eprintid: 10119647 rev_number: 8 eprint_status: archive userid: 638 dir: disk0/10/11/96/47 datestamp: 2021-01-21 15:08:12 lastmod: 2021-01-21 15:08:12 status_changed: 2021-01-21 15:08:12 type: thesis metadata_visibility: show creators_name: Ait-Khaled, Mounir title: Sequence analysis of human immunodeficiency virus type 1: A cross-sectional and longitudinal analysis ispublished: unpub keywords: Biological sciences; HIV-1 note: Thesis digitised by ProQuest. abstract: The replication of HIV-1 and the turnover of CD4 cells in vivo is a highly dynamic process. This environment of continuous de novo virus infection and extensive replication provides an ideal setting for the generation of HIV-1 variants. The objectives of this thesis were to perform a cross-sectional and longitudinal sequence analysis of HIV-1 in blood and multiple tissues of HIV-1 infected individuals. Five to 20 clones of Polymerase Chain Reaction (PCR) amplicons were sequenced and their relationships investigated using phylogenetic methods. An analysis of V3 sequences from a patient at the time of seroconversion revealed a homogeneous quasispecies which contrasted with the high diversity observed in the V3 quasispecies from a patient with AIDS. Phylogenetic analysis of HIV-LTR variants from LN and blood from 4 patients revealed 2 distinct patterns. First, an independent clustering of LN and PBMC variants, indicating a compartmentalisation of the two quasispecies for the patient with an intact lymph node. Second, non-polarised trees with variants from either LN or PBMC present in common branches for the patients with a disrupted LN architecture. These results suggest that the lymph nodes may be important in the sequestration/evolution of distinct HIV-1 variants. A similar phylogenetic analysis has been carried out on LTR variants from multiple postmortem samples (spleen, lung, spinal cord, ganglion, lymph node and blood) of a patient who died with AIDS. The results revealed a genetically distinct LTR quasispecies in the nervous tissues compared to that present in the other tissues. The nervous tissue quasispecies was characterised by 7 mutations in the normally conserved TAR region which would be expected to abrogate tat transactivation. However, this quasispecies showed the maintenance of prototypic NF-kB sites which would allow TAR independent kB tat transactivation to occur. These data provide evidence for a role of the LTR in the adaptation of HIV-1 to the nervous tissue environment by optimising the use of specific cellular transcription factor(s). date: 1996 oa_status: green full_text_type: other thesis_class: doctoral_open thesis_award: Ph.D language: eng thesis_view: UCL_Thesis primo: open primo_central: open_green verified: verified_manual full_text_status: public pages: 275 institution: UCL (University College London) department: Virology thesis_type: Doctoral citation: Ait-Khaled, Mounir; (1996) Sequence analysis of human immunodeficiency virus type 1: A cross-sectional and longitudinal analysis. Doctoral thesis (Ph.D), UCL (University College London). Green open access document_url: https://discovery.ucl.ac.uk/id/eprint/10119647/1/out.pdf