My point is that we should look at the actual evidence to make decisions and prognostications rather than let racism and stupidity make them. With that in mind, here is an odd feature of this current outbreak which sorta validates my initial assessment. It began with an observation about the prognosis of 2019-nCov infections outside China.

As some of you might have heard there are over a couple of hundred confirmed infections of this specific virus outside China, but only one death- thus far. So what is going on? Why is the death rate of patients outside China less than 1%? After posing this question on twitter, I got an interesting reply in the form of an attached table- based on available data from two days ago. Have a look at highlighted row- specifically the low death rate of patients in China (0.21 %) outside Wuhan and the province of Hubei. Note that this rate is rather close to that of cases outside China (0.39%). So, what is going on? Why does the fatality rate for this outbreak drop depending on your distance from Wuhan (4.11%), even in the province of Hubei (0.81%)?

Now let us consider and go through a few hypothesis which might provide an explanation for this unusual pattern. But before we do that, let me say something that is obvious but has to be stated for the benefit of delusional white racists. The numbers provided by Chinese government seem to be as accurate as those which would be provided by the american government under similar circumstances. This is bolstered by the fact that this outbreak seems to noticeably less deadly (on a percentage basis) than SARS. Let me remind you that SARS killed 43 people or almost 20% of the people who got infected in Canada and almost all nations with more than 10 cases ended up with mortality rates over 10%. On to the hypotheses..

1] Are people of Chinese ancestry more susceptible to infection by 2019-nCov and die from it? While the overwhelming majority of those infected and dead, so far, are of Chinese ancestry, the significantly lower death rates outside city of Wuhan (but still in Hubei) suggest that ethnicity and race are unlikely to be an important factor. Also, the majority of 2019-nCov cases outside China (to date) have occurred in travelers of Chinese ancestry from China. In other words, there is no real evidence that people of Chinese ancestry are somehow more susceptible to infection by 2019-nCov or die from it. They were just at the wrong place at a bad time.

2] The virus strain inside Wuhan is different, and more lethal, than the one outside that city? While its certainly possible that more than one strain of 2019-nCov is in circulation, the evidence we have so far suggests that all known isolates are extremely similar and have jumped into human hosts very recently. Having said that, it is common for RNA-based viruses such as Coronaviruses to mutate from more lethal strains into less lethal ones which spread more easily. Need I remind you that some species of coronaviruses are among the many which cause the common cold. In other words, it is possible – but there is a much more likely explanation.

3] In my opinion, the most likely explanation is as follows: there are far more milder infections in Wuhan than have been acknowledged. Imagine that only 1 in 10 or 20 patients have symptoms bad enough to seek medical attention. Now this will result in a 10-20 fold concentration of the worst cases in hospitals. If the infection has a death rate of 0.5%. and only the most ill 10% seek medical attention, the recorded mortality rate at hospitals will immediately jump from 0.5% to 5%. It is therefore likely that, over the next few weeks, we will find out that majority of infections caused by 2019-nCov are mild or asymptomatic and only a small percentage get ill enough to seek medical attention. Not sure if this soothes existing worries, creates new ones or both.

What do you think? Comments?

Some Initial Thoughts about the Recent Coronavirus Outbreak in China

January 31, 2020 12 comments

More than one commentator on my previous post wanted me to write something about the recent Coronavirus outbreak in China, especially regarding how bad it really is or might become in the near future. Since useful and concrete information about this outbreak has been overshadowed by a lot of racist mental projections in the declining west, I thought it was a good idea to write down my initial thoughts about the situation. FYI, one of my degrees is in microbiology. So let us talk about about this outbreak, starting with what we know for sure about the virus in question.

1] The Coronavirus (2019-nCoV) behind this outbreak is fairly close in its sequence to one which caused the SARS outbreak in 2003. And yes, it is closer to some known bat coronaviruses, but not others. Also, both SARS and 2019-nCoV almost certainly jumped from bats to human hosts. The odd thing, though, is that most bat species in Wuhan are currently hibernating and the initial outbreak occurred at a seafood market, suggesting that another mammalian species acted as an intermediate host between bats and humans.. perhaps a sick cat, dog etc.

2] Initial sequence analysis of virus samples from multiple patients and comparing them to each other strongly suggests that the jump from bats to humans occurred very recently, mostly likely within the past 2-3 months. Interestingly it seems to bind to the same human protein (for entry into cells) as the coronavirus which caused SARS. Given the fairly high similarity in sequence, same protein used for entry into cells and similar clinical disease produced by 2019-nCov and SARS we can make an educated guess that many other characteristic (infectivity etc) are also similar. Think of 2019-nCOV as a sibling or cousin of SARS.

3] It therefore follows that 2019-nCov is likely to be similar in its infectivity to the one which caused SARS in 2003. While some preliminary analysis by western scientists pretend that the former is more infectious than the later, everything we know about viruses tells us that they are very similar viruses which use the same protein to gain entry into human cells. I do not expect 2019-nCov to be significantly harder to control than SARS. The key word is ‘harder’ as 2019-nCov might end up infecting more people than SARS- but ease of control will be similar.

4] So far, the percentages of 2019-nCov infections ending in death is around 10%, and is similar to what we saw over the entirety of SARS outbreak. It is well known that viral strains which cause severe infections and high rates of mortality evolve into ones that cause mild infections and low rates of mortality because the former burn themselves out due to lack of new hosts. We can therefore expect the mortality and morbidity rates due to this virus to drop over the course of time due to better quarantine (corrals more aggressive strains) and treatment (lower mortality). Some of you might have noticed that the increase in number of deaths is now far slower than the number of confirmed infections- which is a good sign.

5] It is highly unlikely that 2019-nCov was developed by China as a biological weapon for the simple reason that biological weapons are, for the lack of better words, stupid and dangerous. See.. unlike nuclear weapons (which China posses), biological weapons cannot be controlled once unleashed and are likely to kill as many on your side as the other side. This is especially so, if there is no readily available vaccine or decent drugs to treat that infection. Furthermore, modern scientific techniques allow us to track back their creation to a degree that was unimaginable in even as late as the 1980s. Being greedy is not the same as being stupid.

6] Most hype about 2019-nCov has a lot to do with the increasingly rapid decline of the dying west. To make matters worse, it is now obvious that the western system of corporation-controlled capitalism is vastly inferior to the Chinese system of state-controlled and directed “capitalism”. In case you think otherwise, tell me how people similar to Trump (fraudulent right-wing populists) are increasingly getting elected in western countries. Every white idiot (and non-white idiot from subservient countries) expressing public alarm about 2019-nCov outbreak is subconsciously or consciously driven to do so because of a combination of racism and the unspoken recognition that their own system is in terminal decline with no realistic hope of recovery.

7] To be clear, I am not minimizing the potential problems this outbreak could cause. Having said that, the Chinese system is probably the most capable of actually stopping such an outbreak. As mentioned above, having a state-controlled system of governance not beholden to corporations and other short-sighted moneyed interests allows you to get things done and devote resources in ways that are impossible for corporation-controlled “democracies” such as USA, not to mention semi-functional anarchies such as India. You can be certain that Chinese government will things done, regardless of the financial cost and suppression of worthless “human rights”.

What do you think? Comments?