DT excavator description:
The coronavirus epidemic that started in Wuhan this time first caused the naming of the virus.Generally ,the whole world is accepted as CCP virus in the end.In the second season of digging, the DT excavator will mainly explain why it is more reasonable to be called CCP virus from a more professional perspective. Of course, this is not a scientific name, but a popular naming.
Scientifically, the virus is named SARS-CoV-2? New crown virus (referred to as CCP virus in the article). So what is the relationship between the novel coronavirus, (referred to as CCP virus in the article),SARS coronavirus and SARS-related coronavirus? A scientist provided us with an article and told DT that the article is more comprehensively interpreted, But there are also two key points that non-professionals tend to overlook. More importantly, he made a detailed interpretation of these two key points and mark also the key words in the article.
The following is the article and interpretation:
What is the relationship between the novel coronavirus, SARS coronavirus and SARS-related coronavirus?
Original content: Chinese virology English version IF: 2.467
Author | Hu Ben (Wuhan Institute of Virology, Chinese Academy of Sciences)
On the evening of February 9, New Coronary Pneumonia Epidemic Prevention and Control Headquarters of Hubei Province held a press conference. At the meeting, academician Chen Huanchun, an expert in the epidemic prevention and control research team, error in speaking that the “new coronavirus belongs to SARS coronavirus” caused a public uproar. After the meeting, Academician Chen corrected and clarified the mistake immediately, emphasizing that “the new coronavirus is not a SARS coronavirus” and “belongs to SARS-related coronavirus”.
However, just two days later, the WHO announced officially that the new coronary pneumonia disease was named Coronavirus Disease 2019 (COVID-19). And the international academic institutions responsible for virus naming—International Committee on Taxonomy of Viruses, ICTV. Announced that the name of the new coronavirus was officially defined as SARS coronavirus-2 (severe acute respiratory syndrome coronavirus 2).
As a result, the people who were a little unclear became more and more confused: Now that the relationship between the new coronavirus and SARS has been cleared many times, Why did the international authority ICTV suddenly call it SARS-CoV-2? How to understand SARS-related coronavirus?
This article will give you a rationale from the perspective of coronavirus taxonomy that what is the relationship between the novel coronavirus, SARS coronavirus and SARS-related coronavirus?
I : SARS-associated coronavirus is a virus species in the Coronaviridae family
Viruses in nature are rich and diverse, but they are not disorderly.Scientists classify different viruses according to their genetic information and evolutionary relationship. This is the work done by the subject of virus taxonomy. When a new virus emerges, the researchers will use the genome sequence of the virus, according to specific rules, according to the order , family ,genus, species and other taxonomic levels to identify viruses in turn. The International Virus Classification Committee (ICTV) is the authoritative institution for virus classification.
Let’s take a look at the classification of coronavirus. Coronaviridae is a virus family under Nidovirales, and can be further divided into Coronavirinae and Torovirinae. What we usually call coronavirus does not refer to a certain virus, but a general term for all members of the Coronavirus subfamily. In the ninth ICTV virus classification report published in 2012, we can see that the Coronavirus subfamily is divided into four genera of Alpha Coronavirus, Beta Coronavirus, Gamma Coronavirus and Delta Coronavirus. Coronaviruses of these two genera, Alpha- and Beta-, mainly infect mammals, and all coronaviruses are also located in these two genera. The Beta coronavirus can be further divided into four lines (A, B, C and D), of which lineage B has only one virus species (SARS-related coronavirus), namely SARS-related coronavirus.
Phylogenetic relationships among members of the Coronavirus subfamily (picture taken from ICTV 9th virus classification report, the Ninth Report of the International Committee on Taxonomy of Viruses, 2012）
Over the past eight years, the MERS coronavirus outbreak in the Middle East. In addition to human coronaviruses, more and more animal coronaviruses, especially bat coronaviruses, have been discovered, and many new members have been added to the coronavirus family. The latest ICTV 10th virus classification report is being continuously updated, although the current chapter of the coronavirus classification report has not been officially published. However, in 2018, ICTV issued a new proposal on coronavirus classification (2017.013S), and the number of virus species included in coronavirus has increased significantly compared with the original. Specifically seeing the Beta Coronavirus genus, in the new ICTV proposal, the number of Coronaviruses belonging to Beta Coronavirus has increased from 7 to 12. These 12 species belong to 5 different subgenus (Sub-genus). For example, the sub-genus Merbecovirus contains four species: MERS-associated coronavirus, hedgehog coronavirus 1, vowing coronavirus HKU5, and flat-crowed bat coronavirus HKU4. The subgenus Sarbecovirus corresponds to the Lineage B Beta coronavirus in the past taxonomy, including only the SARS-related coronavirus.
