HIV 874

GUIDELINES

The 2012 southern African ARV
drug resistance testing guidelines

by the
Southern African HIV Clinicians Society

F Conradie, D Wilson
(Chairpersons of the Resistance Testing Guidelines Committee), A Basson, T de Oliveira, G Hunt,

D Joel, M Papathanasopoulos, W Preiser, J Klausner, D Spencer,
W Stevens, F Venter, C van Vuuren (Expert

Panel Members), L Levin, G Meintjes,
C Orrell, H Sunpath, T Rossouw, G van Zyl (Reviewers)

Corresponding

author:
F Conradie
(fconradie@witshealth.co.za)

Disclaimer: Specific recommendations
provided here are intended only as a guide to clinical therapy,
based on expert consensus and best current evidence. Treatment
decisions for patients should be made by their responsible
clinicians, with due consideration for individual circumstances.
The most current version of this document should always be
consulted.

Following the
rapid scale-up of the programme for universal access to
antiretroviral therapy (ART) in southern Africa, resistance to
antiretroviral medications will occur. A detectable viral load
must be treated as an emergency and should trigger intensive
patient tracking and adherence counselling. In contrast to the
developed world, the incidence of transmitted resistance is
still low in most areas in the region. Therefore, in this
consensus statement we do not recommend resistance testing in
HIV-infected adults upon diagnosis or ART initiation. However,
baseline resistance testing is recommended for children who have
been exposed to ART for prevention of
mother-to-child-transmission therapy and subsequently become
HIV-infected. Resistance testing is also recommended after
virological failure of first- and second-line ART regimens.

S Afr J HIV Med 2012;13(4):162-167.
DOI:10.7196/SAJHIVMED.874

1. Opening statement

Antiretroviral
therapy (ART) has converted HIV infection from an almost
universally fatal illness to a chronic manageable disease.
Adherence to therapy is essential for full viral suppression and
optimal immune reconstitution. If antiretroviral (ARV) drug
levels are suboptimal, the risk of developing ARV drug
resistance is high due to the high rate of HIV replication and
the lack of proofreading capacity in the viral reverse
transcriptase enzyme. Continuation of a failing ART regimen can
affect both the treated individual and the community, as
resistant viral strains can be transmitted to other persons.

Resistance can be minimised by
uninterrupted supply of medication, scientifically sound
prescribing practices, long-term adherence support, viral load
(VL) monitoring, and rapid responses to demonstrated
virological failure with timeous changes of therapy.1

We developed consensus guidelines for
HIV resistance testing that consider international best
practice and the financial constraints encountered in southern
Africa. The guidelines, presented here, are based on the
levels of resistance in the community as reported in the 2012
World Health Organization (WHO) HIV drug resistance report.2 The
North American and British resistance testing guidelines,3
,
4
,
5
although ideal, are not affordable nor applicable in most
southern African situations. These guidelines are aimed at
southern African clinicians who manage individuals with HIV
infection in both the private and public sectors in our
region.

Appropriate,

affordable resistance testing needs to be incorporated
strategically into national guidelines relevant to southern
Africa. In late 2012, the South African National Department of
Health sanctioned the formalisation of a National HIV Drug
Resistance Working Group. All relevant stakeholders were
identified and a steering committee was formed. The working
group has 4 clear pillars: (i) a clinical stream; (ii)
a national database development team; (iii) a laboratory team (National
Health Laboratory Service (NHLS) and National Institute for
Communicable Disease (NICD)); and (iv)
an epidemiology stream.

The presence of a VL >1 000 copies/
ml in an individual who has been receiving ART for
>6 months constitutes an adherence emergency, and should
trigger a vigorous response from the healthcare provider,
including increased adherence support, before the VL
measurement is repeated.

