Within-host evolution of X4 HIV-1 in a rare transmission pair revealed by phylogenetic reconstruction of deep-sequence data Anh Q. Le, Jeremy Taylor, Winnie Dong, Rosemary McCloskey, Conan Woods, Kanna Hayashi, M-J Milloy, P. Richard Harrigan, Art F.Y. Poon, Zabrina L. Brumme - Thank you organizers and the title of my poster is shown here.

Putative case of X4 transmission from CCR5-wt/wt donor to CCR5-∆32 homozygous recipient Envelope-V3 - Getting straight into it, through phylogenetic analysis of bulk env-V3 sequences from acute and chronically infected individuals of VIDUS Retrospectively identified a putative transmission case, donor CCR5wt and recipient CCR5∆32 homozygous Shown is a phylogenetic tree created using env-V3 sequences, red branches are X4 and blue are R5 Zoomed in window shows our putative transmission pair, exhibited lowest genetic distances of any two in the tree

Single X4 transmitted/founder virus (TFV) Next performed env-v3 deep sequences on all plasma and pbmc samples Did anc phylogenetic recons using only plasma sequences Shown is a representative time stamped phylogenetic ancestral reconstruction, donor sequences are shown in green and recipient in purple All 10 reconstructions indicated that a single X4 virus was transmitted from donor to recipient indicated by the single line connecting the sequences and labeled Reconstruction by Dr. Art Poon

Transmission via transfer of an HIV infected cell? Donor plasma and PBMC 1 month prior to transmission Tracking the frequency of the exact nucleotide sequence of the TFV in the donor plasma and PBMC compartment 1 month prior to transmission We found that in the plasma shown on the left, this virus represented a minority variant, whereas in the pbmc compartment it was a majority variant representing 33.5% of all sequences This data possibly suggests that transmission and infection in the recipient possibly occurred through transfer of an HIV infected cell rather than free virus spread Plasma PBMC

Differential coreceptor evolution in donor and recipient 41% 60% 59% 40% Lastly we wanted to compare the evolution of X4 in two genetically distinct hosts. On the left are phylogenetic trees constructed using plasma deep sequences from the donor and recipient, again in red are X4 and blue R5 On the right is a summary of the frequency of X4 vs R5 overtime. For the donor you can see a gradual reversion from X4 to R5 whereas the recipient remains consistently X4, this trend is also consistent for the PBMC compartment. 18% 60% 82% 26%

Summary Single X4 T/F virus from the donor to recipient Infection occurred by transfer of HIV infected cell Differential coreceptor evolution In summary anc phylo recon revealed that a single X4 virus was transmitted, a number that is lower than expected for IDU Data also suggests that transmission possibly occurred via the transfer of an HIV infected cell Overtime in the donor and recipient exhibited differential coreceptor evolution

Acknowledgements Dr. Zabrina Brumme Dr. Richard Harrigan Jeremy Taylor Dr. Mark Brockman Gursev Anmole Tallie Kuang Tristan Markle Bemulu Baraki Philip Mwimanzi Aniqa Shahid Natalie Kinloch Dr. Richard Harrigan Jeremy Taylor Winnie Dong VIDUS participants