Representative viruses of the 12 virus species included in the Beta Coronavirus genus (quoted from ICTV Coronavirus Classification Proposal 2018a document number 2017.013S)
Species is a concept in taxonomy, which is further subdivided. Each coronavirus species includes one or more representative viruses. For example, the SARS coronavirus that caused SARS in 2003 is a representative member of the SARS-associated coronavirus. Human coronavirus OC43 is a representative virus of Beta Coronavirus 1.
After reading the above, I believe that everyone has some understanding of the classification of coronaviruses, especially Beta coronaviruses. So the question is, which virus species does the new coronavirus belong to? Does it represent a new coronavirus species?
II. The new coronavirus belongs to the SARS-associated coronavirus
To determine whether a new virus belongs to an existing virus species or a completely new virus species in taxonomy, we need to refer to ICTV’s virus breeding rules. For viruses of different families, the rules for seeding are different. In the case of coronaviruses, it is necessary to compare the sequence consistency of the new viruses and known viruses on the non-structural proteins encoded by ORF1ab. Specifically, seven conserved replicase domains on non-structural proteins are essential for coronavirus identification. The seven domains are: ADRP (adenosine diphosphate nucleose-1 “-phosphatase) located on nsp3, nsp5 (3CLpro, 3C main protease), nsp12 (RdRp, RNA-dependent RNA polymerase), nsp13 (Hel, helicase), nsp14 (ExoN, exonuclease), nsp15 (NendoU, uridine-specific ribonuclease), nsp16 (O-MT, O-methyltransferase). According to ICV’s seeding rules proposed in its ninth classification report: The amino acid sequences of the seven replicase domains are connected in series. If the sequence consistency between the two coronaviruses is greater than the threshold of 90%, it means that the two coronaviruses belong to the same species.
Although the neocoronavirus and SARS coronavirus genomes differ by about 20%, their ORF1b is relatively conserved, and the non-structural protein encoded by ORF1b occupies most of the seven replicase domains. After comparison, the amino acid sequence similarity of the neocoronavirus and SARS coronavirus in these seven domains reached 94%. Therefore, according to the ICTV coronavirus classification rules, the new coronavirus and SARS coronavirus belong to the same virus species, namely SARS-related coronavirus.
Comparison of Amino Acid Sequences of Seven Conserved Replicase Domains of New Coronavirus and SARS Coronavirus
While announcing the name of the new coronavirus, ICTV published a preprint of a research paper on BioRxiv. Called “Severe acute respiratory syndrome-related coronavirus: The species and its viruses – a statement of the Coronavirus Study Group”. The ICTV coronavirus research team passed a phylogenetic analysis based on the five most conserved replicase protein domains of coronavirus ORF1a and 1b. Calculate the genetic distance between the two pairs of common ancestors, determine that the new coronavirus and SARS coronavirus belong to the same species of SARS-related coronavirus, and name the new coronavirus SARS coronavirus-2.
III : The new coronavirus is not a SARS coronavirus
Since it is classified as the same species, does it mean that the new corona virus SARS-CoV-2 and the SARS coronavirus are particularly similar, is it the second SARS virus? It cannot be understood this way. The same coronavirus species may include multiple different viruses. For example, in addition to the human coronavirus OC43, the viruses belonging to the Beta Coronavirus 1 species include bovine coronavirus, equine coronavirus, and porcine hem-agglutinating encephalomyelitis virus. ICTV also clearly mentioned in their preprint paper that SARS-CoV-2 is “a sister to SARS-CoV of the species SARS-related coronavirus”, that is, SARS-CoV-2 and SARS coronavirus are in a sister relationship. Can’t be identified with together.
The new corona virus and the SARS virus have some similarities: both can cause severe pneumonia, are related to wild animals, and the seasons of occurrence are also similar, But the difference is also obvious. The full-length genome sequence similarity between New Corona virus and SARS virus is only about 80%. The S gene of coronavirus encodes the spike protein responsible for receptor binding, which is closely related to the pathogenicity of the virus, while the S gene sequence similarity of the new corona virus and SARS virus is only 73%. From this point of view, there is huge difference between the new corona virus and the SARS virus, Compared with the SARS virus, the pathogenicity of the new coronavirus can only be a younger brother. The rate of development of severe disease and the fatality rate are much lower than SARS, but its ability to spread is stronger than SARS. Moreover, the new coronavirus is more cunning than the SARS virus and has a longer incubation period.
