HIVFacts

Structured knowledge base of HIV-1/HIV-2.

Unusual Mutations

Steps and Criteria

First we calculate the prevalence of an amino acid at a position:

1. Same amino acid at the same position from a single person is only counted once. (PATIENT_PER_MUT_COUNT)
2. Multiple Amino acids at the same position from a single sample are not counted. (EXCLUDE_MIXTURES)
3. Stop codons are not counted. (EXCLUDE_STOP_CODONS)
4. Sequences only used in unpublished studies are not used. (PUBLISHED_ONLY)
5. DNAChip Sequences are not used. (NO_DNACHIP)
6. Sequences with quality issues are not used. (NO_QA_ISSUES)

In general, an amino acid at a position with its prevalence < 0.01% is considered unusual, with the following exception:

• The amino acid is a known drug resistance mutation according to latest HIVDB algorithm.

Sequence QA Criteria

A sequence falls in either of the conditions below is filtered.

Gene	APOBEC cutoff	Score cutoff	Min AA	Max AA
PR	>=2	>=4	>=31	<=89
RT	>=3	>=6	>=66	<=214
IN	>=3	>=5	>=67	<=154

Score cutoff: the "score" here is defined as the total number of problematic mutations. A problematic mutation is defined either an APOBEC mutation or an unusual mutation.

Subtype and treatment distribution

	PR	RT	IN
# Total	186116	189748	22868
# B	102435	100064	12615
# Non-B	83681	89684	10253
% Treated	15.86%	58.14%	6.69%

Signature APOBEC Mutations and APOBEC-context DRMs

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