Subtype-specific differences in the development of accessory mutations associated with high-level resistance to HIV-1 nucleoside reverse transcriptase inhibitors.

OBJECTIVES: To identify accessory mutations associated with high-level resistance to reverse transcriptase (RT) inhibitors in HIV-1 subtypes B and C. METHODS: Changes relative to the wild-type for codons 1-400 of RT were analysed from treatment-experienced patients infected with subtypes B (5464 patients) and C (1920 patients). Positions associated with the accumulation of mutations conferring resistance to thymidine analogues and to non-nucleoside RT inhibitors (NNRTIs) were identified. A subtype-specific single-replication cycle drug susceptibility assay was used to determine whether some of the mutations affected drug susceptibility or viral infectivity. RESULTS: In subtype B, mutations at 31 and 26 positions were associated with the accumulation of thymidine analogue mutations (TAMs) and NNRTI mutations, respectively; in subtype C, 18 and 13 positions were identified, respectively. Amino acid changes at the following positions were differentially associated with (i) the accumulation of 0-4+ TAMs in subtypes B and C (away from consensus): 43 (27.0% B versus 2.5% C); 118 (36.4% B versus 16.2% C); 135 (12.5% B versus 28.0% C); and 326 (2.6% towards consensus in B versus 7.6% away in C) and (ii) the accumulation of 0-3+ NNRTI mutations (away from consensus): 43 (10.2% B versus 0.5% C); and 68 (5.2% B versus 10.3% C). Codon changes K43E, E44D and V118I were found to have no effect on susceptibility to three NRTIs with or without TAMs in either subtype; however, some accessory mutations had subtype-specific effects on viral infectivity. CONCLUSIONS: Differences between subtypes B and C were observed in the development and effect of accessory mutations associated with high-level resistance to RT inhibitors.

Genotypic antiretroviral drug resistance testing at low viral loads in the UK.

BACKGROUND: Antiretroviral drug resistance testing is recommended in HIV-1 infected patients failing therapy in order to inform treatment selection. Although guidelines and test manufacturers recommend a viral load of at least 500-1000 HIV-1 RNA copies/mL for genotypic resistance testing to be performed, prompt management of virological failure could benefit from testing at lower viral load levels. METHODS: Laboratories undertaking genotypic resistance testing were asked to provide figures for the number of resistance tests undertaken at viral loads <2000 copies/mL, the success rates of such tests and the extent of resistance detected, all stratified for viral load levels. RESULTS: Of the replies received, most laboratories were attempting resistance testing at viral loads below the recommended guidelines, with variable success and outcomes. CONCLUSIONS: This audit of current practice in the UK for undertaking genotypic resistance tests at viral loads <1000 copies/mL highlights the widespread use of such testing outside the British HIV Association guidelines.

Detection of hepatitis C virus RNA in serum, by combining reverse transcription and polymerase chain reaction in one tube.

Reverse transcription of viral RNA into cDNA and its subsequent amplification by polymerase chain reaction (PCR) are generally carried out as two separate reactions. Here we describe a novel method for the detection of HCV RNA in serum combining both steps in one reaction tube using a wax interface to separate the two sets of reactants during initial cDNA synthesis. This enabled optimisation of both reactions, simplified the test and thereby reduced the risk of cross-contamination.

A single tube nested PCR for the detection of hepatitis C virus RNA.

An assay was developed for the detection of hepatitis C virus RNA in serum which combined cDNA synthesis and a hot start nested polymerase chain reaction (PCR) in a single tube. This was made possible by separation of the reagents necessary for cDNA synthesis and PCR during cDNA synthesis with a high melting temperature wax interface and by the use of 'drop in-drop out' nested primers which enabled each primer set to be selectively extended within the same reaction tube. The increase in sensitivity following amplification with the internal primer pair was comparable to that achieved when nested reactions are carried out separately.

Pilot scheme for performance assessment of HIV-1 genotypic resistance testing in the UK.

HIV-1 drug susceptibility testing by genotypic methods is now widespread in the UK and it is thus important to determine the reproducibility of such investigations. A pilot study was carried out to determine the reproducibility between laboratories of genotypic testing by nucleotide sequencing of patient samples, and to compare the interpretations of the results provided to the clinicians. Samples were distributed between the participating laboratories. Eight laboratories, using three different methods, sequenced four samples. Nucleotide sequence and reports were collated and compared by one laboratory. Where sequencing data were obtained > 99% concordance was observed for nucleotide designations. No discordances in nucleotide sequencing were found in positions associated with drug resistance. However, there were considerable differences between the laboratories in the interpretation of some of the mutations with respect to their effect on drug susceptibility. This study emphasises the variability in the available interpretation systems, and the importance of joint laboratory-clinical discussion in making decisions about treatment options.

A study of anal intraepithelial neoplasia in HIV positive homosexual men.

OBJECTIVES: To determine the prevalence of high grade anal intraepithelial neoplasia (HGAIN), the value of anal cytology in screening for HGAIN, and the characterisation of epidemiological factors and human papillomavirus (HPV) types. METHODS: Prospective cohort study of HIV positive homosexual men. Subjects were interviewed, underwent STD, anal cytological, and HPV screening at enrolment and at subsequent follow up visits with anoscopy and biopsy at the final visit. 57 enrolled, average CD4 count 273 x 10(6)/l (10-588); 41 completed the cytological surveillance over the follow up period (181 visits, average follow up 17 months), 38 of these had anoscopy and anal biopsy. RESULTS: Oncogenic HPV types were detected in 84% and high grade dyskaryosis in 10.5% (6/57) at enrollment. There was a 70% incidence of high grade dyskaryosis during follow up in patients with negative/warty or low grade dyskaryosis at enrollment. Anoscopy correlated with histology in high grade AIN lesions (sensitivity 91%, specificity 54%) and cytology was 78% sensitive (18/23) for HGAIN on biopsy. CONCLUSIONS: AIN and infection with multiple oncogenic HPV types are very common among immunosuppressed HIV positive homosexual men. Apparent progression from low to high grade cytological changes occurred over a short follow up period, with no cases of carcinoma. All 23 cases of HGAIN were predicted by cytology and/or anoscopy. Future studies focusing on the risk of progression to carcinoma are needed before applying anal cytology as a screening tool for AIN in this population.