Non-B subtypes

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Genotyping of B and Non B Subtypes of Human Immunodeficiency Virus Type 1

Genotyping of B and Non B Subtypes of Human Immunodeficiency Virus Type 1

Current HIV-1 genotyping assays were developed using subtype B viruses prevalent in Western countries. It is not clear whether these assays are appropriate for use among African patients, who are likely to be infected with non-B subtypes. We evaluated the Bayer TRUGENE HIV-1 genotyping (TG) assay using prospectively collected samples from HIV-1-infected individuals who acquired infection in either sub-Saharan Africa or the West (Europe, North America, and Australia). Plasma samples from 208 individuals with an HIV-1 viral load of >1,000 copies/ml were tested using version 1 primers supplied with the TG assay. If these failed, an alternative primer set version 1.5 was used. Of the 208 individuals, the likely origin of infection was Africa (n ⴝ 104), Western (n ⴝ 87) and “Others” (i.e., all other geographic locations or origin not certain; n ⴝ 17). Among the three groups, the version 1 primers were successful in 85 (82%), 77 (89%), and 13 (76%) individuals, respectively (P ⴝ 0.1). Of the remaining 32 samples, 30 were successfully amplified by using the version 1.5 primers. HIV-1 subtypes deduced from the reverse transcriptase sequences correlated with the likely origin of infection: Africa (28A, 3B, 33C, 13D, 6G, 4J, 2K, 5CRF01_AE, and 10CRF02_AG), Western (86B and 1K), and Others (1A and 16B). The success of the version 1 primers correlated with viral load (P < 0.014) and not with HIV-1 subtypes. A protocol based on version 1 primers, followed by 1.5 primers, was successful in sequencing 99% of the samples in this cohort.
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Characteristics of Patients Recently Infected with HIV 1 Non B Subtypes in France: a Nested Study within the Mandatory Notification System for New HIV Diagnoses

Characteristics of Patients Recently Infected with HIV 1 Non B Subtypes in France: a Nested Study within the Mandatory Notification System for New HIV Diagnoses

S ince its introduction in the human species, human immuno- deficiency virus type 1 (HIV-1) group M has diversified into 9 genetic subtypes (A, B, C, D, F, G, H, J, and K) and numerous circulating recombinant forms (CRFs) that arise from recombi- nation between one or several parental viruses in coinfected or superinfected individuals (1). Depending on its epidemiological success, each clade has a specific distribution. Subtype B predom- inates in the Americas, Europe, Japan, and Australia, whereas non-B subtypes predominate in Africa and in most Asian coun- tries. Many studies have reported an increasing prevalence of non-B subtypes in Europe since the beginning of the epidemic (2–10). Whereas there is a common notion that HIV-1 infections with non-B subtypes are mainly associated with migrant popula- tions from the developing world, there is increasing evidence that the epidemiology of non-B viruses in Europe results from both migration and domestic transmissions (11–13). Most of the stud- ies have described the increasing prevalence of non-B variants in Europe among newly diagnosed HIV-1 infections or patients re- ferred for antiretroviral resistance testing (4, 6–9). However, the duration of infection for each new diagnosis was frequently un- known in these studies. Therefore, the dynamic of the non-B sub- epidemics cannot be described accurately since it necessitates fo- cusing on patients with known dates of infection, particularly those who have been infected recently. This includes patients diag- nosed at the time of primary infection (10, 14, 15). Alternatively, serologic assays for recent infection (RI assays) that have been devel- oped and validated during the last decade allow the identification of patients who have been infected for less than a few months, approx- imately 6 months in most of the assays (16–19).
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Prevalence of Human Immunodeficiency Virus Type 1 (HIV 1) Non B Subtypes in Foreigners Living in Madrid, Spain, and Comparison of the Performances of the AMPLICOR HIV 1 MONITOR Version 1 0 and the New Automated Version 1 5

Prevalence of Human Immunodeficiency Virus Type 1 (HIV 1) Non B Subtypes in Foreigners Living in Madrid, Spain, and Comparison of the Performances of the AMPLICOR HIV 1 MONITOR Version 1 0 and the New Automated Version 1 5

subtype-related variation (21), seemed to allow an equivalent quantitation of HIV-1 RNA regardless of the subtype. It uses a set of primers (SK145 and SKCC1B) which are based on a non-B subtype consensus sequence (21, 32). The lower viremia values provided by COBAS in 40% of samples from subjects carrying non-B subtypes and in 18.2% of those with subtype B found in our study was an unexpected finding. It could be due to the difference in how the amplicons are captured (micro- wells versus microbeads) by the detection reagents used in the prototype automated test or the presence of mismatches in sample primer binding sites. The recognition of higher levels of HIV-1 plasma viremia by either assay in two subjects carrying subtypes G (M2773) and B (M1743) and being under triple or quadruple antiretroviral combinations was also unexpected, but it might be explained by noncompliance with the pre- scribed treatment noticed in these subjects.
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Correlation between Sequencing Results from Liquid Plasma and Dried Plasma Spot (DPS) for Determination of HIV Type 1 Non B Subtypes

Correlation between Sequencing Results from Liquid Plasma and Dried Plasma Spot (DPS) for Determination of HIV Type 1 Non B Subtypes

How to cite this paper: Kamangu, E.N., Chatté, A., Vaira, D., de Mol, P., Mvumbi, G.L., Kalala, R.L. and Hayette, M.-P. (2017) Correlation between Sequencing Results from Liquid Plasma and Dried Plasma Spot (DPS) for Determination of HIV Type 1 Non-B Subtypes. Open Access Library Jour- nal, 4: e2922.

