The six strains of SARS-CoV-2
By University of Bologna - 03. August 2020
SARS-CoV-2 mutation rate remains low. Across Europe and Italy, the most widespread is strain G, while the L strain from Wuhan is gradually disappearing. These mutations, however, do not impinge on the process of developing effective vaccines.
The virus causing the COVID-19 pandemic, SARS-CoV-2, presents at least six strains. Despite its mutations, the virus shows little variability, and this is good news for the researchers working on a viable vaccine.
These are the results of the most extensive study ever carried out on SARS-CoV-2 sequencing. Researchers at the University of Bologna drew from the analysis of 48,635 coronavirus genomes, which were isolated by researchers in labs all over the world. This study was published in the journal Frontiers in Microbiology. It was then possible for researchers to map the spread and the mutations of the virus during its journey to all continents.
The first results are encouraging. The coronavirus presents little variability, approximately seven mutations per sample. Common influenza has a variability rate that is more than double.
"The SARS-CoV-2 coronavirus is presumably already optimized to affect human beings, and this explains its low evolutionary change", explains Federico Giorgi, researcher at Unibo and coordinator of the study. "This means that the treatments we are developing, including a vaccine, might be effective against all the virus strains".
Currently, there are six strains of coronavirus. The original one is the L strain, that appeared in Wuhan in December 2019. Its first mutation - the S strain - appeared at the beginning of 2020, while, since mid-January 2020, we have had strains V and G. To date strain G is the most widespread: it mutated into strains GR and GH at the end of February 2020.
"Strain G and its related strains GR and GH are by far the most widespread, representing 74% of all gene sequences we analysed", says Giorgi. "They present four mutations, two of which are able to change the sequence of the RNA polymerase and Spike proteins of the virus. This characteristic probably facilitates the spread of the virus"
If we look at the coronavirus map, we can see that strains G and GR are the most frequent across Europe and Italy. According to the available data, GH strain seems close to non-existence in Italy, while it occurs more frequently in France and Germany. This seems to confirm the effectiveness of last months' containment methods.
In North America the most widespread strain is GH, while in South America we find the GR strain more frequently. In Asia, where the Wuhan L strain initially appeared, the spread of strains G, GH and GR is increasing. These strains landed in Asia only at the beginning of March, more than a month after their spread in Europe.
Globally, strains G, GH and GR are constantly increasing. Strain S can be found in some restricted areas in the US and Spain. The L and V strains are gradually disappearing.
Besides these six main coronavirus strains, researchers identified some infrequent mutations, that, at the moment, are not worrying but should nevertheless be monitored.
"Rare genomic mutations are less than 1% of all sequenced genomes", confirms Giorgi. "However, it is fundamental that we study and analyse them so that we can identify their function and monitor their spread. All countries should contribute to the cause by giving access to data about the virus genome sequences".
This study was published in the journal Frontiers in Microbiology with the title "Geographic and Genomic Distribution of SARS-CoV-2 Mutations". The authors are Daniele Mercatelli and Federico M. Giorgi, both from the Department of Pharmacy and Biotechnology of the University of Bologna.
Prof. Dr. med. Beda Stadler , (* 21. Juni 1950 in Visp) ist ein Schweizer Biologe sowie emeritierter Professor und ehemaliger Direktor des Instituts für Immunologie der Universität Bern. "Das Virus wird langsam harmloser und die ursprünglichen gefährlicheren Stämme verschwinden, genau so wie angenommen."
- Coronaviruses (CoVs) are enveloped positive sense, single-stranded RNA viruses that belong to the subfamily Coronavirinae, family Coronavirdiae, order Nidovirales.
- Four genera of CoVs, namely, Alphacoronavirus (αCoV), Betacoronavirus (βCoV), Deltacoronavirus (δCoV), and Gammacoronavirus (γCoV), are distinguished.
- This group of viruses is of zoonotic origin with αCoV and βCoV found in bats and rodents while δCoV and γCoV are found in avian species.
Structure of SARS-CoV-2
- SARS CoV-2 virus is a betacoronavirus which was discovered in Wuhan City, Hubei Province, China in December 2019.
- They are enveloped, positive-sense, single-stranded RNA viruses of zoonotic origin.
- They are spherical to pleomorphic particles, measuring between 80 and 160 nm in length.
- SARS CoV-2 contains four structural proteins, namely envelope (E), spike (S), membrane (M), and nucleocapsid (N).
- The S, M, and E proteins together form the envelope of the virus. The M protein is the most abundant, mostly responsible for the shape of the envelope. The E protein is the smallest structural protein.
- The S and M proteins are also the transmembrane proteins that are involved in virus assembly during replication.
- N proteins remain associated with the RNA forming a nucleocapsid inside the envelope.
