Publisher Correction: PhIP-Seq characterization of serum antibodies using oligonucleotide-encoded peptidomes

Abstract

The version of this paper originally published contained typesetter-introduced errors in some of the code commands, consisting of conversion of a closing backslash (\) to a forward slash (/). These errors have been corrected in the HTML and PDF versions of the protocol.

Distinct antibody repertoires against endemic human coronaviruses in children and adults

“…Since we detected pan-CoV cross-reactive antibodies less frequently in plasma samples from adult donors, our results argue against a strong therapeutic benefit of intravenous immunoglobulin products to control the spread of COVID-19 disease [67]. In this context, it should be noted that large-scale antibody screening by PhIP-Seq may frequently fail to detect conformational and posttranslationally modified B cell epitopes [29]. Nontheless, we found anti-CoV antibodies in plasma of a COVID-19 patient after prolonged hospitalization and intensive care that targeted largely the same structurally conserved and functionally important regions of the viral N and S proteins (Supplementary Figure S8) as those that we detected in a sizable proportion of children, including antibodies binding to the highly conserved motif and furin-like S2' cleavage site (R¯SA[I/L]ED[I/L]LF), which provides further evidence for the clinical benefit of using convalescent plasma for the prevention and treatment of COVID-19 [68][69][70].…”

“…To gain a deeper insight into human antibody responses to endemic HCoVs, we performed phage-immunoprecipitation sequencing (PhIP-Seq) [29][30][31] on previously collected serum or plasma samples obtained from a total of 1431 human subjects from three different cohorts.…”

“…The samples were collected prior to the current COVID-19 outbreak (Methods). In brief, PhIP-Seq allowed us to obtain comprehensive antiviral antibody repertoires across individuals in our three human cohorts using phage display of oligonucleotide-encoded peptidomes, followed by immunoprecipitation and massive parallel sequencing [29,31]. The VirScan phage library used for PhIP-Seq in the present study comprised peptides derived from viral proteins-each represented by peptide tiles of up to 56 amino acids in length that overlap by 28 amino acids-which collectively encompass the proteomes of a large number of viral species, including HCoV-229E, -NL63, -HKU1 and -OC43 [29,31].…”

“…In brief, PhIP-Seq allowed us to obtain comprehensive antiviral antibody repertoires across individuals in our three human cohorts using phage display of oligonucleotide-encoded peptidomes, followed by immunoprecipitation and massive parallel sequencing [29,31]. The VirScan phage library used for PhIP-Seq in the present study comprised peptides derived from viral proteins-each represented by peptide tiles of up to 56 amino acids in length that overlap by 28 amino acids-which collectively encompass the proteomes of a large number of viral species, including HCoV-229E, -NL63, -HKU1 and -OC43 [29,31]. Proteins of endemic HCoVs which were represented in the VirScan phage library included the Orf1ab replicase polyprotein (pp1ab), the spike glycoprotein (S), the matrix glycoprotein (M), the nucleocapsid protein (N) and gene products of the species-and strainspecific open reading frames (ORFs) encoded in the 3' region of the viral genomes (Supplementary Table S1).…”

Augmenting adaptive immunity: progress and challenges in the quantitative engineering and analysis of adaptive immune receptor repertoires

“…Recently, a potential alternative to peptide arrays has been developed: PhIP-Seq (phage immunoprecipitation sequencing') combines oligonucleotide library synthesis with high-throughput DNA sequencing analysis of phage-displayed libraries. Compared with peptide microarrays, PhIP-Seq features longer and higher-quality peptides 243 . The synthetic oligonucleotide libraries are designed to encode peptide tiles that together span a library of protein sequences (entire proteomes, for example).…”