What is SARS-CoV2 from Genetics perspective and how did it evolve from animal to human?

by PQE Group’s Infodemic Research Team 

Topic: Science

Researchers:
Valentina Izzo, Project Manager
Madan Lal, Consultant

Abstract

The most significant component of a virus is its DNA/RNA, as it is essential for carrying information, its replication and survival in the host. Understanding the genome of SARS-CoV 2 becomes a priority among researchers, since it can give information about its mechanisms of action, which in turn might lead to the treatment of the resulting infection and its related complications but also to the possible development of effective vaccines.

ACE2 Receptor on human cells are normally expressed on the epithelium of many internal organs, such as heart, blood vessels and lungs, especially on some epithelial cells of pulmonary alveoli, where the gas exchanges occur. It is likely the way the virus infects humans. Earliest known cases of infection had a link to a wholesale live food market in Wuhan City in China, suggesting that this specific place could have been the source of this outbreak, where the virus probably spilled over from an animal to a human. Knowing how the virus genome evolved and became a threat for humans is puzzling the researchers all over the world, since knowing how a pandemic starts is a key to prevent the next one. Genetic similarity of SARSCoV-2 to Bat SARS-CoV-like coronaviruses, indicates the likelihood of bats as reservoir hosts for its progenitor. However, SARSCoV-2 passed through an intermediary animal, as the outbreak in 2002 did, from horseshoe bats to civet cats and then humans.

Besides this, different possible explanations of SARS-CoV-2 origins and transmission to human from animals are here presented.

Keywords

ACE (Angiotensin-Converting Enzyme) RBD (Receptor Binding Domain) RaTG13 (one of the bat SARS-related coronaviruses).

What is SARS-CoV2 from a Genetics Perspective?

SARS-CoV 2 mechanisms of action is dependent on the presence of angiotensin-converting enzyme 2 (ACE2 Receptor) on human cells.

ACE2 is normally expressed on the epithelium of many internal organs, such as lungs, heart and blood vessels and it is normally involved in critical biochemical pathways such as blood pressure regulation, wound healing and inflammation. In particular, ACE2 is highly expressed on pneumocytes which are the epithelium cells of pulmonary alveoli, where the exchange between oxygen and carbon dioxide takes place.

Figure 1: ACE2 protein is expressed on external surface of many internal organs, such as lungs, heart and blood vessels. SARS-CoV 2 Spike protein is genetically designed to interact with ACE2. After this interaction, the epithelium is able to change its structure, fold around the virus and include it within the organ, where it starts to replicate and infect the host as well as blocking normal ACE2 functions. (The Conversation, CC BY-SA)

Once in human body, it has been shown that SARS-CoV 2 can specifically bind ACE2 receptor on the surface of epithelial cells using the protein called “Spike”, thus entering into the cell and starting the infection. A specific section of Spike called RBD, is responsible for the modulation of the interaction with ACE2 receptor. In fact this is the most variable part of the coronavirus genome, and the amino acids (building block of proteins) of this section have been shown to be critical for binding to ACE2 receptors and for determining the host susceptibility.
The mechanism is similar to a Key and Lock interaction: while Spike protein is the key, the ACE2 Receptor is the lock to enter human cells. Then the infection triggers an impairment of processes normally mediated through the receptor, precipitates inflammatory processes and alveoli cells death, eventually reducing the amount of oxygen brought into the body, as shown in Figure 1 and Figure 2. In Coronaviruses, Spike gene is not only very important as the most variable part of the viral genome, but it can be used to better classify the viruses. In fact, even a small mutation to Spike gene can determine a big change in the protein structure, changing how the viral particle attaches to receptors in human cells (hence the specificity towards a particular cell). Analyses of SARS-CoV 2 Spike gene have demonstrated that its unique structure creates bonds with the human receptor four times stronger than those of other coronaviruses, which could be one of the reasons why the new coronavirus is so highly contagious [1].

