Steps for Pathogenesis Manuscript Submission

[rando2]

1. Organize into standalone paper: Proposed content of pathogenesis/transmission manuscript #745 ✅
2. Standalone title & abstract: Proposed abstract & title for pathogenesis manuscript #746 ✅
3. Incorporate @byrdjb feedback: Suggestions & Edits from @byrdjb (should be quick to review) #747 ✅
4. Add figure: Add @nilswellhausen's genome structure figure #758 ✅
5. Confirm text with authors ✅
6. Check references (see issue Update reference list prior to manuscript submission #761)
7. Finalize author list Add author order & contributions for Pathogenesis ms #797 (and pending confirmation from a few authors) ✅
8. Final check of text (hopefully not too much changes here! 🤞 ) ✅
9. Generate manuscript for submission (see issue Build stand-alone pathogenesis manuscript  #762) ✅

Questions:

• UK "more contagious" strain (relevant twitter thread)
  • may be able to deal with in evolution section as the data becomes more clear?
  • Address in evolution (Rough outline of evolution manuscript #760)
• Is anything else out of date or missing?

[rando2]

First pass at named author list for pathogenesis

If you are tagged here, please please please let me know what you think about the PRs listed above (PR reviews & approvals especially appreciated!) and please feel free to give feedback on the manuscript. We'd love to get this out ASAP since there has been a TON of collaboration on this and there is a lot of great content here!

I dug through the commit history for this section (pathogenesis) to try to approximate the named authors for this section along with a vague author order. @cgreene has suggested that we will probably end up grouping people into approximate tiers and then randomizing within groups. For this analysis, I ignored commits by @cgreene, @agitter, and myself, because there were just far too many!

These aren't exact because for people who had a large number of contributions, I only categorized the bigger ones that affected several lines -- but here is a rough outline of how we might want to approach author order. The numbers are the number of lines edited by PRs (so if you are someone who had trouble remembering to put each sentence on a separate line, please make sure I accurately estimated your writing!):

Contributor	Edits	Additions	Edits & Additions	Formatting	Outlining	Total Lines	Tier	Role	Approved (date)
@alavendelm	105	26	18		10	159	1	Led infection modeling	pending #790
@ajlee21	29	45	5	5	35	119	1	Led virology	Jan (#784)
@bansalvi	52	55	38	7		152	2	Co-led omics	Jan
@rays1987	5	51	28	4		92	2	Co-led omics	Jan
@anskelly	22	30				52	3	Virology	Jan
@LucyMcGowan	20		28			48	3	Infection Modeling	Jan
@dziakj1*	14	11	15	3		43	3	Symptoms	Jan
@marouenbg	14	16	6	2		38	3	Omics	Jan
@LSH2126	9	34		8		51	3	Immunology	Jan
@scapone01							3	Clinical Presentation	Nov
@ypar			69			70	3	Virology	Yes (but may provide feedback today)
@esell17		29				29	3	Virology	Jan
@Sergey-Knyazev	19	17				36	4	Omics	Jan
@davemai	4		11		4	19	4	Virology	Jan
@SiminaB	60					60	5	Editing	pending #789
@cbrueffer	24	5		10		39	5	Editing/refining	11-11
@jinhui2	10	1				11	5	Virology	Jan
@rdvelazquez	6		3			9	5	infection modeling	Jan
@byrdjb		5				5	5	Symptoms	Jan
@nilswellhausen		2			24	26	5	virology	Jan
@lubianat	32					32	6	Editing	#782
@johnbarton	11					11	6	Editing	11-11
@gregszetoAI	8					8	6	Editing	11-16
@rishirajgoel	5					5	6	Editing	1-20
@RLordan	2			2		4	6	Editing	Jan
@smangul1	19	17				36	6	Editing	11-11
rmrussell	12					12	ack by request	Virology	N/A
yemarshall						94	ack by request	Virology	N/A
@cgreene	24					208	Not analyzed	Editing, Technical & Administration	is doing the submitting
@agitter						32	Not analyzed	Editing, Technical & Administration	Jan (#783)
@rando2						2083	Not analyzed	Writing, Editing, Admin	Will do final proofing!