2. Recommendations for ARV
drug resistance testing

2.1 The
diagnosis of HIV in children aged <2 years

Genotyping

at baseline to detect resistance mutations should be performed
for all HIV-infected infants who have been exposed to any form
of ART taken by the mother or infant for the prevention of
mother-to-child transmission (PMTCT) of HIV, or who have
unknown exposure to PMTCT. Infants and children are a
challenging group to treat with ART, especially in
resource-constrained healthcare settings. Children and their
mothers are likely to have been exposed to ARV medications in
PMTCT programmes. Approximately 52.6% (95% confidence interval
(CI) 37.7 - 67.0) of children who fail PMTCT therapy have at
least one non-nucleoside reverse transcriptase inhibitor
(NNRTI) mutation after single-dose nevirapine (sdNVP), and
about 16.5% (CI 8.9 - 28.3) after sdNVP combined with
antepartum, postpartum or postnatal zidovudine (AZT) with or
without lamivudine (3TC).6 These mutations will
generally have disappeared, or may not be detectable by
routine resistance testing, 2 years after the last dose of
prophylactic ART. Children aged <3 years are treated with a
boosted protease inhibitor (PI) regimen, but it is important
to document NNRTI resistance, as this will have implications
in the choice of second-line regimens.7
Resistance mutations in children failing ART seem to be more
common than in adults.8 Results from baseline
resistance testing will ensure the most appropriate selection
of ARV drugs. Further research on appropriate drug regimens in
paediatric and adolescent populations is, critically, an unmet
need.

2.2 Failure
of ARV regimens

Resistance
testing is recommended for all patients (children and adults)
failing first-line NNRTI-based ARV regimens, with failure
defined as two VL measurements >1 000 RNA copies/ml, with
adherence and other issues addressed in the interval (see
section 5). The accumulation of resistance mutations can be
minimised by repeating the VL measurement within 3 months.9
,
10
,
11 If
the first-line regimen is fully effective, then the VL should
have fallen by 1.0 log10 copies/ml within 4 weeks or
be undetectable by 3 months (or <1 000 RNA copies/ml in
patients whose initial VL was very high).4

Resistance

tests serve two purposes: (i) a fully sensitive pattern may
imply that the patient is not adhering to treatment or has
completely interrupted ART; and (ii) if resistance mutations are
present, then the clinician, preferably together with an
expert, can decide on the most appropriate second-line
regimen. In patients on a stavudine (d4T)- or AZT-containing
NNRTI-regimen, or on a tenofovir (TDF)-containing regimen, the
importance of excluding resistance to TDF is crucial. TDF may
be required as part of the nucleoside reverse transcriptase
inhibitor (NRTI) backbone in second-line ART, or for treatment
of hepatitis B virus (HBV)/HIV co-infection in combination
with 3TC.12

Resistance testing is recommended for
all patients (children and adults) failing a PI-based ARV
regimen. Failure is defined as two VL measurements >1 000
RNA copies/ml, with measurements taken 3 - 6 months apart and
with adherence and other issues addressed in the interval. An
absence of PI mutations during PI-based therapy strongly
suggests non-adherence to treatment.13
Children on any PI regimen are at high risk for PI resistance
if co-treated with rifampicin (for tuberculosis). Repeated VL
measurements and resistance testing are recommended for
patients failing long-term PI regimens with a concurrent
decline in CD4 count.

2.3 Acute
infection

Recent HIV
infection in adults is rarely documented; however, viral
genotyping at this time may give valuable public health insights
into currently circulating strains. Resistance testing
recommendations for specific acute infection scenarios are shown
in Table 1.

Table 1.
Recommendations for HIV resistance testing

Patient
group

Recommendation

Comments

Recent
infection

Infected
infants aged <2 years exposed to PMTCT or infected
children aged >2 years who stopped taking daily NVP
less than 2 years previously

Recommended

As soon as HIV infection is
diagnosed

Infants aged
<2 years where exposure to PMTCT is uncertain

Recommended

As soon as HIV infection is
diagnosed

Documented acute infection*
(seroconversion)

Recommended

Possible public health
surveillance function

HIV diagnosis

Patients without documented
seroconversion presenting for routine clinical care

Not recommended

Background
prevalence of transmitted resistance is low and time
since infection is likely to be long, decreasing the
likelihood of detecting resistance mutations

ARV initiation

Children
aged >2 years about to start first-line ART

Not recommended

Unless within 2 years of stopping
daily NVP

Pregnant women about to start
first-line ART

Not recommended

Pregnant women should have a VL
measurement 3 months after ART initiation. Detectable
viraemia >1 000 RNA
copies/ml should be treated as an adherence emergency.

