Breaking news! The origin of the new coronavirus may not be the Huanan Seafood Market. Chinese scientists have found evidence from the perspective of genetics and evolution by constructing a “genealogy” of the new coronavirus.

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Introduction:This is an academic paper that popped up on the Internet yesterday.According to the article, Yu wenbin, an associate researcher at the Chinese academy of sciences, submitted an English paper to ChinaXiv on February 21.The article suddenly admitted that the Wuhan virus did not come from the seafood market ,it directly gave Shi zhengli a slap in face, a researcher at the Wuhan P4 virus research institute.The shift in the plot is somewhat unexpected.Shi zhengli is a direct participant. Doesn’t she know more about the virus than Yu wenbin?What made her react to the seafood market in the first place?Who let Yu wenbin deny the seafood market in the world when the basic conclusion is man-made drug making?The dark side of the communist party never reaches the bottom. The only thing we know is that both Shi and Yu were scientists trained by the communist party. They respected their superiors instead of science, and they obeyed politics instead of truth.

In any case, the timing of the release of the paper is interesting.Here is the original text.

Chinese scientists have made breakthrough progress in finding the source of new coronavirus pneumonia.

Yu Wenbin, an associate researcher from the Xishuangbanna Tropical Botanical Garden of Chinese Academy of Sciences associated with researchers from South China Agricultural University and Beijing Brain Center published an important research paper on ChinaXiv which is a pre-released platform for scientific papers of the Chinese Academy of Sciences [1].

Through genetic analysis, Yu Wenbin and the others found that the new coronavirus in the Huanan Seafood Market should be imported from other places. In other words, the Huanan Seafood Market is not the birthplace of the new coronavirus. However, the Huanan Seafood Market should be the tipping point for the new coronavirus pneumonia.

They also believe that the new coronavirus may have spread widely in Wuhan in mid-to-late November. The good news is that compared to SARS and MERS viruses, new coronavirus has lower mutation.

The paper’s home page

So how did the scientists from Chinese Academy of Sciences solve the mystery and reach the above conclusions?

We all know that since the outbreak of the new coronavirus pneumonia in Wuhan, scientists and doctors have speculated that the Huanan Seafood Market is the source of the new coronavirus pneumonia. The Huanan Seafood Market was closed on the New Year’s Day of 2020.

However, Professor Huang Chaolin and his colleagues at Wuhan Jinyintan Hospital disclosed the relevant informations [2] of the first batch of 41 new coronavirus infections in the top academic journal “The Lancet” on January 24, had challenged the above assumptions.

Among the 41 first confirmed patients, 13 have never been to Huanan Seafood Market in Wuhan.

More importantly, the earliest patient became ill on December 1, 2019. He has not been to Huanan Seafood Market in Wuhan. Furthermore, two of the three patients of the second group patients on December 10 have not been to Huanan Seafood Market in Wuhan either.

This means that the earliest patients infected with the Wuhan new coronavirus may be infected in an unknown place [3].

New coronavirus (COVID-19, including below related coronavirus) picture (source: NIAID-RML)

However, the Huanan Seafood Market has already been closed, and the current clinical manifestations of patients also show that there are many patients with new coronavirus infection without any symptoms. Therefore, it is almost impossible to analyze the origin of new coronavirus pneumonia from an epidemiological perspective.

With more and more genomic data of new coronavirus, the traceability of its source from the perspective of genetic evolution becomes possible.

Geneticists can be used by the genomic informations of the new coronavirus for us to understand the evolution or genetic relationship between different coronaviruses. To find out who is the father, who is the grandfather, who is the grandson, and then we can draw a family tree for the new coronavirus.

With the genealogy of the new coronavirus, we can find the ancestors of the new coronavirus and follow the line of evidence, we expect to find the birthplace of the new coronavirus.

New coronavirus picture (source: NIAID-RML)

Yu Wenbin and others firstly collected genomic data of 93 new coronavirus’ samples shared by worldwide scientists in the GISAID EpiFluTM database.