Figure 2: Once entered in the cell through the interaction between ACE2 and Spike, SARS CoV2 RNA is released from the virus and, using the host proteins and organelles, the information encoded in it is translated in viral proteins. These proteins are able to assemble again in new structures (Vesicles) containing copies of RNA and membrane proteins. Through the Exocytosis, perfect copied of the initial virus are released again, ready to infect other cells

Understanding SARS-CoV-2 genome is crucial to understand its mechanisms of action, not only to possibly fight the resulting infection and related complications, but also to develop potentially effective vaccines.
Europe has recently funded the GEFACOVID project (Analysis of Genetic Factors influencing infection with SARS-CoV 2 and progression of COVID-19). A consortium of universities, and private companies from Europe, China, India and other countries, will investigate SARS-CoV 2 genome and the human genetic characteristics influencing host susceptibility to the infection, the involvement of immune response and the risk of life-threatening complication.

Mutations in the receptor-binding domain of SARS-CoV 2

As above mentioned, the RBD portion of the Spike protein is the most variable part of the coronavirus genome. Computational analyses predicted that the interaction between RBD of SARS-CoV 2 and human ACE2 is not ideal and that the RBD sequence is different from those shown in SARS-CoV to be optimal for receptor binding. Thus, the high-affinity binding of the SARS-CoV-2 Spike protein to human ACE2 is most likely the result of natural selection on a human or human-like ACE2 that permits another optimal binding solution to arise. This evidence supports that SARS-CoV-2 is not the product of purposeful manipulation [2][3].

How did SARS-CoV2 evolve from animal to human?

First reported case of SARS-CoV2 by officials in Wuhan City, China, was on December 26th 2019. Earliest known cases had a link to a wholesale food market in Wuhan. Many of the initial patients were either stall owners, market employees, or regular visitors to this market [4].
Possible mechanism of SARS-CoV-2 origins and transmission from market animals to human could be:

  1. Natural selection in an animal host before zoonotic transfer.

    Genetic studies have revealed similarity of SARS-Cov-2 to bat SARS-CoV-like coronaviruses like RaTG13. Hence there is a high probability that bats serve as reservoir hosts for its progenitor. Although RaTG13 is ~96% identical to SARS-CoV-2, its Spike deviates in region RBD of the protein, which suggests that it may not bind efficiently to human ACE2 [1], [5].
    On the other hand, it has been shown that Malayan pangolins illegally imported in China contain coronaviruses similar to SARS CoV-2, especially between their RBD region and SARS-CoV-2 one [2],[6].
    RaTG13 virus still remains the closest to SARS-CoV-2, nevertheless similarly with pangolin coronavirus suggest that the SARS-CoV-2 spike protein increased affinity to human-like ACE2 may be the result of natural selection[6]. Further mutations might occur in the Spike protein by a natural evolutionary processed, among which a particular region, called polybasic cleavage site, is shown to be mutated and play a role in determining viral infectivity and host range[7].

    Figure 3: Possible natural selection in an animal host before zoonotic transfer describe, probably bats serve as natural reservoir hosts for its progenitor (based on genomic similarity) there might be intermediate host which is unknown and from unknown source it transferred to human and Couse pandemic
  2. Natural selection in humans after zoonotic transfer.

    The possible progenitor of SARS-CoV-2 then jumped into humans, acquiring the genomic features through adaptation during undetected human-to-human transmission. Once acquired, these adaptations would enable the pandemic to take off and produce a sufficiently large cluster of cases to trigger the surveillance system which detected it. Further serological studies should be conducted to determine the extent of prior human exposure to SARS-CoV-2[5].

    Figure 4: Natural selection in human after zoonotic transfer. It describes that when virus enter in human body, it acquires the genomic features through adaptation during undetected human to-human transmission, causing pandemic.
    Picture Source: Muhammad Adnan Shereen, Suliman Khan, Abeer Kazmi, Nadia Bashir, Rabeea Siddiquea, The Department of Cerebrovascular Diseases, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, PR China b State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, PR China College of Life Sciences, Wuhan University, Wuhan, PR China Journal of Advanced Research 24 (2020) 91–98.
  3. Selection during passage.

