Western University Scholarship@Western Electronic Thesis and Dissertation Repository 8-19-2020 1:00 PM Rates and patterns of indels in HIV-1 gp120 within and among hosts John Lawrence Palmer, The University of Western Ontario Supervisor: Poon, Art F.Y., The University of Western Ontario A thesis submitted in partial fulfillment of the equirr ements for the Master of Science degree in Pathology and Laboratory Medicine © John Lawrence Palmer 2020 Follow this and additional works at: https://ir.lib.uwo.ca/etd Part of the Molecular Genetics Commons Recommended Citation Palmer, John Lawrence, "Rates and patterns of indels in HIV-1 gp120 within and among hosts" (2020). Electronic Thesis and Dissertation Repository. 7308. https://ir.lib.uwo.ca/etd/7308 This Dissertation/Thesis is brought to you for free and open access by Scholarship@Western. It has been accepted for inclusion in Electronic Thesis and Dissertation Repository by an authorized administrator of Scholarship@Western. For more information, please contact
[email protected]. Abstract Insertions and deletions (indels) in the HIV-1 gp120 variable loops modulate sensitivity to neutralizing antibodies and are therefore implicated in HIV-1 immune escape. However, the rates and characteristics of variable loop indels have not been investigated within hosts. Here, I report a within-host phylogenetic analysis of gp120 variable loop indels, with mentions to my preceding study on these indels among hosts. We processed longitudinally-sampled gp120 sequences collected from a public database (n = 11,265) and the Novitsky Lab (n=2,541). I generated time-scaled within-host phylogenies using BEAST, extracted indels by reconstructing ancestral sequences in Historian, and esti- mated variable loop indel rates by applying a Poisson-based model to indel counts and time data.