STABLE REARRANGEMENTS OF THE BETA-3-BETA-4 HAIRPIN LOOP OF HIV-1 REVERSE-TRANSCRIPTASE IN PLASMA VIRUSES FROM PATIENTS RECEIVING COMBINATION THERAPY

Objectives: To study the genetic rearrangements of HIV-1 reverse trans criptase (RT) in circulating viruses from patients under combination t herapy, and to determine the impact of these changes on the virologica l response to treatment.Methods: Blood samples were extracted from tot al RNA and amplified by RT-PCR. The HIV-1 RT and protease genes were s equenced by fluorescent dye terminator cycle sequencing. Results: Spec ific rearrangements in the RT coding region (between amino acids 66 an d 71) were documented in nine patients. This region, which corresponds to a loop between the beta 3 and beta 4 strands of the fingers subdom ain of RT, is involved in the interaction between the enzyme and the t emplate primer. In vitro data with recombinant enzymes have shown the importance of this domain in the processive polymerization of HIV-1 RT . The rearrangements (eight deletions/insertions and one deletion with conservation of the reading frame) did not affect the overall seconda ry structure of the fingers subdomain; as assessed by the Garnier-Osgu thorpe-Robson prediction method. The changes were generally stable ove r a follow-up of 10-12 months. With the exception of two cases, most o f the patients of this study did not respond efficiently to antiretrov iral therapy as assessed by measurements of plasma viraemia. Correspon dingly, the RT and protease genes sequenced from these patients displa yed numerous resistance-associated mutations. Conclusion: Functional a nd stable rearrangements in the beta 3-beta 4 hairpin of HIV-1 RT can be found in circulating viruses from patients under combination therap y. These rearrangements may affect the virological response to antiret roviral therapy by increasing the processivity of RT, an enzymatic par ameter that reflects the fidelity of the polymerization process. (C) 1 998 Lippincott Williams & Wilkins.