Transmitted and acquired HIV drug resistance in Viet Nam

The rollout of antiretroviral therapy (ART) in Viet Nam along with limited resources for treatment monitoring are expected to be accompanied by the emergence of transmitted and acquired drug resistance. Drug resistance challenges the success of ART program and the efforts to curb the HIV epidemic in Viet Nam. Understanding factors that impact treatment outcome and prevalence and patterns of drug resistance provides imperative information for strategic and effective management. The first part of this thesis aims to study the prevalence and patterns of transmitted drug resistance (TDR) in ARTnaïve patients. TDR prevalence was detected in 6.4% of ARVnaïve patients with HIVassociated tuberculous meningitis initiating ART in Ho Chi Minh City (HCMC) from 20052007. This rate is lower than that in developed countries and is comparable to TDR rates reported in similar resourcelimited countries. Pattern of TDR reflected the standard firstline ART regimens with nucleotide and nonnucleotide reverse transcriptase inhibitors in Viet Nam. The second part of this thesis aims to investigate factors that impact treatment outcome and drug resistance in secondline ART in Viet Nam. In a cohort of adult patients on secondline ART at the Hospital for Tropical Diseases, rate of clinical andor immunological failure was 18.2% after a median follow up of 29 months. Older age, history of injecting drug use, lower CD4 count at secondline ART initiation, suboptimal ART adherence, and previous protease inhibitor (PI) use independently predicted treatment failure. Prevalence of virological failure (HIV RNA GT;1000 copiesmL as recommended by the 2013WHO guidelines) in patients who survived and were in active follow up was 9.5%, and high viral load, nonadherence and previous PI use were independent predictors for virological failure to secondline ART. 64% of patients with virological failure carried major PI mutations. Crossresistance to thirdline medications was higher than reported in other studies with cross resistance to ETR, TPV, and DRV of 55%, 45%, and 27% patients, respectively. This information informs selection of appropriate thirdline ART regimen for patients failing secondline ART in Viet Nam. In conclusion, the work of this thesis provides important data on TDR in the chronically HIVinfected population in Viet Nam, provides, for the first time, data on treatment outcome to lopinavirbased secondline ART in the presence of extensive NRTI drug resistance, and identifies modifying risk factors to improve treatment outcomes in Viet Nam. Strategies to diagnose treatment failure accurately, to switch therapy timely, and to provide targeted adherence support will improve the outcomes of patients. Continued surveillance of TDR should be performed to assure the effectiveness of ART at the population level. Costeffectiveness studies should be conducted in order to provide evidence for policy makers to decide whether to apply baseline genotypic testing and viral load monitoring in a resource limited country like Viet Nam. Prospective studies are needed to study the validity of WHO immunologicalclinical criteria in defining virological treatment failure in PIbased secondline ART.

Transmitted and Acquired HIV Drug Resistance in Viet Nam Vu Phuong Thao Kellogg College Clinical Medicine A thesis submitted for the degree of Doctor of Philosophy June 2015 Transmitted and Acquired HIV Drug Resistance in Viet Nam Vu Phuong Thao, Kellogg College, Dphil Thesis, Trinity term 2014 Abstract The roll-out of antiretroviral therapy (ART) in Viet Nam along with limited resources for treatment monitoring are expected to be accompanied by the emergence of transmitted and acquired drug resistance Drug resistance challenges the success of ART program and the efforts to curb the HIV epidemic in Viet Nam Understanding factors that impact treatment outcome and prevalence and patterns of drug resistance provides imperative information for strategic and effective management The first part of this thesis aims to study the prevalence and patterns of transmitted drug resistance (TDR) in ART-naïve patients TDR prevalence was detected in 6.4% of ARV-naïve patients with HIV-associated tuberculous meningitis initiating ART in Ho Chi Minh City (HCMC) from 2005-2007 This rate is lower than that in developed countries and is comparable to TDR rates reported in similar resource-limited countries Pattern of TDR reflected the standard first-line ART regimens with nucleotide and non-nucleotide reverse transcriptase inhibitors in Viet Nam The second part of this thesis aims to investigate factors that impact treatment outcome and drug resistance in second-line ART in Viet Nam In a cohort of adult patients on second-line ART at the Hospital for Tropical Diseases, rate of clinical and/or immunological failure was 18.2% after a median follow up of 29 months Older age, history of injecting drug use, lower CD4 count at second-line ART initiation, suboptimal ART adherence, and previous protease inhibitor (PI) use