HIV molecular immunology database
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.
This is a brief description of the database fields in the variant CTL/CD8+ variant and Helper/CD4+ variant search and results pages.
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unpublished AA, but correspond one-to-one to AAs.
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flanking sequences indicate an unpublished AA, but correspond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.
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.
See the list of variant and mutation types for their definitions.
| 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
|