Under-detection of transmission of transmitted resistance and impact on treatment response

Simon Collins, HIV i-Base

Several studies focused on implications of under-detection of transmitted resistance – both from an individual and epidemiological perspective. Both the limit of sensitivity of genotype tests and the shift to wild-type after infection in the absence of drug pressure are both understood, these reports provided an indication of the level of the problem.

Using real-time PCR point-mutation tests for M184V, D67N, K70R in reverse transcriptase and L90M in protease, Jeffrey Johnson and colleagues analysed 183 samples from treatment naive patients in the US and Canada, with evidence of transmitted resistance by genotype sequence analysis at diagnosis. [1] Although real-time assays are sensitive to detect strains down to 0.05% of the viral population, a cut-off of 0.5% was used for positive screening in this study.

Prevalence for all four mutations was found at a higher level than previously seen with routine genotyping and the results are shown in Table 1 below.

Table 1: Prevalence of mutations in treatment naive patients

Mutation Sequence Point mutation Relative difference
D67N 7% 12% +71%
K70R 9% 14% +60%
M184V 10% 12% +20%
L90M 8% 11% +35%

Detection of additional mutations resulted in 9/183 (5%) samples showing resistance to a new class. The frequency of 2-class resistance increased by 25% from 12% to 15% and the frequency of three-class resistance doubles from 2% to 4%. MDR resistance generally appeared on the same genome.

The relatively low incidence of M184V was attributed to rapid natural decay. Prior exposure to any ARVs (PEP etc) was rules out by a detailed patient questionnaire and review of medical notes.

A similar study was presented from Karin Metzner, who detected transmission of drug resistance in around 20% (10 out of 49) of acute seroconvertors at two German clinics between 1999-2003. [2]

The study used quantitative real-time PCR to look for three key mutations: L90M (protease), K103N (NNRTIs) and M184V (RT) which was detected in 1/49 (2%), 5 /49(10%) and 6/49 (12%) of patients. Half of these mutations were present in less than 25% of the viral population and would have been below the limit of the test to be detected by routine genotypic sequencing analysis.

The clinical implications for missing transmitted resistance prior to initiating treatment were indicated by an analysis of treatment response at 3 months, presented by Marie-Laure Chaix and colleagues from the French primary infection and resistance databases. [3]

Of 297 people treated during primary HIV infection (PHI; within 6 months of infection, median 39 days IQR 33-55 days), 35 people had resistance to at least one drug in their combination (RG) and 262 were wild-type (WT). 21 had resistance to one drug, 10 to two drugs and 4 people had resistance to all three drugs in their regimen.

At baseline, the resistance group tended to have a slightly lower viral load and a higher CD4 cell count than the WT (both non-significant), but a significantly poorer response to treatment, detailed in Table 2 below.

Table 2: Baseline and treatment response

Resistance group Wild-type group p-value
Baseline viral load (log copies/mL) 5.0 5.3 0.11
Baseline CD4 (cells/mm3) 512 475 0.12
% viral load <400 at month 3 63% 82% 0.02
% viral load <50 at month 3 16% 40% 0.01
% viral load <400 at month 6 81% 95% 0.02
% viral load <50 at month 6 57% 79% 0.02

In multivariate logistic regression analysis, taking into account gender, age, plasma HIV-RNA and CD4 cell count at HAART initiation, people with genotypic resistance to at least one drug were significantly less likely to achieve an undetectable viral load.

This study was performed without clinicians having access to the results. Although treatment in PHI rarely occurs outside a clinical trial, the impact on response is startling, and undoubtedly led to treatment failure and resistance long before the patients needed treatment. French guidelines now recommend performing resistance test prospectively in patients with PHI with results available soon after HAART initiation.

The sub-optimal treatment response wouldn’t surprise anyone in the audience. To have this poorer response carefully documented however is very important. It provides additional support for resistance testing prior to starting treatment and additional caution against starting treatment without confirming sensitivity to all drugs in the regimen. The understanding of archived resistance is such that similar differences in responses may be expected even if treatment was initiated during chronic infection, when detection of resistance would also be more difficult.

Finally, Bruna Brenner and colleagues from McGill Medical Centre looking at transmission of drug resistance in Quebec, using high bootstrap (>99%) and short phylogenetic branch length (p<0.015) of reverse transcriptase and protease regions to look at clustering of recent infections from two Canadian cohort databases. [4]

484 unique subtype-B sequences were obtained from people diagnosed within six months of infection, half of which segregated into 71 clusters (range 2-11 individual per cluster). Mean age was 38, 40 and 36 in transmission groups (MSM, IVU, heterosexual respectively), with no difference in CD4, viral load or cluster size between the groups.

There also found no association between primary resistance (10.4% vs 9.4%) and dual/triple class resistance (3.8% vs 2.9%) in the clustered and non-clustered infections respectively.

This study was useful to show that recent infection are often connected – and support the view that much of the ongoing epidemic is driven by newly infected individuals who are unaware of their change in HIV status.

Another comment from the audience, was that results from this study cannot be exptrapolated to actual clustering and behaviour risk as this would require detailed individual patient and partner histories, which by the anonymised nature of this study were not available. The discussion focused on legal implications of this work, although anonymised in this study. In the UK for example similar research was moved for research laboratories by police in recent high profile cases relating to transmission prosecutions.

The results also do not justify the researchers conclusion that this establishes a rationale for earlier treatment. Earlier diagnosis certainly, but not earlier treatment.


SGS screening is probably not appropriate in the UK given the wide range of HIV sub-types that are prevalent (tests need to be recalibrated). However, although BHIVA guidelines recommend resistance testing on diagnosis, this has not been universally adopted in all clinics.

This is unfortunate. Newly diagnosed infection is the ideal time to confirm resistance, and has the practical advantage that laboratories will be seeing patient samples for the first time.

Checking systems between clinicians and labs in some hospitals are finding this a useful way to pick up patients who, for whatever reason, are not receiving resistance test with their initial CD4 and viral load results.


  1. Johnson JA, Li J-F, Brant A et al. Multi-drug resistant HIV-1 are transmitted more frequently than current estimates. 14th International HIV Drug Resistance Workshop (14th IHDRW), 7-11 June 2005, Quebec City, Canada. Abstract 111. Antiviral Therapy 2005; 10:S124.
  2. Metzner KL, Rauch P, Wlater H et al. Detection of minor populations of drug-resistant HIV-1 in acute seroconvertors. 14th International HIV Drug Resistance Workshop (14th IHDRW), 7-11 June 2005, Quebec City, Canada. Abstract 110. Antiviral Therapy 2005; 10:S123.
  3. Chaix1 ML, Desquilbet L, Cottalorda J et al. Sub-optimal response to HAART in patients treated at time of primary HIV-1 infection and infected with HIV resistant strains. 14th International HIV Drug Resistance Workshop (14th IHDRW), 7-11 June 2005, Quebec City, Canada. Abstract 114. Antiviral Therapy 2005; 10:S126.
  4. Brenner BG, Roger M, Moisi D et al. Transmission events within risk groups following primary HIV-1 infection (PHI) in Quebec (1998-2005). Abstract 112. Antiviral Therapy 2005; 10:S125.

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