Adults about to start first-line
ART

Not recommended

Background prevalence resistance
is very low and the time since infection is likely to
be long, decreasing the likelihood of detecting
resistance mutations.

Failure of
NNRTI-based ART

Adults and
children with two VL measurements >1 000 RNA
copies/ml† and/or at
least a <2 log10 drop in VL while on
NNRTI-based ART (measurements at least 4 weeks,
preferably 3 months, apart)

Recommended

Adherence‡ issues should be
addressed comprehensively between the 2 measurements.
Resistance testing should be performed while the
patient is on the failing regimen or within 4 weeks of
discontinuation.

Failure of a boosted PI-based regimen

Adults and
children with two VL measurements >1 000 RNA
copies/ml† and/or a
<2 log10
drop in VL while on PI-based ART (measurements 3 - 6
months apart)

Recommended

Failure

on PI regimens is almost always due to poor
adherence. Adherence‡
issues should be addressed comprehensively between
the 2 measurements. Resistance testing should be
performed while the patient is on the failing
regimen or within 4 weeks of discontinuation.

PMTCT =
prevention of mother-to-child transmission; NVP =
nevirapine; ART = antiretroviral therapy; RNA =
ribonucleic acid; NNRTI = non-nucleoside reverse
transcriptase inhibitor; PI = protease inhibitor; VL =
viral load.

*Some
or all of the following features: high fever,
generalised lymphadenopathy, oral ulcers, pharyngitis,
maculopapular rash, lymphopenia, thrombocytopenia, and
transaminases, in combination with a history
suggestive of HIV exposure.

†Definition of
virological failure may vary between southern African
countries. A persisting VL of 500 - 1 000 copies/ml
could be considered for resistance testing, with
access to sensitive in-house assays.

‡See

section on ARV adherence (section 5).

3.
Scenarios where ARV resistance testing is not
recommended

3.1 HIV
diagnosis in adults and adolescents

At the current
level of transmitted resistance in the community, performing
resistance testing in all individuals who are diagnosed with HIV
infection is not cost-effective.

For pregnant women, although we do not
recommend routine resistance testing, we do recommend HIV VL
testing 3 months after initiating triple ARV therapy (for CD4
counts <350 cells/mm3
)
or at the time that pregnancy is confirmed in women already
receiving ART. A VL >1 000 RNA copies/ml at this point
should be regarded as an emergency, and should lead to
intensive adherence support and screening for drug
interactions or other reasons for failure (section 5), to
minimise fetal transmission risk. The VL measurement should be
repeated after 4 weeks, and, if >1 000 copies/ml, HIV
resistance testing and an immediate switch to a second-line
ART regimen must be performed.

3.2 ARV
initiation in adults and children aged >2 years

Children aged
>2 years who stopped taking prophylactic NVP during
breastfeeding more than 2 years previously do not need a
resistance test prior to ARV initiation. In such cases,
resistance, if present, is very unlikely to be detected by
genotyping. While super-infection with a resistant viral strain
is a theoretical possibility, it is considered to be so rare
that performing resistance tests would not be cost-effective.

3.3
Treatment interruptions without documented failure

Patients
who have interrupted therapy for reasons other than proven
virological failure should not have HIV genotype testing
performed upon presentation for subsequent ART.14 Rather, the previous ART
regimen should be re-started, and VL should be measured after
3 months. Resistance mutations generally disappear rapidly in
the absence of drug pressure and a reliable resistance test
result may not be obtained during treatment interruptions. If
the VL is not suppressed after adherence intervention, a
resistance test can be obtained to document resistance, and an
appropriate second-line regimen can be selected.15

4. National integration of
public sector laboratories

In the public
sector in South Africa, the NHLS has five centralised facilities
capable of conducting sequence-based resistance testing.
Currently, only two of these facilities perform routine
genotyping for patient care on a large scale (Tygerberg and
Johannesburg). Laboratories focus on genotyping assays, most
using in-house assays, with backup from commercial assays such
as Viroseq or TruGene. National surveillance is conducted at the
NICD. As the ARV programme expands and patients receive
treatment for longer periods of time, the capacity for
resistance testing will need to be expanded. Currently,
phenotyping capabilities for resistance are available, largely
for research purposes, at several academic centres. Numerous

research projects are underway to develop and assess more
affordable and accessible approaches to resistance testing
(e.g. sequencing short regions of the reverse transcriptase
gene).

