Discuss about papers

[rshaferw]

1. Paper by Wu describing two different mRNA-1273 boosters. How to represent. ? develop a unique name for the regimen and provide an explanation for the name below the table. 10.1101/2021.05.05.21256716

[rshaferw]

• [x] AZD2816 paper by Spencer - How will we indicate that the antibodies are from vaccinated animals?
• [x] Behrens - Lancet - SARS-CoV-2 delta variant neutralisation after heterologous ChAdOx1-S/BNT162b2 vaccination. ? create a vaccine type "ChAdOx1-S/BNT162b2" with an explanatory footnote (extracted from our vaccine table). Appendix Fig 1A/B
• [x] Barros-Martins (senior author Behrens) Nature Medicine (https://www.nature.com/articles/s41591-021-01449-9) - Note: This paper and the preceding one use a sVNT assay (s=~surrogate) in which the antibody is tested for blocking Ab / ACE2 binding. This is increasingly used because it is high throughput. We should create this assay in the database and add studies that use it. ("sVNT (ACE2 blocking assay))
• [x] Acevedo - Research Square paper has additional data not present in the Acevedo BioRxiv paper. It contains data for BNT162b.

[KaimingTao]

• [x] Wu21, 10.1101/2021.05.05.21256716

[rshaferw]

• [x] Temporal Increase in Neutralization Potency of SARS-CoV-2 Antibodies and Reduced Viral Variant Escape after Sputnik V Vaccination - https://www.medrxiv.org/content/10.1101/2021.08.22.21262186v1
• [x] Neutralization of the SARS-CoV-2 Delta variant after heterologous and homologous BNT162b2 or ChAdOx1 nCoV-19 vaccination. 10.1038/s41423-021-00755-z (Figure 1; also an appendix for methods) sVNT - like Barros-Martins.
• [x] Tea. SARS-CoV-2 neutralizing antibodies: Longevity, breadth, and evasion by emerging viral variants. 10.1371/journal.pmed.1003656. Two assays are described "virus-cell fusion" and "neutralization". Both serve the same purpose but lets just use the neutralization assay. Figure 5H, 5K, 5L. There are two cohorts.
• [x] Corbett mRNA-1273 protects against SARS-CoV-2 beta infection in nonhuman primates. 10.1038/s41590-021-01021-0 (published) Figure 1 I-J-K-L-M-N (Higher priority)
• [x] Annavajhala. Emergence and expansion of SARS-CoV-2 B.1.526 after identification in New York. 10.1038/s41586-021-03908-2. Figure 3.
• [x] Du. A broadly neutralizing humanized ACE2-targeting antibody against SARS-CoV-2 variants. 10.1038/s41467-021-25331-x. mAb vs. different mutations. Schmidt. High genetic barrier to escape from human polyclonal 1 SARS-CoV-2 neutralizing antibodies. 10.1101/2021.08.06.455491. Move to Pending list. Complicated paper.
• [x] Francino-Urdaniz. One-shot identification of SARS-CoV-2 S RBD escape mutants using yeast screening. 10.1016/j.celrep.2021.109627. Low priority. Has binding data (like DMS) and some mAb neutralization 2E, 2F.

[rshaferw]

• [x] Wilhelm pre-print. Antibody mediated neutralization of authentic SARS-CoV-2 B.1.617 variants harboring L452R and T478K/E484Q. 10.1101/2021.08.09.21261704. Figures 1 and 2
• [x] MCCallum pre-print. Molecular basis of immune evasion by the delta and kappa SARS-CoV-2 variants. 10.1101/2021.08.11.455956, Figure 1A-C
• [x] Keeton, R. Prior infection with SARS-CoV-2 boosts and broadens Ad26.COV2.S immunogenicity in a variant dependent manner. 10.1101/2021.07.24.21261037. Attachment has data from the NIH foundation. Figure 2A. J&J vaccine in naive patients, those who were infected before variants, and those who were infected when the Beta variant was circulating. Titers are vs. D614G, Beta variant, and Delta variant.

[rshaferw]

• [x] Hadjadj pre-print (lower priority). Immunogenicity of BNT162b2 vaccine Against the Alpha and Delta Variants in Immunocompromised Patients. 10.1101/2021.08.08.21261766. Figure 2C. But how to represent the immunocompromised patients???

[rshaferw]

• [x] Chen, L. Emergence of Multiple SARS-CoV-2 Antibody Escape Variants in an Immunocompromised Host Undergoing Convalescent Plasma Treatment. 10.1128/mSphere.00480-21. Prolonged infection with emergent mutations. We should discuss placing them in the database - in vivo selection.

[rshaferw]

• [x] Peiffer-Smadja. Emergence of E484K Mutation Following Bamlanivimab Monotherapy among High-Risk Patients Infected with the Alpha Variant of SARS-CoV-2. 10.3390/v13081642. In vivo selection of mutations with bamlanivimab.

[rshaferw]

• [x] Neumann. Development of SARS-CoV-2 Specific IgG and Virus-Neutralizing Antibodies after Infection with Variants of Concern or Vaccination. 10.3390/vaccines9070700. Figure 4a (sVNT). Figure 5 (cVNT) [c=vero cell based neutralization test == live virus]

[rshaferw]

• [x] Fernandez J. Neutralization of Alpha, Gamma, and D614G SARS-CoV-2 variants by CoronaVac vaccine-induced antibodies. J Med Virol. VP (coronovac) vs 614G, alpha, gamma
• [x] Zhao X. Neutralisation of ZF2001-elicited antisera to SARS-CoV-2 variants. Lancet Microbe. Data are in appendix.

[KaimingTao]

• Wilhelm pre-print. Antibody mediated neutralization of authentic SARS-CoV-2 B.1.617 variants harboring L452R and T478K/E484Q. 10.1101/2021.08.09.21261704. Figures 1 and 2

Figure 2 contains mab IC50 results but it's using serial dilution method. It's different with common mAb experiments which using ng/ml to measure the result.

[rshaferw]

• Tang J. Epitope diversity of SARS-CoV-2 hyperimmune intravenous human immunoglobulins and neutralization of variants of concern. iScience. This deals with IVIG. We should add this to those list of papers to keep in our radar. But we should not add this yet. (pending list) Move to pending list

[KaimingTao]

• [x] Hadjadj pre-print (lower priority). Immunogenicity of BNT162b2 vaccine Against the Alpha and Delta Variants in Immunocompromised Patients. 10.1101/2021.08.08.21261766. Figure 2C. But how to represent the immunocompromised patients???

@rshaferw currently we can mark the immunocompomised patients by subject name, another way is to add a new field in subjects table.

[KaimingTao]

• [x] Chen, L. Emergence of Multiple SARS-CoV-2 Antibody Escape Variants in an Immunocompromised Host Undergoing Convalescent Plasma Treatment. 10.1128/mSphere.00480-21. Prolonged infection with emergent mutations. We should discuss placing them in the database - in vivo selection.

It's an update of 10.1101/2021.04.08.21254791

[KaimingTao]

• [x] Neumann. Development of SARS-CoV-2 Specific IgG and Virus-Neutralizing Antibodies after Infection with Variants of Concern or Vaccination. 10.3390/vaccines9070700. Figure 4a (sVNT). Figure 5 (cVNT) [c=vero cell based neutralization test == live virus]

Figure 4a, sVNT is not represented as titer but percentage of inhibition, it's different with other sVNT studies.