Clinical and Laboratory Features of HIV/AIDS in the Kingdom of Saudi Arabia

280 Pages·2015·4.66 MB·English

by  Bajhmoum, Wail

Clinical and Laboratory Features
of HIV/AIDS in the Kingdom of
Saudi Arabia

Thesis submitted in accordance with the requirement of the
University of Liverpool for the degree of Doctor in Philosophy

Wail Bajhmoum
June 2015

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Dedication

To:
Maria, Alaa, Leen and Lama.
My life, love and future.
Wail

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Abstract

Introduction

There are insufficient data on the epidemiology and clinical features of HIV in the
Middle East. WHO statistics show the Kingdom of Saudi Arabia (KSA) to be one of
the least affected countries globally. However, the Saudi National Program for HIV
Control reported a 34.6% increase in cases in 2008 from the previous year. Jeddah
region has the highest proportion of HIV cases in KSA (40%). Infection risk data are
not always complete and coinfection rates have not been studied. The first part of
these studies included a retrospective longitudinal case review of all patients
attending the Jeddah clinic to obtain a clearer view of clinical and epidemiological
features of that population

There are few publications about resistance to antiretroviral therapy (ART) in the
Arabian Peninsula, including KSA, and most are heavily biased towards assessment
of patients with sequential treatment failure. Wider access to resistance testing has
only become available recently and baseline local resistance patterns are largely
unknown. The aim of the second part of the study was to determine patterns of
ART resistance in a systematic fashion in treatment-naïve HIV positive Saudi
patients and to document the presence and frequency of novel resistance HIV
markers in Jeddah.

Study Part 1. Clinical features and epidemiology of HIV and coinfection
with TB and/or viral hepatitis in a large clinic in Jeddah, Kingdom of Saudi
Arabia

Aims: To describe demographic and clinical features of HIV infection in clinics and
hospitals in Jeddah and to document prevalence and risks for coinfections with
tuberculosis (TB) and/or hepatitis

Methods: Retrospective study including all HIV positive Saudi adults attending the
main treatment centre in Jeddah in the 11 years (2000-2010). Data were
systematically collected from case files and summarised. Statistical comparisons
included univariate analyses with a p value <5% considered significant.

Results: 1383 HIV positive adults were reviewed, median (range) age 40 (18-86)
years, of whom 1026 (74.2%) were male. Risk factors included heterosexual
transmission in 709 (51.3%), men having sex with men (MSM) in 264 (26%), blood
products in 148 (10.7%), injecting drug use (IDU) in 97 (7%) and not identified in
165 (11%). The predominant clinical presentation was with respiratory symptoms
611 (44%), followed by gastrointestinal manifestations in 312 (22%), while 29%
(408) were asymptomatic. Past or present TB coinfection (clinical and/or radiology)
was found in 208 (15%); 59 (5.3%) had hepatitis B serology positive (HBsAg
positive) and 82 (7.4%) had hepatitis C coinfection (antibody positive). TB was
associated with IDU (RR 1.67 (CI 1.13-2.41) p< 0.01) and having been in prison
(RR 1.83 (1.18-2.85) p< 0.01) and these two risk factors were closely linked
themselves. HBV coinfection was not linked with IDU (RR 1.89 (0.93-3.85) p=0.08)
but was linked to being in prison (2.38 (1.25-4.54) p <0.01), while HCV was
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strongly linked with IDU (RR 4.22 (2.71-6.57) p<0.01) and MSM but not with
imprisonment (RR 1.94 (1.04-3.63) p=0.07)

Conclusion:

HIV/AIDS and related coinfections are medical problems in Saudi Arabia with many
social challenges. The Saudi National Program for HIV Control actively addresses
prevention of HIV and provision of high quality care for those affected. More
detailed studies are needed on clinical patterns in outpatient and inpatient settings
and on locally appropriate prevention programmes in high risk groups.

Study Part 2. HIV resistance in ART naïve patients in a large treatment
centre in Jeddah, Kingdom of Saudi Arabia

Aims: To document the prevalence and types of ART resistance in ART naïve HIV
patients in Jeddah, and to compare the efficacy of Next Generation Sequencing
(NGS) with standard (Sanger) genotypic methods.

Methods: Plasma samples were collected from all ART-naïve patients sequentially
attending the HIV clinic at King Saud Hospital, the main HIV treatment centre in
Jeddah, between November 2012 and February 2013. Plasma was saved and HIV
protease (Prot) and reverse transcriptase (RT) regions were sequenced according to
routine in-house diagnostic protocols (Sanger) at Liverpool Specialist Virology
Centre. The Stanford database was used for interpretation of resistance profiles.
Neighbour-joining phylogenetic analysis was performed on samples with adequate
sequence data for both Prot and RT. NGS sequencing was later performed at the
Public Health England reference laboratory in Colindale.