(* @dziakj1 has said he doesn't have a lot of bandwidth this semester and would be happy to be moved to acknowledgements -- I'm happy to do that if it's what you want, but you've already put so much work into this project that I just wanted to note that all we really need is thumbs-up level responses from you at this point! It's totally up to you which you'd prefer.)

Please feel free to review and let me know if you think I missed something -- there is a LOT that went into this paper and it's definitely possible something is off! If you worked on this section (#745) and don't see your name here or you feel like something was skipped over in assigning credit, please let me know! (@rdvelazquez, this is just based on your text contribution, not the technical side which was obviously huge -- @cgreene and I are thinking about exactly what we need to do to make sure you and @agitter are properly recognized for everything you did on getting things to run!)

Commits used to generate this table:
gitlogcommits.02.introduction.xlsx
gitlog.02.introduction.xlsx

PS: Obviously these are subject to change and will be re-computed for the final version!

[dziakj1]

Thank you very much @rando2 ! I could give thumbs-up/thumbs-down responses.

[dziakj1]

Dear Halie, I approve of the pathogenesis draft - please let me know if you need anything else. I do think it would be good to add extra info on the new strains from the United Kingdom and from South Africa. Thanks, John

[rando2]

@dziakj1 Thank you so much! I am curious what @Sergey-Knyazev thinks, but I was thinking we might just want to discuss new variants in the evolution section -- although I agree it could also go here! Good luck with everything!

[dziakj1]

Thank you! P.S. I also saw a very recent review you might want to cite: https://www.researchgate.net/publication/348003487_Multifaceted_highly_targeted_sequential_multidrug_treatment_of_early_ambulatory_high-risk_SARS-CoV-2_infection_COVID-19

[Sergey-Knyazev]

Dear Dr. Rando, I am happy with this plan, I will also work on the part in the manuscript that we discussed recently. Thank you! Sergey

