REGA V3 HIV-1 Subtying Classification Rules
1. Decision Tree for sequences longer
than 800 bp:
Rule 1: RULE 1 - PURE
The rule 1 is for pure subtypes classification.
Rule 1A: PURE
Subtype assigned based on sequence > 800 bps, clustering inside a pure subtype with bootstrap > 70% without recombination in the bootscan, and do not clustering with a CRF with bootstrap >70 %.
Rule 1B: PURE-LIKE
Subtype assigned based on sequence > 800 bps, clustering outside a pure subtype with bootstrap > 70% without recombination in the bootscan, and do not clustering with a CRF with bootstrap >70 %.
Rule 1C: PURE (CRF)
Subtype assigned based on sequence > 800 bps, clustering with a pure subtype with bootstrap > 70% without recombination in the bootscan, clustering inside a CRF with bootstrap >70 %.
Rule 1D: NOT ASSIGNED - CHECK THE REPORT
Result assigned based on sequence > 800 bps, not clustering with a pure subtype with bootstrap > 70% without recombination in the bootscan.
Rule 2: RULE 2 - PURE RECOMBINANT
The rule 2 is for the classification of recombinants with pure subtypes.
Rule 2A: PURE RECOMBINANT
Recombinant assigned based on sequence > 800 bps, with pure subtype supported recombination in the bootscan, i.e. two or more pure subtypes with more than 10% of the windows supported by bootstrap > 70%, and not clustering with a CRF with bootstrap > 70%.
Rule 2B: POTENTIAL RECOMBINANT
Potential recombination assigned based on sequence with only one pure recombinant subtype, supported by bootstrap > 70% (failure to classify a second pure subtype with >10% of windows supported by bootstrap >70%), and failure to classify it as a non-recombinant pure subtype or CRF.
Rule 2C: NOT ASSIGNED - CHECK THE BOOTSCAN
Result assigned based on sequence with recombination in the boostscan, i.e < 0.9, however no pure subtype is supported (>70%) in > 50% of the windows.
Rule 3: RULE 3 - CRF
The rule 3 specifies the classification of CRFs.
Rule 3A: CRF
Subtype assigned based on sequence > 800 bps, clustering with a CRF with bootstrap > 70%, with detection of recombination in the pure subtype bootscan, and further confirmed by CRF bootscan analysis (bootscan > 0.9).
Rule 3B: CRF
Subtype assigned based on sequence > 800 bps, clustering inside a CRF with bootstrap > 70%, with detection of recombination in the pure subtype bootscan, and further confirmed by CRF bootscan analysis (bootscan > 0.7 with support of 70%).
Rule 3C: CRF-Like
Subtype assigned based on sequence > 800 bps, clustering outside a CRF cluster with bootstrap > 70% with detection of recombination in the bootscan, and further confirmed by CRF bootscan analysis (bootscan > 0.7 with support of 70%).
Rule 4: RULE 4 - CRF RECOMBINANTS
rule 4 is for the classification of recombinants with CRFs.
Rule 4A: CRF PURE RECOMBINANT
Recombinant assigned based on sequence > 800 bps, with CRF and pure subtype supported recombination in the bootscan (i.e. one CRF and one or more pure subtypes with more than 10% of the windows supported by bootstrap > 70%), and clustering with a CRF with bootstrap > 70%.
Rule 4B: POTENTIAL RECOMBINANT CHECK THE BOOTSCAN
Potential recombination assigned based on sequence > 800 bps, with only one recombinant CRF or pure subtype supported by bootstrap > 70% (failure to classify a second pure subtype or CRF with >10% of windows supported by bootstrap >70%), and failure to classify it as a non-recombinant pure subtype or CRF.
Rule 4C: NOT ASSIGNED - CHECK THE BOOTSCAN
Result assigned based on sequence > 800 bps, with recombination in the boostscan (< 0.9), clustering with a CRF with bootstrap >70% however the CRF is not confirmed by bootscan analysis (>70%) in > 50% of the windows.
2. Decision Tree for sequences shorter than 800 bp:
Rule 11A: PURE
Subtype assigned based on sequence < 800 bps, clustering inside a pure subtype cluster with bootstrap > 70%.
Rule 11B: NOT ASSIGNED CHECK THE REPORT
Result assigned based on sequence < 800 bps, clustering outside a pure subtype cluster with bootstrap > 70%, and clustering outside of a CRF with bootstrap >70 %.
Rule 11C: CRF
Subtype assigned based on sequence < 800 bps, clustering with a pure subtype with bootstrap > 70%, clustering inside a CRF with bootstrap >70 %.
Rule 11D: NOT ASSIGNED CHECK THE REPORT
Result assigned based on sequence > 800bp, clustering with a CRF with bootstrap > 70%,with detection of recombination in the pure subtype bootscan, and further confirmed by CRF by bootscan analysis.
