HIV molecular immunology database

 

HIV Immunology Variant Help

Description

The variant tables contain information about sequence variants and mutations of HIV-1 T-cell epitopes. Variants tested for immunological response as well as those observed in longitudinal intra-patient, subtype comparison, or other inter-patient studies are included. Variants are usually annotated even if the paper only provides sequence or statistical data, this is different from epitope annotations where only immunogenic epitopes or peptides are annotated. Each variant record is attached to one epitope record; an epitope record may have zero, one, or more variants.

For general information about the HIV immunology database and searches, see HIV Immunology Search Help.

Variants Search and Results Fields

This is a brief description of the database fields in the variant CTL/CD8+ variant and Helper/CD4+ variant search and results pages.

HIV protein
The protein for which the epitope was defined.
HXB2 protein location
The HXB2 protein coordinates within the protein selected in the “HIV protein” field above. Three options determine the type of search:
  1. Results overlap with query location: finds epitopes that overlap any residue of the specified location. To find epitopes that contain a single specific residue, you can enter the same coordinate number in both boxes.
  2. Results contained within query location: finds epitopes that are contained within the specified range. Results will be the same length or shorter than the query.
  3. Results exact match to query location: finds epitopes that have exactly the specified start and stop coordinates.
Epitope or variant sequence
The amino acid sequence of the epitope or variant. Three options determine the type of search:
  1. Results contain query sequence: finds epitopes that contain the query sequence. Results will be the same length or longer than the query.
  2. Results exact match to query sequence: finds epitopes with the exact sequence as the query.
  3. Results fuzzy match to query sequence: finds epitopes with up to 25% difference in the amino acid sequence.
Epitope record number
A unique number assigned to an epitope by the database. Please refer to this number if you have any comments or questions about an entry.
Variant record number
A unique number assigned to a variant by the database. Please refer to this number if you have any comments or questions about an entry.
Mutation type
Mutations are classified into various types, depending on the evidence presented in the paper. Assigning the mutation type is sometimes a subjective judgement of the annotator; it is not always clear in the paper. Read the notes for the variant carefully, and refer to the original paper if necessary. Abbreviations are defined below.
Restricting MHC/HLA
The MHC (or HLA) presenting molecules as described by the primary authors.
Variant method
The method(s) used to ascertain the type of mutant.
Note
In the note for the variant, the annotator explains the evidence for assigning the mutation type.
HXB2 location
Epitope position numbers in the HXB2 reference strain. When an epitope spans two proteins that we treat separately in the database, such as p17-p24, both are indicated.
Epitope name
Epitope name as reported by the authors.
Epitope
The amino acid sequence of the epitope or short reactive peptide.
Epitope sequence
The amino acid sequence of the HIV immunogenic epitope or short reactive peptide. There is a limit of 30 amino acids for peptides. This is the “index” epitope sequence mentioned in further definitions on this page.
Variant sequence
The amino acid sequence of the variant (mutated epitope sequence in reference to the index epitope or short reactive peptide).
Mutations
The insertion or absence or change of an amino acid in HIV protein sequence, most often studied in or around epitopes for the purposes of this database.
Epitope mutation location
The position of the mutation within or in reference to the epitope, and the “from” and “to” amino acid values. For example: the mutations in variant sequence RSLYNTiAvLY, in reference to index epitope RSLYNTVATLY, are shown as V7I T9V [“from” AA, location, “to” AA]. Insertions have the form (X.Y) were X is the epitope location/position just before the insertion, and Y is the insertion number. For example, if “ss” is inserted between epitope positions 4 and 5, then the position of the first inserted ‘s’ would be (4.1) and the location of the second inserted 's' would be (4.2). Positions/locations in the left flank (upstream insertions) have a prefix of minus. For example, the ‘a’ in variant {a**}KkWIILGLNK has position -3. Locationns in the right flank have a prefix of ‘+’. For example, the ‘t’ in variant KIRLRPGGK{*t} is position +2. Insertions in the right flank (downstream insertions) have the form (+X.Y) while insertions in the left flank have the form (-X.Y). Flanking sequences are enclosed in curly braces. Asterisks in flanking sequences indicate an unpublished AA, but correspond one-to-one to AAs.
HXB2 mutation location
The position/location of the mutation within or in reference to the protein (HXB2 reference sequence used) it is in and the “from” and “to” values, for example: L64V. Multiple values are separated with by spaces for example L64V I72T. Insertions have the form (X.Y) were X is the protein position/location just before the insertion, and Y is the insertion number. For example, if “ss” is inserted between protein positions 193 and 194, then the position of the first inserted 's' would be (193.1) and the position of the second inserted ‘s’ would be (193.2). Variant positions in the left or right flanks (i.e upstream or downstream regions) are derived by subtracting (or adding) from the beginning (or ending) of the HXB2 position. For example: the mutations in variant sequence RSLYNTiAvLY, in reference to index epitope RSLYNTVATLY and located within Gag, are shown as V82I T84V [“from” AA, location, “to” AA]. Also, the protein position for the ‘r’ in variant {r*}QVPLRPMTYK is 188 because the beginning HXB2 location for the epitope is 190. Similarly the protein position for the ‘g’ in variant QVPLRPMTYK{g} is 200, since the HXB2 ending position for the epitope is 199. Flanking sequences are enclosed in curly brackets. Asterisks in flanking sequences indicate an unpublished AA, but correspond one-to-one to AAs. Locations in the left flank have a prefix of minus.
Epitope subtype
The subtype of HIV in which the index epitope sequence or immunogenic peptide under study is found, sometimes not specified for B subtype.
Variant subtype
The subtype of HIV in which the variant sequence under study is found, sometimes not specified for B subtype.
Download

