Dual-class mutations affection RTI and NNRTI may be common in experienced patients
Simon Collins, HIV i-Base
Gilda Tachedjian and colleagues reported the impact of mutation N348I in the C-terminal region of RT in from retrospective analysis of the British Columbia database, in the December edition of PLoS Medicine.
The prevalence of N348I was <1% in 368 treatment-naive individuals and 12.1% in 1,009 treatment-experienced patients (p = 7.7 x 10-12). N348I was highly associated with thymidine analogue mutations (TAMs) M41L and T215Y/F (p < 0.001), the 3TC mutations M184V/I (p < 0.001), and the NNRTI resistance mutations K103N and Y181C/I (p < 0.001).
The association with TAMs and NNRTI resistance mutations was consistent with the selection of N348I in patients treated with regimens that included both AZT and nevirapine (OR 2.62, 95%CI 1.434.81).
The impact on RTI resistance was assessed by adding N348I into HIV-1 molecular clones with different genetic backbones. N348I decreased AZT susceptibility 2- to 4-fold in the context of wild-type HIV-1 or when combined with TAMs. N348I also decreased susceptibility to nevirapine (7.4-fold) and efavirenz (2.5-fold) and significantly potentiated resistance to these drugs when combined with K103N.
In 31 patients analysed for time to develop N348I, the mutation appeared at the same time as M184V/I and before the appearance of TAMs and also usually appeared at the same time or prior to key NNRTI resistance mutations. Although linked to increases in viral load the study was not powered to report a causal impact unrelated to selection of other RT, NNRTI and PI mutations.
In an editorial comment, Matthias Götte provided a further discussion of the evidence for extending the domain that it is commonly tested. 
These results add to earlier evidence, referenced in the study, implicating changes in RT outside the DNA polymerase domain in RT that is commonly tested in genotypic resistance tests, and is particularly interesting as it indicates mutations that may impact on both nucleoside analogues and NNRTIs.
Although N348I was found in a sample over 3,000 patients in a UK database, it was reported as an NNRTI rather than RTI accessory mutation.  Research into the relative importance of secondary and accessory mutations is likely to expand in the next few years.
Additionally, an abstract from the 2007 Retrovirus conference reported the impact of N348I on in vitro resistance to nevirapine (22-fold) and cross-resistance to AZT and ddI, of 23-fold and 5-fold, respectively.
Also, that while 3% of 328 samples in Los Alamos database contained N348I, it wasnt found in 55 naive patients or 183 unexposed to AZT or ddI, N348I was present in 9% of patients using AZT 7% using ddI and 27% of the 11 patients using both AZT and ddI. 
In the PLoS paper, this mutation didnt occur in the absence of other NNRTI mutations. So, although we may be underestimating the actually fold resistance to a drug, we are not missing resistance all together.
- Yap SH, Sheen CW, Fahey J et al. N348I in the Connection Domain of HIV-1 Reverse Transcriptase Confers Zidovudine and Nevirapine Resistance. PLoS Med. 2007 Dec 1;4(12):e335 [Epub ahead of print]. PMID: 18052601.
- Matthias Götte. Should We Include Connection Domain Mutations of HIV-1 Reverse Transcriptase in HIV Resistance Testing. Editorial perspective, PLoS Med 4(12): e346 doi:10.1371/journal.pmed.0040346
- Cane PA, Green H, Fearnhill E, Dunn D (2007) Identification of accessory mutations associated with high-level resistance in HIV-1 reverse transcriptase. AIDS 21: 447455. (19 February 2007)
- Hachiya A, Hachiya A, Kodam E et al. A Novel Mutation, N348I in HIV-1 Reverse Transcriptase Induced by NRTI Treatment, Confers Nevirapine Resistance. 14th CROI. Abstract 593.