The Southern Africa Treatment and
Resistance Network (SATuRN) has integrated the efforts of
laboratories, researchers and clinicians to monitor HIV
resistance patterns and advise on the clinical management of
patients failing ART. The SATuRN drug resistance database
systems are freely available and include two of the best
public drug resistance databases in the world: the Stanford
HIV Drug Resistance database and the RegaDB Clinical
Management Database. SATuRN databases are used to deliver an
approach to virological failure, delivering resistance
genotyping, interpretation and clinical management to remote
primary healthcare clinics without elaborate computer systems
or infectious diseases specialists at each clinic.

For each case, all laboratories
(non-governmental, public and private) generate a report that
includes clinical and resistance data. This report is sent to
HIV specialists for review and feedback, to advise management at
the primary clinic.

Meaningful interpretation of the results of
genotypic resistance tests requires a detailed knowledge of the
patient’s full ARV history, including drug regimens used, VL and
CD4 test results, any previous resistance test results,
co-occurrence of other infections, and timelines. This
information needs to be provided by the clinician/nurse upon
submitting the resistance test.

4.1
Surveillance of ARV drug resistance

The
ongoing monitoring of ARV drug resistance is a critical public
health activity, particularly in settings where individualised
ARV drug resistance testing (genotyping) is not routinely
performed prior to ART initiation. The success of empiric ART
regimens depends on the regular and timely knowledge and
review of the epidemiology of ARV drug resistance. Recommended
systems for surveillance include prevalence monitoring of HIV
genotype results at sentinel sites among populations who have
recently acquired infection: e.g. recent seroconverters,
HIV-infected pregnant women aged ≤21 years, infants infected
despite ARV exposure and those with acute HIV infection. There
may also be additional value in prevalence monitoring at
sentinel sites of ARV drug resistance among those newly
initiating therapy.

4.2
Monitoring and evaluation

The proportion
of ART-treated patients on first-line, second-line and
subsequent therapy should be monitored routinely. Because a
detectable plasma VL while on ART requires immediate
intervention, national monitoring of the proportion of patients
with detectable plasma VLs is recommended. Thresholds for
response should be determined at the public health level. For
example, a facility or geographic area with >20% detectable
plasma viraemia in patients on ARV who were previously
undetectable, should urgently be investigated. Analyses should
be performed according to demographic and geographic
characteristics, and reported quarterly to national HIV
treatment programmes.

The evaluation of the effect of HIV genotype
testing on the selection of ARV regimens and clinical outcomes
should be supported through networks of clinical programmes.
Indicators to monitor the use of HIV genotype resistance assays
should include: the number of assays per specified time period;
the proportion of assays performed in adults, children and
pregnant women; and the prevalence and type of resistance
(including class of resistance and specific mutations). As the
surveillance of ARV resistance and clinical use of HIV
genotyping increases, additional monitoring and evaluation
activities may be required.

Most settings require increased capacity for
monitoring and evaluation. Resources to sustain adequate data
management and interpretation are a public health priority. The
net cost of incorporating resistance testing, for surveillance
as well as patient management, needs to be evaluated carefully
in ARV programmes in southern Africa.16

Non-adherence: Causes and
interventions

The adherence
requirements of ART are onerous, necessitating adherence rates
>90% for first-line NNRTI-based regimens. The best biological
marker of adherence is an undetectable VL in patients on ART.
The regularity of pharmacy pick-ups is also a good marker of
adherence. Other strategies, including pill counts, have limited
practical utility in busy clinics, and are often inaccurate.17 Pill boxes
and treatment supporters may be useful in selected individuals.18

A detectable VL in patients on ART
should be treated as a medical emergency, with immediate
intervention, prompt evaluation by an experienced clinician
and appropriate support staff (e.g. social workers,
psychologists, and counsellors), and frequent follow-up. In
the case of first-line virological failure, up to 50% of
patients can re-suppress their VL,7
,
8 if
virological failure is identified timeously, and if adherence
can be improved.

