This program is for analyzing the genetic variability in HIV-1 sequences originating from low and middle-income countries (LMICs). It was developed for researchers designing point-of-care HIV-1 drug resistance hybridization assays for detecting drug resistance mutations. The input parameters on this page are used to query a database of 27,203 RT, 24,209 PR, and 2,366 IN sequences from LMICs. Tab-delimited data files are also available for download: PR, RT, and IN.
- Gene: RT, PR, or IN.
- Amino Acid Position (mandatory input)
- Probe Size (mandatory input): Length of sequence to be interrogated - usually about 20 to 30 nucleotides.
- Codon Location (mandatory input): Location of the amino acid position relative to the flanking nucleotides: 5', central, or 3'.
- Subtype: A, B, C, D, G, CRF01_AE, CRF02_AG, or all subtypes.
- Region: Central Africa, East Africa, Southern Africa, West Africa, SSEA (South & Southeast Asia), and India, or all LMIC regions.
- Frequency Threshold: All sequences or just those comprising at least 1% of the total.
- Nucleotide Display: All nucleotides or just those nucleotides that differ from the most common sequence.
- Summary: User-supplied query parameters, number of sequences included in query, number of distinct codons returned, and number of distinct flanking segments returned.
- Distinct Codons table:
- Codons and corresponding amino acid encoding the selected amino acid position in order of descending frequency.
- Number and percent of sequences in query with each codon.
- Distinct Flanking Segments table:
- Distinct flanking sequences in order of descending frequency.
- Number and percent of sequences in query with each flanking segment.
- Codons or flanking segments with nucleotide ambiguities are excluded.
- When all subtypes are queried, sequences for which the subtype is unknown will be included in the results.
- In the Distinct Flanking Segments table, the location of the codon is indicated by . When the Nucleotide Display is set to "Show changes from consensus" bases identical to the most common consensus sequence are indicated by dashes.
- Probe sizes that extend beyond the boundary of a gene will be truncated to fit within gene boundaries.
- Insertions at interrogated positions or in flanking segments are not included in the program output. They occur in less than 0.5% of sequences.