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Objective: The aim of the study was to evaluate the prevalence of periodontal pathogens Aggregatibacter actinomycetemcomitans, Porphyromonas gingivalis, Prevotella intermedia, Tannerella forsythia and Treponema denticola in subgingival plaque collected at different probing depths of type 1 diabetes patients with periodontal disease in correlation to metabolic control. Methods: Twenty-one patients 40 to 50 years old were included in the study. In each patient blood samples were taken for the evaluation of HbA1 c level and subgingival plaque samples were taken with paper points from the two deepest pockets. The presence of five periodontal pathogens was detected by multiplex polymerase chain reaction. Results: The results of 38 plaque samples showed that T. forsythia was found in 48% followed by T. denticola in 31%, P. gingivalis in 26%, P. intermedia in 9% and A. actinomycetemcomitans in 7%. T. forsythia and T. denticola were the most frequent combination of periodontal pathogens found in the same sample. The serum level of HbA1 c in nine patients where T. forsythia was detected (7.5 ± 1.4%) was significantly higher (F-test, p = 0.001) than in 12 patients where T. forsythia was not detected (6.8 + 0.5%). Similarly, the serum level of HbA1c was significantly higher (F-test, p = 0.001) in eight patients where T. denticola was detected (7.5 ± 1.8%) compared to the 13 patients where T. denticola was not detected (7.0 ± 0.5%). No such correlation was found for P. gingivalis, P. intermedia or A. actinomycetemcomitans. Conclusions: We conclude that T. forsythia and T. denticola are most frequently found in subgingival plaque samples of type 1 diabetic patients and these findings correlate with poorer metabolic control of diabetes. [ABSTRACT FROM AUTHOR]

ABSTRACTThe clinical performance of the Abbott RealTime High Risk HPV (human papillomavirus) test (RealTime) and that of the Hybrid Capture 2 HPV DNA test (hc2) were prospectively compared in the population-based cervical cancer screening setting. In women >30 years old (n= 3,129), the clinical sensitivity of RealTime for detection of cervical intraepithelial neoplasia of grade 2 (CIN2) or worse (38 cases) and its clinical specificity for lesions of less than CIN2 (3,091 controls) were 100% and 93.3%, respectively, and those of hc2 were 97.4% and 91.8%, respectively. A noninferiority score test showed that the clinical specificity (P< 0.0001) and clinical sensitivity (P= 0.011) of RealTime were noninferior to those of hc2 at the recommended thresholds of 98% and 90%. In the total study population (women 20 to 64 years old; n= 4,432; 57 cases, 4,375 controls), the clinical sensitivity and specificity of RealTime were 98.2% and 89.5%, and those of hc2 were 94.7% and 87.7%, respectively. The analytical sensitivity and analytical specificity of RealTime in detecting targeted HPV types evaluated with the largest sample collection to date (4,479 samples) were 94.8% and 99.8%, and those of hc2 were 93.4% and 97.8%, respectively. Excellent analytical agreement between the two assays was obtained (kappa value, 0.84), while the analytical accuracy of RealTime was significantly higher than that of hc2. RealTime demonstrated high intralaboratory reproducibility and interlaboratory agreement with 500 samples retested 61 to 226 days after initial testing in two different laboratories. RealTime can be considered to be a reliable and robust HPV assay clinically comparable to hc2 for the detection of CIN2+ lesions in a population-based cervical cancer screening setting.

ABSTRACTA genotyping study of 285 Hybrid Capture 2 low-risk probe cocktail-positive specimens showed cross-reactivity with several untargeted human papillomavirus genotypes. Cross-reactivity was often clinically beneficial due to the detection of untargeted low-risk genotypes. A total of 8.4% of positive results, usually weak, were due to cross-reactivity with high-risk genotypes. Establishment of a gray zone is recommended.

ABSTRACTA prospective unblinded comparative evaluation of three assays for the detection of enteroviral RNA performed on 83 positive and 79 negative cerebrospinal fluid samples showed initial and resolved sensitivities of 90.4% and 98.8%, respectively, for the Cepheid GeneXpert enterovirus assay; 94.0% and 97.6%, respectively, for the Argene enterovirus consensus kit; and 100% and 100%, respectively, for an in-house real-time PCR. The initial and resolved specificities were 100% for all three assays.

