DOI: 10.5061/dryad.qjq2bvqpq
title: Data from: Anti-HLA antibodies may be a subset of polyreactive immunoglobulins generated after viral superinfection

description: Chronic allograft rejection is an insurmountable obstacle to long-term
 allograft survival. Donor-specific anti-HLA antibodies play an important
 role in causing chronic antibody-mediated allograft rejection. Historical
 and current evidence from the literature supports the hypothesis that HLA
 are unreliably immunogenic but definitively antigenic. We hypothesized
 that anti-HLA antibodies may develop following viral superinfection.
description: The NETRAD algorithm is described in "ANTI-HLA ANTIBODIES
 MAY BE A SUBSET OF POLYREACTIVE IMMUNOGLOBULINS GENERATED AFTER VIRAL
 SUPERINFECTION," pending review for publication as of (2025)
 Transplant Immunology, manuscript #TRIM-D-24-00351 and also under United
 States provisional patent application as "SYSTEM AND METHOD FOR
 DETERMINING AND DEVELOPING MONOCLONAL ANTIBODIES AS BIOMARKERS FOR
 DIAGNOSTIC TARGETS AND THERAPEUTIC APPLICATIONS." Patent
 pending.
description: # Data from: Anti-HLA antibodies may be a subset of polyreactive
 immunoglobulins generated after viral superinfection
 [https://doi.org/10.5061/dryad.qjq2bvqpq](https://doi.org/10.5061/dryad.qjq2bvqpq) ### Change Log: Version dated January 30, 2025 was modified to correct typing errors and epitope naming designations in 5 files: NETRAD_CompleteDataforPublishing, 6-HLA-B1302_Influenza_EBV_Epitopes, 6-HLA-DR4_H3N2_EBV_Epitopes, 6-HLA-C0401_H1N1_EBV_Epitopes, 1-CumulativeHLAepitopes. File 6-HLA-B1302_Influenza_EBV_Epitopes had epitope naming convention modified from 76EN to 44MA after identifying epitope specificity correction. File 6-HLA-C0401_H1N1_EBV_Epitopes had epitope naming convention modified from 156RA to 156R after identifying epitope specificity correction. File 6-HLA-DR4_H3N2_EBV_Epitopes had epitope naming convention changed from 80VV to 80V after identifying epitope specificity correction. All epitope specificities align with the HLA Eplet Registry ([https://epregistry.com.br/](https://epregistry.com.br/)). NETRAD_ComleteDatafor Publishing and 1-CumulativeHLAepitopes files were corrected to reflect the naming convention changes in the preceding 3 files. ## Description of the data and file structure Acquired data are structured in two formats: 1) Adobe .pdf and 2) spreadsheet .csv. 1\. Adobe pdf (NETRADCompleteDataForPublishing): Included are a color-coded Key to highlighted sequence motifs, followed by EBV gp350 strain sequences used as the superinfecting primary virus. Each of the following epitopes utilize one of these sequences for analysis (individual Smith Waterman epitope analyses are included as .csv files). Each of the HLA epitopes listed in Table 1 of the manuscript "ANTI-HLA ANTIBODIES MAY BE A SUBSET OF POLYREACTIVE IMMUNOGLOBULINS GENERATED AFTER VIRAL SUPERINFECTION" (submitted Nov 2024, Transplant Immunology [TI], Elsevier) is described chronologically as individual sections, by epitope specificity (i.e., HLA-A*02:01), and includes the corresponding Epitope Registry designation (i.e., 62GK). Epitope analyses are listed according to the order found in Table 1 of the manuscript. Each epitope analysis must be referenced to the corresponding .csv files 4-[a]-[b]-[c], 5-[d]-[e]-[f]-[g], and 6-[h]-[i]-[j]-[k], where 4=file type specific to N-lysozyme digested peptides listed from superinfecting viruses, a=superinfecting secondary virus, b=superinfecting primary virus, c=peptides, 5=file type specific to Smith Waterman analysis of virus peptides obtained from file type 4 and sorting of those peptides as described in the NETRAD algorithm manuscript and supplement text, d=refers to the HLA specificity of the Smith Waterman analysis for viral peptide homology, e=secondary superinfecting virus, f=primary superinfecting virus (always EBV), g=file description that peptides are sorted (SortedPeptides), 6= file type specific to final HLA- specific epitope derivation, h=HLA specificity, i=secondary superinfecting virus, j=primary superinfecting virus (always EBV) and k=epitope(s) designating whether epitope analysis yields one or more epitopes from a superinfecting virus pair. Included in the .pdf in each epitope analysis section are the sequence comparisons (which may be truncated) that highlight the viral peptide patterns (color-coded) that comprise the HLA epitope target of the antibody specificity. These are superimposed onto alleged patient HLA typing or onto patient/donor HLA typing for comparison. Included in the .pdf in each epitope analysis section are the HLA sequences from which the epitope target is derived. Included in the .pdf in each epitope analysis section are the immunogenic viral envelope protein sequences, and individual peptide sequences derived from Expasy PeptideMass in-silico N-lysozyme digestion of the viral envelope protein. All peptides (except those =5 amino acids in length, are included in a corresponding tab in the .csv spreadsheet. Highlighted in each viral protein sequence are SUMO and N-glycan sequons. N-glycan sequons are highlighted for each peptide. A key to color-coding can be found at the very beginning of the pdf. Also, HLA crystal structures obtained from PHLA-3D and/or YASARA software, highlighting the virus-derived epitope, are included. 2\. One .csv file (1-CumulativeHLAepitopes) summarizes the combination(s) of 6 peptides identified to form specific HLA epitopes. This data is included in the .pdf file above. Column A indicates the HLA target specificity and Epitope Registry epitope, Column B= the Expasy PeptideMass generated peptide ID#, Column C= Virus Envelope Protein of origin, Column D= # N-glycans/peptide, E= Smith-Waterman- generated gapped peptide sequence, F= HLA starting residue for the peptide, G= the # Ab accessible residues in the epitope. Epitopes may contain 6 or more rows (corresponding to 6 unique peptides and whether homology was found in forward and/or reverse orientation). The number of peptides in an epitope are distinguished by the target specificity in column A. Below row 487 are tallied peptides used for epitope demarcation. One .csv file (2-PeptideDifferentials) provides measurements between amino acid pairs within individual viral peptides and compare those measurements to the corresponding amino acid pairs of the HLA epitope. The purpose is to provide a statistical analysis for determining whether changes in distances (differential) between the HLA vs viral protein would preclude or support cross-reactivity. Only antibody accessible amino acids are queried. Column A=HLA epitope, column B identifies the superinfecting virus origin of the peptide (column C) from whence the amino acid pair (columns D & E) differential was measured. Column F = # of amino acid gaps between the measured pair, column G indicates the PDB crystal structure designation from which measurements were taken from the virus protein, column H is the distance differential between columns D & E for the virus protein- in Angstroms, column I indicates the corresponding HLA-homologous PDB crystal structure used for measurement (where specific HLA crystal structures were not available, a close approximation was made), column J is the distance differential between columns D & E for the HLA protein, column K is the differential between columns H and J used to compare the amino acid pair differential between the virus protein vs HLA protein. Columns M-Q were used to sum the # Class I vs Class II epitopes and the % which were derived from 6 peptides having &gt;6 motifs (forward and reverse motif). Rows below 46 were used for basic statistical analyses (avg, min, max, % amino acid pairs having 'x' differential[#Angstroms]) & columns U-X were used for ANOVA analysis of differentials across all pairings using GraphPad Prism (M37). One .csv file (3-RadiusMeasurements) provides measurements of epitope diameters for all demarcated epitopes with statistical analysis (t-test; rows 73-77) determining whether the NETRAD-determined epitopes fell within the established diameter of an epitope/paratope interface (15 Angstroms). Column A=HLA Epitope, B=PDB crystal structure from where measurements were taken, C,D= residues used to measure epitope diameter measurement 1(E), F,G=residues used to measure epitope diameter measurement 2 (H), I=measured radius at maximum, J=expected radius (Angstroms)=15. Rows 73-77=statistical analysis to determine whether epitope radii fell within range of standard epitope/paratope interface (t-test). Each of the HLA epitopes listed in Table 1 of "ANTI-HLA ANTIBODIES MAY BE A SUBSET OF POLYREACTIVE IMMUNOGLOBULINS GENERATED AFTER VIRAL SUPERINFECTION" was analyzed in MS Excel (and saved as .csv file according to DYRAD standardization) in chronological order according to the Smith-Waterman (SW) homology assessment of individual peptides generated via Emboss Water web tool (referenced in manuscript). For each epitope, three .csv files exist, labeled 4-[a]-[b]-[c], 5-[d]-[e]-[f]-[g], and 6-[h]-[i]-[j]-[k] as described above. HLA homology is listed by standard amino acid nomenclature. Gapped amino acid positions are listed as "x" or spacers "-". .csv files type 4-[a]-[b]-[c] list peptides, generated by N-lysozyme digestion of viral envelope proteins, to be input into the SW algorithm. Peptides (Column A) are identified by Expasy PeptideMass (EPM) identifier (referenced in manuscript). In silico N-lysozyme digested peptides are listed in forward (Column B) and reverse (Column C) directions. .csv files type 5-[d]-[e]-[f]-[g] file identify HLA homologous virus peptide sequences obtained from Emboss Water SW-generated gapped peptides by row, with separate columns identifying the EPM identifier (Column A), virus protein origin (column B), whether N-glycan sequons are present on the original peptide sequence (Column C), the NETRAD-derived HLA-homologous gapped viral sequence (column D), HLA start residue (column E), the ERP scored location indicating the relative location of the peptide with regard to surface accessibility (described in Methods section of "The Origins of Rejection") (column F), and whether the sequence is HLA specific (Y/N; column G). HLA Class II DQ and DP epitope analyses also have an additional column to distinguish alpha vs beta chain homology. .csv files type 6-[h]-[i]-[j]-[k] file identify complete NETRAD-derived HLA epitopes. Separate columns identify the EPM identifier (Column A), virus protein origin (column B), whether N-glycan sequons are present on the original peptide sequence (Column C), the NETRAD-derived HLA-homologous gapped viral sequence (column D), HLA start residue (column E), the ERP scored location indicating the relative location of the peptide with regard to surface accessibility (described in Methods section of "The Origins of Rejection") (column F), and whether the sequence is HLA specific (Y/N; column G). HLA Class II DQ and DP epitope analyses also have an additional column to distinguish alpha vs beta chain homology. Upon completing gapped peptide data entry into the spreadsheet, each peptide is assessed for antibody accessibility against the crystal structure of the HLA protein. Only gapped homologous amino acids that are identifiable at the protein surface are considered "antibody accessible." Data is sorted by antibody accessibility score (where 1= highest accessibility and 5 (and 0)=least accessible) and by HLA/autoantigen start residue. Peptides that are scored as 1-4 may be considered as potential candidates for antibody binding sites. However, in order to ascertain specificity, a minimum of 4 antibody-accessible residues are required to impute antibody specificity. Between 7-25 residues within a 15 angstrom radius located at the surface of the HLA protein/autoantigen. This typically can be accommodated by 6 peptides (for which forward and reverse sequence matching must be accounted). One of the 6 peptides must be derived from Epstein Barr virus gp350. One of the 6 peptides must contain and N-glycan sequon. ## Sharing/Access information Links to other publicly accessible locations of the data: * HLA and viral protein sequences were obtained from IMGT and NCBI websites:  [https://www.ebi.ac.uk/ipd/imgt/hla/alleles/](https://www.ebi.ac.uk/ipd/imgt/hla/alleles/), [https://www.ebi.ac.uk/ipd/imgt/hla/alignment/](https://www.ebi.ac.uk/ipd/imgt/hla/alignment/), nih.gov * *in silico* N-lysozyme digested viral peptide libraries were created utilizing EXPASY PeptideMass: [https://web.expasy.org/peptide_mass/](https://web.expasy.org/peptide_mass/) * the Smith-Waterman algorithm [https://www.ebi.ac.uk/Tools/psa/emboss_water/](https://www.ebi.ac.uk/Tools/psa/emboss_water/) * HLA crystal structures were obtained from pHLA3D ([https://www.phla3d.com.br/](https://www.phla3d.com.br/) or [https://www.rcsb.org/](https://www.rcsb.org/) and assessed for antibody accessibility to published epitopes, utilizing pHLA3D, YASARA ([http://www.yasara.org/](http://www.yasara.org/) or 1D-3D view at [https://www.rcsb.org/.](https://www.rcsb.org/.) * HLA- homologous viral peptide motifs were sorted (MS Excel) based on IMGT-HLA- referenced amino acid sequence number and then compared to established epitopes (to confirm HLA- specificity including the functional eplet listed according to [https://www.epregistry.com.br/](https://www.epregistry.com.br/) ### Files and variables #### File: NETRAD\_CompleteDataForPublishing.pdf **Description:** Epitope analyses include as described includes listing of HLA specific sequence used to characterize viral-derived epitopes, virus envelope/capsid protein origins of HLA-homologous peptides (includes strain identification), HLA sequence comparison to antibody epitopes specificity containing superimposed Smith Waterman-derived virus peptide subsequences and antibody-accessible residue. #### File: 1-CumulativeHLAepitopes.csv **Description:** Accumulated HLA epitopes derived from NETRAD analysis of virus envelope/capsid protein pairs. ##### Variables * antibody specificity: HLA allele used to identify epitope (HLA Epitope Registry identifier) * Expasy PeptideMass generated peptide ID#: peptide identifier as found in type 4 files column A * Virus Envelope Protein: origin of peptide * \# N-glycans/peptide: number of N-glycan sequons detected in peptide sequence (type 4 files column B) * Smith-Waterman- generated gapped peptide sequence: HLA-homologous peptide subsequence determined by EMBOSS WATER software * HLA start residue: residue of HLA protein sequence mature protein corresponds to 1st residue of peptide * \# Ab accessible residues: number of antibody accessible residues for viral peptides as determined when superimposed upon the corresponding HLA protein * blank cells in columns A and G demarcate distinct epitope groupings (gapped subsequences from 6 peptides may be in forward of reverse sequence or both) #### File: 2-PeptideDifferentials.csv **Description:** measurement of inter-residue distances (in Angstroms) corresponding to viral/HLA homologous amino acid pairs. Used for determine similarities/differences in tertiary/quaternary molecular structure. ##### Variables * Ab Accessible Residues: HLA epitope, as assigned by HLA Eplet Registry, being queried for homology is listed in this column. Only antibody-accessible residues are queried in the table * Virus: virus origin of the peptide * Peptide: peptide identification as listed in type 4 files, column A * Residues: columns D & E are the paired residues being measured. * \#Residues between R1-R2: number of gaps (residues) that exist between residues listed in columns D & E. * Virus PDB: crystal structure identification # at Protein Database (column G for virus protein, column I for correlate HLA protein). * Distance: measured distance between residues R1-R2 (columns D & E) (column H for virus protein, column J for correlate HLA protein) * Differential between columns H and J * Cells N1-N5: instructions for determining inter-residue distance using PDB database (Explore in 3D). * Cells M8-Q11: determination (by counting) number of Class I vs Class II epitopes that were derived from 6 peptides bi-directionally * Columns U-X are replicated from columns F, H, J and K to perform t-test statistical analysis (cells M37,38) * Columns 46-50: basic statistics #### **File: 3-RadiusMeasurements.csv** **Description:** measurement of distance differential between epitope center and outermost amino acid belonging to epitope corresponding to virus-derived peptides ##### Variables * Epitope: NETRAD-derived epitopes correspond to Epitope Registry ([https://www.epregistry.com.br/](https://www.epregistry.com.br/)) * PDB: crystal structure ([https://www.rcsb.org/search](https://www.rcsb.org/search)) corresponding to [HLA] epitope * Residue1: amino acid residue along outermost border of epitope * Residue2: amino acid residue at outermost border of epitope opposite "Residues 1" * Diameter1: distance from Residue 1 to Residue 2 * Residue3: amino acid residue at outermost border of epitope (different position along epitope outer border than Residue 1) * Residue4: amino acid residue at outermost border of epitope opposite "Residues 3" * Diameter2: distance from Residue 3 to Residue 4 * MaxRadius: radius measurement from the points of the epitope having the greatest diameter (normally 1/2 x Diameter1) * Expected: standard epitope radius is 15 Angstroms #### File: CumulativeNegativeControls.csv **Description:** listing of epitopes that could not be derived from selected viral envelope protein pairs (utilizing same file types 4 & 5 for given HLA specificity) ##### Variables: * Virus Pair: Secondary superinfecting virus is listed; EBV gp350 is assumed * Envelope protein or capsid origin * HLA Epitope Registry epitope designation w/ high exposition * HLA specificity included: analysis performed against this HLA specificity #### File: 4-AdenoVpenton\_EBVgp350\_Peptides.csv **Description:** Expasy PeptideMass calculated peptide sequences based on in silico N-lysozyme-digested envelope proteins Adenovirus penton and EBV gp350 ##### Variables * Peptide: Identification # based on peptide mass derived from EXPASY PEPTIDEMASS * Forward: amino terminus  &gt; carboxy terminus orientation of in silico N-lysozyme-digested peptide * Reverse: carboxy terminus &gt; amino terminus orientation of in silico N-lysozyme-digested peptide #### File: 4-BKVvp1\_EBVgp350\_Peptides.csv **Description:** Expasy PeptideMass calculated peptide sequences based on in silico N-lysozyme-digested envelope proteins BK virus VP1 and EBV gp350 ##### Variables * Peptide: Expasy PeptideMass identification # based on peptide mass * Forward: amino terminus  &gt; carboxy terminus orientation of in silico N-lysozyme-digested peptide * Reverse: carboxy terminus &gt; amino terminus orientation of in silico N-lysozyme-digested peptide #### File: 4-CMVgB\_EBVgp350\_HLAClss1Peptides.csv **Description:** Expasy PeptideMass calculated peptide sequences based on in silico N-lysozyme-digested envelope proteins Cytomegalovirus gB and EBV gp350 ##### Variables * Peptide: Expasy PeptideMass identification # based on peptide mass * Forward: amino terminus  &gt; carboxy terminus orientation of in silico N-lysozyme-digested peptide * Reverse: carboxy terminus &gt; amino terminus orientation of in silico N-lysozyme-digested peptide #### File: 4-CMVgB\_EBVgp350\_HLAClss2Peptides.csv **Description:** Expasy PeptideMass calculated peptide sequences based on in silico N-lysozyme-digested envelope proteins Cytomegalovirus gB and EBV gp350 ##### Variables * Peptide: Expasy PeptideMass identification # based on peptide mass * Forward: amino terminus  &gt; carboxy terminus orientation of in silico N-lysozyme-digested peptide * Reverse: carboxy terminus &gt; amino terminus orientation of in silico N-lysozyme-digested peptide #### File: 4-CoronaOC43spike\_EBVgp350\_Peptides.csv **Description:** Expasy PeptideMass calculated peptide sequences based on in silico N-lysozyme-digested envelope proteins coronavirus spike protein and EBV gp350 ##### Variables * Peptide: Expasy PeptideMass identification # based on peptide mass * Forward: amino terminus  &gt; carboxy terminus orientation of in silico N-lysozyme-digested peptide * Reverse: carboxy terminus &gt; amino terminus orientation of in silico N-lysozyme-digested peptide #### File: 4-H1N1\_EBVgp350\_Peptides.csv **Description:** Expasy PeptideMass calculated peptide sequences based on in silico N-lysozyme-digested envelope proteins H1N1 hemagglutinin, neuraminidase and EBV gp350 ##### Variables * Peptide:Expasy PeptideMass identification # based on peptide mass * Forward: amino terminus  &gt; carboxy terminus orientation of in silico N-lysozyme-digested peptide * Reverse: carboxy terminus &gt; amino terminus orientation of in silico N-lysozyme-digested peptide #### File: 4-H3N2\_EBVgp350\_Peptides.csv **Description:** Expasy PeptideMass calculated peptide sequences based on in silico N-lysozyme-digested envelope proteins H3N2 hemmaglutinin, neuraminidase and EBV gp350 ##### Variables * Peptide:Expasy PeptideMass identification # based on peptide mass * Forward: amino terminus  &gt; carboxy terminus orientation of in silico N-lysozyme-digested peptide * Reverse: carboxy terminus &gt; amino terminus orientation of in silico N-lysozyme-digested peptide #### File: 4-EBVgB\_EBVgp350\_Peptides.csv **Description:** Expasy PeptideMass calculated peptide sequences based on in silico N-lysozyme-digested envelope proteins Epstein Barr virus gB and EBV gp350 ##### Variables * Peptide:Expasy PeptideMass identification # based on peptide mass * Forward: amino terminus  &gt; carboxy terminus orientation of in silico N-lysozyme-digested peptide * Reverse: carboxy terminus &gt; amino terminus orientation of in silico N-lysozyme-digested peptide #### File: 4-HHV6BgB\_EBVgp350\_Peptides.csv **Description:** Expasy PeptideMass calculated peptide sequences based on in silico N-lysozyme-digested envelope proteins human herpes virus 6B gB and EBV gp350 ##### Variables * Peptide:Expasy PeptideMass identification # based on peptide mass * Forward: amino terminus  &gt; carboxy terminus orientation of in silico N-lysozyme-digested peptide * Reverse: carboxy terminus &gt; amino terminus orientation of in silico N-lysozyme-digested peptide #### File: 4-hRVvp1\_EBVgp350\_HLAC1Peptides.csv **Description:** Expasy PeptideMass calculated peptide sequences based on in silico N-lysozyme-digested envelope proteins human rhinovirus VP1 (clades B & C) and EBV gp350 ##### Variables * Peptide:Expasy PeptideMass identification # based on peptide mass * Forward: amino terminus  &gt; carboxy terminus orientation of in silico N-lysozyme-digested peptide * Reverse: carboxy terminus &gt; amino terminus orientation of in silico N-lysozyme-digested peptide #### File: 4-hRVvp1\_EBVgp350\_HLAC2Peptides.csv **Description:** Expasy PeptideMass calculated peptide sequences based on in silico N-lysozyme-digested envelope proteins human rhinovirus VP1 (clades A & B) and EBV gp350 ##### Variables * Peptide: Expasy PeptideMass identification # based on peptide mass * Forward: amino terminus  &gt; carboxy terminus orientation of in silico N-lysozyme-digested peptide * Reverse: carboxy terminus &gt; amino terminus orientation of in silico N-lysozyme-digested peptide #### File: 4-HSV1gB\_EBVgp350\_Peptides.csv **Description:** Expasy PeptideMass calculated peptide sequences based on in silico N-lysozyme-digested envelope proteins herpes simplex virus-1 glycoprotein B and EBV gp350 ##### Variables * HSV: Expasy PeptideMass identification # based on peptide mass * Sequence: amino terminus  &gt; carboxy terminus orientation of in silico N-lysozyme-digested peptide * Reverse: carboxy terminus &gt; amino terminus orientation of in silico N-lysozyme-digested peptide #### File: 4-InfluenzaB\_EBVgp350\_Peptides.csv **Description:** Expasy PeptideMass calculated peptide sequences based on in silico N-lysozyme-digested envelope proteins influenza B hemagglutinin, neuraminidase and EBV gp350 ##### Variables * Peptide: Expasy PeptideMass identification # based on peptide mass * Forward: amino terminus  &gt; carboxy terminus orientation of in silico N-lysozyme-digested peptide * Reverse: carboxy terminus &gt; amino terminus orientation of in silico N-lysozyme-digested peptide #### File: 4-MetapnmVfusion\_EBVgp350\_Peptides.csv **Description:** Expasy PeptideMass calculated peptide sequences based on in silico N-lysozyme-digested envelope proteins metapneumovirus fusion protein and EBV gp350 ##### Variables * Peptide: Expasy PeptideMass identification # based on peptide mass * Forward: amino terminus  &gt; carboxy terminus orientation of in silico N-lysozyme-digested peptide * Reverse: carboxy terminus &gt; amino terminus orientation of in silico N-lysozyme-digested peptide #### File: 4-SARSCoV2spike\_EBVgp350\_Peptides.csv **Description:** Expasy PeptideMass calculated peptide sequences based on in silico N-lysozyme-digested envelope proteins SARS-CoV-2 spike protein and EBV gp350 ##### Variables * Peptide: Expasy PeptideMass identification # based on peptide mass * Forward: amino terminus  &gt; carboxy terminus orientation of in silico N-lysozyme-digested peptide * Reverse: carboxy terminus &gt; amino terminus orientation of in silico N-lysozyme-digested peptide #### File: 4-VZVgB\_EBVgp350\_Peptides.csv **Description:** Expasy PeptideMass calculated peptide sequences based on in silico N-lysozyme-digested envelope proteins varicella zoster virus and EBV gp350 ##### Variables * Peptide: Expasy PeptideMass identification # based on peptide mass * Forward: amino terminus  &gt; carboxy terminus orientation of in silico N-lysozyme-digested peptide * Reverse: carboxy terminus &gt; amino terminus orientation of in silico N-lysozyme-digested peptide #### File: 5-HLA-A0201\_CMV\_EBV\_SortedPeptides.csv **Description:** peptide homology derived from comparing viral peptides (found in file type 4) to HLA specificity via Smith Waterman algorithm (EMBOSS Water) ##### Variables * Expasy generated peptide ID: peptide identification as listed in type 4 file column A * Virus protein: origin of peptide * \#N-glycans: # of N-Glycan sequons present on complete peptide as listed in type 4 file column B/C * HLA-[specificity] homologous Gapped Viral Peptide Sequences: Smith Waterman derived sequence homology of peptide including gaps ('x'/'-') * HLA start residue: starting residue of peptide based on location of mature HLA protein * ERP: ectodomain relative score applied according to NETRAD algorithm (see manuscript) * HLA specific: whether peptide contains hypervariable location residues * Chain: HLA Class II epitope analyses (DQ/DP are analyzed for both alpha or beta chains) * Additional columns: spillover from original excel spreadsheet may correspond to epitope derivation #### File: 5-HLA-A0301\_AdenoV\_EBV\_SortedPeptides.csv **Description:** peptide homology derived from comparing viral peptides (found in file type 4) to HLA specificity via Smith Waterman algorithm (EMBOSS Water) ##### Variables * Expasy generated peptide ID: peptide identification as listed in type 4 file column A * Virus protein: origin of peptide * \#N-glycans: # of N-Glycan sequons present on complete peptide as listed in type 4 file column B/C * HLA-[specificity] homologous Gapped Viral Peptide Sequences: Smith Waterman derived sequence homology of peptide including gaps ('x'/'-') * HLA start residue: starting residue of peptide based on location of mature HLA protein * ERP: ectodomain relative score applied according to NETRAD algorithm (see manuscript) * HLA specific: whether peptide contains hypervariable location residues * Chain: HLA Class II epitope analyses (DQ/DP are analyzed for both alpha or beta chains) * Additional columns: spillover from original excel spreadsheet may correspond to epitope derivation #### File: 5-HLA-A3001\_BKV\_EBV\_SortedPeptides.csv **Description:** peptide homology derived from comparing viral peptides (found in file type 4) to HLA specificity via Smith Waterman algorithm (EMBOSS Water) ##### Variables * Expasy generated peptide ID: peptide identification as listed in type 4 file column A * Virus protein: origin of peptide * \#N-glycans: # of N-Glycan sequons present on complete peptide as listed in type 4 file column B/C * HLA-[specificity] homologous Gapped Viral Peptide Sequences: Smith Waterman derived sequence homology of peptide including gaps ('x'/'-') * HLA start residue: starting residue of peptide based on location of mature HLA protein * ERP: ectodomain relative score applied according to NETRAD algorithm (see manuscript) * HLA specific: whether peptide contains hypervariable location residues * Chain: HLA Class II epitope analyses (DQ/DP are analyzed for both alpha or beta chains) * Additional columns: spillover from original excel spreadsheet may correspond to epitope derivation #### File: 5-HLA-A1102\_MetapnV\_EBV\_SortedPeptides.csv **Description:** peptide homology derived from comparing viral peptides (found in file type 4) to HLA specificity via Smith Waterman algorithm (EMBOSS Water) ##### Variables * Expasy generated peptide ID: peptide identification as listed in type 4 file column A * Virus protein: origin of peptide * \#N-glycans: # of N-Glycan sequons present on complete peptide as listed in type 4 file column B/C * HLA-[specificity] homologous Gapped Viral Peptide Sequences: Smith Waterman derived sequence homology of peptide including gaps ('x'/'-') * HLA start residue: starting residue of peptide based on location of mature HLA protein * ERP: ectodomain relative score applied according to NETRAD algorithm (see manuscript) * HLA specific: whether peptide contains hypervariable location residues * Chain: HLA Class II epitope analyses (DQ/DP are analyzed for both alpha or beta chains) * Additional columns: spillover from original excel spreadsheet may correspond to epitope derivation #### File: 5-HLA-A8001\_hRV\_EBV\_SortedPeptides.csv **Description:** peptide homology derived from comparing viral peptides (found in file type 4) to HLA specificity via Smith Waterman algorithm (EMBOSS Water) ##### Variables * Expasy generated peptide ID: peptide identification as listed in type 4 file column A * Virus protein: origin of peptide * \#N-glycans: # of N-Glycan sequons present on complete peptide as listed in type 4 file column B/C * HLA-[specificity] homologous Gapped Viral Peptide Sequences: Smith Waterman derived sequence homology of peptide including gaps ('x'/'-') * HLA start residue: starting residue of peptide based on location of mature HLA protein * ERP: ectodomain relative score applied according to NETRAD algorithm (see manuscript) * HLA specific: whether peptide contains hypervariable location residues * Chain: HLA Class II epitope analyses (DQ/DP are analyzed for both alpha or beta chains) * Additional columns: spillover from original excel spreadsheet may correspond to epitope derivation #### File: 5-HLA-B0702\_HHV6B\_EBV\_SortedPeptides.csv **Description:** peptide homology derived from comparing viral peptides (found in file type 4) to HLA specificity via Smith Waterman algorithm (EMBOSS Water) ##### Variables * Expasy generated peptide ID: peptide identification as listed in type 4 file column A * Virus protein: origin of peptide * \#N-glycans: # of N-Glycan sequons present on complete peptide as listed in type 4 file column B/C * HLA-[specificity] homologous Gapped Viral Peptide Sequences: Smith Waterman derived sequence homology of peptide including gaps ('x'/'-') * HLA start residue: starting residue of peptide based on location of mature HLA protein * ERP: ectodomain relative score applied according to NETRAD algorithm (see manuscript) * HLA specific: whether peptide contains hypervariable location residues * Chain: HLA Class II epitope analyses (DQ/DP are analyzed for both alpha or beta chains) * Additional columns: spillover from original excel spreadsheet may correspond to epitope derivation #### File: 5-HLA-B1512\_InfluenzaB\_EBV\_SortedPeptides.csv **Description:** peptide homology derived from comparing viral peptides (found in file type 4) to HLA specificity via Smith Waterman algorithm (EMBOSS Water) ##### Variables * Expasy generated peptide ID: peptide identification as listed in type 4 file column A * Virus protein: origin of peptide * \#N-glycans: # of N-Glycan sequons present on complete peptide as listed in type 4 file column B/C * HLA-[specificity] homologous Gapped Viral Peptide Sequences: Smith Waterman derived sequence homology of peptide including gaps ('x'/'-') * HLA start residue: starting residue of peptide based on location of mature HLA protein * ERP: ectodomain relative score applied according to NETRAD algorithm (see manuscript) * HLA specific: whether peptide contains hypervariable location residues * Chain: HLA Class II epitope analyses (DQ/DP are analyzed for both alpha or beta chains) * Additional columns: spillover from original excel spreadsheet may correspond to epitope derivation #### File: 5-HLA-B2705NegCtrl\_H3N2\_EBV\_SortedPeptides.csv **Description:** peptide homology derived from comparing viral peptides (found in file type 4) to HLA specificity via Smith Waterman algorithm (EMBOSS Water) ##### Variables * Expasy generated peptide ID: peptide identification as listed in type 4 file column A * Virus protein: origin of peptide * \#N-glycans: # of N-Glycan sequons present on complete peptide as listed in type 4 file column B/C * HLA-[specificity] homologous Gapped Viral Peptide Sequences: Smith Waterman derived sequence homology of peptide including gaps ('x'/'-') * HLA start residue: starting residue of peptide based on location of mature HLA protein * ERP: ectodomain relative score applied according to NETRAD algorithm (see manuscript) * HLA specific: whether peptide contains hypervariable location residues * Chain: HLA Class II epitope analyses (DQ/DP are analyzed for both alpha or beta chains) * Additional columns: spillover from original excel spreadsheet may correspond to epitope derivation #### File: 5-HLA-B3701\_CMV\_EBV\_SortedPeptides.csv **Description:** peptide homology derived from comparing viral peptides (found in file type 4) to HLA specificity via Smith Waterman algorithm (EMBOSS Water) ##### Variables * Expasy generated peptide ID: peptide identification as listed in type 4 file column A * Virus protein: origin of peptide * \#N-glycans: # of N-Glycan sequons present on complete peptide as listed in type 4 file column B/C * HLA-[specificity] homologous Gapped Viral Peptide Sequences: Smith Waterman derived sequence homology of peptide including gaps ('x'/'-') * HLA start residue: starting residue of peptide based on location of mature HLA protein * ERP: ectodomain relative score applied according to NETRAD algorithm (see manuscript) * HLA specific: whether peptide contains hypervariable location residues * Chain: HLA Class II epitope analyses (DQ/DP are analyzed for both alpha or beta chains) * Additional columns: spillover from original excel spreadsheet may correspond to epitope derivation #### File: 5-HLA-B2705\_InfluenzaB\_EBV\_SortedPeptides.csv **Description:** peptide homology derived from comparing viral peptides (found in file type 4) to HLA specificity via Smith Waterman algorithm (EMBOSS Water) ##### Variables * Expasy generated peptide ID: peptide identification as listed in type 4 file column A * Virus protein: origin of peptide * \#N-glycans: # of N-Glycan sequons present on complete peptide as listed in type 4 file column B/C * HLA-[specificity] homologous Gapped Viral Peptide Sequences: Smith Waterman derived sequence homology of peptide including gaps ('x'/'-') * HLA start residue: starting residue of peptide based on location of mature HLA protein * ERP: ectodomain relative score applied according to NETRAD algorithm (see manuscript) * HLA specific: whether peptide contains hypervariable location residues * Chain: HLA Class II epitope analyses (DQ/DP are analyzed for both alpha or beta chains) * Additional columns: spillover from original excel spreadsheet may correspond to epitope derivation #### File: 5-HLA-B4402\_InfluenzaB\_EBV\_SortedPeptides.csv **Description:** peptide homology derived from comparing viral peptides (found in file type 4) to HLA specificity via Smith Waterman algorithm (EMBOSS Water) ##### Variables * Expasy generated peptide ID: peptide identification as listed in type 4 file column A * Virus protein: origin of peptide * \#N-glycans: # of N-Glycan sequons present on complete peptide as listed in type 4 file column B/C * HLA-[specificity] homologous Gapped Viral Peptide Sequences: Smith Waterman derived sequence homology of peptide including gaps ('x'/'-') * HLA start residue: starting residue of peptide based on location of mature HLA protein * ERP: ectodomain relative score applied according to NETRAD algorithm (see manuscript) * HLA specific: whether peptide contains hypervariable location residues * Chain: HLA Class II epitope analyses (DQ/DP are analyzed for both alpha or beta chains) * Additional columns: spillover from original excel spreadsheet may correspond to epitope derivation #### File: 5-HLA-B1302\_InfluenzaB\_EBV\_SortedPeptides.csv **Description:** peptide homology derived from comparing viral peptides (found in file type 4) to HLA specificity via Smith Waterman algorithm (EMBOSS Water) ##### Variables * Expasy generated peptide ID: peptide identification as listed in type 4 file column A * Virus protein: origin of peptide * \#N-glycans: # of N-Glycan sequons present on complete peptide as listed in type 4 file column B/C * HLA-[specificity] homologous Gapped Viral Peptide Sequences: Smith Waterman derived sequence homology of peptide including gaps ('x'/'-') * HLA start residue: starting residue of peptide based on location of mature HLA protein * ERP: ectodomain relative score applied according to NETRAD algorithm (see manuscript) * HLA specific: whether peptide contains hypervariable location