HIV molecular immunology database

 

List of Variant and Mutation Types

Code Mutation type Description
? unclear Not clear from the paper, for example "E ?" Or "IE ?"
A HLA association Variant is statistically associated with a particular HLA molecule. Since we focus on experimentally verified epitope variants, the variant with this mutation is entered only if it is already described as an experimentally determined mutation.
CE calculated escape Predicted escape as shown by statistical correlation or other computational methods in a large cohort. Since we focus on experimentally verified epitope variants, the variant with this mutation is entered only if it is already described as an experimentally determined mutation.
CHB calculated diminished HLA binding Predicted decrease in binding to HLA as shown by algorithm(s). Since we focus on experimentally verified epitope variants, the variant with this mutation is entered only if it is already described as an experimentally determined mutation.
CM compensatory mutation Variant is associated with a compensatory mutation. This could be a compensatory mutation outside epitope boundaries, or a mutation within epitope boundaries, compensating for the same epitope or for a variant of another epitope. Each particular entry is explained in the variant note.
DHB diminished HLA binding or increased off-rate Decreased binding (or increased off-rate) to presenting HLA as compared to binding by original epitope.
DI drug induced Treatment with antiretroviral drugs induces this variant.
DR diminished response Experimental data suggests a partial escape by decreased CTL response, but authors do not call it an escape (judgment call of annotator).
E escape documented in this paper Same as NSF (non-susceptible form) but called an escape when dynamic changes seen in a longitudinal or transmission study or when author claims escape.
EL epitope loss Entire sequence of epitope lost in variant virus.
IE inferred escape Variant is predicted to be an escape by longitudinal study or transmission study (but the reactivity of the variant is not tested experimentally).
LE literature escape Escape previously documented in the literature (according to the authors).
NSF non-susceptible form No CTL response when patient cells are challenged with the variant peptide.
NSF-2 non-susceptible form-2 Neither index nor variant peptides are recognized by CTL, but the index peptide is a known epitope and, in most cases, there was a prior patient response to it.
OV observed variant variant sequence observed in longitudinal or transmission study.
P processing Variant escapes CTL detection by altering epitope processing in subcellular organelles, experimentally verified.
R reversion Variant reverts to wild type epitope sequence as documented by sequence, experimental studies or literature.
RCOK replicative capacity is not abrogated Variant does not cause loss of viral replication, as shown by replication assays.
RCR replicative capacity reduced Variant is associated with a reduction or loss (abrogation) of replication of the virus, as shown by replication assays.
SF susceptible form CTL response is elicited when patient cells are challenged with the variant peptide.
SNSF subtype-specific non-susceptible form No CTL response when patient cells are challenged with the variant peptide in the course of subtype comparative studies, however the same epitope from a different subtype does elicit CTL response.
SSF subtype-specific susceptible form CTL response is elicited when patient cells are challenged with the variant peptide in the course of subtype comparative studies, i.e. patient cells can recognize at least two different viral subtype variants.
TCR TCR related mutation Variant does not bind or shows decreased binding to TCR.

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