Results: Blood samples were collected from 109/116 (94%) eligible patients
approached to join the study. 71 (65%) were male and 52 (48%) had been
diagnosed with HIV within the last 6 months. HIV RNA was successfully amplified
from 96, and sequence data obtained from 93 Prot amplicons and 87 RT amplicons
by Sanger and 105 by NGS. Mutations at putative resistance sites for NNRTI NRTI
and PI were detected by Sanger in 9/87 (10.3%), 1/87 (1.1%) and 6/93 (6.5%)
and 24/105 (22.9%), 6/105 (5.7%) and 34/105 (32.4%) respectively by NGS.
Those with significant potential to confer resistance to NNRTI were found in 9/87
(10.3%), with resistance to NRTI in 1/87 (1.1%) and PI in 6/93 (6.5%). 4.5% of
the samples showed resistance to efavirenz and nevirapine. The most common HIV-
1 subtype was C (38%); although a cluster of CRF2_A (7%) was also prominent.

Conclusion: Clinically significant resistance is emerging (16 %) in this population.
A variety of other markers included some clustering suggesting local transmission
of primary resistance. The results are probably generalizable in KSA and we
recommend the introduction of routine resistance testing for all HIV positive
patients in the region before starting ART.

Overall:
These findings provide evidence for introduction of several changes to enhance the
National HIV/AIDS programme in the Kingdom of Saudi Arabia.

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Acknowledgements

This work could not be completed without the assistance and support of
many people. I would like to express my deep thanks and appreciation to Dr.
Nick Beeching for his endless support, guidance and close supervision.
Thank you for the great organizing of every detail of this study along the
past years. This work could not be done without your meticulous
supervision.
Also I am greatly thankful to Dr. Anu Chawla my second supervisor for her
advice and contiguous care.
Dr. Mark Hopkins, thank you very much for your cooperation and support in
lab work. Professor Anna Maria Geretti, Professor David Lalloo and Professor
Brian Faragher thank you all very much for your care and advice. Also I’m
grateful to Colindale Centre for their assistance in processing samples for
next generation sequencing (NGS) particularly Dr. Jean Lutamyo Mbisa,
Acting Head, Antiviral Unit Virus Reference Department.
To all members of the staff of King Saud Hospital in Jeddah, I can’t thank
you enough. I’m also greatly thankful to Saudi Ministry of Health in Riyadh
for the care and useful support particularly Dr. Ziad Memish, former Deputy
Minister for Saudi Public Health.
Finally I’d like to express my deep appreciation to my family and friends,
specially my lovely mom Maria and wonderful wife Alaa.

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Contents Page
Dedication…………………………………………….…………………………… 2
Abstract …………………………………………….……………………………… 3
Acknowledgements ……………………………………………………………. 5
Abbreviations …………………………………………………………………….. 13
Tables……………………………………………………………………………….. 16
Figures……………………………………………………………………………….. 20
Chapter 1……………………………………………………………………………. 22
1.1 Introduction…………………………………………………………………… 23
1.1.1 Global view…………………………………………………………………. 23
1 .1.2 Regional view……………………………………………………………… 26
1 .1.3 Aims…………………………………………………………………………… 31
1 .2 Literature Review……………………………………………………………. 32
1 .2.1 Global epidemiology………………….…………………………………. 34
1 .2.1.1 Asia…………………………………………………………………………. 36
1 .2.1.2 Sub-Saharan and Africa …………………………………………….. 36
1 .2.1.3 East Europe and Central Asia…………………..…………….…… 37
1 .2.1.4 Middle East and North Africa MENA ………………….………… 37
1 .2.2.1 Bahrain…………………..…………………………………………………. 48

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# Contents Page
1 .2.2.2 Iran …………………………………………..………………………………….. 50
1 .2.2.3 Jordan ……………………….………………………………………………….. 51
1 .2.2.4 Kuwait ……………………………………………………………………………. 52
1 .2.2.5 Lebanon...…………….…………………………………………………………. 53
1 .2.2.6 Oman.…………………………………………………………………………….. 54
1 .2.2.7 Palestine Israel ……………………………………………………………….. 56
1 .2.2.8 Syria ……………………………………………………………….…………….. 58
1 .2.2.9 Turkey ………………………………………………………………………….. 59
1 .2.2.10 United Arab Emirates…………………………………………………….. 60
1 .2.2.11 Yemen…………………………………………………………………………. 61
1 .2.3.1 Saudi Arabia…………………………………………………………………… 62
1 .2.3.2 HIV clinic protocols…………………………………………………………. 70
1 .2.3.3 Links between Islam and HIV prevalence………………………….. 74
1 .3. Coinfections………………………………………….……………………………. 79
1 .3.1 Syphilis and STI in Saudi Arabia…………….……………………………. 80
1 .3.2 Hepatitis A Viral Infection HAV ……………………………………………. 82
1 .3.3 Hepatitis B Viral Infection HBV …………………………………………….. 84
1 .3.4 Hepatitis C Viral Infection HCV …………………………………………….. 87
1 .3.5 Tuberculosis Infection TB ……………………………………………………. 94