residues * Chain: HLA Class II epitope analyses (DQ/DP are analyzed for both alpha or beta chains) * Additional columns: spillover from original excel spreadsheet may correspond to epitope derivation #### File: 5-HLA-B5501\_VZV\_EBV\_SortedPeptides.csv **Description:** peptide homology derived from comparing viral peptides (found in file type 4) to HLA specificity via Smith Waterman algorithm (EMBOSS Water) ##### Variables * Expasy generated peptide ID: peptide identification as listed in type 4 file column A * Virus protein: origin of peptide * \#N-glycans: # of N-Glycan sequons present on complete peptide as listed in type 4 file column B/C * HLA-[specificity] homologous Gapped Viral Peptide Sequences: Smith Waterman derived sequence homology of peptide including gaps ('x'/'-') * HLA start residue: starting residue of peptide based on location of mature HLA protein * ERP: ectodomain relative score applied according to NETRAD algorithm (see manuscript) * HLA specific: whether peptide contains hypervariable location residues * Chain: HLA Class II epitope analyses (DQ/DP are analyzed for both alpha or beta chains) * Additional columns: spillover from original excel spreadsheet may correspond to epitope derivation #### File: 5-HLA-A0201\_HSV1\_EBV\_SortedPeptides.csv **Description:** peptide homology derived from comparing viral peptides (found in file type 4) to HLA specificity via Smith Waterman algorithm (EMBOSS Water) ##### Variables * Expasy generated peptide ID: peptide identification as listed in type 4 file column A * Virus protein: origin of peptide * \#N-glycans: # of N-Glycan sequons present on complete peptide as listed in type 4 file column B/C * HLA-[specificity] homologous Gapped Viral Peptide Sequences: Smith Waterman derived sequence homology of peptide including gaps ('x'/'-') * HLA start residue: starting residue of peptide based on location of mature HLA protein * ERP: ectodomain relative score applied according to NETRAD algorithm (see manuscript) * HLA specific: whether peptide contains hypervariable location residues * Chain: HLA Class II epitope analyses (DQ/DP are analyzed for both alpha or beta chains) * Additional columns: spillover from original excel spreadsheet may correspond to epitope derivation #### File: 5-HLA-B5101\_HSV1\_EBV\_SortedPeptides.csv **Description:** peptide homology derived from comparing viral peptides (found in file type 4) to HLA specificity via Smith Waterman algorithm (EMBOSS Water) ##### Variables * Expasy generated peptide ID: peptide identification as listed in type 4 file column A * Virus protein: origin of peptide * \#N-glycans: # of N-Glycan sequons present on complete peptide as listed in type 4 file column B/C * HLA-[specificity] homologous Gapped Viral Peptide Sequences: Smith Waterman derived sequence homology of peptide including gaps ('x'/'-') * HLA start residue: starting residue of peptide based on location of mature HLA protein * ERP: ectodomain relative score applied according to NETRAD algorithm (see manuscript) * HLA specific: whether peptide contains hypervariable location residues * Chain: HLA Class II epitope analyses (DQ/DP are analyzed for both alpha or beta chains) * Additional columns: spillover from original excel spreadsheet may correspond to epitope derivation #### File: 5-HLA-B5701\_EBVgB\_EBV\_SortedPeptides.csv **Description:** peptide homology derived from comparing viral peptides (found in file type 4) to HLA specificity via Smith Waterman algorithm (EMBOSS Water) ##### Variables * Expasy generated peptide ID: peptide identification as listed in type 4 file column A * Virus protein: origin of peptide * \#N-glycans: # of N-Glycan sequons present on complete peptide as listed in type 4 file column B/C * HLA-[specificity] homologous Gapped Viral Peptide Sequences: Smith Waterman derived sequence homology of peptide including gaps ('x'/'-') * HLA start residue: starting residue of peptide based on location of mature HLA protein * ERP: ectodomain relative score applied according to NETRAD algorithm (see manuscript) * HLA specific: whether peptide contains hypervariable location residues * Chain: HLA Class II epitope analyses (DQ/DP are analyzed for both alpha or beta chains) * Additional columns: spillover from original excel spreadsheet may correspond to epitope derivation #### File: 5-HLA-C0701\_SARS\_EBV\_SortedPeptides.csv **Description:** peptide homology derived from comparing viral peptides (found in file type 4) to HLA specificity via Smith Waterman algorithm (EMBOSS Water) ##### Variables * Expasy generated peptide ID: peptide identification as listed in type 4 file column A * Virus protein: origin of peptide * \#N-glycans: # of N-Glycan sequons present on complete peptide as listed in type 4 file column B/C * HLA-[specificity] homologous Gapped Viral Peptide Sequences: Smith Waterman derived sequence homology of peptide including gaps ('x'/'-') * HLA start residue: starting residue of peptide based on location of mature HLA protein * ERP: ectodomain relative score applied according to NETRAD algorithm (see manuscript) * HLA specific: whether peptide contains hypervariable location residues * Chain: HLA Class II epitope analyses (DQ/DP are analyzed for both alpha or beta chains) * Additional columns: spillover from original excel spreadsheet may correspond to epitope derivation #### File: 5-HLA-A2501\_H1N1\_EBV\_SortedPeptides.csv **Description:** peptide homology derived from comparing viral peptides (found in file type 4) to HLA specificity via Smith Waterman algorithm (EMBOSS Water) ##### Variables * Expasy generated peptide ID: peptide identification as listed in type 4 file column A * Virus protein: origin of peptide * \#N-glycans: # of N-Glycan sequons present on complete peptide as listed in type 4 file column B/C * HLA-[specificity] homologous Gapped Viral Peptide Sequences: Smith Waterman derived sequence homology of peptide including gaps ('x'/'-') * HLA start residue: starting residue of peptide based on location of mature HLA protein * ERP: ectodomain relative score applied according to NETRAD algorithm (see manuscript) * HLA specific: whether peptide contains hypervariable location residues * Chain: HLA Class II epitope analyses (DQ/DP are analyzed for both alpha or beta chains) * Additional columns: spillover from original excel spreadsheet may correspond to epitope derivation #### File: 5-HLA-A2901\_CoronaOC43\_EBV\_SortedPeptides.csv **Description:** peptide homology derived from comparing viral peptides (found in file type 4) to HLA specificity via Smith Waterman algorithm (EMBOSS Water) ##### Variables * Expasy generated peptide ID: peptide identification as listed in type 4 file column A * Virus protein: origin of peptide * \#N-glycans: # of N-Glycan sequons present on complete peptide as listed in type 4 file column B/C * HLA-[specificity] homologous Gapped Viral Peptide Sequences: Smith Waterman derived sequence homology of peptide including gaps ('x'/'-') * HLA start residue: starting residue of peptide based on location of mature HLA protein * ERP: ectodomain relative score applied according to NETRAD algorithm (see manuscript) * HLA specific: whether peptide contains hypervariable location residues * Chain: HLA Class II epitope analyses (DQ/DP are analyzed for both alpha or beta chains) * Additional columns: spillover from original excel spreadsheet may correspond to epitope derivation #### File: 5-HLA-DP1\_hRV\_EBV\_SortedPeptides.csv **Description:** peptide homology derived from comparing viral peptides (found in file type 4) to HLA specificity via Smith Waterman algorithm (EMBOSS Water) ##### Variables * Expasy generated peptide ID: peptide identification as listed in type 4 file column A * Virus protein: origin of peptide * \#N-glycans: # of N-Glycan sequons present on complete peptide as listed in type 4 file column B/C * HLA-[specificity] homologous Gapped Viral Peptide Sequences: Smith Waterman derived sequence homology of peptide including gaps ('x'/'-') * HLA start residue: starting residue of peptide based on location of mature HLA protein * ERP: ectodomain relative score applied according to NETRAD algorithm (see manuscript) * HLA specific: whether peptide contains hypervariable location residues * Chain: HLA Class II epitope analyses (DQ/DP are analyzed for both alpha or beta chains) * Additional columns: spillover from original excel spreadsheet may correspond to epitope derivation #### File: 5-HLA-DR3\_CMV\_EBV\_SortedPeptides.csv **Description:** peptide homology derived from comparing viral peptides (found in file type 4) to HLA specificity via Smith Waterman algorithm (EMBOSS Water) ##### Variables * Expasy generated peptide ID: peptide identification as listed in type 4 file column A * Virus protein: origin of peptide * \#N-glycans: # of N-Glycan sequons present on complete peptide as listed in type 4 file column B/C * HLA-[specificity] homologous Gapped Viral Peptide Sequences: Smith Waterman derived sequence homology of peptide including gaps ('x'/'-') * HLA start residue: starting residue of peptide based on location of mature HLA protein * ERP: ectodomain relative score applied according to NETRAD algorithm (see manuscript) * HLA specific: whether peptide contains hypervariable location residues * Chain: HLA Class II epitope analyses (DQ/DP are analyzed for both alpha or beta chains) * Additional columns: spillover from original excel spreadsheet may correspond to epitope derivation #### File: 5-HLA-A2301\_HSV1\_EBV\_SortedPeptides.csv **Description:** peptide homology derived from comparing viral peptides (found in file type 4) to HLA specificity via Smith Waterman algorithm (EMBOSS Water) ##### Variables * Expasy generated peptide ID: peptide identification as listed in type 4 file column A * Virus protein: origin of peptide * \#N-glycans: # of N-Glycan sequons present on complete peptide as listed in type 4 file column B/C * HLA-[specificity] homologous Gapped Viral Peptide Sequences: Smith Waterman derived sequence homology of peptide including gaps ('x'/'-') * HLA start residue: starting residue of peptide based on location of mature HLA protein * ERP: ectodomain relative score applied according to NETRAD algorithm (see manuscript) * HLA specific: whether peptide contains hypervariable location residues * Chain: HLA Class II epitope analyses (DQ/DP are analyzed for both alpha or beta chains) * Additional columns: spillover from original excel spreadsheet may correspond to epitope derivation #### File: 5-HLA-A3001NegCntrl\_HSV1\_EBV\_SortedPeptides.csv **Description:** peptide homology derived from comparing viral peptides (found in file type 4) to HLA specificity via Smith Waterman algorithm (EMBOSS Water) ##### Variables * Expasy generated peptide ID: peptide identification as listed in type 4 file column A * Virus protein: origin of peptide * \#N-glycans: # of N-Glycan sequons present on complete peptide as listed in type 4 file column B/C * HLA-[specificity] homologous Gapped Viral Peptide Sequences: Smith Waterman derived sequence homology of peptide including gaps ('x'/'-') * HLA start residue: starting residue of peptide based on location of mature HLA protein * ERP: ectodomain relative score applied according to NETRAD algorithm (see manuscript) * HLA specific: whether peptide contains hypervariable location residues * Chain: HLA Class II epitope analyses (DQ/DP are analyzed for both alpha or beta chains) * Additional columns: spillover from original excel spreadsheet may correspond to epitope derivation #### File: 5-HLA-DR4\_H3N2\_EBV\_SortedPeptides.csv **Description:** peptide homology derived from comparing viral peptides (found in file type 4) to HLA specificity via Smith Waterman algorithm (EMBOSS Water) ##### Variables * Expasy generated peptide ID: peptide identification as listed in type 4 file column A * Virus protein: origin of peptide * \#N-glycans: # of N-Glycan sequons present on complete peptide as listed in type 4 file column B/C * HLA-[specificity] homologous Gapped Viral Peptide Sequences: Smith Waterman derived sequence homology of peptide including gaps ('x'/'-') * HLA start residue: starting residue of peptide based on location of mature HLA protein * ERP: ectodomain relative score applied according to NETRAD algorithm (see manuscript) * HLA specific: whether peptide contains hypervariable location residues * Chain: HLA Class II epitope analyses (DQ/DP are analyzed for both alpha or beta chains) * Additional columns: spillover from original excel spreadsheet may correspond to epitope derivation #### File: 5-HLA-DR7\_InfluenzaB\_EBV\_SortedPeptides.csv **Description:** peptide homology derived from comparing viral peptides (found in file type 4) to HLA specificity via Smith Waterman algorithm (EMBOSS Water) ##### Variables * Expasy generated peptide ID: peptide identification as listed in type 4 file column A * Virus protein: origin of peptide * \#N-glycans: # of N-Glycan sequons present on complete peptide as listed in type 4 file column B/C * HLA-[specificity] homologous Gapped Viral Peptide Sequences: Smith Waterman derived sequence homology of peptide including gaps ('x'/'-') * HLA start residue: starting residue of peptide based on location of mature HLA protein * ERP: ectodomain relative score applied according to NETRAD algorithm (see manuscript) * HLA specific: whether peptide contains hypervariable location residues * Chain: HLA Class II epitope analyses (DQ/DP are analyzed for both alpha or beta chains) * Additional columns: spillover from original excel spreadsheet may correspond to epitope derivation #### File: 5-HLA-DR11\_AdenoV\_EBV\_SortedPeptides.csv **Description:** peptide homology derived from comparing viral peptides (found in file type 4) to HLA specificity via Smith Waterman algorithm (EMBOSS Water) ##### Variables * Expasy generated peptide ID: peptide identification as listed in type 4 file column A * Virus protein: origin of peptide * \#N-glycans: # of N-Glycan sequons present on complete peptide as listed in type 4 file column B/C * HLA-[specificity] homologous Gapped Viral Peptide Sequences: Smith Waterman derived sequence homology of peptide including gaps ('x'/'-') * HLA start residue: starting residue of peptide based on location of mature HLA protein * ERP: ectodomain relative score applied according to NETRAD algorithm (see manuscript) * HLA specific: whether peptide contains hypervariable location residues * Chain: HLA Class II epitope analyses (DQ/DP are analyzed for both alpha or beta chains) * Additional columns: spillover from original excel spreadsheet may correspond to epitope derivation #### File: 5-HLA-DR15\_HHV6B\_EBV\_SortedPeptides.csv **Description:** peptide homology derived from comparing viral peptides (found in file type 4) to HLA specificity via Smith Waterman algorithm (EMBOSS Water) ##### Variables * Expasy generated peptide ID: peptide identification as listed in type 4 file column A * Virus protein: origin of peptide * \#N-glycans: # of N-Glycan sequons present on complete peptide as listed in type 4 file column B/C * HLA-[specificity] homologous Gapped Viral Peptide Sequences: Smith Waterman derived sequence homology of peptide including gaps ('x'/'-') * HLA start residue: starting residue of peptide based on location of mature HLA protein * ERP: ectodomain relative score applied according to NETRAD algorithm (see manuscript) * HLA specific: whether peptide contains hypervariable location residues * Chain: HLA Class II epitope analyses (DQ/DP are analyzed for both alpha or beta chains) * Additional columns: spillover from original excel spreadsheet may correspond to epitope derivation #### File: 5-HLA-DR15\_SARS\_EBV\_SortedPeptides.csv **Description:** peptide homology derived from comparing viral peptides (found in file type 4) to HLA specificity via Smith Waterman algorithm (EMBOSS Water) ##### Variables * Expasy generated peptide ID: peptide identification as listed in type 4 file column A * Virus protein: origin of peptide * \#N-glycans: # of N-Glycan sequons present on complete peptide as listed in type 4 file column B/C * HLA-[specificity] homologous Gapped Viral Peptide Sequences: Smith Waterman derived sequence homology of peptide including gaps ('x'/'-') * HLA start residue: starting residue of peptide based on location of mature HLA protein * ERP: ectodomain relative score applied according to NETRAD algorithm (see manuscript) * HLA specific: whether peptide contains hypervariable location residues * Chain: HLA Class II epitope analyses (DQ/DP are analyzed for both alpha or beta chains) * Additional columns: spillover from original excel spreadsheet may correspond to epitope derivation #### File: 5-HLA-DQ8\_BKV\_EBV\_SortedPeptides.csv **Description:** peptide homology derived from comparing viral peptides (found in file type 4) to HLA specificity via Smith Waterman algorithm (EMBOSS Water) ##### Variables * Expasy generated peptide ID: peptide identification as listed in type 4 file column A * Virus protein: origin of peptide * \#N-glycans: # of N-Glycan sequons present on complete peptide as listed in type 4 file column B/C * HLA-[specificity] homologous Gapped Viral Peptide Sequences: Smith Waterman derived sequence homology of peptide including gaps ('x'/'-') * HLA start residue: starting residue of peptide based on location of mature HLA protein * ERP: ectodomain relative score applied according to NETRAD algorithm (see manuscript) * HLA specific: whether peptide contains hypervariable location residues * Chain: HLA Class II epitope analyses (DQ/DP are analyzed for both alpha or beta chains) * Additional columns: spillover from original excel spreadsheet may correspond to epitope derivation #### File: 5-HLA-DQ9\_BKV\_EBV\_SortedPeptides.csv **Description:** peptide homology derived from comparing viral peptides (found in file type 4) to HLA specificity via Smith Waterman algorithm (EMBOSS Water) ##### Variables * Expasy generated peptide ID: peptide identification as listed in type 4 file column A * Virus protein: origin of peptide * \#N-glycans: # of N-Glycan sequons present on complete peptide as listed in type 4 file column B/C * HLA-[specificity] homologous Gapped Viral Peptide Sequences: Smith Waterman derived sequence homology of peptide including gaps ('x'/'-') * HLA start residue: starting residue of peptide based on location of mature HLA protein * ERP: ectodomain relative score applied according to NETRAD algorithm (see manuscript) * HLA specific: whether peptide contains hypervariable location residues * Chain: HLA Class II epitope analyses (DQ/DP are analyzed for both alpha or beta chains) * Additional columns: spillover from original excel spreadsheet may correspond to epitope derivation #### File: 5-HLA-DQ6\_H1N1\_EBV\_SortedPeptides.csv **Description:** peptide homology derived from comparing viral peptides (found in file type 4) to HLA specificity via Smith Waterman algorithm (EMBOSS Water) ##### Variables * Expasy generated peptide ID: peptide identification as listed in type 4 file column A * Virus protein: origin of peptide * \#N-glycans: # of N-Glycan sequons present on complete peptide as listed in type 4 file column B/C * HLA-[specificity] homologous Gapped Viral Peptide Sequences: Smith Waterman derived sequence homology of peptide including gaps ('x'/'-') * HLA start residue: starting residue of peptide based on location of mature HLA protein * ERP: ectodomain relative score applied according to NETRAD algorithm (see manuscript) * HLA specific: whether peptide contains hypervariable location residues * Chain: HLA Class II epitope analyses (DQ/DP are analyzed for both alpha or beta chains) * Additional columns: spillover from original excel spreadsheet may correspond to epitope derivation #### File: 5-HLA-DQ2\_InfluenzaB\_EBV\_SortedPeptides.csv **Description:** peptide homology derived from comparing viral peptides (found in file type 4) to HLA specificity via Smith Waterman algorithm (EMBOSS Water) ##### Variables * Expasy generated peptide ID: peptide identification as listed in type 4 file column A - Virus protein: origin of peptide - \#N-glycans: # of N-Glycan sequons present on complete peptide as listed in type 4 file column B/C - HLA-[specificity] homologous Gapped Viral Peptide Sequences: Smith Waterman derived sequence homology of peptide including gaps ('x'/'-') - HLA start residue: starting residue of peptide based on location of mature HLA protein - ERP: ectodomain relative score applied according to NETRAD algorithm (see manuscript) - HLA specific: whether peptide contains hypervariable location residues - Chain: HLA Class II epitope analyses (DQ/DP are analyzed for both alpha or beta chains) - Additional columns: spillover from original excel spreadsheet may correspond to epitope derivation #### File: 5-HLA-B4501\_InfluenzaB\_EBV\_SortedPeptides.csv **Description:** peptide homology derived from comparing viral peptides (found in file type 4) to HLA specificity via Smith Waterman algorithm (EMBOSS Water) ##### Variables * Expasy generated peptide ID: peptide identification as listed in type 4 file column A - Virus protein: origin of peptide - \#N-glycans: # of N-Glycan sequons present on complete peptide as listed in type 4 file column B/C - HLA-[specificity] homologous Gapped Viral Peptide Sequences: Smith Waterman derived sequence homology of peptide including gaps ('x'/'-') - HLA start residue: starting residue of peptide based on location of mature HLA protein - ERP: ectodomain relative score applied according to NETRAD algorithm (see manuscript) - HLA specific: whether peptide contains hypervariable location residues - Chain: HLA Class II epitope analyses (DQ/DP are analyzed for both alpha or beta chains) - Additional columns: spillover from original excel spreadsheet may correspond to epitope derivation #### File: 5-HLA-DQ8\_BKV\_EBV\_SortedPeptides.csv **Description:** peptide homology derived from comparing viral peptides (found in file type 4) to HLA specificity via Smith Waterman algorithm (EMBOSS Water) ##### Variables * Expasy generated peptide ID: peptide identification as listed in type 4 file column A - Virus protein: origin of peptide - \#N-glycans: # of N-Glycan sequons present on complete peptide as listed in type 4 file column B/C - HLA-[specificity] homologous Gapped Viral Peptide Sequences: Smith Waterman derived sequence homology of peptide including gaps ('x'/'-') - HLA start residue: starting residue of peptide based on location of mature HLA protein - ERP: ectodomain relative score applied according to NETRAD algorithm (see manuscript) - HLA specific: whether peptide contains hypervariable location residues - Chain: HLA Class II epitope analyses (DQ/DP are analyzed for both alpha or beta chains) - Additional columns: spillover from original excel spreadsheet may correspond to epitope derivation #### File: 5-HLA-DQ9\_BKV\_EBV\_SortedPeptides.csv **Description:** peptide homology derived from comparing viral peptides (found in file type 4) to HLA specificity via Smith Waterman algorithm (EMBOSS Water) ##### Variables * Expasy generated peptide ID: peptide identification as listed in type 4 file column A - Virus protein: origin of peptide - \#N-glycans: # of N-Glycan sequons present on complete peptide as listed in type 4 file column B/C - HLA-[specificity] homologous Gapped Viral Peptide Sequences: Smith Waterman derived sequence homology of peptide including gaps ('x'/'-') - HLA start residue: starting residue of peptide based on location of mature HLA protein - ERP: ectodomain relative score applied according to NETRAD algorithm (see manuscript) - HLA specific: whether peptide contains hypervariable location residues - Chain: HLA Class II epitope analyses (DQ/DP are analyzed for both alpha or beta chains) - Additional columns: spillover from original excel spreadsheet may correspond to epitope derivation #### File: 5-HLA-DQ6\_H1N1\_EBV\_SortedPeptides.csv **Description:** peptide homology derived from comparing viral peptides (found in file type 4) to HLA specificity via Smith Waterman algorithm (EMBOSS Water) ##### Variables * Expasy generated peptide ID: peptide identification as listed in type 4 file column A - Virus protein: origin of peptide - \#N-glycans: # of N-Glycan sequons present on complete peptide as listed in type 4 file column B/C - HLA-[specificity] homologous Gapped Viral Peptide Sequences: Smith Waterman derived sequence homology of peptide including gaps ('x'/'-') - HLA start residue: starting residue of peptide based on location of mature HLA protein - ERP: ectodomain relative score applied according to NETRAD algorithm (see manuscript) - HLA specific: whether peptide contains hypervariable location residues - Chain: HLA Class II epitope analyses (DQ/DP are analyzed for both alpha or beta chains) - Additional columns: spillover from original excel spreadsheet may correspond to epitope derivation #### File: 5-HLA-DQ2\_InfluenzaB\_EBV\_SortedPeptides.csv **Description:** peptide homology derived from comparing viral peptides (found in file type 4) to HLA specificity via Smith Waterman algorithm (EMBOSS Water) ##### Variables * Expasy generated peptide ID: peptide identification as listed in type 4 file column A - Virus protein: origin of peptide - \#N-glycans: # of N-Glycan sequons present on complete peptide as listed in type 4 file column B/C - HLA-[specificity] homologous Gapped Viral Peptide Sequences: Smith Waterman derived sequence homology of peptide including gaps ('x'/'-') - HLA start residue: starting residue of peptide based on location of mature HLA protein - ERP: ectodomain relative score applied according to NETRAD algorithm (see manuscript) - HLA specific: whether peptide contains hypervariable location residues - Chain: HLA Class II epitope analyses (DQ/DP are analyzed for both alpha or beta chains) - Additional columns: spillover from original excel spreadsheet may correspond to epitope derivation #### File: 5-HLA-DR3\_H3N2\_EBV\_SortedPeptides.csv **Description:** peptide homology derived from comparing viral peptides (found in file type 4) to HLA specificity via Smith Waterman algorithm (EMBOSS Water) ##### Variables * ##### * Expasy generated peptide ID: peptide identification as listed in type 4 file column A * Virus protein: origin of peptide * \#N-glycans: # of N-Glycan sequons present on complete peptide as listed in type 4 file column B/C * HLA-[specificity] homologous Gapped Viral Peptide Sequences: Smith Waterman derived sequence homology of peptide including gaps ('x'/'-') * HLA start residue: starting residue of peptide based on location of mature HLA protein * ERP: ectodomain relative score applied according to NETRAD algorithm (see manuscript) * HLA specific: whether peptide contains hypervariable location residues * Chain: HLA Class II epitope analyses (DQ/DP are analyzed for both alpha or beta chains) * Additional columns: spillover from original excel spreadsheet may correspond to epitope derivation #### File: 5-HLA-C0401\_H1N1\_EBV\_SortedPeptides.csv **Description:** peptide homology derived from comparing viral peptides (found in file type 4) to HLA specificity via Smith Waterman algorithm (EMBOSS Water) ##### Variables * Expasy generated peptide ID: peptide identification as listed in type 4 file column A * Virus protein: origin of peptide * \#N-glycans: # of N-Glycan sequons present on complete peptide as listed in type 4 file column B/C * HLA-[specificity] homologous Gapped Viral Peptide Sequences: Smith Waterman derived sequence homology of peptide including gaps ('x'/'-') * HLA start residue: starting residue of peptide based on location of mature HLA protein * ERP: ectodomain relative score applied according to NETRAD algorithm (see manuscript) * HLA specific: whether peptide contains hypervariable location residues * Chain: HLA Class II epitope analyses (DQ/DP are analyzed for both alpha or beta chains) * Additional columns: spillover from original excel spreadsheet may correspond to epitope derivation #### File: 6-HLA-A0201\_CMV\_EBV\_Epitopes.csv **Description:** identification of 6 HLA-homologous viral peptide subsequences (listed in file type 5) needed to demarcate an HLA specific epitope (may be more than 1 listed per file) ##### Variables * Expasy generated peptide ID: peptide identifier as listed in type 4 file column A * Virus protein: origin of peptide * \#N-glycans: # of N-Glycan sequons present on complete peptide as listed in type 4 file column B/C * HLA-[specificity] homologous Gapped Viral Peptide Sequences: Smith Waterman derived sequence homology of peptide including gaps ('x'/'-') * HLA start residue: starting residue of peptide based on location of mature HLA protein * ERP: ectodomain relative score applied according to NETRAD algorithm (see manuscript) * HLA specific: whether peptide contains hypervariable location residues * Chain: HLA Class II epitope analyses (DQ/DP are analyzed for both alpha or beta chains) #### File: 6-HLA-A0201\_HSV1\_EBV\_Epitopes.csv **Description:** identification of 6 HLA-homologous viral peptide subsequences (listed in file type 5) needed to demarcate an HLA specific epitope (may be more than 1 listed per file) ##### Variables * Expasy generated peptide ID: peptide identifier as listed in type 4 file column A * Virus protein: origin of peptide * \#N-glycans: # of N-Glycan sequons present on complete peptide as listed in type 4 file column B/C * HLA-[specificity] homologous Gapped Viral Peptide Sequences: Smith Waterman derived sequence homology of peptide including gaps ('x'/'-') * HLA start residue: starting residue of peptide based on location of mature HLA protein * ERP: ectodomain relative score applied according to NETRAD algorithm (see manuscript) * HLA specific: whether peptide contains hypervariable location residues * Chain: HLA Class II epitope analyses (DQ/DP are analyzed for both alpha or beta chains) #### File: 6-HLA-A0301\_AdenoV\_EBV\_Epitope.csv **Description:** identification of 6 HLA-homologous viral peptide subsequences (listed in file type 5) needed to demarcate an HLA specific epitope (may be more than 1 listed per file) ##### Variables * Expasy generated peptide ID: peptide identifier as listed in type 4 file column A * Virus protein: origin of peptide * \#N-glycans: # of N-Glycan sequons present on complete peptide as listed in type 4 file column B/C * HLA-[specificity] homologous Gapped Viral Peptide Sequences: Smith Waterman derived sequence homology of peptide including gaps ('x'/'-') * HLA start residue: starting residue of peptide based on location of mature HLA protein * ERP: ectodomain relative score applied according to NETRAD algorithm (see manuscript) * HLA specific: whether peptide contains hypervariable location residues * Chain: HLA Class II epitope analyses (DQ/DP are analyzed for both alpha or beta chains) #### File: 6-HLA-A1102\_MetapnV\_EBV\_Epitopes.csv **Description:** identification of 6 HLA-homologous viral peptide subsequences (listed in file type 5) needed to demarcate an HLA specific epitope (may be more than 1 listed per file) ##### Variables * Expasy generated peptide ID: peptide identifier as listed in type 4 file column A * Virus protein: origin of peptide * \#N-glycans: # of N-Glycan sequons present on complete peptide as listed in type 4 file column B/C * HLA-[specificity] homologous Gapped Viral Peptide Sequences: Smith Waterman derived sequence homology of peptide including gaps ('x'/'-') * HLA start residue: starting residue of peptide based on location of mature HLA protein * ERP: ectodomain relative score applied according to NETRAD algorithm (see manuscript) * HLA specific: whether peptide contains hypervariable location residues * Chain: HLA Class II epitope analyses (DQ/DP are analyzed for both alpha or beta chains) #### File: 6-HLA-A2301\_HSV1\_EBV\_Epitopes.csv **Description:** identification of 6 HLA-homologous viral peptide subsequences (listed in file type 5) needed to demarcate an HLA specific epitope (may be more than 1 listed per file) ##### Variables * Expasy generated peptide ID: peptide identifier as listed in type 4 file column A * Virus protein: origin of peptide * \#N-glycans: # of N-Glycan sequons present on complete peptide as listed in type 4 file column B/C * HLA-[specificity] homologous Gapped Viral Peptide Sequences: Smith Waterman derived sequence homology of peptide including gaps ('x'/'-') * HLA start residue: starting residue of peptide based on location of mature HLA protein * ERP: ectodomain relative score applied according to NETRAD algorithm (see manuscript) * HLA specific: whether peptide contains hypervariable location residues * Chain: HLA Class II epitope analyses (DQ/DP are analyzed for both alpha or beta chains) #### File: 6-HLA-A2501\_H1N1\_EBV\_Epitopes.csv **Description:** identification of 6 HLA-homologous viral peptide subsequences (listed in file type 5) needed to demarcate an HLA specific epitope (may be more than 1 listed per file) ##### Variables * Expasy generated peptide ID: peptide identifier as listed in type 4 file column A * Virus protein: origin of peptide * \#N-glycans: # of N-Glycan sequons present on complete peptide as listed in type 4 file column B/C * HLA-[specificity] homologous Gapped Viral Peptide Sequences: Smith Waterman derived sequence homology of peptide including gaps ('x'/'-') * HLA start residue: starting residue of peptide based on location of mature HLA protein * ERP: ectodomain relative score applied according to NETRAD algorithm (see manuscript) * HLA specific: whether peptide contains hypervariable location residues * Chain: HLA Class II epitope analyses (DQ/DP are analyzed for both alpha or beta chains) #### File: 6-HLA-A2901\_CoronaOC43\_EBV\_Epitopes.csv **Description:** identification of 6 HLA-homologous viral peptide subsequences (listed in file type 5) needed to demarcate an HLA specific epitope (may be more than 1 listed per file) ##### Variables * Expasy generated peptide ID: peptide identifier as listed in type 4 file column A * Virus protein: origin of peptide * \#N-glycans: # of N-Glycan sequons present on complete peptide as listed in type 4 file column B/C * HLA-[specificity] homologous Gapped Viral Peptide Sequences: Smith Waterman derived sequence homology of peptide including gaps ('x'/'-') * HLA start residue: starting residue of peptide based on location of mature HLA protein * ERP: ectodomain relative score applied according to NETRAD algorithm (see manuscript) * HLA specific: whether peptide contains hypervariable location residues * Chain: HLA Class II epitope analyses (DQ/DP are analyzed for both alpha or beta chains) #### File: 6-HLA-A3001\_BKV\_EBV\_Epitopes.csv **Description:** identification of 6 HLA-homologous viral peptide subsequences (listed in file type 5) needed to demarcate an HLA specific epitope (may be more than 1 listed per file) ##### Variables * Expasy generated peptide ID: peptide identifier as listed in type 4 file column A * Virus protein: origin of peptide * \#N-glycans: # of N-Glycan sequons present on complete peptide as listed in type 4 file column B/C * HLA-[specificity] homologous Gapped Viral Peptide Sequences: Smith Waterman derived sequence homology of peptide including gaps ('x'/'-') * HLA start residue: starting residue of peptide based on location of mature HLA protein * ERP: ectodomain relative score applied according to NETRAD algorithm (see manuscript) * HLA specific: whether peptide contains hypervariable location residues * Chain: HLA Class II epitope analyses (DQ/DP are analyzed for both alpha or beta chains) #### File: 6-HLA-A8001\_hRV\_EBV\_Epitopes.csv **Description:** identification of 6 HLA-homologous viral peptide subsequences (listed in file type 5) needed to demarcate an HLA specific epitope (may be more than 1 listed per file) ##### Variables * Expasy generated peptide ID: peptide identifier as listed in type 4 file column A * Virus protein: origin of peptide * \#N-glycans: # of N-Glycan sequons present on complete peptide as listed in type 4 file column B/C * HLA-[specificity] homologous Gapped Viral Peptide Sequences: Smith Waterman derived sequence homology of peptide including gaps ('x'/'-') * HLA start residue: starting residue of peptide based on location of mature HLA protein * ERP: ectodomain relative score applied according to NETRAD algorithm (see manuscript) * HLA specific: whether peptide contains hypervariable location residues * Chain: HLA Class II epitope analyses (DQ/DP are analyzed for both alpha or beta chains) #### File: 6-HLA-B0702\_HHV6B\_EBV\_Epitopes.csv **Description:** identification of 6 HLA-homologous viral peptide subsequences (listed in file type 5) needed to demarcate an HLA specific epitope (may be more than 1 listed per file) ##### Variables * Expasy generated peptide ID: peptide identifier as listed in type 4 file column A * Virus protein: origin of peptide * \#N-glycans: # of N-Glycan sequons present on complete peptide as listed in type 4 file column B/C * HLA-[specificity] homologous Gapped Viral Peptide Sequences: Smith Waterman derived sequence homology of peptide including gaps ('x'/'-') * HLA start residue: starting residue of peptide based on location of mature HLA protein * ERP: ectodomain relative score applied according to NETRAD algorithm (see manuscript) * HLA specific: whether peptide contains hypervariable location residues * Chain: HLA Class II epitope analyses (DQ/DP are analyzed for both alpha or beta chains) #### File: 6-HLA-B1302\_InfluenzaB\_EBV\_Epitopes.csv **Description:** identification of 6 HLA-homologous viral peptide subsequences (listed in file type 5) needed to demarcate an HLA specific epitope (may be more than 1 listed per file) ##### Variables * Expasy generated peptide ID: peptide identifier as listed in type 4 file column A * Virus protein: origin of peptide * \#N-glycans: # of N-Glycan sequons present on complete peptide as listed in type 4 file column B/C * HLA-[specificity] homologous Gapped Viral Peptide Sequences: Smith Waterman derived sequence homology of peptide