Cdominguez Week 11
Purpose
To critically understand and examine the biology of the current Coronavirus pandemic in order to use our scientific knowledge to better understand the mechanisms that govern its infectivity and origin.
Definitions
- angiotensin: family of oligopeptides known for their regulation of blood pressure (BiologyOnline, 2020)
- spike protein: multifunctional molecular machine that mediates entry into host cells (BiologyOnline, 2020)
- iterative:Recital or performance a second time; repetition (BiologyOnline, 2020)
- reiterative:repeating for emphasis or quality (Merriam-Webster, 2020)
- palm civets:type mammal from the civet family that is predominant in South and Southeast Asia (Merriam-Webster, 2020)
- B-genus:beta level is the second stage of the activity and involves the morphology and arrangement of these species into further biological categories of same species (Ernst, 1968)
- envelope-anchored:attached to the envelope (outer layer) of the virus (NCI Dictionary of Cancer Terms, 2020)
- orthologues:Genes related by common phylogenetic descent and usually with a similar organization (Dictionary of Cell and Molecular Biology)
- putative:an entity or a concept that is based on what is generally accepted or inferred even without evidence (BiologyOnline, 2020)
- steric: interference with or inhibition of a seemingly feasible reaction because the size of one or another reactant prevents approach to the required interatomic distance (BiologyOnline, 2020)
Outline
What is the importance or significance of this work?
This work is extremely significant in a time where a global pandemic has consumed all forefronts of every country in the world. 2019-nCOV has proven to be highly infectious and has thus resulted in government regulations to be put in place and life as we know it to greatly change. As scientists and medical professionals look to fight this, understanding more about its origin, transmission, and cell infectivity are crucial to understanding both how to stop its transmission and prevent a pandemic like this again. As vaccines and testing remain important avenues into allowing this virus to be slowed down, understanding the mechanism as to how 2019-nCOV attacks is extremely essential to developing such accurate tests as well as vaccines. Using previous knowledge and research on SARS-CoV to find relationships and significance between the two is an important avenue that is being taken to gage how a previous epidemic was stopped and how this one can be too. This type of work can be argued to be some of the most important scientific work of the time as almost every person in the world in some how effected by this virus and its transmission.
What were the limitations in previous studies that led them to perform this work?
Previous studies focused on SARS-CoV as much research was done on its transmission after the 2002 outbreak. SARS- CoV presents many similarities to 2019-nCOV including symptoms of respiratory distress, animal origin, and B-genus grouping. These studies only focused on SARS-CoV and the affinity between viral RBM and host ACE2. They found two spots that RBM and ACE2 bind as well as amino acid position that allow for the binding of ACE2. They claim to “establish a structure-function predictive framework” for SARS-CoV which allowed them to have credibility in the beginning of looking to 2019-nCOV predictive framework. Overall, the only limitation of previous studies is that it applies to SARS-CoV and not 2019-nCOV, although they do highly base their findings on previous work and their similarities.
How did they overcome these limitations?
Sequencing of 2019-nCOV was released and thus allowed them to be able to compare SARS-CoV to 2019-nCOV. The amount of research done on SARS-CoV was very crucial for them to be able to relate between the two and understand the similarities and differences in their transmission human to human and cross species.
What is the main result presented in this paper? (Hint: look at the last sentence of the introduction and restate it in plain English.)
Their main results relate to understanding the capability of 2019-nCOV’s receptor usage between the spike protein receptor binding domain (RBD) and receptor angiotension-converting enzyme 2 (ACE2). Based on sequencing, they found that 2019-nCOV receptor binding motif (RBM) is like SARS-CoV meaning that it potentially uses ACE2 as receptor. They also found that the finding of residue Glnc493 indicates that interaction between it and ACE2 would be likely. This provides evidence for how 2019-nCOV infects human cells through ACE2. Residue Asn501 indicates that interaction between it and ACE2 is less favorable than Glnc493. This demonstrates the difference found between 2019-nCOV and SARS-CoV where transmission is distinct. They also found that potential animal origin of 2019-nCOV shows potential from a diversity of animals, including but not limited to bats.
