20200512T Day 133: Year of the RaTG13 – Origin of SARS-CoV-2 In the Multiverse

Screen Shot 2020-05-12 at 7.58.11 PM
From Ang Ku Kueh Girl and Friend’s Chinese New Year sticker pack

20200512T Santa Cruz, CA: In this post, I’ll be discussing the origins of the coronavirus known as SARS-CoV-2 in the different sets of universes around us. Some of these universes will match the official view and some of these universes will align with conspiracy theories. Most of these universes will interfere with one another and have overlapping characteristics.

The first statement out of China was that SARS-CoV-2 was believed to have originated at a wet market in Wuhan, a large city in Hubei Province, China. Many of the early cases of COVID-19, the disease caused by SARS-CoV-2, were found in individuals who shopped at Huanan Seafood Wholesale Market. The market was closed on Jan 1, 2020, and any evidence of origin was believed to have been destroyed. A few days ago, a WHO scientist Dr. Peter Ben Embarek stated that samples taken from the wet market show that the market likely played a role in the COVID-19 outbreak. Specifically, he stated:

The market played a role in the event, that’s clear. But what role we don’t know. Whether it was the source or amplifying setting or just a coincidence that some cases were detected in and around that market,” said Dr Peter Ben Embarek in a press briefing.

Notice how this statement does not limit us to universes in which SARS-CoV-2 originated in the wet market, but also includes universes where it amplified the spread of COVID-19 and also universes in which it played no role and was only coincidentally connected.

The main unofficial and so-called conspiracy theory is that SARS-CoV-2 originated in the Wuhan Biolab not far from the wet market. This theory is circumstantial based mainly on the fact that the biolab does perform research on bat coronaviruses. This theory has two sub-theories – one in which the virus is a bioweapon and one in which it is a natural virus. There are also two overlapping sub-theories – one in which the virus was intentionally released and one in which it was accidentally released. The accidentally released theory can be further divided into one in which a lab worker is accidentally infected and one in which samples are improperly discarded.

If we assume that there is a set of universes for each of these theories and sub-theories, then the reality we see will likely be an interference pattern of these different sets of universes until one set reveals itself.

Let’s make the hypothesis/assumption that sets of universes that are in conflict will repel each other and sets of universes that are congruent will attract one another. We can begin to see a set of universes that fit together with the following features:

  1. The Huanan Seafood Wholesale Market, a wet market, played a role in the outbreak.
  2. The Wuhan Institute of Virology (WIV), a Biosafety Level 4 Laboratory, played a role in the outbreak.
  3. SARS-CoV-2 was a coronavirus being studied at WIV.
  4. SARS-CoV-2 found a way from WIV to individuals at the wet market, which was the first identified outbreak.

There are also universes where the WIV is not involved and SARS-CoV-2 is found to have come from livestock sold at the wet market. However, the future in which this is true does not appear to be sending any indications to the present that are detectible. It doesn’t fit in well with the other universes. If SARS-CoV-2 is found in live animals, it is most likely in bats not local to the Wuhan area and most likely bats from which virus samples had been collected by lab workers at WIV.

Since the SARS-CoV-2 coronavirus has been sequenced, two other coronavirus sequences have been released. The first one released is labeled RaTG13, from a sample collected in 2013 in the Yunnan province. Comparison between RaTG13 (MN996532.1) and SARSCoV2-Wuhan-Hu1 (MN908947.3) show that they had a most recent common ancestor estimated at 50 years ago. The second one released is labeled RmYN02, which is shown to have a most recent common ancestor estimated at 35 years ago. Neither one of these is likely to be the natural ancestor of the virus, due to the number of mutations between each and SARS-CoV-2.

The Bat coronavirus RaTG13 complete genome sequence references the Nature paper: A pneumonia outbreak associated with a new coronavirus of probable bat origin.

Figure 1 showing RaTG13 phylogeny (https://doi.org/10.1038/s41586-020-2012-7)

Key quotes from the paper:

Full-length genome sequences were obtained from five patients at an early stage of the outbreak. The sequences are almost identical and share 79.6% sequence identity to SARS-CoV. Furthermore, we show that 2019-nCoV is 96% identical at the whole-genome level to a bat coronavirus.

This second one I wish was explained more in how the “then found” occurred.

We then found that a short region of RNA-dependent RNA polymerase (RdRp) from a bat coronavirus (BatCoV RaTG13)—which was previously detected in Rhinolophus affinis from Yunnan province—showed high sequence identity to 2019-nCoV.

More thoughts to come…


20200416h Day 107: Behind the Curve

I just finished watching Behind the Curve, a documentary about people who believe that the Earth is flat instead of a globe. For these people, the rest of the world believes in a conspiracy that the Earth is a globe. This belief is rooted in a belief that scientific research is censored and only research allowed to be published is that which aligns with the dogma of the community in power.