CLASSIFICATION OF MAJOR DRUG RESISTANCE MUTATIONS: NRTI-resistance mutations are classified into those that inhibit NRTI incorporation into the HIV-1 primer DNA strand ('Discriminatory' Mutations) and those that promote excision of chain-terminating NRTIs via ATP-mediated pyrophosphorolysis ('Excision' Mutations). Excision mutations are usually called TAMs (Thymidine Analog Mutations) because they are selected by AZT and d4T. Two mutation complexes are associated with high-levels of multi-NNRTI resistance: (i) A 2-amino acid insertion at codon 69, which nearly always occurs in combination with multiple TAMS; and (ii) Q151M which usually occurs with several otherwise uncommon accessory mutations: A62V, V75I, F77L, and F116Y.
M184V: M184V is the most common NRTI-resistance mutation because all recommended first-line regimens contain the highly potent cytidine analogs 3TC or FTC, each of which exerts strong selective antiretroviral pressure. Although M184V causes high-level resistance to 3TC and FTC, M184V is not a contraindication to the use of 3TC or FTC because it increases susceptibility to AZT, d4T, and TDF, and is associated with a clinically significant reduction in HIV-1 replication. M184I is an uncommon mutation which generally occurs before M184V in patients developing 3TC or FTC resistance because the G to A transition causing ATG (M) => ATA (I) generally occurs before the A to G transition ATG (M) => GTG (V). However, M184I is usually rapidly replaced by M184V because it replicates less well than M184V.
TAMS: Although they are selected only by AZT and d4T, the presence of multiple TAMs confer clinically significant resistance to ABC, DDI, and TDF, and low-level phenotypic resistance to 3TC and FTC of uncertain clinical significance. The TAMs occur in two overlapping patterns referred to as Type I (M41L, L210W, and T215Y) and Type II (67N, K70R, T215F, and K219QE). Type I TAMs are associated with higher levels of cross-resistance. Among the Type II TAMs, D67N and K219QE appear to be solely accessory, whereas K70R and T215F appear to directly reduce susceptibility to AZT, d4T, and probably TDF, ABC, and ddI. The TAMs are decreasing in prevalence with the decrease use of AZT and d4T.
MDR MUTATIONS: There are two uncommon patterns of mutations associated with pan-NRTI resistance:(i) Multiple TAMs + T69ins + M184V and (ii) Q151M (with 2-3 of its accessory mutations) + K65R + M184V. T69ins usually indicates T69S_SS -- the substitution of S for T and the addition of two amino acids. Single amino acid insertions occur less commonly (usually in combination with Type II TAMs) and are associated with lower levels of multidrug resistance. Other double amino acid insertions such as SA and SG occur commonly and appear to have similar effects to the SS insertion. Q151M is a two-base pair (CAG => ATG) discriminatory mutation which rarely occurs in combination with TAMs (particularly the Type I TAMs). Two other patterns of mutations are associated with multi-NRTI resistance: (i) 4 to 5 TAMs + M184V confers clinically significant resistance to all NRTIs, although TDF may retain some activity because M184V partially reverses the effect of the multiple TAMs; and (ii) K65R + M184V decreases susceptibility to all NRTIs except AZT (to which it increases susceptibility) and possibly TDF because M184V partially reverse the phenotypic (but probably not the clinical) resistance caused by K65R.
ADDITIONAL MUTATIONS AT MAJOR DRUG-RESISTANCE POSITIONS: (i) T69D is a nonpolymorphic mutation associated with decreased ddI susceptibility. T69S/N/A/I/K/E/G are additional NRTI-selected mutations of unknown clinical significance; (ii) V75T/M/A/S are nonpolymorphic mutations that have been associated with decreased susceptibility to d4T and ddI. (iii) K70G/E. In contrast to K70R, K70G/E/Q are selected by non-TAM containing regimens and affect susceptibility in a manner similar to but less prominently than K65R. The effect of other mutations at position 70 such as K70Q/T/N/S has been less well studied. (iv) D67G/E/S/T are uncommon poorly characterized mutations. (v) K219N/R. In contrast to K219Q/E, K219N and particularly R usually occur in combination with multiple Type I TAMs. (vi) T215S/C/D/E/I/V are often called 'revertant' mutations because they arise in patients with T215Y/F who have discontinued therapy. They are also common in patients primarily infected with T215Y/F. They are more fit than T215Y/F in the absence of therapy and do not appear to decrease NRTI susceptibility. (vii) K65N is an extremely rare mutation that has affects susceptibility in a manner similar to but less prominently than K65R. (viii) Additional insertions and deletions between codons 67 and 70. A deletion at codon 67 occurs in about 0.1% of viruses from treated persons. It usually occurs in combination with T69G and Q151M. Although there have been reports of insertions at positions other than 69 and deletions at positions other than 67, most insertions appear to be associated with TAMs like the T69 insertions whereas most deletions appear to be associated with Q151M like the codon 67 deletion. (ix) Q151L is an extremely rare poorly characterized one-base pair transitional mutation occasionally observed in viruses developing Q151M: CAG (Q) => CTG (L) => ATG (M).
ADDITIONAL NON-POLYMORPHIC AND MINIMALLY POLYMORPHIC MUTATIONS: E40F, K43Q/N, E44A, E203K, H208Y, D218E, K223E/Q, and L228H/R are non-polymorphic mutations that occur exclusively in viruses that also contain TAMs. E44D and V118I are minimally polymorphic mutations that occur with increased frequency in patients receiving NRTIs. The combination of E44D and V118I appears to minimally reduce susceptibility to most PIs. The effects of the remaining NRTI-associated mutations are not well characterized.
CONNECTION DOMAIN MUTATIONS: There have been an increasing number of reports of mutations downstream of the 5' polymerase-coding region extending into the RT connection domain (up to codon 440). With the notable exception of N348I most of these mutations are polymorphic and may owe their association with therapy to their association with primary 5' polymerase coding mutations. Indeed, the prevailing hypothesis for why connection domain mutations are associated with NRTI therapy is that they slow primer-template translocation and as a result provide an increased opportunity for TAMs' associated nucleotide excision.