A total of 150 specimens of anogenital hairs plucked from the scrotal, pubic, and perianal region of 51 immunocompetent healthy male individuals were tested for the presence of beta‐papillomaviruses (beta‐HPV) using the nested Ma/Hapolymerase chain reaction. Beta‐HPV were found in a total of 38 (25.3%) of 150 hair samples. According to the sampling sites, beta‐HPV were detected in 18/51 (35.3%), 13/50 (26.0%), and 7/49 (14.3%) plucked hair samples obtained from the pubic, scrotal, and perianal region, respectively. The prevalence of beta‐HPV in the plucked pubic hairs was significantly higher than in the perianal hairs (P= 0.013). In contrast, the difference in the prevalence of beta‐HPV in the pubic and scrotal hairs as well as in scrotal and perianal hairs did not reach statistical significance (P= 0.302 and P= 0.227, respectively). The difference in the lifetime‐cumulative sun exposure is the most likely explanation for the differences obtained on beta‐HPV prevalence. Beta‐HPV genotype HPV‐38 was detected most frequently, followed by HPV‐36, HPV‐15, and HPV‐14D. In addition to the beta‐HPV recognized officially five partial DNA sequences suggesting putative new HPV genotypes were identified. J. Med. Virol. 78:1673–1678, 2006. © 2006 Wiley‐Liss, Inc.

Various studies have demonstrated the increasing prevalence of non‐B HIV‐1 subtypes in Western Europe. In contrast, knowledge about the molecular epidemiology of HIV‐1 in Central and Eastern Europe is limited. The objective of present study was to investigate the HIV‐1 molecular diversity as well as time trends in HIV‐1 subtype distribution in Slovenia. A retrospective molecular epidemiological survey was conducted on a cohort representing 88% (131/149) of all HIV‐1 infected patients diagnosed between January 1996 and June 2005. The study revealed that subtype B is a predominant HIV‐1 subtype in Slovenia (110/131; 84%), although a relatively high proportion (21/131; 16%) of non‐B subtypes was found. Among them, a high proportion of recombinant (10/21; 48%) and different unclassified strains (8/21; 38%) were identified. Non‐B subtype viruses were predominant among heterosexuals (19/21; 90%) and subtype B viruses among men who have sex with men (84/110; 76%). Importantly, 86% (18/21) of patients infected with non‐B subtypes were of Slovenian nationality. In contrast to Western European countries, a significant increase (P= 0.015) in the proportion of men who have sex with men was observed recently among newly diagnosed HIV‐1 infected patients in Slovenia. J. Med. Virol. 78:997–1002, 2006. © 2006 Wiley‐Liss, Inc.

The aim of this study was to investigate the genetic diversity of HIV-1 strains circulating in Slovenia. Proviral DNA isolated from peripheral blood mononuclear cells (PBMCs) of 20 randomly selected HIV-1-infected individuals was classified into subtypes by sequence-based phylogenetic analysis of the env (C2V3) and gag (p24) regions of the viral genome. The phylogenetic tree based on env C2V3 sequences showed that 15 of the 20 samples were subtype B, two A1, one F1, one CRF01_AE, and one CRF02_AG. The phylogenetic analysis of the gag gene yielded identical results expect for one sample that had a discordant subtype; it was identified as subtype A1 in the env and AE in the gag region. Our study confirmed that although subtype B predominates, other subtypes and circulating recombinant forms (CRFs) are also present in Slovenia. The high intrasubtype genetic diversity of subtype B sequences suggests a multiple introduction of subtype B strains into Slovenia.

With the exception of Lyme borreliosis, tick-borne encephalitis (TBE) is the most prevalent tick-transmitted disease in Europe. Here we report clinical and epidemiologic features of the largest number of children with TBE reported to date and the longest (i.e. 42-year) retrospective survey of pediatric TBE cases from one geographic region.

