Sierra 3.5.5

• HIVDB Algorithm 10.1: This version updates scores of IN:Q146PRLI: 5 for DTG and BIC and 10 for CAB.

Sierra 3.5.4-1

• HIVDB algorithm 10.0-1: This is a bugfix version that added the missing L74I score for Cabotegravir (score=10).

Sierra 3.5.4

• HIVDB algorithm 10.0: This latest update includes major score and comment updates for all drug classes (NRTI, NNRTI, PI, INSTI and CAI/Lenacapavir). Visit algorithm updates
  page for more information.

Sierra 3.5.3

• HIVDB algorithm 9.8: This latest update includes score and comment updates for Lenacapavir (LEN), the Capsid Inhibitor. In addition, we added score interpretation for Dapivirine (DPV), an NNRTI drug recommended by the WHO. Visit algorithm updates
  page for more information.

Sierra 3.5.1

Bugfixes:

1. Fixed a bug that failed to exclude low quality alignment from the final results (hivdb/sierra-core@95a442d)
2. Fixed several bugs that related to genotyper/subtyper.
3. Fixed an issue that missing DRPs are not reported by NGS program (hivdb/hivfacts@13b743c)

Sierra 3.5.0

HIVDB algorithm 9.6: This latest algorithm update incorporates significant modifications and enhancements in the rules and comments for NRTI, NNRTI, INSTI, and PI drug classes. A detailed comparison between algorithm versions 9.3 and 9.6 can be found in this zip file: algV9.6.zip.

Sierra 3.4.13

Bugfix: Fix a bug that MINIMAP2 argument -w 5 was accidentally removed by the previous version 3.4.12.

Sierra 3.4.12

Bugfixes:

1. Previously, minimizer window size=5 (-w 5) was employed for aligning HIV-1 sequences by minimap2. We changed this config to minimizer k-mer length=10 (-k 10 -w 5) for increase alignment sensitivity for super short sequences.
2. (3.4.11, forgot to release) Address an issue that certain CRFs were incorrectly called due to an insufficient regional subtyping rule, or a misconfiguration of region subtype (X29).

Sierra 3.4.10

HIVDB-HIV2 algorithm 9.0: Comments update since 2020.

Sierra 3.4.9

Subtyping/genotyping updates:

Subtype A is divided into A1/3/4/6/7. Two reference sequences of subtype A8 are added (MW353966/MW353967). Subtypes of six reference sequences are changed from A to X22 (CRF22_01A1) after further re-analysis is performed: AH011123, AY371167, EU743963, JN864048, KP109498, and KU168256.