What were the methods used in the study?
The methods used for this study are broken up into 3 parts. The first is structural analysis where mutations were made for structural models. The second is phylogenetic analysis where spike phylogenetic tree was made of B-genus coronaviruses . The third was sequence alignment to compare 2019-nCOV and SARS-CoV.
Briefly state the result shown in each of the figures and tables, not just the ones you are presenting.
Figure 1: (A) This is a representation of the structure of SARS-CoV including its core and RBM. There is also the Human ACE2 in order to demonstrate how they interact with one another during viral attachment. (B) This table demonstrates residue changes for both 2019-nCOV and SARS-CoV, which have been shown to determine host range. The five residues, 442, 472, 479. 480, and 487 are along the top of the table were due to natural selection and critical for SARS-CoV infectivity. Residue numbers were different for 2019-nCOV and thus shown in parenthesis. The SARS virus is shown in different species during different years as well as in vitro and viral adaption to human ACE2. The letters in the table represent amino acids are mutations that occurred causing amino acid to change. The >, >>>, or = is indicative of how much more adapted it is for attachment to ACE2. (C) The displays a model of human SARS-CoV optimized RBD and human ACE2. This means that all ACE2 favoring residues were incorporated and showed high affinity with viral RBD allowing for more efficient entry into the cell. (D) The displays a model of 2019-nCOV RBD and human ACE2.
Figure 2: This is a phylogenetic tree of the spike phylogeny of B-genus coronaviruses using GenBank accession number. This was done through aligning protein sequences. It shows that 2019-nCOV is rooted with other bat coronaviruses but has ancestry with SARS-CoV strains.
Figure 3: (A) This is a sequence alignment of 2019-nCOV and SARS-CoV where RBM residues, critical residues, and ACE2 contacting residues are emphasized. It was also looked as how conserved the residues are. The similiarties are 76%-78% for whole protein, 73% for RBD, and 50% for RBM. Most of the ACE2 contacting residues were fully conserved. (B) This table shows the percentage of sequence similarities of SARS-CoV and 2019-nCOV in the spike protein, RBD, and RBM. (C) This table shows sequene similarities between MERS- CoV and HKU4 virus in the spike protein, RBD, and RBM. This shows that although they recognize the same receptor, they have a lower amount of sequence similarities in spike. This offers more prove for why there is strong evidence that SARS-CoV and 2019-nCOV have very similar host infectivity receptors.
Figure 4: (A) This table shows the changes in virus contacting residues of ACE2 from 10 different species. Hot spot 31 and 353 for the civet ACE2 were the two spot that showed the most significant change. These changes are important as they can become optimal for viral binding. (B) A model of SARS-CoV RBD and civet ACE2 to showing optimal binding based on residue changes. (C) A model of human 2019-nCOV RBD and Civet ACE2 with mutations that would allow for binding. However it is shown that it would probably not bind to mouse or rat but would bind pigs, ferrets, cats, bats, orangutans, monkeys, and humans.
How do the results of this study compare to the results of previous studies (See Discussion).
The previous studies relate to this study by using the same predictive modeling in order to apply it for 2019-nCOV. They were able to make these connections by being able to use data from the previous studies on SARS-CoV strains and ACE2 receptors. It is different by now applying this model for the first time to 2019-nCOV. There are two current studies mentioned that also confirmed ACE2 as the host receptor in which this study found that to be consistent. This study was also able to make comparisons on how well SARS-CoV uses ACE2 receptors as compared to 2019-nCOV which can be a critical evaluation on how to implement epidemiological strategies.
What are the important implications of this work?
This work is crucial to this time as more is needed to be learned how exactly the virus infects humans. Most importantly they find that a single mutation can potentially enhance binding which is important to keeping this virus at bay and not allowing for mutations to exacerbate the current situation. They also give a hypothesis on the animal origin given its close relation to bat coronaviruses on the phylogenetic tree. However, there was strong evidence for cross-species adaptability of the RBM residues. The implications of this work are huge as people look to understand where it originated from as to prevent something like this from happening again as well as how to potentially target the virus in vaccines or medicines to stop the viral attachment to ACE2.