ABSTRACTComparative evaluation of the semiautomated COBAS AMPLICOR hepatitis B virus (HBV) MONITOR Test (COBAS-HBV) and manual AMPLICOR HBV MONITOR Test (AMPLICOR-HBV) on 208 serum samples revealed no significant difference in the sensitivities of the two assays. Twenty samples tested HBV DNA negative and 183 samples tested HBV DNA positive by both assays. Three samples tested positive by COBAS-HBV only and two samples tested positive by AMPLICOR-HBV only. HBV DNA concentrations determined by the two assays were significantly related (n= 183, r= 0.97,P< 0.0001), which indicates that COBAS-HBV could replace AMPLICOR-HBV. The major inconvenience of COBAS-HBV is the required performance of appropriate predilutions of high-titer samples in order to extend the narrow dynamic range of the assay.

Background:To search for a possible source of hepatitis C virus (HCV) in saliva, the presence and shedding patterns of HCV in gingival crevicular fluid (GCF) and saliva of HCV viremic patients were assessed based on clinical, biochemical, histological, virological, and oral health parameters. Methods:Saliva and GCF samples of 50 HCV viremic patients were collected to detect HCV RNA by a modified commercial polymerase chain reaction (PCR) assay. Clinical oral examination was performed and periodontal status at the collection sites was monitored. The results were correlated to specified parameters. Results:HCV RNA was detected in 59% (29/49) of the GCF specimens and in 35% (17/48) of the saliva specimens. In saliva specimens, HCV RNA was detected only in cases which also had detectable HCV RNA in the GCF samples (P= 0.00002) and was significantly related to the presence of blood in saliva (P= 0.03). Higher, but not significant, values of oral clinical parameters at the sites of fluid collection were found in GCF specimens harboring HCV RNA. In GCF specimens with no blood detected, HCV RNA was more often present in cases with higher plasma viral load (P= 0.05). Conclusions:The results suggest that besides blood, the other most probable source of HCV in saliva is GCF. Unknown endogenous HCV inhibitory mechanisms in the oral cavity may explain the discrepancies in HCV appearance between saliva and GCF. The results provide a biologic basis for further investigation of the role of HCV in the pathogenesis of periodontal disease. J Periodontol 2001;72:11‐16.

To evaluate the usefulness of a standardized commercial amplification assay for detection of hepatitis C virus (HCV) RNA, Amplicor® HCV Test (Roche), a total of 1,204 serum samples from 888 patients was examined. Seven out of 443 anti-HCV-negative samples, 638 out of 729 anti-HCV-positive samples and four out of 32 anti-HCV-indeterminate samples tested HCV RNA positive by Amplicor® in initial testing. One false-negative and five false-positive Amplicor® results were found in initial testing, giving an overall sensitivity and specificity of the Amplicor® HCV Test of 99.8% and 99.1%, respectively. Our study confirmed that the Amplicor® HCV Test is a practical, rapid, sensitive and specific assay for detection of HCV RNA. However, the results must be interpreted with some caution and with the patient's anti-HCV status and clinical data in mind.

The prevalence of hepatitis G virus (HGV) infection was assessed by the detection of viral genome and HGV E2 antibodies in hemodialysis patients from a dialysis unit with the highest prevalence of hepatitis C virus infection in Slovenia. HGV RNA was detected in 7 (11.9%) and HGV E2 antibodies in 20 (33.9%) of 59 hemodialysis patients. One patient had detectable HGV RNA as well as HGV E2 antibodies in her serum sample at the time of the study. The total prevalence of HGV infection was 44.1%. Our results clearly indicate that the mere detection of HGV RNA in serum samples would seriously underestimate the real prevalence of HGV infection in hemodialysis patients. Therefore, when assessing the prevalence of HGV infection in hemodialysis patients, detection of both antibody and nucleic acid is requisite.