The search results may be downloaded in JSON or CSV (comma separated value) format. Individual records may be downloaded in JSON format. Note that the CSV files are encoded in UTF-8; please set Excel and other programs to UTF-8 when importing. Refer to the API Guide for details of the JSON format.

List of Variant and Mutation Types

See the list of variant and mutation types for their definitions.

Codes and Symbols in Variants

Symbol Meaning Example
x Lower case letters indicate a mutation. Variant SLYNTVAvL indicates a mutation from T to V in the epitope SLYNTVATL.
(x) Parentheses in the epitope variant designate an insertion. Variant PLTF(a)GWCYKL has an A inserted between 4F and 5G (Nef 139F and 140G) in the epitope PLTFGWCYKL. Insertion position within the epitope is reported as (4.1)A, and insertion position in the protein is reported as Nef (139.1)A.
- Dash in the epitope variant denotes a deletion. Variant RAEQ-SQdV of epitope RAEQASQEV has lost amino acid A at position 5.
{xxx} Curly braces in the variant are used to designate a flanking region when there is a mutation upstream or downstream of the epitope. Variant {p}ISPRTLNAW of epitope {A}lSPRTLNAW means that there is an A-to-P mutation upstream of the epitope N-terminus.
'+n' Mutation in the downstream epitope flanking region. Variant SPAIFQSSM{TKILd} of the epitope SPAIFQSSM{TKILE} has an E-to-D mutation 5 amino acids downstream of the epitope C-terminus. Report as “extra-epitopic mutation seen at +5 position”
'-n' Mutation in the upstream epitope flanking region. Variant {rWEKI}RLRPGGKKK of the epitope {KWEKI}RLRPGGKKK has a K-to-R mutation 5 amino acids upstream of the epitope N-terminus. Report as “extra-epitopic mutation seen at -5 position”
* An asterisk represents a non-mutated amino acid in the epitope flanking region either upstream or downstream of the epitope. Each * is one amino acid, and its sequence location is specific. This notation is used when the amino acids between the epitope and the mutation site are not reported in the original publication. Variant KIRLRPGGK{*t} of epitope KIRLRPGGK has an R-to-T processing mutation 2 amino acids downstream. The intervening amino acid was not reported.
... An unspecified number of amino acids were present between the mutation position in the flanking region and the epitope. This notation is used when the exact mutation position upstream or downstream is more than 5 amino acids away, or was not reported in the original publication. In the former case, the mutation position is reported. Variant {q...}TSnLQEQIGW of epitope {H...}TSTLQEQIGW has an unspecified number of non-mutated amino acids between the N-terminus of the epitope and the upstream H-to-Q mutation.
[/] A forward slash between two amino acids in an epitope or variant indicates that either of the two amino acids on either side of the forward slash, /, could be functionally found in that epitope or variant. The two possible amino acids at that position are placed in square brackets. WKEM[D/N]R
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