…

On Fri, Jan 8, 2021 at 4:09 PM HM Rando ***@***.***> wrote: First pass at named author list for pathogenesis If you are tagged here, please please please let me know what you think about the PRs listed above (PR reviews & approvals especially appreciated!) and please feel free to give feedback on the manuscript. We'd love to get this out ASAP since there has been a TON of collaboration on this and there is a lot of great content here! I dug through the commit history for this section (pathogenesis) to try to approximate the named authors for this section along with a vague author order. @cgreene <https://github.com/cgreene> has suggested that we will probably end up grouping people into approximate tiers and then randomizing within groups. For this analysis, I ignored commits by @cgreene <https://github.com/cgreene>, @agitter <https://github.com/agitter>, and myself, because there were just far too many! These aren't exact because for people who had a large number of contributions, I only categorized the bigger ones that affected several lines -- but here is the rough logic used to estimate author order: Contributor Edits Additions Edits & Additions Formatting Outlining Total Lines Tier Role @alavendelm <https://github.com/alavendelm> 105 26 18 10 159 1 Led infection modeling @ajlee21 <https://github.com/ajlee21> 29 45 5 5 35 119 1 Led virology @bansalvi <https://github.com/bansalvi> 52 55 38 7 152 2 Co-led omics @rays1987 <https://github.com/rays1987> 5 51 28 4 92 2 Co-led omics @anskelly <https://github.com/anskelly> 22 30 52 3 Virology @LucyMcGowan <https://github.com/LucyMcGowan> 20 28 48 3 Infection Modeling @dziakj1 <https://github.com/dziakj1>* 14 11 15 3 43 3 Symptoms @marouenbg <https://github.com/marouenbg> 14 16 6 2 38 3 Omics @LSH2126 <https://github.com/LSH2126> 9 34 8 51 3 Immunology @ypar <https://github.com/ypar> 69 70 3 Virology @esell17 <https://github.com/esell17> 29 29 3 Virology @Sergey-Knyazev <https://github.com/Sergey-Knyazev> 19 17 36 4 Omics @davemai <https://github.com/davemai> 4 11 4 19 4 Virology @SiminaB <https://github.com/SiminaB> 60 60 5 Editing @cbrueffer <https://github.com/cbrueffer> 24 5 10 39 5 Editing/refining @jinhui2 <https://github.com/jinhui2> 10 1 11 5 Virology @rdvelazquez <https://github.com/rdvelazquez> 6 3 9 5 infection modeling @byrdjb <https://github.com/byrdjb> 5 5 5 Symptoms @nilswellhausen <https://github.com/nilswellhausen> 2 24 26 5 virology @lubianat <https://github.com/lubianat> 32 32 6 Editing @johnbarton <https://github.com/johnbarton> 11 11 6 Editing @gregszetoAI <https://github.com/gregszetoAI> 8 8 6 Editing @rishirajgoel <https://github.com/rishirajgoel> 5 5 6 Editing @RLordan <https://github.com/RLordan> 2 2 4 6 Editing rmrussell 12 12 ack by request Virology yemarshall 94 ack by request Virology @cgreene <https://github.com/cgreene> 24 208 Not analyzed Editing, Technical & Administration @agitter <https://github.com/agitter> 32 Not analyzed Editing, Technical & Administration @rando2 <https://github.com/rando2> 2083 Not analyzed Writing, Editing, Admin (* @dziakj1 <https://github.com/dziakj1> has said he doesn't have a lot of bandwidth this semester and would be happy to be moved to acknowledgements -- I'm happy to do that if it's what you want, but you've already put so much work into this project that I just wanted to note that all we really need is thumbs-up level responses from you at this point! It's totally up to you which you'd prefer.) Please feel free to review and let me know if you think I missed something -- there is a LOT that went into this paper and it's definitely possible something is off! If you worked on this section (#745 <#745>) and don't see your name here or you feel like something was skipped over in assigning credit, please let me know! ***@***.*** <https://github.com/rdvelazquez>, this is just based on your text contribution, not the technical side which was obviously huge -- @cgreene <https://github.com/cgreene> and I are thinking about exactly what we need to do to make sure you and @agitter <https://github.com/agitter> are properly recognized for everything you did on getting things to run!) Commits used to generate this table: gitlogcommits.02.introduction.xlsx <https://github.com/greenelab/covid19-review/files/5789342/gitlogcommits.02.introduction.xlsx> gitlog.02.introduction.xlsx <https://github.com/greenelab/covid19-review/files/5789347/gitlog.02.introduction.xlsx> — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#744 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABLLHXZ7APH2AJDYSCZRSJTSY5YAXANCNFSM4VEKALWA> .

-- Thank you! Sergey Knyazev, Ph.D. student at Georgia State University, Computer Science Department, Bioinformatics laboratory; ORISE fellow at CDC, Division of HIV/AIDS Prevention.

[nilswellhausen]

Dear Halie,

I reviewed and approved the pathogenesis section. Please let me know if there is anything I can help with. This collaboration has been a blast.

Best,
Nils

[dziakj1]

P.S. I guess you could consider mentioning yesterday's article about asymptomatic transmission:
https://jamanetwork.com/journals/jamanetworkopen/fullarticle/2774707
It's not really an empirical study but it was a warm heaping delivery of bad news in case anybody needed more of that.

[byrdjb]

Hi, I’m struggling a little because I don’t see PRs listed above. I think it’s because I’m looking at an email, and that is probably structured around the way it looks in GitHub. But I’m not sure how to find the right link in GitHub. Sorry I’m not more facile with GitHub :grimace:

[SiminaB]

@byrdjb: I think @rando2 is referring to the PRs in the first post at #744
@rando2: It seems like those PRs have been reviewed and only have suggested changes from 1/3 reviewers. Let us know how else we can help.

[marouenbg]

Hi @rando2 ,

Sounds good to me. Glad to see the first piece of this project coming together so nicely.

Cheers,

[bansalvi]

Hi @rando2 <https://github.com/rando2> Looks good to me :) Best, Vikas

…

On Mon, Jan 11, 2021 at 11:39 AM Marouen ***@***.***> wrote: Hi @rando2 <https://github.com/rando2> , Sounds good to me. Glad to see the first piece of this project coming together so nicely. Cheers, — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#744 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AMLWRN2ESPRYJQJVN3YYKWDSZKI3DANCNFSM4VEKALWA> .