In patients failing
second-line therapies, and where expensive third-line options
are being evaluated, newer measures such as the use of
electronic pill boxes (e.g. Medication Event Monitoring System
(MEMS) caps) and hair PI levels may be used, if available.

In a
significant minority of cases, patients will have no
resistance on resistance testing. Data from South Africa
reveal that this can be as high as 15 - 20% where patients
have been genotyped.19
,
20 This means the patient is
missing a large number of doses, consequently resulting in
insufficient drug pressure to induce or select out existing
resistance. These patients have a poorer prognosis,
paradoxically, than patients with established resistance,21
,
22 as their poor adherence is
often difficult to remedy, and may persist into subsequent
regimen choices. Such patients often require the intervention
of a psychologist or experienced counsellor.

Common causes of poor
adherence (sections 5.1 - 5.12) are often complex and linked to
social issues.

5.1
Inadequate treatment literacy

Most HIV
programmes have extraordinary adherence rates when compared with
other chronic diseases – largely due to efforts by clinic staff
to ensure that patients understand HIV infection and ART. If a
patient fails therapy, then some examination of the pre-ART
counselling may be merited.

5.2
Side-effects

Side-effects
are a very common reason for patients to default therapy. A
careful history of often subtle but distressing side-effects
(bad dreams, sleepiness, poor concentration, nausea, loss of
appetite), in conjunction with a work history (shift work in
particular) may allow for drug substitutions. Subtle signs of
lipo-atrophy due to NRTIs are often not taken seriously by
healthcare providers. Regular enquiry and immediate drug
substitutions should form part of every healthcare worker
encounter. Single drug substitutions should only be performed if
the VL is undetectable.

5.3
Depression and mental illness

Undiagnosed or
under-treated depression and other mental illnesses are often
overlooked. The frequency of major depression is twice as high
in HIV-infected patients as in matched HIV-negative patients.23 Patients
with depression usually respond well to treatement with an
antidepressant in combination with other non-pharmaceutical
interventions. Patients who respond to antidepressant medication
should be treated accordingly for at least 6 months.

5.4 Poverty
and food insecurity

Both poverty
and food insecurity have been related to poor adherence and an
increased frequency of missed clinic visits. Patients often lose
their jobs due to ill health in the period leading up to ART
initiation. Patients should be encouraged to return to the job
market as soon as is feasible, or to seek support. The need to
seek work may cause patients to move away from the current
clinic; therefore, referral must be facilitated. Access to
available grants, social support and employment NGOs may provide
additional support.

5.5
Work-related issues

Work-related
issues, including shift work and an inability to attend clinic
visits on weekdays, are a major cause of poor adherence. Long
clinic waiting times and monthly medication pick-ups, may make
holding down a job untenable, especially with an unsympathetic
employer.

5.6
Substance use

Alcohol use
may cause significant problems with adherence. In addition,
other recreational drugs may cause problems in certain parts of
the country. Use may fluctuate according to availability and
peer pressure.

5.7 Social
problems

Social
problems that affect adherence include stigma, both external and
internal, and poor social support networks. Perceived stigma is
correlated with poor adherence. This may manifest in: a fear of
tablets being found; an inability to solicit family or partner
support; fear around visiting the clinic or pharmacy; or anxiety
regarding an employer, neighbours or a community. Social support
groups may assist in this regard.

5.8 Denial

ART initiation
in ambivalent, conflicted patients is unlikely to have a
successful outcome. The involvement of family members and
partners may be an effective mechanism for addressing denial.

5.9 Pill
burden

Pill burden is
less of an issue with current regimens, but must be considered
in patients who are failing treatment. Pill burden due to
treatment for other conditions, such as hypertension or
diabetes, should also be addressed. Dosing simplification, such
as provision of fixed-dose combination regimens, where possible,
should be a major part of advocacy within public programmes.