What future directions should the authors take?
The paper acknowledges that there should be other factors that should be looked into that can play a part in 2019-nCOV infecting cells. This could be interesting to examine other factors that can play a role in infectivity. Specifically, I have noticed that some cases have been unpredictable with seemingly healthy young people getting extremely sick or dying from 2019-nCOV. This paper makes me wonder if this has anything to do with RBD and ACE2 attachment and how this effected the person. It would be interesting for the authors to consider this as a factor in how bad someone’s symptoms are or if there are genetic predispositions.
Give a critical evaluation of how well you think the authors supported their conclusions with the data they showed.Are there any limitations or major flaws to the paper?
I thought that this paper was mostly well supported. They did a good job of connecting data on SARS-CoV and 2019-nCOV to allow for a model that shows evidence for ACE2 as the receptor. They made good inferences about how the changing of critical residues thus amino acids would effect the ability of ACE2 to bind to RBD. It was not too hard to follow. One limitation of the paper was the lack of methods on how SARS-CoV sequence differences from 2019-nCOV were applied to the optimized 2019-nCOV interfaced with human ACE2 model.
Presentation
Wan_Journal_Club_Presentation_CDDCMP_S2020.pdf
Conclusion
This paper used the similarities of SARS-CoV and 2019-nCoV coronaviruses in order to better understand how 2019-nCoV potentially originated and infects its hosts. Based on their modeling of SARS-CoV, it is very likely that 2019-nCoV uses ACE2 receptor in order to bind to the host. They also found potential links to its origin in bats or civets. Overall, this paper found evidence in their research of SARS-CoV and modeling to predict the mechanism of 2019-nCoV.
Acknowledgments
- I worked with user:Dcartmel and user:Mpaniag1 where we met via Zoom to work on the presentation for this week.
- Except for what is noted above, this individual journal entry was completed by me and not copied from another source.
Cdominguez (talk) 13:26, 3 April 2020 (PDT)
References
- Biology Online. (2020). Angiotensin. Retrieved April 3, 2020, from https://www.biologyonline.com/dictionary/angiotensin.
- Biology Online. (2020). Spikeprotein. Retrieved April 3, 2020, from https://www.biologyonline.com/dictionary/spikeprotein.
- Biology Online. (2020). Putative. Retrieved April 3, 2020, from https://www.biologyonline.com/dictionary/putative.
- Biology Online. (2020). Iteration. Retrieved April 3, 2020, from https://www.biologyonline.com/dictionary/iteration.
- Biology Online. (2020). Steric. Retrieved April 3, 2020, from https://www.biologyonline.com/dictionary/steric.
- Dictionary of Cell and Molecular Biology eBook. (2020). Orthologues. Retrieved April 5, 2020, from https://electra.lmu.edu:2110/lib/lmu/reader.action?docID=311420.
- Mayr, Ernst (9 February 1968), "The Role of Systematics in Biology: The study of all aspects of the diversity of life is one of the most important concerns in biology", Science, 159 (3815), pp. 595–599, Bibcode:1968Sci...159..595M, doi:10.1126/science.159.3815.595.
- Merriam-Webster. (2020). Reiteration. Retrieved April 5, 2020, from https://www.merriam-webster.com/thesaurus/reiteration.
- Merriam-Webster. (2020). Palm Civet. Retrieved April 5, 2020, from https://www.merriam-webster.com/dictionary/palm%20civet.
- NCI Dictionary of Cancer Terms. (2020). Enveloped-vurs. Retrieved April 5, 2020, from https://www.cancer.gov/publications/dictionaries/cancer-terms/def/enveloped-virus.
- OpenWetWare. (2020). BIOL368/S20:Week 11. Retrieved April 3, 2020, from https://openwetware.org/wiki/BIOL368/S20:Week_11.
- Wan, Y., Shang, J., Graham, R., Baric, R. S., & Li, F. (2020). Receptor recognition by the novel coronavirus from Wuhan: an analysis based on decade-long structural studies of SARS coronavirus. Journal of virology, 94(7). DOI: 10.1128/JVI.00127-20.