- Although N protein is largely involved in processes relating to the viral genome, it is also involved in other aspects of the CoV replication cycle (assembly and budding) and the host cellular response to viral infection.
- Polymers of S proteins remain embedded in the envelope giving it a crown-like appearance, thus the name coronavirus.
Figure: Structure of SARS-CoV-2, created with biorender.com
Figure: Spike protein conformation of SARS-CoV-2, created with biorender.com
- Spike glycoprotein comprised of S1 and S2 subunits. The S1 subunit contains a signal peptide, followed by an N-terminal domain and receptor-binding domain.
- The S2 subunit contains conserved fusion peptide, heptad repeat 1 and 2, a transmembrane domain, and a cytoplasmic domain.
- The S2 subunit of 2019-nCoV is highly conserved and shares 99% identity with those of the two bats SARS-like CoVs and human SARS-CoV.
- The S1 subunit shares 70% to these CoVs but the core receptor binding domain is highly conserved. These amino-acid differences are responsible for the direct interaction of spike protein with the host receptor.
- Spike glycoprotein binds to the human ACE2 receptor present in the target cells in the respiratory tract. This protein has a compact ridge that allows the virus to attach more strongly than other viruses of the same origin.
- After the spike protein binds with the receptor in the target cell, the viral envelope fuses with the cell membrane and releases the viral genome into the target cell.
Genomic Organization of SARS-CoV-2
Figure: Genomic organization of SARS-CoV-2, created with biorender.com
- The genome of SARS-CoV-2 is a single-stranded positive-sense RNA of 30kb (29891 nucleotides) encoding 9860 amino acids. The G + C content is 38%.
- There are 12 functional open reading frames (ORFs) along with a set of nine subgenomic mRNAs carrying a conserved leader sequence, nine transcription-regulatory sequences, and 2 terminal untranslated regions.
- The genome of this virus lacks the haemagglutinin-esterase gene, which is characteristically found in lineage A βCoV.
- Two-thirds of viral RNA, mainly located in the first ORF translates two polyproteins, pp1a and pp1ab, and encodes 16 non-structural proteins (NSP), while the remaining ORFs encode accessory and structural proteins.
- The 16 non-structural proteins include two viral cysteine proteases, namely, NSP3 (papain-like protease) and NSP5 (main protease), NSP12 (RNA-dependent RNA polymerase, NSP13 (helicase), and other NSPs which are likely involved in the transcription and replication of the virus
- The rest part of the viral genome codes for four structural proteins E, M, S, and E along with a number of accessory proteins that interfere with the host immune response.
- The organization of the coronavirus genome is 5′-leader-UTR-replicase-S (Spike)–E (Envelope)-M (Membrane)-N (Nucleocapsid)-3′UTR-poly (A) tail with accessory genes interspersed within the structural genes at the 3′ end of the genome.
- SARS-CoV-2 is closer to the SARS-like bat CoVs in terms of the whole genome sequence.
- However, mutations are observed in NSP2 and NSP3 and the spike protein, that play a significant role in infectious capability and differentiation mechanism of SARS-CoV-2
- Besides, two strains, namely L-type and S-type, are discovered. It was found that L lineage was more prevalent than the S lineage within the limited patient samples that were examined. The study (https://academic.oup.com/nsr/article/7/6/1012/5775463) states that, “The implication of these evolutionary changes on disease etiology remains unclear”.
