Dorota Bander

Characteristics of HIV-1 non-B subtype infections in Northwest Poland.

The number of non‐B subtype HIV‐1 infections in Europe has been increasing even though major regional differences have been observed. This trend was investigated in northwestern Poland using sequence and epidemiological data from a cohort of 102 HIV‐1‐infected patients from Szczecin, Poland. HIV‐1 subtypes were defined by phylogenetic analysis of viral reverse transcriptase‐ and protease‐partial coding regions, and results were compared with online subtyping by Standford and REGA tools. Subtype analysis using on‐line subtyping methods produced varying results if compared to phylogenesis, with concordant variant assignment obtained for 98% (100/102) of sequences by Stanford and 85% (87/102) by REGA. In the population studied, non‐B subtype infections comprised 21% of the infections and consisted of subtype D (57%, n = 12), CRF01_AE (19%, n = 4), A and C clades (9.5%, n = 2), and the CRF13_cpx recombinant isolate (4.8%, n = 1). Patients carrying non‐B subtypes were predominantly heterosexuals with high percentage (57%) of women observed in the group. All HIV‐1 non‐B women were Caucasian with majority (83%) of infections acquired in Poland; however, among 12 travelers included in the study a higher proportion of non‐B infections was noted (50%, P = 0.01). Moreover, lower baseline lymphocyte CD4 counts (P = 0.01), higher baseline HIV‐1 viremia (P = 0.08), and a more advanced stage of the disease (P = 0.03) were observed among individuals infected with non‐B subtypes. The data indicated that the proportion of HIV‐1 non‐B subtype infections was higher than previously reported in Poland consisting of a high subtype D prevalence. Furthermore, subtype D transmission occurred primarily between heterosexual Caucasian individuals from this region. J. Med. Virol. 82:1306–1313, 2010.

HIV-1 integrase resistance among antiretroviral treatment naive and experienced patients from Northwestern Poland

BackgroundHIV integrase inhibitor use is limited by low genetic barrier to resistance and possible cross-resistance among representatives of this class of antiretrovirals. The aim of this study was to analyse integrase sequence variability among antiretroviral treatment naive and experienced patients with no prior integrase inhibitor (InI) exposure and investigate development of the InI drug resistance mutations following the virologic failure of the raltegravir containing regimen.MethodsSequencing of HIV-1 integrase region from plasma samples of 80 integrase treatment naive patients and serial samples from 12 patients with observed virologic failure on raltegravir containing treatment whenever plasma vireamia exceeded >50 copies/ml was performed. Drug resistance mutations were called with Stanford DB database and grouped into major and minor variants. For subtyping bootstrapped phylogenetic analysis was used; Bayesian Monte Carlo Marcov Chain (MCMC) model was implemented to infer on the phylogenetic relationships between the serial sequences from patients failing on raltegravir.ResultsMajority of the integrase region sequences were classified as subtype B; the remaining ones being subtype D, C, G, as well as CRF01_AE , CRF02_AG and CRF13_cpx recombinants. No major integrase drug resistance mutations have been observed in InI-treatment naive patients. In 30 (38.5%) cases polymorphic variation with predominance of the E157Q mutation was observed. This mutation was more common among subtype B (26 cases, 54.2%) than non-B sequences (5 cases, 16.7%), p=0.00099, OR: 5.91 (95% CI:1.77-22.63)]. Other variants included L68V, L74IL, T97A, E138D, V151I, R263K. Among 12 (26.1%) raltegravir treated patients treatment failure was observed; major InI drug resistance mutations (G140S, Q148H and N155H, V151I, E92EQ, V151I, G163R) were noted in four of these cases (8.3% of the total InI-treated patients). Time to the development of drug resistance ranged from 2.6 to 16.3 months with mean increase of HIV viral load of 4.34 (95% CI:1.86-6.84) log HIV-RNA copies/ml at the time of emergence of the major mutations. Baseline polymorphisms, including E157Q were not associated with the virologic failure on raltegravir.ConclusionsIn InI treatment naive patients polymorphic integrase sequence variation was common, with no major resistance mutants. In the treatment failing patients selection of drug resistance occurred rapidly and followed the typical drug resistance pathways. Preexisting integrase polymorphisms were not associated with the treatment failure.

