HIV
What are the unique virological features of retroviruses?
- diploid genome
- integration into the cellular genome as obligate step of replication cycle
Explain the naming/nomenclature of specific mutations
G48V
the number denotes position of a codon/AA
the letters denote AA in wt (left) and mutated strain (right)
Name/describe methods and approaches to ARV resistance testing
genotypic resistance testing
- based on DNA sequencing
- "Sanger" and "NGS"
phenotypic resistance testing
What is the difference between primary/baseline resistance testing and pretreatment resistance testing
Baseline resistance testing and pretreatment resistance testing both involve assessing drug resistance before starting treatment, with "pretreatment" referring to resistance at the point of starting a new regimen, and "baseline" meaning the resistance present at the initial diagnosis of infection.
What are HIV-1 subtypes?
How many are there and how do they differ?
HIV-1 is further classified into four groups; M, N, O and P. Of these, group M is the most widespread worldwide. Group M is divided into nine distinct subtypes; A, B, C, D, F, G, H, J and K;
Novel HIV-1 M subtype L!
What is the difference between major and minor drug resistance mutations?
Major drug resistance mutations typically arise early during HIV treatment failure, conferring significant reductions in a drug's effectiveness.
Minor resistance mutations, in contrast, tend to appear later, often after a major mutation, provi
How do we interpret results of genotypic HIV DR tests?
Interpretation of HIV DR relies on bioinformatic algorithms that link the obtained genotypic result to large databases of genotypic results corelated to phenotypic results and/or clinical outcomes (e.g. Stanford Drug Resistance Database) and are based on interpretation rules that include list of known mutations (e.g. the IAS-USA guidelines)
According to current guidelines, when should resistance testing be performed?
-Baseline genotypic resistance test should be performed on the first available sample at diagnosis
-Genotypic resistance testing is recommended prior to initiation of ART
-Resistance testing should be performed at virological failure
What does the concept of HIV quasispecies denote
An HIV quasispecies is the genetically heterogeneous "cloud" or "swarm" of closely related but distinct viral variants that co-exist within an infected individual.
Which statement is the most accurate regarding HIV drug resistance?
HIV drug resistance has never been found in patients who are naive to treatment
HIV drug resistance is always the result of poor treatment adherence
Specific mutations associated with HIV drug resistance may vary between HIV subtypes
Cross-resistance among ART drug classes is common
"Specific mutations associated with HIV drug resistance may vary between HIV subtypes"
Drug resistance pathways vary between different subtypes, certain resistance mutations are more likely to appear in some subtypes than others, influencing treatment strategies. For example, the L90M mutation is a key primary DRM for protease inhibitors (PIs) in subtype C, while subtype B commonly sees the D30N mutation for nelfinavir (NFV). Another example is the V106M mutation, a non-nucleoside reverse transcriptase inhibitor (NNRTI) resistance mutation, which is more easily acquired in subtype C
What are the indications for proviral DNA resistance testing?
1. Repeated failure of RNA amplification at baseline or time of virologic failure, especially at lower levels of viremia when amplification of HIV-RNA may fail.
2. A switch to a new regimen in individuals who are virally suppressed in the absence of a clearly documented treatment history, or insufficient access to historic resistance tests performed at baseline or during previous failure
3. The initiation of therapy in individuals not on ART, since in the absence of selective pressure, resistant variants may be archived in the DNA but replaced in the plasma by more replication-competent variants with less or no resistance.
On the basis of current data, which is most accurate regarding acquired drug resistance?
-Delaying ART initiation is associated with increased risk for acquired drug resistance
-If therapy is deferred, repeat testing at ART initiation to identify drug resistance is unnecessary
- Similar rates of acquired drug resistance have been shown with immediate and delayed ART initiation
- The rates of acquired drug resistance are significantly lower with immediate/early ART initiation vs delayed initiation
"Similar rates of acquired drug resistance have been shown with immediate and delayed ART initiation"
Name three mechanisms of HIV viral evolution / genomic change
1.RT high mutation rate
~ 1 substitution per genome
EVERY possible mutation EVERY day
2. Recombination
rate: 7-30 crossing-overs per genome
resulting in mosaic genome
3. APOBEC related mutagenesis
Deamination dC to dU in ss-cDNA resulting in
G to A hypermutation in a complementary strand
What makes ARV mutation RT M184V so special?
What are the advantages of Sanger sequencing in HIV resistance genotype testing?
name three
•Well-established analytical method in every molecular laboratory with a variety of in house and commercial assays (decades of clinical experience)
•Bioinformatic algorithms with easily interpreted and highly reproducible results of HIV drug resistance
•Good performance regarding different molecular forms of HIV
•An impressive number of sequences available in genomic databases freely available to the scientific community
TRUE or FALSE
It is possible for individuals who have received preexposure prophylaxis to develop pretreatment drug resistance
TRUE
The prevalence of pre-exposure prophylaxis (PrEP)-associated resistance (defined as resistance to tenofovir and/or lamivudine) is low for individuals who acquire HIV while receiving tenofovir-containing PrEP. However, the prevalence of tenofovir and or lamivudine resistance is more than 10-fold higher if PrEP is initiated during undiagnosed acute HIV infection.
Current taxonomic name of HIV-1 according to the International Committee on Taxonomy of Viruses: ICTV
Lentivirus humindef1
TRUE or FALSE
All resistance associated mutations involve target viral genes coding for specific viral product
FALSE
3’PPT: potential sequencing target in patients failing INSTI without adherence issues and no resistance based on pol region sequencing
Env region: potential relevance in patients with unexplained INSTI failure, highly diverse region
What are the advantages of NGS sequencing in HIV resistance genotype testing?
name three
-ability to detect low-frequency drug-resistant variants (LA-DRVs)
-high throughput and efficiency - NGS enables the simultaneous sequencing of millions of DNA fragments in a single run
-easier to access whole genome and test for resistance across multiple drug targets
Which statement best describes a recommendation for HIV drug resistance testing?
Drug resistance testing should be performed for all patients who are changing ART regimens regardless of their HIV viral load
ART initiation should be delayed while awaiting resistance testing results in patients who are pregnant and have HIV
In the setting of virologic failure, drug resistance testing is recommended within 6 weeks after discontinuing therapy
Results of drug resistance testing must be factored into the adjustment of ART regimens in patients experiencing virologic failure
"Results of drug resistance testing should be factored into the adjustment of ART regimens in patients experiencing virologic failure"