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hivdb / covid-drdb-payload

A relational database of SARS-CoV-2 resistance data.
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Add antibody neutralization studies #73

Closed KaimingTao closed 2 years ago

KaimingTao commented 3 years ago
philiptzou commented 2 years ago

@KaimingTao Isn't the term "in Vitro" used for selection data? I checked several ones in this list and they are not selection data but mAb neutralization test (of course they are in vitro). Where can I find a list of in Vitro selection data pending for entering? I thought we have one.

KaimingTao commented 2 years ago

@KaimingTao Isn't the term "in Vitro" used for selection data? I checked several ones in this list and they are not selection data but mAb neutralization test (of course they are in vitro). Where can I find a list of in Vitro selection data pending for entering? I thought we have one.

"in vitro" is just mean not "in vivo" data. We can use neutralization to replace the title.

KaimingTao commented 2 years ago

@KaimingTao Isn't the term "in Vitro" used for selection data? I checked several ones in this list and they are not selection data but mAb neutralization test (of course they are in vitro). Where can I find a list of in Vitro selection data pending for entering? I thought we have one.

Please check the OmicronPaper excel file to see which papers need to be entered. This list is for papers that are entered or decided to be entered but haven't been released.

KaimingTao commented 2 years ago

Please also check the supplementary content if they contain neutralization test results.

shegocaga commented 2 years ago

Taking Assawakosri

shegocaga commented 2 years ago

@KaimingTao For Assawakosri22, what would the control_iso_name be if the study is making a comparison of vaccines' efficacies for delta against BBIBP, and then the same vaccines' efficacies for omicron against BBIBP?

KaimingTao commented 2 years ago

@KaimingTao For Assawakosri22, what would the control_iso_name be if the study is making a comparison of vaccines' efficacies for delta against BBIBP, and then the same vaccines' efficacies for omicron against BBIBP?

@zachandfox This paper is special, the control is delta variant

shegocaga commented 2 years ago

Taking Chatterjee22

shegocaga commented 2 years ago

Taking Chen22b 10.1080/22221751.2022.2035195

shegocaga commented 2 years ago

For Chen22b, how do I represent the fold data (figure 2) in the rx_potency table?

shegocaga commented 2 years ago

For Chen22b, the infection isolate is of lineage B.1.36.27, but we haven't that in the isolates table atm, how would I add it?

KaimingTao commented 2 years ago

For Chen22b, how do I represent the fold data (figure 2) in the rx_potency table?

You can enter the data to rx_folder tables. I would update the document later, please check the rx_folder and use one file as an example.

KaimingTao commented 2 years ago

For Chen22b, the infection isolate is of lineage B.1.36.27, but we haven't that in the isolates table atm, how would I add it?

Please check the document Method: Variants, isolates and mutations and 3.1.3 tables/variants.csv

If you can get the GISAID or Genbank sequence you can recheck the variant name (lineage name) using our Analysis program. If you want to know the mutations of the B.1.36.27, please check outbreak.info.

shegocaga commented 2 years ago

If you can get the GISAID or Genbank sequence you can recheck the variant name (lineage name) using our Analysis program. If you want to know the mutations of the B.1.36.27, please check outbreak.info.

The paper doesn't provide the GISAID, so I'm not able to check the variant/lineage name in the analysis program. Outbreak.info does provide the mutation list, so I should be able to add it to isolate_mutations.csv, but then I don't know what the name should be (B.1.36.27 full genome?).

In the variants.csv table, what does the consensus_availability represent, and how do I find this?

If I understand correctly, what I need to do is add a variant to variants.csv, which implies that I must also add to isolates.csv and isolate_mutations.csv.

KaimingTao commented 2 years ago

If you can get the GISAID or Genbank sequence you can recheck the variant name (lineage name) using our Analysis program. If you want to know the mutations of the B.1.36.27, please check outbreak.info.

The paper doesn't provide the GISAID, so I'm not able to check the variant/lineage name in the analysis program. Outbreak.info does provide the mutation list, so I should be able to add it to isolate_mutations.csv, but then I don't know what the name should be (B.1.36.27 full genome?).

In the variants.csv table, what does the consensus_availability represent, and how do I find this?

If I understand correctly, what I need to do is add a variant to variants.csv, which implies that I must also add to isolates.csv and isolate_mutations.csv.

Yes, you're correct, the name would be B.1.36.27 full genome. It would be a reference for B.1.36.27. consensus_availability please use FALSE, I will use program to automatically fetch the information later.

Yes, for a new variant, you need fill in three tables variants, isolates, and isolate_mutations

shegocaga commented 2 years ago

I'll take Cheng22 (10.1038/s41591-022-01704-7)

shegocaga commented 2 years ago

In Cheng22, is there anything particular to the PRNT50 neutralization titers that differentiates them from NT50 in other studies?

shegocaga commented 2 years ago

If you can get the GISAID or Genbank sequence you can recheck the variant name (lineage name) using our Analysis program. If you want to know the mutations of the B.1.36.27, please check outbreak.info.