HIV-1 Subtype D Infections among Caucasians from Northwestern Poland—Phylogenetic and Clinical Analysis

Background HIV-1 subtype D infections, which are associated with a faster rate of progression and lymphocyte CD4 decline, cognitive deficit and higher mortality, have rarely been found in native Europeans. In Northwestern Poland, however, infections with this subtype had been identified. This study aimed to analyze the sequence and clinical data for patients with subtype D using molecular phylogeography and identify transmission clusters and ancestry, as well as drug resistance, baseline HIV tropism and antiretroviral treatment efficacy. Methods Phylogenetic analyses of local HIV-1 subtype D sequences were performed, with time to the most recent common ancestor inferred using Bayesian modeling. Sequence and drug resistance data were linked with the clinical and epidemiological information. Results Subtype D was found in 24 non-immigrant Caucasian, heterosexually infected patients (75% of females, median age at diagnosis of 49.5 years; IQR: 29–56 years). Partial pol sequences clustered monophyletically with the clades of Ugandan origin and no evidence of transmission from other European countries was found. Time to the most common recent ancestor was 1989.24 (95% HPD: 1968.83–1994.46). Baseline drug resistance to nucleoside reverse transcriptase inhibitors was observed in 54.5% of cases (mutations: M41L, K103N, T215S/D) with evidence of clustering, no baseline integrase or protease resistance and infrequent non-R5 tropism (13.6%). Virologic failure was observed in 60% of cases and was associated with poor adherence (p<0.001) and subsequent development of drug resistance (p = 0.008, OR: 20 (95%CI: 1.7–290). Conclusions Local subtype D represented an independently transmitted network with probably single index case, high frequency of primary drug resistance and evidence of transmission clusters.

Genotypic tropism of antiretroviral‐treated patients with drug resistant HIV‐1

CCR5 inhibitors remain an attractive antiretroviral treatment option for HIV‐infected patients; however, tropism testing should be utilized prior their introduction. This study analyzed genotypic HIV‐1 tropisms in patients with evidence of genotypic drug resistance to antiretroviral therapies in Northwest Poland. V3 loop sequences were analyzed from plasma samples obtained from patients presenting with virologic treatment failure while on combined antiretroviral treatment and with evidence of genotypic drug resistance. Genotypic X4 and R5 tropisms were identified using the geno2pheno algorithm with a false positive rate threshold set at 10%. Clinical data for all patients examined was collected, in addition to determining the CCR5 Δ32 genotype and calculating the genotypic susceptibility score (GSS). Virologic treatment failure and the presence of drug resistant mutations were observed in 37/450 (8.4%) patients on cART (combination antiretroviral therapy) with successful tropism analysis carried out on 35 (95%) cases. In 22 (62.9%) and 13 (37.1%) cases the R5 and X4 tropisms were predicted, respectively. An association between viral X4 tropism and the M41L (P = 0.04) resistance mutation and R5 tropism and the K103N (P = 0.07) resistance mutation were observed. GSS values were lower in the group with NRTI (P = 0.01) and NNRTI resistance (P = 0.048). In the majority of the drug resistant patients, R5 tropic viruses were found. As genotypic tropism testing is easy to carry out and interpret, its use in clinical practice would be highly useful in determining the use of appropriate drug therapies. J. Med. Virol. 83:1869–1875, 2011.

Introduction of pharmacogenetic screening for the human leucocyte antigen (HLA) B*5701 variant in Polish HIV-infected patients.

Prospective pharmacogenetic screening for the human leucocyte antigen (HLA) B*5701 allele can significantly reduce the number of cases of abacavir‐related hypersensitivity among HIV‐infected patients treated with this drug. The aim of this study was to establish the frequency of the HLA B*5701 variant in HIV‐infected Poles.

Risk of all-cause mortality in HIV infected patients is associated with clinical, immunologic predictors and the CCR5 Δ32 deletion.

Objective Investigation of the interplay between the CCR5 Δ32/wt genotype and demographic, epidemiological, clinical and immunological factors associated with mortality in the cART era. Design Longitudinal data from 507 HIV-infected patients following the Δ32 allele detection were analyzed. Methods Cumulative 15 years mortality was calculated using Kaplan-Meyer methodology. Hazard ratios were estimated using univariate Cox models. Basing on Akakie information criteria and statistical significance multivariate Cox model was constructed and effect plots presenting adjusted hazard ratio time-dependency were drawn. Analysis of the association of all-cause mortality and CCR5 Δ32/wt genotype prior to the antiretroviral treatment (cART) initiation (n = 507) and on the therapy (n = 422) was also performed. Results A mortality rate of 2.66 (CI 2.57–3.19) per 100 person-years was observed. Univariate analysis factors modifying the risk of death included the CCR5 genotype, gender, history of cART, AIDS diagnosis and also CD4 lymphocyte nadir, zenith, the latest CD4 count and stable levels >500 cells/µl. For multivariate analysis the following predictors were selected: CCR5 genotype (HR for wt/wt 2.53, CI 1.16–5.53, p = 0.02), gender (HR for males 1.91, 95%CI 1.1–3.36, p = 0.023), introduction of combined antiretroviral treatment (HR 4.85, CI 3.0–7.89, if untreated or treated <1 month, p<0.0001) CD4 count of 500 cells/µl for six months or more (HR 4.16, CI 1.95–8.88 if not achieved, p = 0.028), the latest CD4 count (HR 5.44, CI 3.39–8.74 for <100 cells/µl, p<0.0001) and history of AIDS (HR 1.69, CI 1.03–2.79, p = 0.039). Among untreated individuals the Δ32/wt genotype was associated with notably better survival (p = 0.026), while among cART treated individuals the Δ32 mutation did not correlate significantly with higher survival rates (p = 0.23). Conclusions The Δ32 CCR5 allele is associated with a reduction of the risk of all-cause mortality in HIV (+) patients alongside clinical and immunologic predictors such as AIDS, history of cART, lymphocyte CD4 cell count and gender.