- Chan JF, Kok K, Zhu Z, Chu H, To KK, Yuan S and Yuen K (2020). Genomic characterization of the 2019 novel humanpathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan, Emerging Microbes & Infections, 9:1, 221-236, DOI: 10.1080/22221751.2020.1719902
- Xia S, Liu M, Wang C, et al.Inhibition of SARS-CoV-2 (previously 2019-nCoV) infection by a highly potent pan-coronavirus fusion inhibitor targeting its spike protein that harbors a high capacity to mediate membrane fusion. Cell Res 30, 343–355 (2020). https://doi.org/10.1038/s41422-020-0305-x
- Fehr, A. R., & Perlman, S. (2015). Coronaviruses: an overview of their replication and pathogenesis. Methods in molecular biology (Clifton, N.J.), 1282, 1–23. https://doi.org/10.1007/978-1-4939-2438-7_1
- Schoeman, D., Fielding, B.C. Coronavirus envelope protein: current knowledge. Virol J16, 69 (2019). https://doi.org/10.1186/s12985-019-1182-0
- Ou X, Liu Y, Lei X, et al. Characterization of spike glycoprotein of SARS-CoV-2 on virus entry and its immune cross-reactivity with SARS-CoV. Nature Communications (2020) 11:1620 | https://doi.org/10.1038/s41467-020-15562-9
- Guo Y, Cae Q, Hong Z, et al. The origin, transmission and clinical therapies on coronavirus disease 2019 (COVID-19) outbreak – an update on the status. Millitary Medical Reasearch. (2020) 7:11. https://doi.org/10.1186/s40779-020-00240-0
- Adhikari et al. Epidemiology, causes, clinical manifestation and diagnosis, prevention and control of coronavirus disease (COVID-19) during the early outbreak period: a scoping review. Infectious Diseases of Poverty. (2020) 9:29. https://doi.org/10.1186/s40249-020-00646-x
- 9% – https://mmrjournal.biomedcentral.com/articles/10.1186/s40779-020-00240-0
- 3% – https://www.tandfonline.com/doi/pdf/10.1080/22221751.2020.1719902
- 3% – https://www.researchgate.net/publication/264547924_The_Coronavirus_Nucleocapsid_Is_a_Multifunctional_Protein
- 3% – https://cmr.asm.org/content/cmr/28/2/465.full.pdf
- 2% – https://www.tandfonline.com/doi/full/10.1080/22221751.2020.1719902
- 2% – https://www.researchgate.net/publication/339176245_Fusion_mechanism_of_2019-nCoV_and_fusion_inhibitors_targeting_HR1_domain_in_spike_protein
- 1% – https://www.scientificamerican.com/article/researchers-map-structure-of-coronavirus-spike-protein/
- 1% – https://www.sciencedirect.com/science/article/pii/S0378111912011122
- 1% – https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4369385/
- 1% – https://www.ncbi.nlm.nih.gov/books/NBK554776/
- 1% – https://www.cdc.gov/sars/lab/sequence.html
- 1% – https://taskboot.com/2020/03/05/new-coronavirus-mutants-misread-s-subtype-is-actually-the-ancestor-of-l-subtype/
- 1% – https://pubs.acs.org/doi/pdf/10.1021/acsinfecdis.0c00052
- 1% – https://bestpractice.bmj.com/topics/en-gb/3000168/aetiology
- 1% – https://atlanticbusinesssystems.com/2020/04/03/heres-why-the-new-coronavirus-is-so-good-at-infecting-human-cells/
The most troubling thing is coming for scientific researchers. An undeniable fact is that the new coronavirus is still changing in ways we do not know. Compared to the new coronavirus that defeats the SARS virus.
on March 3, Lei Feng News, the National Science Review published an article with the title “On the origin and continuing evolution of SARS-CoV- 2)”. The National Science Review – sponsored by the Chinese Academy of Sciences
In the thesis, a large analysis of the genome-wide molecular evolution of 103 new coronaviruses revealed that there were 149 mutations in virus strain. Of which 101 could be classifieds into two subtypes, L and S. The S type is a relatively older version. While the L subtype is more aggressive and more infectious. By proportion, the L subtype is more common. The L type reaching 70% and the S subtype is 30%.
The new coronavirus maybe divided into two types, not recent mutations
According to the Interface News report, It is noteworthy that the industry media bio-art team analyzed the research of the relevant scientific research team. And said that some media said that ” New coronavirus has been mutated! was misunderstood”. The correct understanding should be this: New coronavirus can be divided into two types, L and S, according to different mutational locations in the genome, but these two types may be present at the early stage of the virus’s spread. And they had not changed recently.
The L subtype is relatively older and closer to the phylogenetic tree from bats to coronaviruses. The s S subtype is more aggressive and contagious but accounts for 30% of the total.
According to reports, the difference between the two subtypes is on the 28144th site of the viral RNA genome. According to leucine Leu, The L is the base of type T. According to Serine Ser S is type C base.
The subtype S is the “ancestor” of the subtype L, has it not been restored?
The L subtype is relatively older and closer to the phylogenetic tree from bats to coronaviruses. The s S subtype is more aggressive and contagious but accounts for 30% of the total. The L subtype is T base, which is equivalent to leucine Leu. And S subtype is C base, which is equivalent to Siren serine Ser
The Public account: Leifeng.com found that the study selected 103 viral genome sequences in total. And also found that 149 mutations in virus strain were-detected with 43 synchronous mutations and 83 errors. Including
- Sense mutation (nonsynonymous mutation)
- 70% of the virus sequences have 7 identical sense mutations, plus 1 identical missense mutation (L84S). Thus affecting the function of the virus’s 6 proteins.
Spectrum analysis of 103 derivative variations of the new Coronavirus strain. Orange is a non-synonymous variable. Green is a synonymous mutation
In this study, 70% of these viruses were-classified with these mutations as the L subtype of SARS Cov2 (L misunderstanding mutant iss derived from L84S). The S84L called the S subtype.