including gaps ('x'/'-') * HLA start residue: starting residue of peptide based on location of mature HLA protein * ERP: ectodomain relative score applied according to NETRAD algorithm (see manuscript) * HLA specific: whether peptide contains hypervariable location residues * Chain: HLA Class II epitope analyses (DQ/DP are analyzed for both alpha or beta chains) #### File: 6-HLA-B1512\_InfluenzaB\_EBV\_Epitopes.csv **Description:** identification of 6 HLA-homologous viral peptide subsequences (listed in file type 5) needed to demarcate an HLA specific epitope (may be more than 1 listed per file) ##### Variables * Expasy generated peptide ID: peptide identifier as listed in type 4 file column A * Virus protein: origin of peptide * \#N-glycans: # of N-Glycan sequons present on complete peptide as listed in type 4 file column B/C * HLA-[specificity] homologous Gapped Viral Peptide Sequences: Smith Waterman derived sequence homology of peptide including gaps ('x'/'-') * HLA start residue: starting residue of peptide based on location of mature HLA protein * ERP: ectodomain relative score applied according to NETRAD algorithm (see manuscript) * HLA specific: whether peptide contains hypervariable location residues * Chain: HLA Class II epitope analyses (DQ/DP are analyzed for both alpha or beta chains) #### File: 6-HLA-B3701\_CMV\_EBV\_Epitopes.csv **Description:** identification of 6 HLA-homologous viral peptide subsequences (listed in file type 5) needed to demarcate an HLA specific epitope (may be more than 1 listed per file) ##### Variables * Expasy generated peptide ID: peptide identifier as listed in type 4 file column A * Virus protein: origin of peptide * \#N-glycans: # of N-Glycan sequons present on complete peptide as listed in type 4 file column B/C * HLA-[specificity] homologous Gapped Viral Peptide Sequences: Smith Waterman derived sequence homology of peptide including gaps ('x'/'-') * HLA start residue: starting residue of peptide based on location of mature HLA protein * ERP: ectodomain relative score applied according to NETRAD algorithm (see manuscript) * HLA specific: whether peptide contains hypervariable location residues * Chain: HLA Class II epitope analyses (DQ/DP are analyzed for both alpha or beta chains) #### File: 6-HLA-B2705\_InfluenzaB\_EBV\_Epitopes.csv **Description:** identification of 6 HLA-homologous viral peptide subsequences (listed in file type 5) needed to demarcate an HLA specific epitope (may be more than 1 listed per file) ##### Variables * Expasy generated peptide ID: peptide identifier as listed in type 4 file column A * Virus protein: origin of peptide * \#N-glycans: # of N-Glycan sequons present on complete peptide as listed in type 4 file column B/C * HLA-[specificity] homologous Gapped Viral Peptide Sequences: Smith Waterman derived sequence homology of peptide including gaps ('x'/'-') * HLA start residue: starting residue of peptide based on location of mature HLA protein * ERP: ectodomain relative score applied according to NETRAD algorithm (see manuscript) * HLA specific: whether peptide contains hypervariable location residues * Chain: HLA Class II epitope analyses (DQ/DP are analyzed for both alpha or beta chains) #### File: 6-HLA-B4501\_InfluenzaB\_EBV\_Epitope.csv **Description:** identification of 6 HLA-homologous viral peptide subsequences (listed in file type 5) needed to demarcate an HLA specific epitope (may be more than 1 listed per file) ##### Variables * Expasy generated peptide ID: peptide identifier as listed in type 4 file column A * Virus protein: origin of peptide * \#N-glycans: # of N-Glycan sequons present on complete peptide as listed in type 4 file column B/C * HLA-[specificity] homologous Gapped Viral Peptide Sequences: Smith Waterman derived sequence homology of peptide including gaps ('x'/'-') * HLA start residue: starting residue of peptide based on location of mature HLA protein * ERP: ectodomain relative score applied according to NETRAD algorithm (see manuscript) * HLA specific: whether peptide contains hypervariable location residues * Chain: HLA Class II epitope analyses (DQ/DP are analyzed for both alpha or beta chains) #### File: 6-HLA-B5101\_HSV1\_EBV\_Epitopes.csv **Description:** identification of 6 HLA-homologous viral peptide subsequences (listed in file type 5) needed to demarcate an HLA specific epitope (may be more than 1 listed per file) ##### Variables * Expasy generated peptide ID: peptide identifier as listed in type 4 file column A * Virus protein: origin of peptide * \#N-glycans: # of N-Glycan sequons present on complete peptide as listed in type 4 file column B/C * HLA-[specificity] homologous Gapped Viral Peptide Sequences: Smith Waterman derived sequence homology of peptide including gaps ('x'/'-') * HLA start residue: starting residue of peptide based on location of mature HLA protein * ERP: ectodomain relative score applied according to NETRAD algorithm (see manuscript) * HLA specific: whether peptide contains hypervariable location residues * Chain: HLA Class II epitope analyses (DQ/DP are analyzed for both alpha or beta chains) #### File: 6-HLA-B5501\_VZV\_EBV\_Epitopes.csv **Description:** identification of 6 HLA-homologous viral peptide subsequences (listed in file type 5) needed to demarcate an HLA specific epitope (may be more than 1 listed per file) ##### Variables * Expasy generated peptide ID: peptide identifier as listed in type 4 file column A * Virus protein: origin of peptide * \#N-glycans: # of N-Glycan sequons present on complete peptide as listed in type 4 file column B/C * HLA-[specificity] homologous Gapped Viral Peptide Sequences: Smith Waterman derived sequence homology of peptide including gaps ('x'/'-') * HLA start residue: starting residue of peptide based on location of mature HLA protein * ERP: ectodomain relative score applied according to NETRAD algorithm (see manuscript) * HLA specific: whether peptide contains hypervariable location residues * Chain: HLA Class II epitope analyses (DQ/DP are analyzed for both alpha or beta chains) #### File: 6-HLA-B5701\_EBVgB\_EBVgp350\_Epitopes.csv **Description:** identification of 6 HLA-homologous viral peptide subsequences (listed in file type 5) needed to demarcate an HLA specific epitope (may be more than 1 listed per file) ##### Variables * Expasy generated peptide ID: peptide identifier as listed in type 4 file column A * Virus protein: origin of peptide * \#N-glycans: # of N-Glycan sequons present on complete peptide as listed in type 4 file column B/C * HLA-[specificity] homologous Gapped Viral Peptide Sequences: Smith Waterman derived sequence homology of peptide including gaps ('x'/'-') * HLA start residue: starting residue of peptide based on location of mature HLA protein * ERP: ectodomain relative score applied according to NETRAD algorithm (see manuscript) * HLA specific: whether peptide contains hypervariable location residues * Chain: HLA Class II epitope analyses (DQ/DP are analyzed for both alpha or beta chains) #### File: 6-HLA-C0701\_SARS\_EBV\_Epitopes.csv **Description:** identification of 6 HLA-homologous viral peptide subsequences (listed in file type 5) needed to demarcate an HLA specific epitope (may be more than 1 listed per file) ##### Variables * Expasy generated peptide ID: peptide identifier as listed in type 4 file column A * Virus protein: origin of peptide * \#N-glycans: # of N-Glycan sequons present on complete peptide as listed in type 4 file column B/C * HLA-[specificity] homologous Gapped Viral Peptide Sequences: Smith Waterman derived sequence homology of peptide including gaps ('x'/'-') * HLA start residue: starting residue of peptide based on location of mature HLA protein * ERP: ectodomain relative score applied according to NETRAD algorithm (see manuscript) * HLA specific: whether peptide contains hypervariable location residues * Chain: HLA Class II epitope analyses (DQ/DP are analyzed for both alpha or beta chains) #### File: 6-HLA-DP1\_hRV\_EBV\_Epitopes.csv **Description:** identification of 6 HLA-homologous viral peptide subsequences (listed in file type 5) needed to demarcate an HLA specific epitope (may be more than 1 listed per file) ##### Variables * Expasy generated peptide ID: peptide identifier as listed in type 4 file column A * Virus protein: origin of peptide * \#N-glycans: # of N-Glycan sequons present on complete peptide as listed in type 4 file column B/C * HLA-[specificity] homologous Gapped Viral Peptide Sequences: Smith Waterman derived sequence homology of peptide including gaps ('x'/'-') * HLA start residue: starting residue of peptide based on location of mature HLA protein * ERP: ectodomain relative score applied according to NETRAD algorithm (see manuscript) * HLA specific: whether peptide contains hypervariable location residues * Chain: HLA Class II epitope analyses (DQ/DP are analyzed for both alpha or beta chains) #### File: 6-HLA-DQ8\_BKV\_EBV\_Epitope.csv **Description:** identification of 6 HLA-homologous viral peptide subsequences (listed in file type 5) needed to demarcate an HLA specific epitope (may be more than 1 listed per file) ##### Variables * Expasy generated peptide ID: peptide identifier as listed in type 4 file column A * Virus protein: origin of peptide * \#N-glycans: # of N-Glycan sequons present on complete peptide as listed in type 4 file column B/C * HLA-[specificity] homologous Gapped Viral Peptide Sequences: Smith Waterman derived sequence homology of peptide including gaps ('x'/'-') * HLA start residue: starting residue of peptide based on location of mature HLA protein * ERP: ectodomain relative score applied according to NETRAD algorithm (see manuscript) * HLA specific: whether peptide contains hypervariable location residues * Chain: HLA Class II epitope analyses (DQ/DP are analyzed for both alpha or beta chains) #### File: 6-HLA-DQ9\_BKV\_EBV\_Epitope.csv **Description:** identification of 6 HLA-homologous viral peptide subsequences (listed in file type 5) needed to demarcate an HLA specific epitope (may be more than 1 listed per file) ##### Variables * Expasy generated peptide ID: peptide identifier as listed in type 4 file column A * Virus protein: origin of peptide * \#N-glycans: # of N-Glycan sequons present on complete peptide as listed in type 4 file column B/C * HLA-[specificity] homologous Gapped Viral Peptide Sequences: Smith Waterman derived sequence homology of peptide including gaps ('x'/'-') * HLA start residue: starting residue of peptide based on location of mature HLA protein * ERP: ectodomain relative score applied according to NETRAD algorithm (see manuscript) * HLA specific: whether peptide contains hypervariable location residues * Chain: HLA Class II epitope analyses (DQ/DP are analyzed for both alpha or beta chains) #### File: 6-HLA-DR3\_H3N2\_EBV\_Epitopes.csv **Description:** identification of 6 HLA-homologous viral peptide subsequences (listed in file type 5) needed to demarcate an HLA specific epitope (may be more than 1 listed per file) ##### Variables * Expasy generated peptide ID: peptide identifier as listed in type 4 file column A * Virus protein: origin of peptide * \#N-glycans: # of N-Glycan sequons present on complete peptide as listed in type 4 file column B/C * HLA-[specificity] homologous Gapped Viral Peptide Sequences: Smith Waterman derived sequence homology of peptide including gaps ('x'/'-') * HLA start residue: starting residue of peptide based on location of mature HLA protein * ERP: ectodomain relative score applied according to NETRAD algorithm (see manuscript) * HLA specific: whether peptide contains hypervariable location residues * Chain: HLA Class II epitope analyses (DQ/DP are analyzed for both alpha or beta chains) #### File: 6-HLA-DR4\_H3N2\_EBV\_Epitopes.csv **Description:** identification of 6 HLA-homologous viral peptide subsequences (listed in file type 5) needed to demarcate an HLA specific epitope (may be more than 1 listed per file) ##### Variables * Expasy generated peptide ID: peptide identifier as listed in type 4 file column A * Virus protein: origin of peptide * \#N-glycans: # of N-Glycan sequons present on complete peptide as listed in type 4 file column B/C * HLA-[specificity] homologous Gapped Viral Peptide Sequences: Smith Waterman derived sequence homology of peptide including gaps ('x'/'-') * HLA start residue: starting residue of peptide based on location of mature HLA protein * ERP: ectodomain relative score applied according to NETRAD algorithm (see manuscript) * HLA specific: whether peptide contains hypervariable location residues * Chain: HLA Class II epitope analyses (DQ/DP are analyzed for both alpha or beta chains) #### File: 6-HLA-DRB0301\_CMV\_EBV\_Epitope.csv **Description:** identification of 6 HLA-homologous viral peptide subsequences (listed in file type 5) needed to demarcate an HLA specific epitope (may be more than 1 listed per file) ##### Variables * Expasy generated peptide ID: peptide identifier as listed in type 4 file column A * Virus protein: origin of peptide * \#N-glycans: # of N-Glycan sequons present on complete peptide as listed in type 4 file column B/C * HLA-[specificity] homologous Gapped Viral Peptide Sequences: Smith Waterman derived sequence homology of peptide including gaps ('x'/'-') * HLA start residue: starting residue of peptide based on location of mature HLA protein * ERP: ectodomain relative score applied according to NETRAD algorithm (see manuscript) * HLA specific: whether peptide contains hypervariable location residues * Chain: HLA Class II epitope analyses (DQ/DP are analyzed for both alpha or beta chains) #### File: 6-HLA-DRB0701\_InfluenzaB\_EBV\_Epitope.csv **Description:** identification of 6 HLA-homologous viral peptide subsequences (listed in file type 5) needed to demarcate an HLA specific epitope (may be more than 1 listed per file) ##### Variables * Expasy generated peptide ID: peptide identifier as listed in type 4 file column A * Virus protein: origin of peptide * \#N-glycans: # of N-Glycan sequons present on complete peptide as listed in type 4 file column B/C * HLA-[specificity] homologous Gapped Viral Peptide Sequences: Smith Waterman derived sequence homology of peptide including gaps ('x'/'-') * HLA start residue: starting residue of peptide based on location of mature HLA protein * ERP: ectodomain relative score applied according to NETRAD algorithm (see manuscript) * HLA specific: whether peptide contains hypervariable location residues * Chain: HLA Class II epitope analyses (DQ/DP are analyzed for both alpha or beta chains) #### File: 6-HLA-DRB1101\_AdenoV\_EBV\_Epitope.csv **Description:** identification of 6 HLA-homologous viral peptide subsequences (listed in file type 5) needed to demarcate an HLA specific epitope (may be more than 1 listed per file) ##### Variables * Expasy generated peptide ID: peptide identifier as listed in type 4 file column A * Virus protein: origin of peptide * \#N-glycans: # of N-Glycan sequons present on complete peptide as listed in type 4 file column B/C * HLA-[specificity] homologous Gapped Viral Peptide Sequences: Smith Waterman derived sequence homology of peptide including gaps ('x'/'-') * HLA start residue: starting residue of peptide based on location of mature HLA protein * ERP: ectodomain relative score applied according to NETRAD algorithm (see manuscript) * HLA specific: whether peptide contains hypervariable location residues * Chain: HLA Class II epitope analyses (DQ/DP are analyzed for both alpha or beta chains) #### File: 6-HLA-DRB1501\_HHV6B\_EBV\_Epitope.csv **Description:** identification of 6 HLA-homologous viral peptide subsequences (listed in file type 5) needed to demarcate an HLA specific epitope (may be more than 1 listed per file) ##### Variables * Expasy generated peptide ID: peptide identifier as listed in type 4 file column A * Virus protein: origin of peptide * \#N-glycans: # of N-Glycan sequons present on complete peptide as listed in type 4 file column B/C * HLA-[specificity] homologous Gapped Viral Peptide Sequences: Smith Waterman derived sequence homology of peptide including gaps ('x'/'-') * HLA start residue: starting residue of peptide based on location of mature HLA protein * ERP: ectodomain relative score applied according to NETRAD algorithm (see manuscript) * HLA specific: whether peptide contains hypervariable location residues * Chain: HLA Class II epitope analyses (DQ/DP are analyzed for both alpha or beta chains) #### File: 6-HLA-DRB1501\_SARS\_EBV\_Epitopes.csv **Description:** identification of 6 HLA-homologous viral peptide subsequences (listed in file type 5) needed to demarcate an HLA specific epitope (may be more than 1 listed per file) ##### Variables * Expasy generated peptide ID: peptide identifier as listed in type 4 file column A * Virus protein: origin of peptide * \#N-glycans: # of N-Glycan sequons present on complete peptide as listed in type 4 file column B/C * HLA-[specificity] homologous Gapped Viral Peptide Sequences: Smith Waterman derived sequence homology of peptide including gaps ('x'/'-') * HLA start residue: starting residue of peptide based on location of mature HLA protein * ERP: ectodomain relative score applied according to NETRAD algorithm (see manuscript) * HLA specific: whether peptide contains hypervariable location residues * Chain: HLA Class II epitope analyses (DQ/DP are analyzed for both alpha or beta chains) #### File: 6-HLA-C0401\_H1N1\_EBV\_Epitopes.csv **Description:** identification of 6 HLA-homologous viral peptide subsequences (listed in file type 5) needed to demarcate an HLA specific epitope (may be more than 1 listed per file) ##### Variables * Expasy generated peptide ID: peptide identifier as listed in type 4 file column A * Virus protein: origin of peptide * \#N-glycans: # of N-Glycan sequons present on complete peptide as listed in type 4 file column B/C * HLA-[specificity] homologous Gapped Viral Peptide Sequences: Smith Waterman derived sequence homology of peptide including gaps ('x'/'-') * HLA start residue: starting residue of peptide based on location of mature HLA protein * ERP: ectodomain relative score applied according to NETRAD algorithm (see manuscript) * HLA specific: whether peptide contains hypervariable location residues * Chain: HLA Class II epitope analyses (DQ/DP are analyzed for both alpha or beta chains) #### File: 6-HLA-B4402\_InfluenzaB\_EBV\_Epitope.csv **Description:** identification of 6 HLA-homologous viral peptide subsequences (listed in file type 5) needed to demarcate an HLA specific epitope (may be more than 1 listed per file) ##### Variables * Expasy generated peptide ID: peptide identifier as listed in type 4 file column A * Virus protein: origin of peptide * \#N-glycans: # of N-Glycan sequons present on complete peptide as listed in type 4 file column B/C * HLA-[specificity] homologous Gapped Viral Peptide Sequences: Smith Waterman derived sequence homology of peptide including gaps ('x'/'-') * HLA start residue: starting residue of peptide based on location of mature HLA protein * ERP: ectodomain relative score applied according to NETRAD algorithm (see manuscript) * HLA specific: whether peptide contains hypervariable location residues * Chain: HLA Class II epitope analyses (DQ/DP are analyzed for both alpha or beta chains) #### File: 6-HLA-DQ2\_InfluenzaB\_EBV\_Epitopes.csv **Description:** identification of 6 HLA-homologous viral peptide subsequences (listed in file type 5) needed to demarcate an HLA specific epitope (may be more than 1 listed per file) ##### Variables * Expasy generated peptide ID: peptide identifier as listed in type 4 file column A * Virus protein: origin of peptide * \#N-glycans: # of N-Glycan sequons present on complete peptide as listed in type 4 file column B/C * HLA-[specificity] homologous Gapped Viral Peptide Sequences: Smith Waterman derived sequence homology of peptide including gaps ('x'/'-') * HLA start residue: starting residue of peptide based on location of mature HLA protein * ERP: ectodomain relative score applied according to NETRAD algorithm (see manuscript) * HLA specific: whether peptide contains hypervariable location residues * Chain: HLA Class II epitope analyses (DQ/DP are analyzed for both alpha or beta chains) #### File: 6-HLA-DQ6\_H1N1\_EBV\_Epitopes.csv **Description:** identification of 6 HLA-homologous viral peptide subsequences (listed in file type 5) needed to demarcate an HLA specific epitope (may be more than 1 listed per file) ##### Variables * Expasy generated peptide ID: peptide identifier as listed in type 4 file column A * Virus protein: origin of peptide * \#N-glycans: # of N-Glycan sequons present on complete peptide as listed in type 4 file column B/C * HLA-[specificity] homologous Gapped Viral Peptide Sequences: Smith Waterman derived sequence homology of peptide including gaps ('x'/'-') * HLA start residue: starting residue of peptide based on location of mature HLA protein * ERP: ectodomain relative score applied according to NETRAD algorithm (see manuscript) * HLA specific: whether peptide contains hypervariable location residues * Chain: HLA Class II epitope analyses (DQ/DP are analyzed for both alpha or beta chains) ## Code/software [https://www.ebi.ac.uk/ipd/imgt/hla/](https://www.ebi.ac.uk/ipd/imgt/hla/alleles/) used to obtain HLA protein sequence which correlates with anti-HLA antibody specificity. [Release 3.58 (2024-10) Version Report](https://www.ebi.ac.uk/ipd/imgt/hla/release/v358/) - Build 6fc03c9. Click "Alleles". Under "Allele Name Query" enter HLA allele (e.g. A*02:01) and click "Submit." A list of alleles will populate. Choose the appropriate allele under "Name" column. When allele page loads, scroll to "Sequence" and click "Protein" tab. Protein sequence can be highlighted, copied and pasted for later use. [https://www.ncbi.nlm.nih.gov](https://www.ncbi.nlm.nih.gov) used to obtain virus envelope protein sequences. Perform search and scroll to identify protein(s) with suspected homology to correlate HLA (e.g. "Influenza A, H1 hemagglutinin 2016"). Higher specificity descriptors work best. Under "Proteins", click "Protein". Open link to suspected protein of interest. Copy/paste protein title, Genebank identification information (e.g., hemagglutinin [Influenza A virus (A/Tennessee/26/2016(H1))] GenBank: AOZ86615.1). Scroll down to obtain, copy paste strain identifier (e.g., strain="A/Tennessee/26/2016") and protein sequence at bottom of page: e.g.:  1 mkailvvlly tfttanadtl cigyhannst dtvdtvlekn vtvthsvnll edkhngklck 61 lrgvaplhlg kcniagwilg npeceslsta sswsyivets nsdngtcypg dfinyeelre 121 qlssvssfer feifpktssw pnhdsnkgvt aacphagaks fyknliwlvk kgnsypklnq 181 syindkgkev lvlwgihhps ttadqqslyq nadayvfvgt sryskkfkpe iatrpkvrdq 241 egrmnyywtl vepgdkitfe atgnlvvpry aftmernags giiisdtpvh dcnttcqtpe 301 gaintslpfq nihpitigkc pkyvkstklr latglrnvps iqsrglfgai agfieggwtg 361 mvdgwygyhh qneqgsgyaa dlkstqnaid kitxkvnsvi ekmntqftav gkefnhlekr 421 ienlnkkvdd gfldiwtyna ellvllener tldyhdsnvk nlyekvrnql knnakeigng 481 cfefyhkcdn tcmesvkngt ydypkyseea klnrekidgv klestriyqi laiystvass 541 lvlvvslgai sfwmcsngsl qcrici EXPASY PeptideMass: [https://web.expasy.org/peptide_mass (2024)/](https://web.expasy.org/peptide_mass%20\(2024\)/) (RRID SCR_008508). Software (beta version) used to digest virus protein in silico. After deleting residue numbers from virus sequence to make contiguous sequence, enter sequence into window under "Submit a protein sequence/Examples". Select "Lys N" from drop down under "Select an enzyme". Click "Perform cleavage". Under "Peptide masses for your input sequence", mass, position and peptide sequence can be copied/pasted to build type 4 data file and for later use with EMBOSS WATER (Smith Waterman algorithm). [https://www.ebi.ac.uk/jdispatcher/psa/emboss_water](https://www.ebi.ac.uk/jdispatcher/psa/emboss_water) (EMBOSS Water Pairwise Sequence Alignment) used to identify HLA homology from viral peptides. Make sure "Protein" is checked. Copy/paste HLA sequence of identified allele, according to website format, to be used for characterizing anti-HLA antibody epitope under "Paste your first sequence here - or use the example sequence" (e.g.,  \&gt;A0201  MAVMAPRTLVLLLSGALALTQTWAGSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYWDGETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAYDGKDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKETLQRTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDGTFQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRWEPSSQPTIPIVGIIAGLVLFGAVITGAVVAAVMWRRKSSDRKGGSYSQAASSDSAQGSDVSLTACKV Be sure to include space after allele (e.g., &gt;0201_) Under "Paste your second sequence here - or use the example sequence" copy/paste the peptide sequence of interest using website formatting. Remember to designate forward [F] vs reverse [R] orientation. (e.g.,  \&gt;18440236F KTLIITRTATNATTTTH) Leave parameters default as "pair". Title job and submit to your email. Will receive email with job title identifier including virus and HLA subsequence with homologous residues, EMBOSS score, and starting residues. e.g., xTL(8x)AxTxT. Gaps in sequence are depicted with an "x" or "-". See website details for differences in gapping. Depending on the sequence, start residue numbering may require adjustment. Refer to original sequence. Smith-Waterman derived sequence can be copied for use with NETRAD algorithm.