independently i predicted treatment failure Prevalence of virological failure (HIV RNA >1000 copies/mL as recommended by the 2013WHO guidelines) in patients who survived and were in active follow up was 9.5%, and high viral load, nonadherence and previous PI use were independent predictors for virological failure to second-line ART 64% of patients with virological failure carried major PI mutations Cross-resistance to third-line medications was higher than reported in other studies with cross resistance to ETR, TPV, and DRV of 55%, 45%, and 27% patients, respectively This information informs selection of appropriate third-line ART regimen for patients failing secondline ART in Viet Nam In conclusion, the work of this thesis provides important data on TDR in the chronically HIV-infected population in Viet Nam, provides, for the first time, data on treatment outcome to lopinavirbased second-line ART in the presence of extensive NRTI drug resistance, and identifies modifying risk factors to improve treatment outcomes in Viet Nam Strategies to diagnose treatment failure accurately, to switch therapy timely, and to provide targeted adherence support will improve the outcomes of patients Continued surveillance of TDR should be performed to assure the effectiveness of ART at the population level Cost-effectiveness studies should be conducted in order to provide evidence for policy makers to decide whether to apply baseline genotypic testing and viral load monitoring in a resource limited country like Viet Nam Prospective studies are needed to study the validity of WHO immunological/clinical criteria in defining virological treatment failure in PI-based second-line ART ii Acknowledgements This thesis would not have been possible without the help and support of many people who in one or another way contributed the completion of this study With great pleasure and satisfaction I would like to convey my sincere gratitude and thanks to everyone I would like to express my utmost gratitude to my principal supervisor, Dr Sarah Dunstan who gave me the opportunity to work in the field of clinical research I am very grateful to you for your guidance, patience, encouragement and providing me excellent atmosphere of doing research and patiently reviewing my thesis Thank you for your care and kindness This work would not be accomplished without the support and supervision from Dr Thuy Le Under her guidance and supervision I successfully overcame many difficulties and learned a lot I am very grateful to her for her knowledge and clinical expertise in HIV treatment, her many insightful discussions and suggestions, and her patience in reviewing the thesis Chị Thùy ơi, you are like my big sister comforting me and walking me through the ups and downs Thank you for everything you have shared with me whether it was academic or personal matter I would like to thank Prof Menno de Jong, Dr Suzanne Jurriaans, Dr Nicole Back, and Mr Ronald Rientsma from Amsterdam Medical Center for HIV genotyping and kind hostage I am thankful to Dr Estee M Török for her collaboration, giving me access to the HIV-associated tuberculosis meningitis clinical trial cohort, and Dr Hue for assistance with sample arrangement I am grateful to Dr Marcel Wolbers at Oxford iii University Clinical Research Unit for his statistical training using R software and for his assistance with the multiple imputation analyses in chapter I would like to acknowledge the doctors and nurses in the HIV Out-patient Clinic at the Hospital for Tropical Diseases for their assistance with enrolling patients in the secondline ART cohorts Special thanks to Dr Vo Minh Quang, head of the clinic for his support and insightful discussions of the project Most important is my gratitude to the patients who participated in the tuberculous meningitis clinical trial and the second-line cohorts from the Pham Ngoc Thach hospital and the Hospital for Tropical Diseases Many thanks to all of my colleagues in Oxford University Clinical Research Unit especially Ms Cam Binh, Ms Thuy Hang, Ms Phuong Tu, Ms Ai Hien, Ms Bich Tram, Ms Hoang Thu and Ms Mai Thu for patiently listening to my troubles I specially thank my parents, sisters and brothers for their unending support My mere expression of thanks does not suffice Last and not least I would like to thank my dearest husband and children for their unconditional love and support during my good and bad times These past several years have not been an easy ride yet thanks for being by my side, cheering me up and pulling me out of depression and troubles Finally, I would like to thank everybody who was important to make this thesis possible, as well as expressing my apology that I could not mention personally one by one iv Declaration The work described in this thesis is my own work and was conducted under the supervision of Drs Sarah Dunstan and Thuy Le at the Oxford University Clinical Research Unit (OUCRU) – Vietnam Thesis result chapter 3: I was in charge of the data management, performed all the sequencing, sequence analysis, and the analysis