[rays1987]

Dear Halie, That's great. Many thanks for this update. Sounds good. Best regards, Sandipan

…

________________________________ From: HM Rando <notifications@github.com> Sent: Friday, January 8, 2021 4:09 PM To: greenelab/covid19-review <covid19-review@noreply.github.com> Cc: Ray, Sandipan <Sandipan.Ray@pennmedicine.upenn.edu>; Mention <mention@noreply.github.com> Subject: [External] Re: [greenelab/covid19-review] Steps for Pathogenesis Manuscript Submission (#744) First pass at named author list for pathogenesis If you are tagged here, please please please let me know what you think about the PRs listed above (PR reviews & approvals especially appreciated!) and please feel free to give feedback on the manuscript. We'd love to get this out ASAP since there has been a TON of collaboration on this and there is a lot of great content here! I dug through the commit history for this section (pathogenesis) to try to approximate the named authors for this section along with a vague author order. @cgreene<https://github.com/cgreene> has suggested that we will probably end up grouping people into approximate tiers and then randomizing within groups. For this analysis, I ignored commits by @cgreene<https://github.com/cgreene>, @agitter<https://github.com/agitter>, and myself, because there were just far too many! These aren't exact because for people who had a large number of contributions, I only categorized the bigger ones that affected several lines -- but here is the rough logic used to estimate author order: Contributor Edits Additions Edits & Additions Formatting Outlining Total Lines Tier Role @alavendelm<https://github.com/alavendelm> 105 26 18 10 159 1 Led infection modeling @ajlee21<https://github.com/ajlee21> 29 45 5 5 35 119 1 Led virology @bansalvi<https://github.com/bansalvi> 52 55 38 7 152 2 Co-led omics @rays1987<https://github.com/rays1987> 5 51 28 4 92 2 Co-led omics @anskelly<https://github.com/anskelly> 22 30 52 3 Virology @LucyMcGowan<https://github.com/LucyMcGowan> 20 28 48 3 Infection Modeling @dziakj1<https://github.com/dziakj1>* 14 11 15 3 43 3 Symptoms @marouenbg<https://github.com/marouenbg> 14 16 6 2 38 3 Omics @LSH2126<https://github.com/LSH2126> 9 34 8 51 3 Immunology @ypar<https://github.com/ypar> 69 70 3 Virology @esell17<https://github.com/esell17> 29 29 3 Virology @Sergey-Knyazev<https://github.com/Sergey-Knyazev> 19 17 36 4 Omics @davemai<https://github.com/davemai> 4 11 4 19 4 Virology @SiminaB<https://github.com/SiminaB> 60 60 5 Editing @cbrueffer<https://github.com/cbrueffer> 24 5 10 39 5 Editing/refining @jinhui2<https://github.com/jinhui2> 10 1 11 5 Virology @rdvelazquez<https://github.com/rdvelazquez> 6 3 9 5 infection modeling @byrdjb<https://github.com/byrdjb> 5 5 5 Symptoms @nilswellhausen<https://github.com/nilswellhausen> 2 24 26 5 virology @lubianat<https://github.com/lubianat> 32 32 6 Editing @johnbarton<https://github.com/johnbarton> 11 11 6 Editing @gregszetoAI<https://github.com/gregszetoAI> 8 8 6 Editing @rishirajgoel<https://github.com/rishirajgoel> 5 5 6 Editing @RLordan<https://github.com/RLordan> 2 2 4 6 Editing rmrussell 12 12 ack by request Virology yemarshall 94 ack by request Virology @cgreene<https://github.com/cgreene> 24 208 Not analyzed Editing, Technical & Administration @agitter<https://github.com/agitter> 32 Not analyzed Editing, Technical & Administration @rando2<https://github.com/rando2> 2083 Not analyzed Writing, Editing, Admin (* @dziakj1<https://github.com/dziakj1> has said he doesn't have a lot of bandwidth this semester and would be happy to be moved to acknowledgements -- I'm happy to do that if it's what you want, but you've already put so much work into this project that I just wanted to note that all we really need is thumbs-up level responses from you at this point! It's totally up to you which you'd prefer.) Please feel free to review and let me know if you think I missed something -- there is a LOT that went into this paper and it's definitely possible something is off! If you worked on this section (#745<#745>) and don't see your name here or you feel like something was skipped over in assigning credit, please let me know! (@rdvelazquez<https://github.com/rdvelazquez>, this is just based on your text contribution, not the technical side which was obviously huge -- @cgreene<https://github.com/cgreene> and I are thinking about exactly what we need to do to make sure you and @agitter<https://github.com/agitter> are properly recognized for everything you did on getting things to run!) Commits used to generate this table: gitlogcommits.02.introduction.xlsx<https://github.com/greenelab/covid19-review/files/5789342/gitlogcommits.02.introduction.xlsx> gitlog.02.introduction.xlsx<https://github.com/greenelab/covid19-review/files/5789347/gitlog.02.introduction.xlsx> — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub<#744 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AO5KTRMORN7VYZGS2ECY54LSY5YAZANCNFSM4VEKALWA>.