5.10
Altered fertility intentions

HIV-discordant
or -concordant couples may spontaneously decide to cease their
ART regimen with the intent to begin a family. Empathetic
fertility counselling during ART initiation should prevent this
from occurring.

5.11
Conflict of opinions

Conflict of
opinions on the use of ARVs occurs frequently between healthcare
providers, certain alternative health providers and churches.
This is best addressed with an honest and non-judgmental
conversation.

5.12 Other

Drug doses
should be checked, especially in patients referred from the
private sector or inexperienced sites. Drug interactions (e.g.
rifampicin with a PI), absorption issues and primary acquisition
of resistant virus may also result in failure.

6. Laboratory objectives

6.1
Recommendations and requirements

A meaningful
interpretation of genotypic resistance test results requires
detailed knowledge of the patient’s full ARV history, including
drug regimens used, VL and CD4 test results, any previous
resistance test results, and timelines.

It is desirable that national databases be
built, using unique patient identifiers (e.g. ID numbers), to
allow the easy retrieval of information for patients who have
been cared for at different clinics and tested by different
laboratories. Besides improving patient care and easing clinical
workload, this approach is cost-effective, as it prevents
unnecessary repeat testing.

All resistance test results (including
clinical information and sequences obtained) should be entered
into a central database, such as the one maintained by SATuRN,
to enable research and surveillance.

6.2
Genotypic ARV resistance testing: Practical issues

Testing
requires ethylenediaminetetra-acetic acid (EDTA) whole blood or
EDTA plasma (purple-top tubes). Alternatively, where
established, dried blood spots (DBSs) may be used. To ensure
sample integrity, whole-blood and plasma samples must be
maintained and shipped cooled (4°C – fridge temperature) and
reach the laboratory within 48 hours. For longer delays,
whole-blood specimens must be centrifuged and the plasma
stored at -20°C (frozen). Repeat freeze-thaw cycles must be
avoided. DBSs can be maintained at room temperature for up to
4 weeks, and must be frozen at -20°C if the delay is longer
than 4 weeks.

Current commercial tests have been licensed
for specimens with a VL value of at least 1 000 RNA copies/ml.
If DBSs are used, then the minimum usable VL is 2 000 - 5 000
RNA copies/ml. Nevertheless, many in-house assays can detect VLs
of 500 - 1 000 RNA copies/ml. The probability of harbouring
resistance in the VL range of 500 - 1 000 RNA
copies/ml is only marginally less than in the 1 000 - 10 000

copies/ ml range.24 The acquisition of additional
mutations is not necessarily associated with incremental
increases in VL.25

Once a failing ART regimen has been
discontinued, most resistant viral variants quickly become
undetectable. Samples must therefore be obtained while the
patient is still on the failing regimen or very shortly after
discontinuation (to a maximum of 4 weeks).

Current test methods do not detect minority
resistant viral variants (quasi-species present at less than
approximately 20% of the total population) or archived
resistance.26

Even in the best hands, the rate of failure
to amplify virus is 5 - 10%, so not all samples submitted to the
laboratory will have a genotype result.

6.3
Genotypic ARV resistance assays

Currently
available genotype tests evaluate only the viral reverse
transcriptase and protease genes. Mutations in the genes
encoding these enzymes underlie resistance to the NRTIs, NNRTIs
and PIs.

Raltegravir (RAL),27
,
28 the first of the integrase
strand-transfer inhibitors (ISTIs), is now registered in South
Africa. Currently, no entry inhibitors – e.g. maraviroc (a CCR5
co-receptor inhibitor) or enfuvirtide (a fusion inhibitor ) –
have been registered. Future genotype tests will also need to
incorporate these drug classes.

Current resistance testing is performed
by means of polymerase chain reaction (PCR) amplification and
sequencing/genotyping of the HIV-1 protease and reverse
transcriptase genes, using commercial or validated in-house
assays. The turnaround time of these assays is approximately 2
weeks. Current United States Food and Drug Administration
(FDA)-approved commercial assays, including ViroSeq and
Trugene, can be performed at a cost of approximately R5 000
per assay. In-house assays are about 50% cheaper. Results can
provide data on the presence or absence of resistance
mutations, with resistance mutations interpretable by drug
resistance algorithms, many of which are available online.

