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PhIP-Seq/VirScan Coronavirus phage display assay in maternal-infant dyads


Prahl, Mary (2022), PhIP-Seq/VirScan Coronavirus phage display assay in maternal-infant dyads, Dryad, Dataset,


We investigated antibody linear epitope binding and transplacental transfer using the PhIP-seq/VirScan SARS-CoV-2 Spike protein phage display array in mother-infant dyads at the time of birth. SARS-CoV-2 antibody linear epitope binding after vaccination during pregnancy showed high levels of binding in carboxy terminal of N-terminal, S1/S2 cleavage site, and S2 — with multiple immunodominant regions found in the majority of mothers and infants.


Description of methods used for collection/generation of data:

PhIP-Seq/VirScan Coronavirus phage display assay

Immunoprecipitation of phage-bound patient antibodies

Maternal plasma at delivery and cord plasma were evaluated by PhIP-Seq/Virscan Coronavirus phage display. Construction of the Coronavirus PhIP-Seq library and detailed methods for immunoprecipitation, sequencing, and bioinformatic processing of data are identical to what has previously been described. For the purposes of the analysis conducted in this study, analysis was restricted to sero-reactivity against the SARS-CoV-2 Spike protein. As previously described, a total of two rounds of amplification and selection were performed for all PhIP-Seq analyses.

Next Generation Sequencing library prep

Amplicon sequencing library preps were performed using the Labcyte Echo 525 and an Integra Via Flow 96 and were identical to what has previously been described. All libraries were pooled by equal volume, cleaned and size selected using Ampure XP beads at 1.0X per manufacturer’s protocol. Libraries were quantified by High Sensitivity DNA Qubit and quality-checked by High Sensitivity DNA Bioanalyzer. Sequencing was then performed on a NovaSeq S1 (300 cycle kit with 1.3 billion clusters) aiming for sequencing depths of at least 1 million reads per sample.

Bioinformatic Analysis of PhIP-Seq Data

Sequencing reads were aligned to a Human coronavirus reference database of the full viral peptide library using the Bowtie2 aligner. For all VirScan libraries, the null distribution of each peptide’s log10(rpK) was modeled using a set of 95 pre-pandemic, healthy control sera. All counts were augmented by 1 to avoid zero counts in the healthy control sera samples. 


National Institutes of Health