of correlates of clinical outcomes Thesis result chapter 4: I designed the data collection form, enrolled all the patients, collected data from patients’ clinic chart, generated the clinical databases and performed the data analysis Thesis result chapter 5: I enrolled and followed all patients, collected data from patients’ clinic chart, generated the clinical databases, performed viral load measurement, sequencing, sequence analysis, and the analysis of resistance mutations and correlates of clinical outcome This thesis has not been submitted for a degree or other qualification to this or any other university v Table of Content Acknowledgements iii  Declaration v  Table of Content vi  List of figures xii  List of tables xiv  Abbreviations xvi  List of Publications xx  1  INTRODUCTION 1  1.1  HIV Epidemiology .1  1.2  Human Immunodeficiency virus 3  1.2.1  HIV Structure 3  1.2.2  HIV Life Cycle 6  1.2.3  Subtypes and diversity 9  1.3  Course of HIV infection 12  1.3.1  Primary infection 12  1.3.2  Clinical latency 13  1.3.3  Clinical AIDS 14  1.4  Laboratory diagnosis 18  vi 1.5  HIV treatment 21  1.5.1  History of HIV treatment 21  1.5.2  Antiretroviral drugs 22  1.5.3  Antiretroviral (ARV) treatment 26  1.6  HIV drug resistance 34  1.6.1  How does resistance develop? 34  1.6.2  Types of drug resistance 34  1.6.3  Prevalence of drug resistance 38  1.6.4  Impact of resistance to treatment outcome 43  1.6.5  Mechanisms of HIV-1 drug resistance 46  1.6.6  Subtypes and drug resistance 52  1.6.7  HIV drug resistance testing 53  1.7  HIV infection in Viet Nam 57  1.7.1  Epidemiology 57  1.7.2  ARV Treatment and monitoring in Viet Nam 63  1.7.3  HIV drug resistance and treatment outcome in Viet Nam 67  1.8  2  Study objectives 70  METHODS .73  2.1  Study sites 73  vii 2.1.1  Hospital for Tropical Diseases 73  2.1.2  Pham Ngoc Thach Hospital for tuberculosis and lung diseases 73  2.2  Molecular-based methods 74  2.2.1  Quantification of HIV by Abbott Real-Time HIV-1 m2000rt 74  2.2.2  In-house drug resistance testing 76  3  HIV-1 drug resistance in antiretroviral-naïve individuals with HIV-associated tuberculous meningitis initiating antiretroviral therapy in Viet Nam 89  3.1  Abstract 89  3.2  Introduction 90  3.3  Methods 94  3.3.1  Study settings and population 94  3.3.2  Statement of ethics 95  3.3.3  HIV-1 drug resistance testing 95  3.3.4  Statistical method 96  3.4  Results 96  3.4.1  Presence of pre-existing HIV drug resistance mutations in chronicallyinfected subjects with HIV-associated tuberculous meningitis 96  3.4.2  HIV-1 sub-typing and polymorphisms not associated with drug resistance in Ho Chi Minh City, Viet Nam 99  3.4.3  HIV drug resistance development in subjects with virological failure 103  viii 3.5  4  Discussion 105  Second-Line Antiretroviral Therapy Outcome in HIV-Infected Adults in Ho Chi Minh City, Viet Nam 112  4.1  Abstract 112  4.2  Introduction 113  4.3  Methods 115  4.3.1  Study population 115  4.3.2  Outcome measurements 116  4.3.3  Data collection 116  4.3.4  Therapy adherence measurement and Visual Analogue Scale 117  4.3.5  Statistical analysis 118  4.4  Results 120  4.4.1  Study population and baseline characteristics 120  4.4.2  Second-line ART and outcome 123  4.4.3  Predictors of time to second-line ART failure 126  4.4.4  Causes and predictors of death 130  4.4.5  Tuberculosis co-infection on second-line ART 132  4.4.6  Virological outcome in patients with protocol-defined treatment failure 132  4.5  Discussion 134  ix Page 35 of 37 573 Journal of Antimicrobial Chemotherapy Co nf id en tia l: fo rp ee 574 rr ev iew 575 Figure 3: Predicted antiretroviral susceptibility among 22 patients experiencing virological failure on second-line 576 antiretroviral therapy in Ho Chi Minh City using the Stanford’s algorithm 577 578 579 580 NRTIs, nucleoside reverse transcriptase inhibitors; NNRTIs, non-nucleotide reverse transcriptase inhibitors; PIs, protease inhibitors; AZT, zidovudine; d4T, stavudine; 3TC, lamivudine; FTC, emtricitabine; ABC, abacavir; ddI, didenosine; TDF, tenofovir; EFV, efavirenz; NVP, nevirapine; ETR, etravirine; RPV, rilpivirine; LPV, lopinavir; IDV, indinavir; NFV, nelfinavir; ATV, atazanavir; FPV, fosamprenavir; SQV, saquanavir; TPV, tipranavir; DRV, darunavir; r, ritonavir-boosted on ly 581 Journal of Antimicrobial Chemotherapy: under review Journal of Antimicrobial Chemotherapy 582 Co Table 3: Factors associated with virological failure in 231 patients on second-line antiretroviral therapy in Ho Chi Minh city Covariates nf id CD4 counta (by -50 cells/µl) HIV RNAa (by + log10 copies/ml) 583 584 Page 36 of 37 Patients without virological failure en (N=209) Patients with virological failure (N=22) Univariate effect Multivariate effect OR (95% CI) p-value OR (95% CI) p-value 47 (17-88)(n=205) 33 (9-59) 1.39 (0.92-2.38) 0.184 1.52 (0.84-3.45) 0.248 5.1 (4.6-5.5)(n=194) 5.6 (5-5.9)(n=21) 3.14 (1.56-6.69) 0.002 2.70 (1.08-7.35) 0.039 9(3-21) 1.01 (0.97-1.05) 0.537 1.01 (0.95-1.07) 0.786 4.18 (1.46-11.16) 0.005 7.81 (2.06-31.00) 0.002 5.50 (2.02-14.91)