BACKGROUND:
In co-infected individuals two or more HIV-1 strains established close to the time of PHI, whereas in super-infection a second strain established several months to years after PHI. Does this lead over time to differential replication of the strains?

PATIENTS AND METHODS:
Three intravenous drug users (IVDUs) co-infected with B subtype and CRF-11, two IVDUs initially infected with B subtype and lateron infected with CRF-11. Population sequencing of reverse transcriptase, protease and gag p24, subtype -specific nested PCR with a first generic PCR (amplification of a 1397 bp gag/pol fragment –1872–3251 in ref to HXB2–) followed by a nested B and CRF-11-specific PCR. Population sequencing of the B and CRF-11 amplicons.

RESULTS:
Using subtype-specific PCR and limiting dilutions with constant amount of the heterologous subtype (250000 HIV-1 RNA copies) and decreasing amount of the homologous subtype (1000–10 HIV-1 RNA copies), the detection limit was <10 copies of the homologous subtype in 250000 copies of the heterologous subtype, and there was no amplification of the heterologous subtype in presence of 250000 copies. In the three co-infected patients, both CRF-11 and B subtypes were detected in plasma and proviral DNA analysed over a follow-up of 14, 20 and 24 months, respectively. Two of the three patients had viraemia >400000 copies/ml during the follow-up. A genetic tree based on sequences of the B-specific amplicons of 10 IVDUs infected with B subtypes and of the three coinfected patients indicated that two over three coinfected patients were infected with different B strains.

The two super-infected patients, initially infected by a B subtype, can be referred as LTNPs since they control their viraemia without treatment to <50 copies/ml and had <500 CD4/mm3 for, respectively, 3 and 5 years before becoming infected with CRF-11. In these two patients, super-infection with CRF-11 was associated with high viraemia, steep drop in CD4 and an acute retroviral syndrome (ARS). CFR-11 was the only detectable subtype in the plasma at the time of superinfection and later on in follow-up samples. Both subtypes were detectable in proviral DNA after the superinfection and during the follow-up. Genetic trees performed on B and CRF-11 amplicons indicate that the patients were initially infected with different B strains, whereas results for CRF-11 were inconclusive due to the high degree of homogeneity of sequences of the CRF-11 amplicons for both the super-infected IVDUs and other IVDUs infected with CRF-11 only.