Increasing role of arthropod bites in tularaemia transmission in Poland – case reports and diagnostic methods

The study describes four cases of tularaemia - one developed after contact with rabbits and three developed after an arthropod bite. Due to non-specific clinical symptoms, accurate diagnosis of tularaemia may be difficult. The increasing contribution of the arthropod vectors in the transmission of the disease indicates that special effort should be made to apply sensitive and specific diagnostic methods for tularaemia, and to remind health-care workers about this route of Francisella tularensis infections. The advantages and disadvantages of various diagnostic methods - molecular, serological and microbiological culture - are discussed. The PCR as a rapid and proper diagnostic method for ulceroglandular tularaemia is presented.

Analysis of V3 loop sequences using various bioinformatic tools designed for genotypic HIV-1 tropism testing

Summary Background Interest in genotypic tropism prediction using bioinformatic tools trained on phenotype-genotype data has recently been rekindled by introduction of coreceptor inhibitors into clinical practice. In this study it was aimed to compare predictions obtained by six algorithms and investigate concordance of prediction. Material and Methods Fifty V3 loop sequences were analysed with geno2pheno (g2p) used as reference and PSSM_sinsi, SVM, charge rule, PART and C4.5 tools. For every patient sample Δ32 CCR5 genotyping and subtyping basing on partial pol sequence was also performed. Phylogenetic tree of V3 sequences was reconstructed by maximum likelihood with example 3D protein structure visualized. Results Subtype B was noted in 72.0% while CCR5 Δ32 allele in 25.0% of cases. X4 tropism was found in 30.0% of patients by g2p with 10% false positivity rate (FPR), 8% – PSSM_sinsi, 32% – SVM, 12% – C4.5, 18% – PART and 20% by charge rule. Mean 76.2% concordance among the tools for X4 tropism prediction was noted with g2p FPR 20%. In phylogeny no clustering between the X4 and R5 sequences was observed except for one taxonomical unit. Conclusions Genotype V3 predictions are concordant for geno2pheno 0%-5% and 20-100% FPR while g2p based interpretation of sequences with false positive rate of 5-20% or derived from non-B subtype should be cautious. In data interpreted with g2p 10% FPR neither X4 nor R5 tropism was associated with presence of single Δ32 CCR5 allele or HIV-1 non-B variant and no significant clustering of sequences with the same tropism was noted.

Osteoporosis associated selected single nucleotide polymorphisms frequency in HIV-infected and non-infected Polish population

INTRODUCTION Non-functioning pituitary adenomas (NFPA) are often diagnosed late as invasive macroadenomas. The surgical resection is usually incomplete and about 50% of patients require additional surgery. Recent data suggest that somatostatin analogues (SSA), so important in the pharmacotherapy of acromegaly, can also be effective in the management of NFPA. MATERIAL AND METHODS We analysed data of patients who had been treated up to 10 years previously with SSA: 40 with acromegaly (23 - primary, 17 - recurrent tumours) and 22 with NFPA (4 - primary, 18 - recurrent tumours). Hormonal profile, dynamics of tumour size change, ophthalmic syndromes, somatostatin receptor (SSTR) scintigraphy, and immunohistochemistry of SSTR subtypes of operated tumours as well as side effects were investigated. RESULTS Biochemical cure of acromegaly was achieved in 57.5% of patients, while reduction of tumour size was observed in 37% of patients and it was more frequent in not-operated cases. Regarding NFPA, stabilisation of tumour size was noticed in 68% of patients. Tumour shrinkage was reported in 9% of cases, but in 23% of the study group the adenoma size increased with indication for reoperation. CONCLUSIONS The efficacy of SSA in NFPA is much lower in comparison to their well-established effects in the treatment of acromegaly. Stabilisation of tumour size, which is observed in the majority of NFPA, is significantly more frequent in comparison to the natural history of untreated NFPA and our previous studies as well. Analysis of SSTR subtypes is an argument in favour of introduction of novel broad-spectrum SSA that may be more effective in the treatment of NFPA. Referring to acromegaly, adenoma size decrease was reported more frequently in primary therapy. Considering recurrent tumours better outcomes were achieved in patients who were pre-treated with SSA before planned surgery. (Endokrynol Pol 2016; 67 (3): 292-298).

CCR5 D32 modifies 15-year mortality risk associated with well-established clinical and immunological factors among HIV-infected patients

7‐11 November 2010, Tenth International Congress on Drug Therapy in HIV Infection, Glasgow, UK