7. Research priorities

7.1
Resistance assays

The main
thrust of research activities remains the need to develop rapid,
affordable, accessible resistance assays, including:

• advocacy to drive down
current commercial assay costs

• the evaluation of
innovative new testing approaches, e.g. the use of more
cost-effective strategies such as allele-specific assays (e.g.
M184V) to determine adherence

• improved logistics using
creative approaches such as DBS technology

• national
standardisation of technology and reporting across the country

• continual review to ensure
the incorporation of new drug classes into assays

• integrase assays

• tropism assays for CCR5
inhibitors

• the constant evaluation of
new testing platforms, e.g. ultra-deep sequencing strategies

• the suitability of assays
for relevant local HIV subtypes.

7.2
Operational research activities

7.2.1
Laboratory-based activities

Laboratory-based

activities should include:

• the upgrading and
up-scaling of infrastructure, human resource skills,
interpretation skills, and improved emergency reporting within
and by the laboratory

• national data flow and
reporting

• a monitoring and evaluation
framework to evaluate the effect of the intervention

• ongoing cost-effectiveness
modelling and analyses to assess cost-effectiveness

• ensured support for
strengthened national surveillance activities (i.e. increased
numbers processed in realtime).

7.2.2
Clinical activities

Clinical
activities must include:

• strategies to develop a
hierarchy of specialist support for interpretation, e.g. failure
clinics

• resistance testing to
support ongoing clinical research and guideline development

• strategising for the
components of an appropriate standardised third-line regimen.

7.2.3 Basic
research questions

Future work
should address:

• the contribution of
detecting minority variants and their effect on patient outcome
(including ultra-deep sequencing)

• the significance and role
of PI mutations in the local population

• the development of a
national reference facility that conducts phenotyping and other
sophisticated assays to support and develop a strong scientific
agenda for resistance testing.

8. Closing comment

These
guidelines reflect the current status quo
in terms of levels of HIV resistance in southern Africa in late
2012, and will be reviewed every few years. Implementation of
the recommendations herein will require a drastic expansion of
the laboratory capacity in the region.

Conflict of interest. All expert panel members and
reviewers have completed and submitted conflict of interest
disclosure forms. Disclosure information represents the
previous 3 years (updated 13 October 2012) and pertains to
relationships with pharmaceutical companies and medical aids.
F Conradie has received research support from Bristol-Myers
Squibb, Gilead, GlaxoSmithKline and Tibotec. She is also a
consultant for Discovery Health. L Levin has received
honoraria from Abbott, Aspen, Novagen, Optipharm and ViiV
Healthcare for speaking engagements, and served as a
consultant to Optipharm and Discovery Health. G Meintjes has
received honoraria from Sanofi-Aventis for speaking
engagements and is a consultant to Aid for AIDS. C Orrell
received funding support from Merck Sharp & Dohme (MSD) to
attend a workshop, and received honoraria from Abbott for a
speaking engagement. T Rossouw received honoraria from Abbott
for a speaking engagement, and serves as a consultant to
Discovery Health. D Spencer has received honoraria from
Abbott, Adcock Ingram, Aspen, MSD and Janssen for speaking
engagements. H Sunpath received research support from Gilead
Sciences. G van Zyl has received honoraria from Abbott for
speaking engagements. F Venter has received support from
Adcock Ingram to attend conferences and honoraria from Johnson
and Johnson, Merck and Tibotec for speaking engagements. A Basson, T de Oliveira, G Hunt, D Joel, M
Papathanasopoulos, W Preiser, J Klausner, W Stevens, C van
Vuuren and D Wilson have no conflicts of interest to declare.

Acknowledgement. This work was supported and
funded by the Southern African HIV Clinicians Society through
an educational grant from Atlantic Philanthropies. The authors
wish to acknowledge Lynsey Isherwood for her assistance in the
development of this document.

References

1. Kantor R, Shafer RW, Follansbee S, et al. Evolution of
resistance to drugs in HIV-1-infected patients failing
antiretroviral therapy. AIDS 2004;18(11):1503-1511.

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