Sierra 2.3.5: new HIVDB algorithm release

We upgraded the HIVDB Drug Resistance Algorithm to V8.9.

Sierra 2.3.4: bugfix release

In this bugfix release, we identified and fixed an issue: when a reverse complement of sequence was entered, the subtype and "pretty pairwise" output were incorrect.

As far as we know, the mutation list and drug resistance interpretation result are not affected.

Sierra 2.3.3

In this release, we updated the list of usual/unusual mutations, the list of signature APOBEC mutations, and the list of APOBEC context drug resistance mutations. The latest version of the three lists are included in the HIVFacts library (previously known as "HIV-AAPcnt") as version 2019.8.

This is the first time since 2016 we updated our APOBEC-related lists. The steps of identifying signature APOBEC mutations and APOBEC context DRMs were described in this document: HIV-1 Signature APOBEC Mutations.

Sierra 2.3.2

1. Upgrade ASI Interpreter to version 1.4.0.0 (HIVDB modified version ee4481).
2. Fix an issue that in certain circumstance, part of a mixture mutation is not included in "partialScores" explanation. Although the mutation is not included, we can confirm that the final drug resistance score is not affected at all.

Sierra 2.3.1

Follow changes was made in this release:

1. A list of 24 INSTI SDRMs has been added for our analyses.
2. GraphQL API is now accepting a custom list of mutations as a filter option for retrieving a list of mutations.

Sierra 2.3.0

Two major updates are introduced in this release:

1. HIVDB Drug Resistance Algorithm V8.8: INSTI rule and comment changes.
2. A new set of subtype & CRF sequences is created for determining the subtype for each input HIV-1 sequence. These subtype & CRF sequences and their description can be found in following study:
   Rhee SY and Shafer RW (2018). Geographically-stratified HIV-1 group M pol subtype and circulating recombinant form sequences. Scientific Data. 2018 July 31.

Sierra 2.2.11

ANRS Algorithm has been upgraded to v29 (Nov 2018): Rules were added for two new drugs: FTR (fostemsavir) and BIC (bictegravir). Three rules were changed for DOR (doravirine).

In addition, we changed the type of mutation RT:106I from "Other" to "NNRTI".

Sierra 2.2.10

Switch to hiv-aapcnt 2018.11-2 for detecting unusual mutations.

Sierra 2.2.9

Release of HIVDB Drug Resistance Algorithm 8.7.

Sierra 2.2.8

Two major upgrades are introduced in this release:

1. Upgrade to NucAmino 0.2.0-beta.2.
2. Improve performance by adding an option to use AWS Lambda for sequence alignment (NucAmino). The detail can be found here: README.md#nucamino-on-aws-lambda.