The author of this article believes that according to the evolution of the new coronavirus, There can be a big difference between the transmission capacity and the severity of the L and S subtype.
To further study the relationship between L-type and S-type strains. The researchers reconstructed their phylogenetic tree. This tree based on the entire genome sequence of 103 SARS-Co-2 viruses.
The following further confirmed the differences between L-type and S-type strains
The L subtype is relatively older and closer to the phylogenetic tree from bats to coronaviruses. The s S subtype is more aggressive and contagious but accounts for 30% of the total.
According to the SARS-COV family, the first other virus is S84L. Therefore, research shows that the L subtype that is currently popular derived from the S subtype. And the S subtype is actually the “ancestor” of the L subtype.
It is noteworthy that the research analysis concludes that both subtypes are not reorganizing cycles in nature. SNP analysis further confirmed the classification of this lineage. The 72 virus sequence was T28144, which encodes L. The 29 virus sequences were C28144, which code S. According to leucine Leu, The L is the base of type T. According to Serine Ser S is type C base.
Comparing with other coronaviruses the authors found that the S subtype is closer to the coronavirus originating from the bat on the new coronavirus phylogenetic tree. And the authors concluded that the S subtype is relatively older.
The L subtype was more common in the early stages of the Wuhan outbreak. And the frequency of the L subtype decreased in early January 2020. The authors believe that human intervention can exert more selective pressure on the L subtype. The L subtype may spread more aggressively and rapidly. On the other hand, since selection pressure is relatively weak. Primitive and less aggressive S types can increase in relative frequency.
One very natural reason is that the relatively old S-type new coronavirus should create more stress as it takes longer to spread to people. However, genomic data show that L-type 70% and S-type accounts for 30% and that each strain of L-type causes relatively newborn changes from S-type.
Why does the new coronavirus cause more stress than the young L-type?
The authors speculate that L-type viruses are more capable of spreading or replicating faster in the body. Which may mean they are more virulent.
The authors further compared changes in the proportion of S type and L type before and after January 7. They found that the proportion of L-type decreased in virus strain while that type increased. Regarding this slight change, the author also made his own speculation. Because China has taken stringent anti-pandemic measures. The patients with type L virus are more likely to show symptoms and thus need manual intervention. Is more likely to become a target, thus becoming L. The new type of coronavirus is under more negative selection pressure and the number of infected people decreases.
In addition, these 103 samples showed that most patients were-infected with only one of the L or S subtypes. However, the virus isolated from one of the US patients with recent travel history in Wuhan suggests that they may be infected with both the L and S variants of the new coronavirus. However, the authors say the possibility of new mutations cannot be ruled out at this time.
Overall, this study routinely elucidated the evolutionary dynamics of the virus during human transmission through genome analysis of 103 SARS-CoV-2. At the same time, the authors also stated that these results mean that in 2019, it is imperative to conduct more comprehensive studies by combining genomic data, epidemiological data and chart records of the clinical symptoms of coronavirus patients in 2019. Required.
Where does the New Coronavirus Come from? Does it change?
This is a problem that is of great concern to the general public in the scientific field, and scientific research has been successful.
On March 3, The Chinese Academy of Sciences published a paper entitled “On the origin and continuing evolution of SARS-CoV-2”. This paper is published by Lu Jian and Cui Jie. Lu Jian is a researcher at the Bioinformatics Center of Peking University. And Cui Jie is a researcher at the Chinese Academy of Sciences of Shanghai Pasteur Institute.
The article states that through the analysis of the largest genome of 103 new coronaviruses so far, it has been found that the new coronavirus has recently developed 149 mutation points and developed into two subtypes, 101 belong to both species of sub-types.
New Coronavirus has recently generated 149 mutation points and evolved into two subtypes
An L subtype, which is relatively older and closer to the phylogenetic tree from bats to coronaviruses, accounting for about 70% higher;
The second is the S subtype, which is more aggressive and contagious but accounts for 30% of the total.
According to reports, the difference between the two subtypes is on the 28144th site of the viral RNA genome. The L subtype is T base, which is equivalent to leucine Leu. And S subtype is C base, which is equivalent to Siren serine Ser.
According to this article, according to the evolution of the new Coronavirus. There can be a significant difference between the transmission and the severity of the disease transmission between the L subtype and the S subtype. Of these, the type of L was more common at the beginning of the outbreak in Wuhan. But the human intervention has reduced it since early January this year.
So far, most patients with new coronavirus pneumonia have been affected by only one of this subtype. The virus has been isolated from a recent US patient who moved to Wuhan. Suggesting that they may be affected by both subtypes. But new mutations have not been excluded.
Some experts have commented that this study has a strong guide to the discrimination, prevention and control of new coronavirus artery disease.