Rule 11E: CRF
Result assigned based on sequence < 800 bps, clustering with a CRF inside with bootstrap > 70%, and not clustering with a pure subtype with bootstrap < 70%.
The rule 1 is for pure subtypes classification.
Rule 1A: PURE
Subtype assigned based on sequence > 800 bps, clustering inside a pure subtype with bootstrap > 70% without recombination in the bootscan, and do not clustering with a CRF with bootstrap >70 %.
Rule 1B: PURE-LIKE
Subtype assigned based on sequence > 800 bps, clustering outside a pure subtype with bootstrap > 70% without recombination in the bootscan, and do not clustering with a CRF with bootstrap >70 %.
Rule 1C: PURE (CRF)
Subtype assigned based on sequence > 800 bps, clustering with a pure subtype with bootstrap > 70% without recombination in the bootscan, clustering inside a CRF with bootstrap >70 %.
Rule 1D: NOT ASSIGNED - CHECK THE REPORT
Result assigned based on sequence > 800 bps, not clustering with a pure subtype with bootstrap > 70% without recombination in the bootscan.
Rule 2: RULE 2 - PURE RECOMBINANT
The rule 2 is for the classification of recombinants with pure subtypes.
Rule 2A: PURE RECOMBINANT
Recombinant assigned based on sequence > 800 bps, with pure subtype supported recombination in the bootscan, i.e. two or more pure subtypes with more than 10% of the windows supported by bootstrap > 70%, and not clustering with a CRF with bootstrap > 70%.
Rule 2B: POTENTIAL RECOMBINANT
Potential recombination assigned based on sequence with only one pure recombinant subtype, supported by bootstrap > 70% (failure to classify a second pure subtype with >10% of windows supported by bootstrap >70%), and failure to classify it as a non-recombinant pure subtype or CRF.
Rule 2C: NOT ASSIGNED - CHECK THE BOOTSCAN
Result assigned based on sequence with recombination in the boostscan, i.e < 0.9, however no pure subtype is supported (>70%) in > 50% of the windows.
Rule 3: RULE 3 - CRF
The rule 3 specifies the classification of CRFs.
Rule 3A: CRF
Subtype assigned based on sequence > 800 bps, clustering with a CRF with bootstrap > 70%, with detection of recombination in the pure subtype bootscan, and further confirmed by CRF bootscan analysis (bootscan > 0.9).
Rule 3B: CRF
Subtype assigned based on sequence > 800 bps, clustering inside a CRF with bootstrap > 70%, with detection of recombination in the pure subtype bootscan, and further confirmed by CRF bootscan analysis (bootscan > 0.7 with support of 70%).
Rule 3C: CRF-Like
Subtype assigned based on sequence > 800 bps, clustering outside a CRF cluster with bootstrap > 70% with detection of recombination in the bootscan, and further confirmed by CRF bootscan analysis (bootscan > 0.7 with support of 70%).
Rule 4: RULE 4 - CRF RECOMBINANTS
rule 4 is for the classification of recombinants with CRFs.
Rule 4A: CRF PURE RECOMBINANT
Recombinant assigned based on sequence > 800 bps, with CRF and pure subtype supported recombination in the bootscan (i.e. one CRF and one or more pure subtypes with more than 10% of the windows supported by bootstrap > 70%), and clustering with a CRF with bootstrap > 70%.
Rule 4B: POTENTIAL RECOMBINANT CHECK THE BOOTSCAN
Potential recombination assigned based on sequence > 800 bps, with only one recombinant CRF or pure subtype supported by bootstrap > 70% (failure to classify a second pure subtype or CRF with >10% of windows supported by bootstrap >70%), and failure to classify it as a non-recombinant pure subtype or CRF.
Rule 4C: NOT ASSIGNED - CHECK THE BOOTSCAN
Result assigned based on sequence > 800 bps, with recombination in the boostscan (< 0.9), clustering with a CRF with bootstrap >70% however the CRF is not confirmed by bootscan analysis (>70%) in > 50% of the windows.
2. Decision Tree for sequences shorter than 800 bp:
Subtype assigned based on sequence < 800 bps, clustering inside a pure subtype cluster with bootstrap > 70%.
Rule 11B: NOT ASSIGNED CHECK THE REPORT
Result assigned based on sequence < 800 bps, clustering outside a pure subtype cluster with bootstrap > 70%, and clustering outside of a CRF with bootstrap >70 %.
Rule 11C: CRF
Subtype assigned based on sequence < 800 bps, clustering with a pure subtype with bootstrap > 70%, clustering inside a CRF with bootstrap >70 %.
Rule 11D: NOT ASSIGNED CHECK THE REPORT
Result assigned based on sequence > 800bp, clustering with a CRF with bootstrap > 70%,with detection of recombination in the pure subtype bootscan, and further confirmed by CRF by bootscan analysis.
Rule 11E: CRF
Result assigned based on sequence < 800 bps, clustering with a CRF inside with bootstrap > 70%, and not clustering with a pure subtype with bootstrap < 70%.