Preliminary analysis found that there were 140 locus aberrances in these 93 coronaviruses, 120 of them were located in the gene coding sequence.  Based on this, they divided these new coronaviruses into 58 haplotypes (which can be simply understood as 58 different new coronaviruses).

Combining other data, they found that the new coronavirus had lower aberrance than the SARS and MERS viruses. In other words: the current new coronavirus is still relatively stable.  This may be because the new coronaviruses are relatively mild and the immune system does not release much pressure on them.

Aberrance Location Analysis

Next is the most important analysis process: analyzing the evolutionary relationship among these 58 haplotypes, that is to draw their genealogy.

I am directly uploading the picture here. The picture below is the genealogy of these 58 new crown viruses.

Evolutionary Maps of Different Haplotypes of New Coronavirus

The picture above is complicated at first glance.  Let’s firstly look the branch-like thing on the right.

You can clearly see that it consists of three parts. The top group A is light green and is in the shape of a foot. The middle lilac group B is rectangular. The bottom group C has no background color and a large circle surrounded by small circles. Groups D and E respectively protrude from the left and right corners of group C.

In other words, the haplotypes of the 58 new coronaviruses (numbered H1-H58) were divided into five groups: A, B, C, D, and E.  Their relationship is that group A is the oldest and can be said to be the ancestor of the new cronavirus.  This is an approximate situation.

Then, I request everyone to pay attention to H13 of group A, H38 (pink) and H3 (four-colored round-cake shape) in group B, and H1 (largest multi-colored, round-cake shamp) in group C.  You can even ignore all the small circles around the above haplotypes and pull them out individually.

In order to make it easier for you to see the pictures in combination with the text, I locate this key picture again.

In this case, you can easily find two simplified routes: H13 → H3 → H1, and H38 → H3 → H1.  We can simply think of these two lines as the relationship between the three generations.  H13 and H38 are the oldest, H3 is the middle, and H1 is the youngest.  Researchers also believe that through phylogenetic networks, H13 and H38 can basically be considered as the ancestral haplotypes of the new coronavirus.

However, the researchers do not rule out the existence of other ancient haplotypes, because the data of the earliest infected persons and those infected in early December (2019) were not included in this study.

Diagram of two possible evolutionary pathways of the new coronavirus

What I want to illustrate next is that the new coronavirus from the Huanan Seafood Market in Wuhan is H1 and its descendants (the circle around H1), without H13 and H38; even only one H3 appeared in the entire Wuhan sample, and Huanan Seafood Market has nothing to do with it.

So from where the earlier H13 and H38 isolated from?

H13 appeared in five Shenzhen patients, and they were also the first confirmed infection in Guangdong.  H38 came from the first confirmed patient in USA.  Their travel records indicate that they had been to Wuhan between December 2019 and January 2020, but they had no history of Huanan Seafood Market exposure.

This shows that the viruses in the five H13 infected persons of Shenzhen and the H38 infected person of USA may have been infected through hospitals in Wuhan or other unknown channels.

Geographical distribution of different haplotypes of New Coronavirus

Based on the data above, Yu Wenbin and his colleagues believe that the speculation of other scientists should be correct: the new coronavirus of the Huanan Seafood Market was imported from other places.

However, researchers are still looking forward to having early infected samples for further analysis, maybe they can find traces of H13 and H38 from these patients, which is very important to find the source of the new coronavirus.

It is hoped that a hospital in Wuhan still holds the sample of an unknown early patient.

References:

[1]. https://eprint.las.ac.cn/abs/202002.00033

[2]. https://www.thelancet.com/journals/lancet/article/PIIS0140-6736(20)30183-5/fulltext

[3]. https://www.sciencemag.org/news/2020/01/wuhan-seafood-market-may-not-be-source-novel-virus-spreading-globally

Author of this article丨BioTalker

Source of this article in original Chinese

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