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.

Input

1. Gene: RT, PR, or IN.
2. Amino Acid Position (mandatory input)
3. Probe Size (mandatory input): Length of sequence to be interrogated - usually about 20 to 30 nucleotides.
4. Codon Location (mandatory input): Location of the amino acid position relative to the flanking nucleotides: 5', central, or 3'.
5. Subtype: A, B, C, D, G, CRF01_AE, CRF02_AG, or all subtypes.
6. Region: Central Africa, East Africa, Southern Africa, West Africa, SSEA (South & Southeast Asia), and India, or all LMIC regions.
7. Frequency Threshold: All sequences or just those comprising at least 1% of the total.
8. Nucleotide Display: All nucleotides or just those nucleotides that differ from the most common sequence.

Output

1. Summary: User-supplied query parameters, number of sequences included in query, number of distinct codons returned, and number of distinct flanking segments returned.
2. 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.
3. Distinct Flanking Segments table:
   • Distinct flanking sequences in order of descending frequency.
   • Number and percent of sequences in query with each flanking segment.

1. Codons or flanking segments with nucleotide ambiguities are excluded.
2. When all subtypes are queried, sequences for which the subtype is unknown will be included in the results.
3. 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.
4. Probe sizes that extend beyond the boundary of a gene will be truncated to fit within gene boundaries.
5. Insertions at interrogated positions or in flanking segments are not included in the program output. They occur in less than 0.5% of sequences.