(Note: The original author is a virology expert. This sentence describes the difference between the biological characteristics of the two viruses very clearly! This sentence unintentionally revealed nature ´s mystery: This is the purpose of the CCP virus as a biochemical weapon. It is to have a controllable virus with moderate pathogenicity and super capability spreading the virus into Hong Kong to suppress the resistance of Hong Kong warriors, and force them go home from the street. Unexpectedly, the CCP shot itself in the foot and the virus was completely out of control!)
From this we can see that there are many obvious differences between the new corona virus and the SARS virus, which are two different things. The WHO also stated on its official website: 2019-nCoV is from the same family of viruses as SARS-CoV but it is not the same virus, which clearly indicates that the new crown virus and SARS virus are different viruses.
Screenshot source: WHO official website (https://www.who.int/news-room/q-a-detail/q-a-coronaviruses)
If Coronaviridae is a large family, SARS-associated coronaviruses are a small family. But there are many members of this family. In addition to SARS coronavirus and new coronavirus, SARS-related coronaviruses also include the abundant and diverse SARS-like coronaviruses found in bats in China and in many parts of the world. From the evolutionary tree of SARS-related coronavirus, we can see that the new coronavirus and SARS coronavirus are located on two different branches, and on these two branches, there are also different bat SARS-like coronaviruses. The evolution tree also intuitively shows that the new coronavirus is not an evolutionary or mutant version of the SARS coronavirus, not SARS 2.0, but a parallel relationship with the SARS coronavirus.
Phylogenetic tree based on full-length genome sequence of SARS-associated coronavirus
Some people may ask: “You said that ICTV determined that the new corona virus and SARS virus are the same species, but experts said that the new corona virus and SARS virus are not the same virus. Isn’t this contradictory? Who should I believe? “In fact, both of these statements are true. It is said that the new crown virus and the SARS virus are the same species. The “species” here refers to “species”, which is a proper term in taxonomy. While it is said that the new crown virus and SARS are not a kind of virus, the “species” here is our popular saying. As if to say, Chihuahua and Teddy are not a kind of dog, but they are both dogs. Therefore, both of these statements are understandable.
(Note: The Bat CoV RaTG13 here is a manually modified virus sequence uploaded by Zhengli Shi)
Because Shi claimed that this sequence was detected in the virus in 2013, but Shi did not have the actual virus! (Zhengli Shi, you know what I mean). This sequence was uploaded by Zhengli Shi only after the CCP virus became outbreak ,This is a fake virus sequence after manual modification (will be described in detail later).
Therefore, the viruses most similar to the CCP virus are ZXC21 and ZC45, the two Zhoushan bat viruses that revealing on January 19 on the Luther´s we-Media.
Finally, let ’s summarize the relationship between the new coronavirus SARS-CoV-2 and SARS coronavirus: Taxonomically they belong to the same coronavirus species, but they are two different viruses, two brothers in this small family of coronaviruses related to SARS.
We summarise the key sentences in this article:
The new coronavirus (CCP virus) and SARS coronavirus belong to the same virus species, namely SARS-associated coronavirus.
It was determined that the new coronavirus (CCP virus) and SARS coronavirus belong to the same species of SARS-related coronavirus, and the new coronavirus was named SARS coronavirus-2.
The full-length genomic sequence similarity between the new crown virus New Crown Virus (CCP virus) and SARS virus is only about 80%.
However, the similarity of the S-gene sequence between New Coronavirus (CCP virus) and SARS virus is only 73%.
Compared with the SARS virus, the pathogenicity of the new coronavirus can only be a younger brother. The rate of development of severe disease and the fatality rate are much lower than SARS, but its ability to spread is stronger than SARS. Moreover, the new coronavirus is more cunning than the SARS virus and has a longer incubation period.
New Corona virus New Corona virus (CCP virus) and SARS virus are different viruses.
New coronavirus New coronavirus (CCP virus) is not an evolutionary or mutant version of SARS coronavirus, not SARS 2.0, but a parallel relationship with SARS coronavirus.
Taxonomically they belong to the same coronavirus species, but they are two different viruses, two brothers in this small family of coronaviruses related to SARS.
Bat CoV RaTG13 is an artificially modified virus sequence uploaded by Zhengli Shi Because Shi claimed that this sequence was detected in the virus in 2013, but the real thing of this virus isn’t exist.
Therefore, the viruses most similar to the CCP virus are ZXC21 and ZC45, the two Zhoushan bat viruses that revealing on January 19 on the Luther We-media.
Finally, we consummate the following table:
This series of conclusions and this table are the basis of the discussion later.