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HIV Subclustering

- Single consensus estimation of all full length genome runs



- Hypothesis: SGAs runs 0021-463M-D6 or 0020-463M_I3 are possible
founders to the 463F SGA recipient.

- Best outcome: identify the exact HIV founder genome to the base in
  the bulk PCR runs that transmitted between the donor and the
  recipient.

Next

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HIV Subclustering Overview

- What is the recipient identity?

  -0015-463F_28 and -0024-463F_74 consensus have a single difference
  (A deletion after TTTT).

- Cluster high coverage bulk PCR run -0003.

- Original cluster. 154 variant feature positions.

  

- Cut at 0.5 which is near the theoretical threshold for 154 selected
features.

- There are 17 groups at 0.5 cutoff of which 10 have 28 or more
sequences.

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HIV Subclustering Clusters

- 10 clustering plots after subsetting (number of features, cluster plots):

1, 2, 70
  

10, 10, 45
  

13, 0, 0
  

0



- Alignment of the 10 cluster consensus groups

  getQuiverSubpop.aln

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HIV Subclustering Identification

- Align the 10 clusters to the 28 full-run consensus estimates

- Two subclusters mapped to SGA estimates:

  - cg_2->0022-463M_I1 and cg_3->0020-463M_I3.

    - Subcluster cg_2->463M_I1 is exact for the 9067 bases with NO
      error.

    - Subclustering cg_3->0020-463M_I3 is 99.3821% concordant with 49
      mismatches, 2 deletions, and 5 insertions.

- Subcluster 2 perfect (green) and subcluster 3 99.38% concordance (blue)

    

- Alignment of the 10 cluster consensus to the recipient estimate (run
  -0024) shows cg_3 to be the closest but still errors (47 mismatch 17
  deletion 4 insertion).

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HIV Subclustering Ambiguity

- subcluster cg-3 still has a larger variation with 70 identified
variant positions in the subcluster.

- There are 116 degenerate positions at 10% or greater in cluster group 3!
     61 R
     30 Y
     10 K
     10 M
      3 W
      2 H

- There are 177 degerate positions at 10% in the bulk PCR before subclustering.
     84 R
     56 Y
     15 M
     10 K
      4 W
      3 S
      2 D
      1 H
      1 N
      1 V

- There is no ambiguity at the 10% level in the closest matched
recipient SGA -0022-463M_I3.