Summary To evaluate the usefulness of two standardized commercially available amplification assays for the detection ofMycobacterium tuberculosis: Amplicor® test (Roche) and MTD-Amplified direct test (Gen-Probe) a total of 281 respiratory specimens from 198 patients with symptoms of pulmonary diseases were examined and compared with conventional methods. Fifty-seven specimens were positive and 218 negative by both amplification assays. Three specimens were reactive by Amplicor® only, and three by MTD only. In comparison with culture, the sensitivity, specificity, positive predictive value and negative predictive value were 96.0, 94.8, 80.0, and 99.1%, respectively, for the Amplicor® test; the corresponding values were 94.0, 94.4, 78.3, and 98.6%, respectively, for the MTD. However, when 28 specimens from 14 patients on antituberculous therapy were excluded the improvement in PPV and specificity of both assays was obtained. In conclusion, both commercially available amplification tests are almost equally sensitive and specific and are suitable for the implementation in daily routine work in the specialized clinical laboratories.

The Alinity m (Abbott Molecular, Des Plaines, IL) automated molecular analyzer allows continuous loading of samples and sample-to-result molecular detection of several microorganisms. The detection of SARS-CoV-2 by the Alinity m was compared with that of the Cobas 6800 (Roche Molecular Systems, Branchburg, NJ; standard comparator) in a manufacturer-independent clinical evaluation of samples from 2157 consecutive nasopharyngeal swabs. Valid initial results on Alinity m and Cobas 6800 were obtained from 2129 (98.7%) and 2157 (100%) samples, respectively. The overall percent agreement (95% CI) was 98.3% (2092/2129 [97.6%–98.7%]); positive percent agreement, 100% (961/961 [99.6%–100%]); negative percent agreement, 96.8% (1131/1168 [95.7%–97.7%]); and high κ value, 0.965 (0.954–0.976). There were 37 discordant results on Alinity m and, based on discordant analyses, including previous and/or follow-up PCR results, 22 could be considered analytically true positive with high probability. Due to a lack of additional information and an inability to perform repeated/further testing, the status of the remaining 15 discordant results remained unresolved. The throughput of the two analyzers was compared using testing on 564 samples in parallel across two 8-hour shifts in clinical practice. The turnaround times were compared using processing of 94 routine samples in parallel on each working day for 5 consecutive days. The two analyzers showed similar performance, with certain differences that have potential importance in some laboratory settings.

The Alinity m HR HPV assay (Alinity) is a novel human papillomavirus (HPV) assay that individually identifies genotypes HPV16, HPV18, and HPV45 while reporting on 11 other high-risk HPV (hrHPV) genotypes in two aggregates: HPV31/33/52/58 and HPV35/39/51/56/59/66/68. The clinical performance of Alinity for screening for cervical cancer was evaluated in population-based settings.

To determine the prevalence of HCV genotypes in Slovenia, 203 subjects infected with hepatitis C virus (HCV) were studied using the Inno-Lipa HCV II assay (Innogenetics, Belgium). Of 21 patients infected by blood transfusion 19% had HCV subtype 1a, 81% had subtype 1b, and none of them was infected with genotype 3. In chronic hepatitis C patients infected by unknown cause subtype 1b was the most prevalent (54.4%), followed by subtype 1a (24.6%), genotype 3 (15.8%) and genotype 2 (5.2%). Genotype 3 (45.9%) and subtype 1a (43.2%) predominated among 74 intravenous drug users. In 37 haemodialysis patients genotypes 1 and 2 were almost equally frequent (40.5% and 37.8%, respectively), followed by genotype 3 (21.6%). Significant differences in HCV genotype distribution among distinct epidemiological groups observed in Slovenia indicate a close relationship between certain HCV genotypes and particular routes of viral transmission.

ABSTRACTIn the present study we comparatively evaluated the first- and second-generation Digene Hybrid Capture assays for detection of human papillomaviruses (HPV) associated with high or intermediate risk for cervical cancer in cervical specimens. Concordant results were obtained with 468 of 483 (96.8%) specimens. All 15 specimens which gave repeatedly discordant results were positive by the second-generation test only, and 14 of them tested PCR positive. The enhanced sensitivity of the second-generation assay is mainly a result of the reformulation of hybridization reagents and, to a lesser extent, a result of the addition of new HPV probes.