Exploring nasopharyngeal microbiota profile in children affected by SARS-CoV-2 infection

[SvetlanaUP]

Exploring nasopharyngeal microbiota profile in children affected by SARS-CoV-2 infection – L Roman – Microbiology Spectrum https://journals.asm.org/doi/10.1128/spectrum.03009-23

[Druscillaa]

@SvetlanaUP please assign me this project

[omojokunoluwatomisin10]

kindly assign me this project @SvetlanaUP

[Druscillaa]

Thank you

[Druscillaa]

@SvetlanaUP please review

https://bugsigdb.org/Study_965

[Omabekee]

This was a good second curation attempt @Druscillaa. Here are some corrections to the error you made, I've presented them as simply as I can. Please implement all and ask for help in the slack community where you're not sure. Corrections

1. Statistical test: LEfSe was used not ANOVA (see method section).
2. Matched on: Age is the only variable that was matched on (confirm by using ctrl + f).
3. Incomplete signatures: From figure 3, there should be about 28 taxa in total for COVID-19 (increased signature) and 17 for ctrls (decreased signature).
4. Source descriptions: for signatures should be more descriptive "Differences in bacterial taxa abundance of nasopharyngeal (NP) microbiota in COVID-19 patients VS CTRL groups" should be more appropriate.
5. Group descriptions should also be more descriptive, "healthy control group, COVID-19 patients
6. Additional experiment: Figure S4 of the supplemental file should be curated as an additional experiment. COVID-19 vs NO COVID-19 Please read the paper again to understand the group descriptions of this new experiment so that you can curate well.

CURATION RESULTS

1. All elements marked "Needs review" (none "Incomplete") (1 point): 1
2. Correct study design (1 point): 1
3. Entered all relevant experiments and no irrelevant experiments (1 point): 0.5
4. Body site correctly identified (i.e. does not include multiple sites) (1 point): 1
5. Condition entered according to contrast (correct EFO ontology) (1 point): 1
6. Contrast groups correctly identified (1 point): 1
7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): 1
8. Antibiotic exclusion correctly identified (1 point): 1
9. Correctly identified sequencing details (2 points): 2
10. Identified correct statistical test (1 point): 0
11. Identified MHT correction (1 point): 1
12. Correctly recorded matched on factors (1 point): 0.5
13. Entered correct number of statistical tests per experiment (1 point): 0
14. All diversity measures identified (1 point): 1
15. Diversity results correctly entered as increased/decreased/unchanged (1 point): 1
16. All signature sources correctly identified (-1 for each error) (2 points): 1
17. Abundance direction correctly selected (1 point): 1
18. Members of Signatures identified correctly (2 points): 0.5
19. Correct use of NCBI taxonomy (2 points): 2

Total = 17.5 @SvetlanaUP, grading of Study 965 complete. ✅ Review still in progress

[Omabekee]

Hi @Analyst-Joan, I need your assistance here. Can you work with @Druscillaa to complete this curation?

[Analyst-Joan]

Alright @Omabekee, I'll do that. @Druscillaa please what's your slack username, so we continue the discussion there? Mine is @Joan_Chuks. Hoping to hear from you 🤗

[Analyst-Joan]

Good evening @Omabekee, I reached out to @Druscillaa on slack channel yesterday morning but yet to get any feedback.

[Omabekee]

@Analyst-Joan Let's wait till evening, if they don't respond please proceed with the curation. Thanks a bunch.!

[Analyst-Joan]

Alright, Thanks.

[Analyst-Joan]

Alright, Thanks.

Good afternoon @Omabekee

I'm now working on the required corrections. I'd revert here once i'm done.

Thank you

[Analyst-Joan]

Good afternoon @Omabekee

I'm done effecting the corrections for Study_965 and it's now ready for review.

Thanks.

[Omabekee]

@SvetlanaUP 2nd review complete. ✅ This issue can now be closed. Thank you.

[SvetlanaUP]

https://bugsigdb.org/Study_965 reviewed.