Genotype-Rx Datasets
2019-2-19
Genotype-rx correlaton datasets include all publicly available HIV-1 isolates in HIVdb and the lists of ARVs (antiretrovials) received prior to the isolations.
| Gene | Dataset | Number of isolates included | Description |
|---|---|---|---|
| protease | PR.txt | 138,433 isolates from 131,196 persons, 1,023 references | protease isolates and the lists of protease inhibitors received |
| RT | RT.txt | 147,590 isolates from 139,609 persons, 1,036 references | RT isolates and the lists of RT inhibitors received |
| integrase | IN.txt | 17,604 isolates from 16,959 persons, 368 references | integrase isolates and the lists of integrase inhibitors received |
Note: (a) isolates with unknown treatment status were excluded; (b) isolates obtained from CPZ were excluded; (c) only a consensus amino acid sequence was included if an isolate was cloned; (d) primary references from which the isolates were descrived can be found Ref.txt; (e) suggested citation can be found on FAQ page.
Description of fields in the datasets (fields are tab-delimited.)
| Field Name | Description |
|---|---|
| RefID | Reference identifier;linked to Ref.txt |
| PtID | Patient identifier |
| IsolateName | Isolate identifier |
| Region | Region of sampling; |
| Year | Year of sampling; preceded by '=' when the exact year of sampling is available or '<' otherwise |
| Subtype | Subtype of sequence; 'NA' if subtype could not be classifed because nucleotide sequence was not available; 'Others' if the subtype of sequence is a circulating recombinant form other than CRF01_AE and CRF02_AG or a non-CRF recombinant or other non-classifiable group M sequence. |
| PIList (or RTIList or INIList) | List of protease (or RT or integrase) inhibitors received prior to sequencing; 'None' when no ARVs received; 'Unknown' when an ARV was received or not is not known; 'PI' when a protease inhibitor was received but which protease inhibitor was recceived is not known; 'NRTI' when a NRTI was received but which NRTI was received is not known; 'NNRTI' when a NNRTI was received but which NNRTI was received is not known; 'RTI' when a RTI (either NRTI or NNRTI) was received but which RTI was received is not known |
| P1...Pn | Amino acid at this position. '-' indicates consensus; '.' indicates no sequence; '#' indicates an insertion; '~' indicates a deletion; '*' indicates a stop codon and a letter indicates one letter Amino Acid substitution. Two and more amino acid codes indicates a mixture. The consensus B amino acid sequences can be found here. |
| AccessionID | Genbank AccessionID number |
| NASeq | Nucelotide sequence |