The paper doesn't provide the GISAID, so I'm not able to check the variant/lineage name in the analysis program. Outbreak.info does provide the mutation list, so I should be able to add it to isolate_mutations.csv, but then I don't know what the name should be (B.1.36.27 full genome?). In the variants.csv table, what does the consensus_availability represent, and how do I find this? If I understand correctly, what I need to do is add a variant to variants.csv, which implies that I must also add to isolates.csv and isolate_mutations.csv.

Yes, you're correct, the name would be B.1.36.27 full genome. It would be a reference for B.1.36.27. consensus_availability please use FALSE, I will use program to automatically fetch the information later.

Yes, for a new variant, you need fill in three tables variants, isolates, and isolate_mutations

For (B.1.36.27)[https://outbreak.info/situation-reports?pango=B.1.36.27], there are mutations in ORF1a, ORF1b, but these genes are not present in the (genes.csv)[https://github.com/hivdb/covid-drdb-payload/blob/master/tables/genes.csv] table. Is the genes.csv table subject to change, if so, how? If not, do I exclude the ORF1a, ORF1b mutations?

shegocaga commented 2 years ago

In Cheng22, there is a new isolate hCoV-19/Hong Kong/VM20001061-2/2020 (gisaid 412028) that has a mutation list that is identical to an existing isolate, hCoV-19/Hong Kong/HKU-001a/2020, as shown below

hCoV-19/Hong Kong/HKU-001a/2020,S,367,F,NULL,NULL
hCoV-19/Hong Kong/HKU-001a/2020,ORF8,62,L,NULL,NULL
hCoV-19/Hong Kong/HKU-001a/2020,ORF8,84,S,NULL,NULL
...
hCoV-19/Hong Kong/VM20001061-2/2020,S,367,F,NULL,NULL
hCoV-19/Hong Kong/VM20001061-2/2020,ORF8,62,L,NULL,NULL
hCoV-19/Hong Kong/VM20001061-2/2020,ORF8,84,S,NULL,NULL

Does it still get added?

shegocaga commented 2 years ago

In Cheng22, sera is collected for infected individuals (pre-Omicron) but without a specified variant or date of infection, as quoted:

We also evaluated sera from the following groups of previously infected individuals: (1) indi- viduals 143–196 d postinfection who had recovered from COVID- 19 (pre-Omicron emergence) and had not yet received a vaccine (n = 30) 12 , (2) convalescent individuals with COVID-19 who had received one dose of BNT162b2 (n = 30) or (3) convalescent indi- viduals with COVID-19 who had received one dose of CoronaVac (n = 28)

In order to represent these subjects in cheng22-pth.csv, what would I use for their iso_name and their event_date?

shegocaga commented 2 years ago

I'll take Hu22 (10.1038/s41423-021-00836-z)

shegocaga commented 2 years ago

I'll take Kurahashi22 (10.1101/2022.02.24.22271262)

KaimingTao commented 2 years ago

Alidjinou1, 10.1007/s15010-021-01732-4

EPI_ISL_3750532 is currently not available at the Submitter's request. (Mar 31, 2022)

KaimingTao commented 2 years ago

10.3390/v14010144, Chatterjee22b

KaimingTao commented 2 years ago

Alvarez-Diaz22,10.3390/vaccines10020180 Alvarez-Diaz21,10.1016/j.virusres.2021

KaimingTao commented 2 years ago

Banerjee22, 10.1101/2022.01.13.475409

shegocaga commented 2 years ago

Taking Mannar22 (10.1126/science.abn7760)

shegocaga commented 2 years ago

For Mannar22, the Delta CP is specified as B.1.617.2 in the paper, but the B.1.617.2 variant is not listed in the variants.csv table, though B.1.617 is in the table. What should I use? Delta, or B.1.617.2?

shegocaga commented 2 years ago

The vaccine(s) for vaccinated patients is not provided in Mannar22, and there doesn't appear to be an "Unknown vaccine" in the vaccines.csv table. What should value should I use when filling out mannar22-vacc.csv?

KaimingTao commented 2 years ago

For Mannar22, the Delta CP is specified as B.1.617.2 in the paper, but the B.1.617.2 variant is not listed in the variants.csv table, though B.1.617 is in the table. What should I use? Delta, or B.1.617.2?

Please use Delta as infected_var_name, B.1.617.2 is Delta defaultly.

KaimingTao commented 2 years ago

The vaccine(s) for vaccinated patients is not provided in Mannar22, and there doesn't appear to be an "Unknown vaccine" in the vaccines.csv table. What should value should I use when filling out mannar22-vacc.csv?

Please more all data to the excluded folder, if the vaccine is unknown. Please keep the file in the corresponding folders.

shegocaga commented 2 years ago

Taking Muik22 (10.1126/science.abn7591)

shegocaga commented 2 years ago

Taking Edara22 (10.1101/2022.01.24.22269189)

shegocaga commented 2 years ago

For Edara22, the researchers are based in the USA, but the sera were collected in India. Do I use India in the plasma and vaccine tables, or USA?

philiptzou commented 2 years ago

For Edara22, the researchers are based in the USA, but the sera were collected in India. Do I use India in the plasma and vaccine tables, or USA?

I think for this case it should be India if they were collected in India.

KaimingTao commented 2 years ago

This issue is closed. In the future, all new studies will have its own issue number.