FM DECEMBER 2018 ISSUE - digital edition

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Can NextGeneration
Sequencing help tackle HIV?
No routine testing for ART-related drug resistance
in low-income settings
DR RAJANI KANTH
VENGALA
Writer is medical scientist
and former director of
SGRF, Bangalore
Advances in nucleic acid sequencing
have been taking place at a great
pace since 2005, resulting in several
novel Next Generation Sequencing (NGS)
systems. Current NGS technology has a
three-step approach, in which a DNA library
is prepared, enriched and sequenced or
identified. Adding bioinformatics tools to this
data gives an immense power to detect and
identify microbiomes which are hitherto not
known. This enables identification of new
viruses or mutations using metagenomics
approaches. Continuous and dynamic
development of NGS technology, coupled
with metagenomics, will change the scope of
the application of this technology, and enable
identifying intraspecies changes within a
given biospecimen. Present day diagnostics
use a Sanger sequencing-based method
for molecular detection, which is not very
sensitive.
For example, in case of Transmitted
drug-resistance mutations (TDRM) of HIV-1
infection, a comparative study of NGS and
Sanger sequencing (Roy Moscona et al.,
2017) was performed. It is well known that
TDRM frequency may vary in the viral pool.
It was noted that one could observe more
non-synonymous amino acid substitutions
and TDRM using NGS compared to the
Sanger method. In the study, an overall
TDRM prevalence of 8.8% was identified via
Sanger method out of a reported prevalence
of 10.1% in treatment-naïve individuals
with NRTI as the most affected drug class.
However, NGS was able to identify 31.3%
of the patients, including those with very
low HIV-1 viral load -- even below 5%. This
suggests that NGS can truly identify viral
populations with high genetic diversity and
can evaluate at an early stage patients who
may develop resistance in the long run.
Another study (Casadellà et al., 2016) using
an NGS platform found a K65R prevalence of
nearly 70% in subjects developing virological
failure in first-line antiretroviral therapy (ART)
containing TDF (tenofovir), which was missed
by Sanger sequencing.
ART is provided in low- and middleincome
countries (LMIC) as a public health
approach and policy. This leads to HIV drug
resistance. However, no regular testing for
the drug resistance is done. The present drug
resistance testing is primarily for surveying
to inform national and regional ART. NGS can
become the best-suited technology platform
if it is used in centralized laboratories to
reduce the cost. This approach can enable
large population coverage and identify
non-responders or patients who are yet to
develop drug resistance.
NGS is likely to soon become a very
important cornerstone technology for
improved capabilities in diagnosing HIV drug
resistance. The clinical value, prevalence
of certain mutations and genetic barriers
in drug resistance can be best understood
and evaluated using NGS. Ultrasensitive
genotyping has been proven to improve
ART outcome predictions in treatment
naïve subjects who are about to start
on nevirapine or efavirenz and CCR5
antagonists. It has become very clear that if
we are to tackle HIV global pandemic, the
question of making NGS accessible to LMICs
must be resolved. In the best case scenario
-- in which global HIV-1 eradication is seen
as a possibility -- reducing costs in library
preparation and bioinformatic analysis will
be a good place to start.
54 / FUTURE MEDICINE / DECEMBER 2018