Applying ballpark rates of viral evolution, Rambaut estimates that the Adam (or Eve) virus from which all others are descended first appeared no earlier than Oct. 30, 2019, and no later than Nov. 29.
This information (originally posted by Emma Robertson from an article at Statnews) needs to be updated. This estimate was based on the first 24 samples of the virus to be sequenced, as of last Jan. 24th. Now over 100 samples have been sequenced, including many more samples from cases around the world.
The news is paradigm changing. The virus is several months older than we thought, and it didn't originate at the meat market in Wuhan, China. The information is contained within two recent scientific papers:
On the origin and continuing evolution of SARS-CoV-2 (Tang et al.)
Population genetic analyses of 103 SARS-CoV-2 genomes indicated that these viruses evolved into two major types (designated L and S), that are well defined by two different SNPs that show nearly complete linkage across the viral strains sequenced to date. Although the L type (~70%) is more prevalent than the S type (~30%), the S type was found to be the ancestral version. Whereas the L type was more prevalent in the early stages of the outbreak in Wuhan, the frequency of the L type decreased after early January 2020.
Decoding evolution and transmissions of novel pneumonia coronavirus using the whole genomic data
In this study, we used 93 complete genomes of SARS-CoV-2 from the GISAID EpiFluTM database to investigate the evolution and human-to-human transmissions of SARS-CoV-2 in the first two months of the outbreak.... The 58 haplotypes (31 found in samples from China and 31 from outside China) were identified in 93 viral genomes under study and could be classified into five groups. By applying the reported bat coronavirus genome (bat-RaTG13-CoV) as the outgroup, we found that haplotypes H13 and H38 might be considered as ancestral haplotypes, and later H1 (whose descendants included all samples from the Huanan Seafood Wholesale Market) was derived from the intermediate haplotype H3. The population size of the SARS-CoV-2 was estimated to have undergone a recent expansion on 06 January 2020, and an early expansion on 08 December 2019. Phyloepidemiologic analyses suggested that the SARS-CoV-2 source at the Huanan Seafood Wholesale Market was potentially imported from elsewhere.
The "Type S" ancestral strain discussed in the first paper, corresponds to haplotypes H13 and H38 in the second paper, and their descendants. The "Type L" strain that exploded suddenly into the Wuhan epidemic, is described in the 2nd paper as haplotype H1 and its descendants. These two strains are separated by two sequential genetic mutations, and the second paper identifies a haplotype H3 which is the intermediate step.
So the original strain (H13/H38) must have existed early enough for those two mutations to occur before the onset of the Wuhan epidemic.
The 2nd paper was analyzed by a virologist on a TV news show in Taiwan, and from there it was picked up by Larry Romanoff at Global Research:
China’s Coronavirus: A Shocking Update. Did The Virus Originate in the US?
Taiwan ran a TV news program on February,27,(click here to access video (Chinese), that presented diagrams and flow charts suggesting the coronavirus originated in the US. (6)
Below is a rough translation, summary and analysis of selected content of that newscast. (see map below)
The man in the video is a top virologist and pharmacologist who performed a long and detailed search for the source of the virus. He spends the first part of the video explaining the various haplotypes (varieties, if you will), and explains how they are related to each other, how one must have come before another, and how one type derived from another. He explains this is merely elementary science and nothing to do with geopolitical issues, describing how, just as with numbers in order, 3 must always follow 2.
One of his main points is that the type infecting Taiwan exists only in Australia and the US and, since Taiwan was not infected by Australians, the infection in Taiwan could have come only from the US.
The basic logic is that the geographical location with the greatest diversity of virus strains must be the original source because a single strain cannot emerge from nothing. He demonstrated that only the US has all the five known strains of the virus (while Wuhan and most of China have only one, as do Taiwan and South Korea, Thailand and Vietnam, Singapore, and England, Belgium and Germany), constituting a thesis that the haplotypes in other nations may have originated in the US. ....
The Virologist further stated that the US has recently had more than 200 “pulmonary fibrosis” cases that resulted in death due to patients’ inability to breathe, but whose conditions and symptoms could not be explained by pulmonary fibrosis. He said he wrote articles informing the US health authorities to consider seriously those deaths as resulting from the coronavirus, but they responded by blaming the deaths on e-cigarettes, then silenced further discussion. …
The Taiwanese doctor then stated the virus outbreak began earlier than assumed, saying, “We must look to September of 2019”.
He stated the case in September of 2019 where some Japanese traveled to Hawaii and returned home infected, people who had never been to China. This was two months prior to the infections in China and just after the CDC suddenly and totally shut down the Fort Detrick bio-weapons lab claiming the facilities were insufficient to prevent loss of pathogens.
While the TV show was in Chinese, the virologist took his map and phylogenic tree (with notations in English) from the 2nd scientific paper linked above. (The first paper provides a very similar tree diagram, while the 2nd paper mentions that its classification the virus into 5 "Groups" can easily be further classified into two clades, "Clade I" and "Clade II". Thus it's clear to me that the two papers are reaching very similar conclusions from the data.)
Chris Martenson discussed the 1st paper yesterday in his daily podcast. Starting at about 23:40:
All right, a lot of people sent me this. It's a recent study that came out. It's pretty intriguing because it talks about two different types, two different clades of groups of the coronavirus … Whereas the L type was more prevalent in the early stages of the outbreak in Wuhan, the frequency of the L type decreased after early January 2020. So the L type looks to be more virulent, in the sense that it transfers faster more aggressively, and it actually causes higher levels of complications. So the L type, though, decreased after early January 2020. Human intervention may have placed more severe selective pressure on the L type. So: severe selective pressure means we're gonna stop this one. So if somebody got sick, they would be they would be quarantined right away. If somebody got sick, then everybody they were in contact with retraced, and they would all be quarantined right away. So because the L type presented itself more aggressively (right), and it spread more quickly, it was found faster. And so the L type would have gone away, because that one was contained and collapsed, right? So the quarantine found the L type right away. On the other hand, the S type, which is evolutionarily older and less aggressive, might have increased in relative frequency due to the relatively weaker selective pressure. Meaning, jeez you know, if you just had very minor symptoms or you were even asymptomatic; you didn't notice it; hey nobody would have come and quarantined you. You might have spread that one around. … If there is an L type and there is an S type, you might even want to encourage the S type to spread while you're doing everything you can to contain the L type.
So Martenson is saying, in other words, that the "S" type might work almost like a vaccination against the much more dangerous "L" type. And, the Taiwanese virologist is arguing that the "S" type has been multiplying and spreading throughout the USA since last September. If that's true, then it implies that the "S" type couldn't be too much more lethal than any other flu virus. If it was anything like the Wuhan coronavirus, there's no way it could have been here in the USA since September without creating a panic and collapsing our entire hospital system.
Now, it's important to notice that Romanoff titled his paper "Did the virus originate in the US?" with a Question Mark, indicating that this is all highly speculative. It's possible that H13/H38 originated in the US, but then again it's possible that the US has the greatest genetic diversity of the virus here because we have more flights connecting us everywhere in the world. Or there might be something else wrong with this long chain of scientific reasoning.
But if turns out that the US has basically been vaccinated against "Type L" by a largely asymptomatic, silent epidemic of "Type S" virus... maybe Trump knows what he's talking about when he says the threatened pandemic will disappear "like a miracle"?