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added 8 commits
January 19, 2021 17:42
rando2
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Jan 19, 2021
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Feedback from @SiminaB and my responses to a couple of things. I need to dig into a lot of the deeper comments, and would love to hear what others think (perhaps @LucyMcGowan for the IFR & other modeling questions, @rays1987 and/or @bansalvi for the omics?)
content/07.pathogenesis.md
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| A) The genomic structure of coronaviruses is highly conserved, including the order and organization of genes such as the spike (S), envelope (E), membrane (M) and nucleocapsid (N) proteins. | ||
| B) The physical structure of the coronavirus virion, including the components encoded by conserved genes S, E, M and N. | ||
| B) The physical structure of the coronavirus virion, including the components encoded by conserved genes S, E, M and N. |
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@SiminaB says:
This caption only seems to focus on the 3rd region. Should provide more details for ORF1a and ORF2b. ORF1b has the replicase, but what about the proteases? What are they used for? (I mean, I know they break down proteins, but what does the virus use them for?)
content/07.pathogenesis.md
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| R~0~ and the timescale of infection (measured by the infectious period and the exposed period) govern population-level epidemic dynamics, with R~0~ being one of the most important epidemiological parameters [@isbn:9780691116174]. | ||
| R~0~ is the average number of new (secondary) infections caused by one infected person, assuming a wholly susceptible population [@doi:10.1111/j.1467-9574.1996.tb01482.x]. | ||
| A simple mechanistic model used to describe infectious disease dynamics is a susceptible-infected-recovered (SIR) compartmental model. | ||
| In this formulation individuals move through three states: susceptible, infected, and recovered; two parameters, $\gamma$ and $\beta$, specify the rate at which the infectious recover, and the infection transmission rate, respectively. | ||
| In this simple formulation, R~0~ is estimated as the ratio of $\beta$ and $\gamma$.[@doi:10.1126/science.abb5659; @isbn:9780691116174]. | ||
| A pathogen can invade a susceptible population only if R~0~ > 1 [@isbn:9780691116174; @isbn:9780199209996]. | ||
| A pathogen can invade a susceptible population only if R~0~ > 1 [@isbn:9780691116174; @isbn:9780199209996]. |
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@SiminaB says:
I’m a bit unclear on this. It only takes 1 person to be infected. I know that if Rt < 1 eventually the infectious dies down, but I’m confused on this issue of “invading a susceptible population”.
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I'm tagging @LucyMcGowan, @alavendelm, and @rdvelazquez for help on this one! I think I understand the idea being communicated but I'm not sure exactly how to adjust the phrasing.
content/07.pathogenesis.md
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| R~0~ and the timescale of infection (measured by the infectious period and the exposed period) govern population-level epidemic dynamics, with R~0~ being one of the most important epidemiological parameters [@isbn:9780691116174]. | ||
| R~0~ is the average number of new (secondary) infections caused by one infected person, assuming a wholly susceptible population [@doi:10.1111/j.1467-9574.1996.tb01482.x]. | ||
| A simple mechanistic model used to describe infectious disease dynamics is a susceptible-infected-recovered (SIR) compartmental model. | ||
| In this formulation individuals move through three states: susceptible, infected, and recovered; two parameters, $\gamma$ and $\beta$, specify the rate at which the infectious recover, and the infection transmission rate, respectively. | ||
| In this simple formulation, R~0~ is estimated as the ratio of $\beta$ and $\gamma$.[@doi:10.1126/science.abb5659; @isbn:9780691116174]. | ||
| A pathogen can invade a susceptible population only if R~0~ > 1 [@isbn:9780691116174; @isbn:9780199209996]. | ||
| A pathogen can invade a susceptible population only if R~0~ > 1 [@isbn:9780691116174; @isbn:9780199209996]. |
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Suggested change
| A pathogen can invade a susceptible population only if R~0~ > 1 [@isbn:9780691116174; @isbn:9780199209996]. | |
| A pathogen can invade a susceptible population only if R~0~ > 1 [@isbn:9780691116174; @isbn:9780199209996]. |
rando2
commented
Jan 19, 2021
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AppVeyor build 1.0.2779 for commit 7100491 is now complete.... Found 5 potential spelling error(s). Preview:content/07.pathogenesis.md:1:Symptomatologycontent/07.pathogenesis.md:9:symptomatology content/07.pathogenesis.md:133:ffrom content/07.pathogenesis.md:461:symptomatology content/07.pathogenesis.md:477:symptomatology The rendered manuscript from this build is temporarily available for download at: |