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Contents Page
1. 3.6 IDU and HIV infection…………………………………………………….. 100
1. 3.7 Summary………………………………………………………………………. 103
1. 4. Antiretroviral Therapy ART ……………………………………………….. 104
1. 4.1 Types of ART resistance tests………………………………............. 108
Ch apter 2………………………………………………………………………….……. 115
2. Methodoloy …………………………………………………………………………. 115
2. 1 Clinical Features of HIV in KSA ……………………..………..………….. 116
2. 2 Data collection and anonymizing……….…………………………………. 119
2. 3.1 Important definitions……………………..……………………..…………. 120
2. 3.2 TB co infection patients ……………………………………………………. 120
2. 3.3 HCV coinfection…………………………………………………..…………… 121
2. 3.4 HBV coinfection …………………………………………………...…………. 121
2. 4.1 1 WHO AIDS Staging…………………………………………...…………… 122
2. 5. Antiretroviral resistance in treatment naïve HIV patients in
Jeddah…………………………………………………………….....…..…………….. 124
2. 5.1 Patient recruitment …………………..……………………..….…………. 125
2. 6. Samples storage and transport………………………………....……….. 127
2. 7. Lab work methodology……………………………...…….......…………… 128
2. 7.1 Principles of examination………………………….....……………........ 128
2. 7.2 HIV drug-resistance testing/nucleic acid sequencing……......... 129

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Content Page
2.7.3 Specimen requirements, means of identification and collection
procedure…………………………………………………………........................ 129
2.7.4. Instrumentation, equipment and special supplies……….......... 129
2.7.5. Reagents………………………………………………………………......... 130
2. 7.6. HIV-RNA extraction (purification)……………………………........... 130
2. 7.7. PCR……………………………………………………………………….......... 131
2. 7.8 Nested Protease and Reverse Transcriptase PCRs……….......... 131
2. 7.9. PCR Product Quantification……………………………………........... 132
2. 7.10 Big Dye Cycle Sequencing PCR…….………………………….......... 133
2. 8. Data Collection Software and Data Analysis………………….......... 136
2. 9. Sample size and ethics………………………………………………......... 136
2. 10. Next Generation Sequencing methodology……………............... 137
2. 10.1. RNA extraction……………………………………………………………... 137
2. 10.2. PCR amplification……………………………………………………....... 137
2. 10.3 Library preparation for sequencing………………………………..... 138
2. 10.4 Bioinformatic analysis……………………………………………......... 139
2. 11. Definitions………………………………………………………………......... 140
2. 11.1. Primary HIV drug resistance……………………………………....... 140
2. 11.2. Treatment emerging HIV Drug Resistance……………….......... 140
2. 11.3. Recruitment and tests…………………………………………............ 140

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Contents Page
Ch apter 3………………………………………………………………………… 142
3. 1. Introduction……………………………………………………………… 143
3. 2. Results……………………………………………………………………… 144
3. 2.1. Age and features of HIV infection……………………………… 144
3. 2.2. Educational level…………………………………………………….. 145
3. 2.3. Marital status………………………………………………………….. 146
3. 2.4. Reasons for HIV testing…………………………………………… 146
3. 2.5 Risk Factors for HIV…………………………………………………. 147
3. 2.6. Presenting history…………………………………………………… 153
3. 2.7. Laboratory results…………………………………………………… 156
3. 2.8. Viral load……………………………………………………………….. 157
3. 2.9. IDU and History of prison………………………………………… 158
3. 3. IDU and STI………………………………………………………………. 158
3. 4. Patients on ART…………………………………………………………. 158
3. 5. WHO classification……………………………………………………. 159
3. 6. Discussion………………………………………………………………… 160
3. 6.1 HIV/AIDS in the Kingdom of Saudi Arabia…………………… 160
Ch apter 4………………………………………………………………………… 169
H IV coifections………………………………………………………………… 169
4. 1 Introduction………………………………………………………………. 170

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