One of the important reasons why the Taiwan program traces the source of the new coronavirus to the United States is:
Samples of haplotype h38 were found in the United States.
What is haplotype?
Zhao Xumao, who is engaged in the research of climate change ecology and conservation biology, makes an example: just as a company can operate effectively only when multiple departments with different responsibilities cooperate with each other, the characteristics of the virus are also determined by many genes, and a single gene can not play a role, each haplotype is like an independent department. In short, haplotypes are gene combinations that determine the same trait.
A novel coronavirus sample covering 12 continents in four continents was collected by Yu Wenbin, who was working in the Tropical Botanical Garden of the Chinese Academy of Sciences (up to February 12th). It was found that the 93 virus samples contained 58 haplotypes in February 12th. The data of the 93 new coronavirus samples from all countries in China were collected.
Moreover, in this paper, the haplotype evolution relationship shows that haplotypes H13 and h38 are relatively old haplotypes, and they are associated with bat coronavirus ratg13 through an intermediate vector, MV1 (maybe ancestral haplotype, or from intermediate host or patient No.0), and haplotype H1 is derived from haplotype H3.
According to this haplotype evolution relationship, if we simply comb, we can get the following two groups of schematic diagrams:
What does this mean? The beginning is the haplotype MV1. According to Zhao Xumaos interpretation, Xinguan virus is like a family business. H38 and H13 are the first generation founders of the virus, which we can call grandpa haplotype; H3 is the second generation leader of the virus, which we can call the parent haplotype; and H3 derived the grandson H1, which is the third generation leader of the virus. It is this grandson H1 that makes the virus as powerful as ever. H1 is derived from h56 and MV2 of great grandson, as the fourth generation leader.
According to the normal logic, the haplotypes of grandfathers are the ancestors of the virus. However, the research team found that the sample haplotypes of patients associated with the seafood market in South China are all the H1 of their grandchildren and their descendants (i.e. haplotypes H2 and h8-h12), and the only sample haplotype H3 in Wuhan, that is, the H3 of their parents, has nothing to do with the seafood market in South China.
Novel coronavirus in Southern China seafood market was introduced from other places, and spread rapidly in the market to the market. In other words, the paper argues that the South China seafood market is not the origin of the virus.
Here comes the question:
Is the source in the United States?
This is not the end of the study. Along the way, the research team traced the source of two ancient haplotypes, namely, grandfather haplotypes H13 and h38, and found that they were patients from Shenzhen (the first in Guangdong) and Washington State (the first in the United States). Among them, the patient in the United States is the sample of haplotype h38 mentioned in the Taiwan program.
Things are not as simple as you think. Zhang Wenhong, director of novel coronavirus pneumonia treatment team and Huashan Hospital Affiliated to Fudan University director of infectious diseases, said in an interview with relevant media about the source of the new crown virus, Shanghai new crown pneumonia.
1u3001 When and where the virus first appeared should be investigated;
2u3001 To find its position on the top of the evolutionary tree, the evolution of the genes behind is based on the former.
Tracking the infection time and activity track of grandfathers haplotypes H13 and h38, the research team found that the travel records of the two patients showed that they should be infected during the activity in Wuhan from the end of December 2019 to the beginning of January 2020. In other words, the research team believes that the two grandparent haplotypes H13 and h38 are from Wuhan.
In addition, the Taiwan program believes that there are five haplotypes in the virus in the United States, so the United States is the origin of the virus. This shows that there are many ways to infect the virus in the United States, such as Wuhan, Australia, Shenzhen and so on. Zhao Xumaos analysis.
Therefore, based on this paper, we can not conclude that the source of the new coronavirus is in the United States.
According to genome analysis, the source of the new coronavirus is not in the South China seafood market. Where is the source? It needs to be tracked by relevant researchers, but according to the current relevant research, it should still be in Wuhan. Zhao Xumao said.
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In this case, the existing Wuhan sample, why did not detect the grandfather generation haplotype? The research team believes that this may be because the existing samples are mainly collected from several designated hospitals, and the sample collection time is limited to December 24, 2019 and January 5, 2020.
According to Zhao Xumao, Wuhan virus samples were collected later. With the development of the virus, its haplotypes are growing and its diversity is increasing. Due to the late collection time in Wuhan, it is likely that the haplotypes of grandfathers have been replaced by those of grandsons.
In fact, Yu Wenbin, the author of the paper, also admitted in an interview about the limitations of this study. There is a shortage in this study, that is, of the 93 samples, Wuhan samples are mainly early. If there are more Wuhan samples for genome sequencing, more evidences may be found in traceability, such as finding the H13 and h38 haplotypes, which may be able to Help find the source of the virus.
Why did Wuhan become the main outbreak area, while Guangdong, which had earlier haplotypes, was relatively better?
Zhao Xumaos analysis: first, the amount of virus in Guangdong is less, and second, the local authorities have taken relatively strict measures after finding it. In contrast, Wuhan has a large population of viruses, which did not take more stringent measures in time and effectively in the early stage, which led to more and more people infected.
In this regard, Zhao Xumao believes that this kind of conjecture without data basis is not reliable enough. He said that although novel coronavirus pneumonia and influenza have similar clinical symptoms, two of them belong to RNA virus. Novel coronavirus pneumonia is a new type of virus. But it is two different viruses, and it is not related to each other. Human beings have a long history of dealing with influenza viruses, and the detection of influenza is far more mature than the new coronavirus. It only needs a simple rapid influenza nucleic acid amplification test to judge. Therefore, there is little possibility of miscalculation. Zhao Xumao said.
In fact, just 28 local time, who experts said that the source of the new coronavirus can not be determined. Novel coronavirus pneumonia emergency technology program director Kohof said there are still many work to be done to identify the intermediate host animal that causes new crowns. At present, there is no definite answer, but it is under active research.