agitter
reviewed
Jan 20, 2021
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AppVeyor build 1.0.2784 for commit 446cabc is now complete. Found 1 potential spelling error(s). Preview:content/07.pathogenesis.md:133:ffrom... |
Co-authored-by: Anthony Gitter <agitter@users.noreply.github.com>
rando2
commented
Jan 21, 2021
content/07.pathogenesis.md
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| R~0~ and the timescale of infection (measured by the infectious period and the exposed period) govern population-level epidemic dynamics, with R~0~ being one of the most important epidemiological parameters [@isbn:9780691116174]. | ||
| R~0~ is the average number of new (secondary) infections caused by one infected person, assuming a wholly susceptible population [@doi:10.1111/j.1467-9574.1996.tb01482.x]. | ||
| A simple mechanistic model used to describe infectious disease dynamics is a susceptible-infected-recovered (SIR) compartmental model. | ||
| In this formulation individuals move through three states: susceptible, infected, and recovered; two parameters, $\gamma$ and $\beta$, specify the rate at which the infectious recover, and the infection transmission rate, respectively. | ||
| In this simple formulation, R~0~ is estimated as the ratio of $\beta$ and $\gamma$.[@doi:10.1126/science.abb5659; @isbn:9780691116174]. | ||
| A pathogen can invade a susceptible population only if R~0~ > 1 [@isbn:9780691116174; @isbn:9780199209996]. | ||
| A pathogen can invade a susceptible population only if R~0~ > 1 [@isbn:9780691116174; @isbn:9780199209996]. |
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I'm tagging @LucyMcGowan, @alavendelm, and @rdvelazquez for help on this one! I think I understand the idea being communicated but I'm not sure exactly how to adjust the phrasing.
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AppVeyor build 1.0.2794 for commit 6214578 is now complete. Found 1 potential spelling error(s). Preview:content/20.pharmaceuticals.md:327:rishirajgoel... |
Co-authored-by: HM Rando <halie.rando@pennmedicine.upenn.edu>
Co-authored-by: HM Rando <halie.rando@pennmedicine.upenn.edu>
Co-authored-by: HM Rando <halie.rando@pennmedicine.upenn.edu>
Co-authored-by: HM Rando <halie.rando@pennmedicine.upenn.edu>
Co-authored-by: HM Rando <halie.rando@pennmedicine.upenn.edu>
Co-authored-by: HM Rando <halie.rando@pennmedicine.upenn.edu>
Co-authored-by: HM Rando <halie.rando@pennmedicine.upenn.edu>
Co-authored-by: HM Rando <halie.rando@pennmedicine.upenn.edu>
Co-authored-by: HM Rando <halie.rando@pennmedicine.upenn.edu>
Co-authored-by: HM Rando <halie.rando@pennmedicine.upenn.edu>
Co-authored-by: HM Rando <halie.rando@pennmedicine.upenn.edu>
Co-authored-by: HM Rando <halie.rando@pennmedicine.upenn.edu>
Co-authored-by: HM Rando <halie.rando@pennmedicine.upenn.edu>
Co-authored-by: HM Rando <halie.rando@pennmedicine.upenn.edu>
Co-authored-by: HM Rando <halie.rando@pennmedicine.upenn.edu>
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AppVeyor build 1.0.2883 for commit 803da23 is now complete. Found 1 potential spelling error(s). Preview:content/07.pathogenesis.md:196:signalling... |
rando2
commented
Jan 24, 2021
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AppVeyor build 1.0.2884 for commit e063fda is now complete. Found 1 potential spelling error(s). Preview:content/07.pathogenesis.md:195:signalling... |
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Thanks for all your responses. These make sense to me, especially the one about the time course of the virus ..much clearer! |
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AppVeyor build 1.0.2890 for commit 3cee000 is now complete. Found 2 potential spelling error(s). Preview:content/07.pathogenesis.md:195:signallingcontent/07.pathogenesis.md:394:IFRs... |
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Hi @bansalvi I saw your comment in my email but can't find it here -- could you open a PR to do that? I can make sure it gets merged in before submission this morning!!! |
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[ci skip] This build is based on 1a0933d. This commit was created by the following CI build and job: https://github.com/greenelab/covid19-review/commit/1a0933d778a86e5047da677f66ee26bab0dd1d83/checks https://github.com/greenelab/covid19-review/runs/509493318
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[ci skip] This build is based on 1a0933d. This commit was created by the following CI build and job: https://github.com/greenelab/covid19-review/commit/1a0933d778a86e5047da677f66ee26bab0dd1d83/checks https://github.com/greenelab/covid19-review/runs/509493318
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Description of the proposed additions or changes
@SiminaB sent me proposed changes by email.
Hopefully this is a faithful representation of all the feedback!
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