    Basic research been ongoing for many years across the world, therefore possibility of an inadvertent laboratory release of SARS-CoV-2 cannot be ruled out completely. In theory, it is possible that SARS-CoV-2 acquired RBD mutations during adaptation to passage in cell culture. Although possible, the finding of pangolin SARS-CoV like viruses with nearly identical RBDs, would suggest otherwise, requiring a more meaningful explanation of how SARS-CoV-2 acquired these RBD via in-vitro recombination or mutation[8] [9]. Furthermore, a hypothetical generation of SARS-CoV-2 by cell culture or animal passage would have required prior isolation of a progenitor virus with very high genetic similarity, which has not been described[5] [10].

  4. Phylogenetic Analyses

    Other research suggested SARS-CoV2 was the recombinant virus of bat coronavirus and snake coronavirus, by comparison in conjunction with relative synonymous codon usage bias among different animal species[11].

    Figure 5: phylogenetic analyses shows, Bat as probable animal reservoir. Based on genome sequencing matching, SARS-CoV2 is 89% similar to Bat, 82% to Human SARS-CoV1, and 50% similar to MERS-CoV [10]. Both SARS-CoV1 and MERS-CoV were transmitted through intermediate to humans, in case of SARS-CoV2 Pangolins were suggested as the possible intermediate hosts, because their genome had approximately 85.5%-92.4% [11]

Conclusion

As the virus is new to the world and the outbreak of SARS-CoV-2 has caused severe damages at all levels, understanding its genetics, origin, evolution and transmission to humans becomes a prime necessity. Based on available data there is no specific evidence available to prove the exact origin of SARS-CoV-2. Further investigation is required to have a broader and deeper knowledge. Investigation shall be focused on ‘how and why’ it happened, not on “what” happened. Country leaders should pay more attention, share more initial information about the origin and be more inclusive in the fight against such a virus. Only working together with proper knowledge, scientists all over the word could identify origin’s virus, and, in this way, the process of a vaccine development could be speed up.

References:

[1] J. Shang et al., “Structural basis of receptor recognition by SARS-CoV-2,” Nature, vol. 581, no. 7807, pp. 221–224, May 2020, doi: 10.1038/s41586-020-2179-y.

[2] Y. Wan, J. Shang, R. Graham, R. S. Baric, and F. Li, “Receptor Recognition by the Novel Coronavirus from Wuhan: an Analysis Based on Decade-Long Structural Studies of SARS Coronavirus,” J. Virol., 2020, doi: 10.1128/jvi.00127-20.

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[4] F. Wu et al., “A new coronavirus associated with human respiratory disease in China,” Nature, 2020, doi: 10.1038/s41586-020-2008-3.

[5] P. Zhou et al., “A pneumonia outbreak associated with a new coronavirus of probable bat origin,” Nature, 2020, doi: 10.1038/s41586-020-2012-7.

[6] T. Zhang, Q. Wu, and Z. Zhang, “Pangolin homology associated with 2019-nCoV,” bioRxiv, 2020, doi: 10.1101/2020.02.19.950253.

[7] Y. Yamada and D. X. Liu, “Proteolytic Activation of the Spike Protein at a Novel RRRR/S Motif Is Implicated in Furin-Dependent Entry, Syncytium Formation, and Infectivity of Coronavirus Infectious Bronchitis Virus in Cultured Cells,” J. Virol., 2009, doi: 10.1128/jvi.00613-09.

[8] T. Sheahan et al., “Mechanisms of Zoonotic Severe Acute Respiratory Syndrome Coronavirus Host Range Expansion in Human Airway Epithelium,” J. Virol., 2008, doi: 10.1128/jvi.02041-07.

[9] J. Cui, F. Li, and Z. L. Shi, “Origin and evolution of pathogenic coronaviruses,” Nature Reviews Microbiology. 2019, doi: 10.1038/s41579-018-0118-9.

[10] T. Ito et al., “Generation of a Highly Pathogenic Avian Influenza A Virus from an Avirulent Field Isolate by Passaging in Chickens,” J. Virol., 2001, doi: 10.1128/jvi.75.9.4439-4443.2001.

[11] W. Ji, W. Wang, X. Zhao, J. Zai, and X. Li, “Cross-species transmission of the newly identified coronavirus 2019-nCoV,” J. Med. Virol., 2020, doi: 10.1002/jmv.25682.

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