Upper respiratory tract microbiome profiles in SARS-CoV-2 Delta and Omicron infected patients exhibit variant specific patterns and robust prediction of disease groups

[SvetlanaUP]

Upper respiratory tract microbiome profiles in SARS-CoV-2 Delta and Omicron infected patients exhibit variant specific patterns and robust prediction of disease groups – Shankha Nath – Microbiology Spectrum https://journals.asm.org/doi/10.1128/spectrum.02368-23

[TitilayoMG]

@SvetlanaUP Please I'll like to curate this paper

[TitilayoMG]

@leenaaize, @Scholarpat and @Lonercode thank you for reviewing my curation

[SvetlanaUP]

Ready for review https://bugsigdb.org/Study_883

[Folakunmi21]

Hello @TitilayoMG Here are a few things to note about your curation:

• Signatures were incomplete in experiment 1

• Experiments 2 and 4 were wrongly curated. The signature source for the comparison between controls and the 2 sars-cov-2 variants is figure 6, and not table 3. The comparison has both groups having decreased signatures, and no increases (figure 6). The signatures appear to be the same for the comparison between controls and both variants, so I created only 1 experiment for this and created a talk page for it.

CURATION RESULT

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
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): 0.5
7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): 0.5
8. Antibiotic exclusion correctly identified (1 point): 1
9. Correctly identified sequencing details (2 points): 2
10. Identified correct statistical test (1 point): 0.5
11. Identified MHT correction (1 point): 0
12. Correctly recorded matched on factors (1 point): 1
13. Entered correct number of statistical tests per experiment (1 point): 1
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): 0.5
18. Members of Signatures identified correctly (2 points): 0.5
19. Correct use of NCBI taxonomy (2 points): 2

Total (maximum 23 points): 16.5

@SvetlanaUP study 883 reviewed

[TitilayoMG]

Noted all the corrections with thanks @Folakunmi21 It will definitely guide my subsequent curation. Thank you.