[rando2]

All major PRs have been merged in, in case anyone wants to take a look at the final proposed text! @alavendelm and @SiminaB are both taking a look, and I will do a final read-through next week to clean up abbreviations, grammar, etc. We're getting so close!

Also, this is a note to myself to make sure @nilswellhausen gets authorship credit for his amazing genome/viral structure figure!

[rdvelazquez]

Hi @rando2,
The pathogenesis manuscript looks good to me I opened two minor pull requests (#772 and #781) with suggested edits but they are both minor and the section can definitely be published without them. Congrats to everyone on completing the first section! 🎉
Best,
Ryan

[rando2]

OK! Looking through final approvals, I just wanted to double-check (thumbs up are fine, or comment/reach out if there are issues!)
@ajlee21, @agitter: I'm assuming you are OK with the manuscript since your PRs proofing it merged, but just wanted to confirm!
@SiminaB, @alavendelm, @lubianat: Once the PRs with your edits merge, is there anything else you want to see addressed? (I'm assuming that was the bulk of your concerns but just want to be sure!)
@RLordan: You've given tons of feedback on everything but I just wanted to give you a chance to speak up if you aren't okay with it getting submitted!

[RLordan]

Looks great @rando2 thank you!

[ajlee21]

Thank @rando2 looks great to me too!

[SiminaB]

Same here!

[rando2]

Happy to report that @cgreene submitted this manuscript earlier this afternoon! 🎉 I believe you should have received an email from mSystems confirming. I'll keep everyone updated on what happens! Thank you all SO much for all of your work getting this out -- this was a huge piece of the review that connects several different fields, and it's been so amazing working with all of you to see how it all comes together!

[dziakj1]

Thank you! I got the email! Thank you for coordinating this.

[cgreene]

I clicked the button but, wow, this manuscript was a truly remarkable amount of work! I'm excited to see this continue to move forward! 🚀 Also, this is an experiment for the journal in that these will be "living" documents that we can continue to update and improve.

[RLordan]

Thank you all, great achievement!

[bansalvi]

That's great. It was really fun working online with Manubot. Great teamwork. Best wishes, Vikas

…

On Mon, Jan 25, 2021 at 11:18 PM RLordan ***@***.***> wrote: Thank you all, great achievement! — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#744 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AMLWRN3XHWERHR5AN72MCA3S3XUZZANCNFSM4VEKALWA> .

[agitter]

I added the tag pathogenesis-v1 to the output branch commit that contains the submitted docx. If we need to get the corresponding source commit, it is in the commit message of the tagged commit.

[cgreene]

This is now available on arXiv, and I've tweeted out a thread if folks want to share. Tweet your own and post here and I'm happy to retweet too.

https://twitter.com/GreeneScientist/status/1356943381453287426?s=20

Also, we'll get the arXiv paper password sent out so those of you who want to can claim the manuscript on arXiv.