Published in elife. Authors: Meghan E. Garrett*, Jared G. Galloway*, Caitlin Wolf, Jennifer K. Logue, Nicholas Franko, Helen Chu, Frederick A. Matsen IV^, Julie Overbaugh^
* these authors contributed equally to this work. ^ co-corresponding authors
A repository for hosting all Phage Deep Mutational Scanning (Phage-DMS) data presented in Comprehensive characterization of the antibody responses to SARS-CoV-2 Spike protein finds additional vaccine- induced epitopes beyond those for mild infection. Here, we break our entire dataset into more manageable subsets and provide links to view all the data using the DMS-view tool. Below we describe the data subsets which are split by cohort and sample condition -- while keeping all respective time points and replicates from a single participant (biologically distinct) in the same data subset. To view, simply click on the link next to the participant list and you'll be re-directed to the interactive tool, with all data for the samples listed already loaded for youi exploration.
To observe the enrichment and/or mutation-induced pathways of escape data for any of the samples in the manuscript (and more), follow the steps below, replacing participant 10C with any participant of your choosing.
- Click on the relevant dataset link Dataset #1 below under Cohort 2 (HAARVI), which will pull up DMS-View website
- In the "condition" drop-down menu, select "10C, SPIKE2, Pre-vaccine draw". SPIKE<X> is the batch replicate identifier - Select the respective SPIKE2 to see the replicate. So the pattern, generally, for condition naming id "<Participant ID>, <Batch Replicate>, <Time point>"
- Brush over the enriched region around peptide location 800.
- Brush over the peptides you would like to see enrichment for.
Dataset #1 : ['M01', 'M02', 'M03', 'M04', 'M05', 'M06']
Dataset #2 : ['M07', 'M08', 'M09', 'M10', 'M11', 'M12']
Dataset #3 : ['M13', 'M14', 'M15', 'M16', 'M17', 'M18']
Dataset #4 : ['M19', 'M20', 'M21', 'M22', 'M23', 'M24']
Dataset #5 : ['M25', 'M26', 'M27', 'M28', 'M29', 'M30']
Dataset #6 : ['M31', 'M32', 'M33', 'M34', 'M35', 'M36']
Dataset #7 : ['M37', 'M38', 'M39', 'M40', 'M41', 'M42']
Dataset #8 : ['M43', 'M44', 'M45', 'M46', 'M47', 'M48', 'M49']
Infection -> Vaccinated
Dataset #1 : ['103C', '10C', '110C', '118C', '120C', '136C']
Dataset #2: ['146C', '149C', '154C', '161C', '163C', '191C']
Dataset #3 : ['194C', '210C', '213C', '217C', '238C', '239C']
Dataset #4 : ['242C', '24C', '26C', '79C']
Healthy -> Vaccinated
Dataset #1 :['12H', '16H', '20H', '24H', '27H', '35H']
Dataset #2 :['36H', '38H', '3H', '4H', '50H', '53H', '54H']
Dataset #3 :['55H', '56H', '58H', '59H', '65H', '67H', '75H']
Infection (Hospitalized)
- Participant 6C shows hospitalized infection pre and post infection
Dataset #1: ['12001', '12004', '12101', '12104', '6', '6C'],
Infection (Non-hospitalized)
Dataset #1: ['1', '2', '3', '4', '5']
Dataset #2: ['7', '8', '9', '10', '11', '12']
Dataset #3: ['13', '14', '15', '16', '17', '18']