Background:  The presence of innate resistance mutations and polymorphisms in drug-naïve, HIV-infected persons may affect subsequent responses to antiviral therapy. Recent findings suggest bidirectional antagonisms between K65R and thymidine analogue mutations (TAM) in treatment-experienced patients. Our studies show facilitated development of K65R in subtype C due to a signature KKK motif at codons 64, 65, and 66. This present study addressed the effects of innate polymorphisms (T69N, V75I, V118I, L210N, T215S, and K219E) in HIV-2 on emergent resistance to nucleoside/nucleotide analogues.

Methods:  Emergent drug-resistance profiles in HIV-2 subtype A (n = 3) and B (n = 1) were compared with HIV-1 subtypes B and C. Drug resistance was evaluated in cord blood mononuclear cells (CBMC), using selective pressure with tenofovir (TFV), zidovudine (ZDV), stavudine (d4T), didanosine (ddI), abacavir (ABC), and lamuvidine (3TC), and dual combinations of TFV-DDI, TFV-ABC, TFV-3TC, ZDV-3TC, and d4T-ddI. Culture fluids were analyzed weekly for virus production by RT assay. Resistance was evaluated using conventional and ultra-sensitive sequencing approaches.

Results:  In agreement with our previous findings, dual drug combinations of TFV, ddI, ABC, d4T, ZDV, and 3TC preferentially selected for the K65R mutation in HIV-1 subtype C isolates within 22 weeks. In single drug selections, K65R was observed with TFV and ddI and M184V with 3TC. In HIV-1 subtype B, TFV-3TC and ZDV-3TC selected for M184I and D67N respectively. In stark contrast, selections with all 4 HIV-2 cultures favored development of M184I in all dual drug combinations that included 3TC. With single drugs, M184V appeared within 6 weeks while some HIV-2 isolates developed S134A, V167I, and A174V under TFV selective pressure. Since HIV-2 cultures did not develop K65R, an ultra-sensitive codon-specific real-time polymerase chain reaction (RT-PCR) assay was developed and the latter distinguished the presence of the K65R mutation from the wild type HIV-2 plasmid by 16 cycles (∆CT). Furthermore, TAM were antagonistic to the development of K65R in HIV-2.

Conclusions:  These results underscore potential differences in emergent drug-resistance pathways in HIV-1 and HIV-2 and show that polymorphisms may determine the resistance pathways that emerge. These studies may have implications in the design of TAM-sparing regimens used against HIV-1 subtype C.