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First-line HIV treatment failures in non-B subtypes and recombinants: a cross-sectional analysis of multiple populations in Uganda

First-line HIV treatment failures in non-B subtypes and recombinants: a cross-sectional analysis of multiple populations in Uganda

This study represents the largest database of first-line treatment failures in Uganda to date, drawing from every available study cohort associated with the JCRC. In a pre- vious cross-sectional study of a clinical HIV database in Uganda, we reported a statistical association between HIV subtype D infections and treatment failures on sec- ond-line and salvage therapies ( n = 843 ) [33], which are generally associated with higher failure rates than first- line therapies [34]. Furthermore, suboptimal modification of drug regimens in second-line and salvage therapies may allow substantial virus replication to amplify incipi- ent differences among HIV-1 subtypes. In this study, we observed limited evidence for significant variation with respect to genotype susceptibility scores and plasma viral loads among HIV-1 subtypes within the first-line treat- ment failures. We acknowledge some insurmountable limitations in this retrospective cross-sectional study of all available records of first-line treatment failures in the JCRC databases. For instance, matched baseline and fail- ure samples or duration of treatment were not available for the majority of cases, which would have permitted a longitudinal analysis of these populations. Moreover, our Bayesian network analysis was limited to the n = 1750 (42%) records with complete information on drug regi- mens and sampling region.
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Characteristics and spread to the native population of HIV 1 non B subtypes in two European countries with high migration rate

Characteristics and spread to the native population of HIV 1 non B subtypes in two European countries with high migration rate

HIV-1 pol sequences 857 nucleotides nt long concatenated sequence fragments comprising codon 4 to 99 of the Protease gene and codon 30 to 226 of the Reverse transcriptase gene, were coll[r]

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High prevalence of CXCR4 usage among treatment naive CRF01 AE and CRF51 01B infected HIV 1 subjects in Singapore

High prevalence of CXCR4 usage among treatment naive CRF01 AE and CRF51 01B infected HIV 1 subjects in Singapore

because they were built using datasets of genotype- phenotype correlations from subtype B viruses [15-17]. According to a study evaluating the reliability of several V3-based genotypic predictors, the sensitivity to identify X4 variants was 90% for B subtypes and 61% for non-B subtypes using Geno2pheno compared with the pheno- typic assay [15]. Seclen et al. determined a sensitivity of 58% and specificity of 79% for non-B subtypes, compared with a sensitivity of 94% and specificity of 51% for subtype B, using the Geno2pheno tool [17]. The inadequacy of current genotypic tools for predicting CXCR4-using viruses among non-B subtypes thus underscores the need to improve the information on the correlation between phenotypic and genotypic methods for viral tropism determination in patients infected with non-B HIV-1.
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Sensitivity and Specificity of Human Immunodeficiency Virus Rapid Serologic Assays and Testing Algorithms in an Antenatal Clinic in Abidjan, Ivory Coast

Sensitivity and Specificity of Human Immunodeficiency Virus Rapid Serologic Assays and Testing Algorithms in an Antenatal Clinic in Abidjan, Ivory Coast

To evaluate serologic testing algorithms for human immunodeficiency virus (HIV) based on a combination of rapid assays among persons with HIV-1 (non-B subtypes) infection, HIV-2 infection, and HIV-1–HIV-2 dual infections in Abidjan, Ivory Coast, a total of 1,216 sera with known HIV serologic status were used to evaluate the sensitivity and specificity of four rapid assays: Determine HIV-1/2, Capillus HIV-1/HIV-2, HIV-SPOT, and Genie II HIV-1/HIV-2. Two serum panels obtained from patients recently infected with HIV-1 subtypes B and non-B were also included. Based on sensitivity and specificity, three of the four rapid assays were evaluated prospectively in parallel (serum samples tested by two simultaneous rapid assays) and serial (serum samples tested by two consecutive rapid assays) testing algorithms. All assays were 100% sensitive, and specificities ranged from 99.4 to 100%. In the prospective evaluation, both the parallel and serial algorithms were 100% sen- sitive and specific. Our results suggest that rapid assays have high sensitivity and specificity and, when used in parallel or serial testing algorithms, yield results similar to those of enzyme-linked immunosorbent assay-based testing strategies. HIV serodiagnosis based on rapid assays may be a valuable alternative in implementing HIV prevention and surveillance programs in areas where sophisticated laboratories are difficult to establish.
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Development and Evaluation of an Oligonucleotide Ligation Assay for Detection of Drug Resistance Associated Mutations in the Human Immunodeficiency Virus Type 2 pol Gene

Development and Evaluation of an Oligonucleotide Ligation Assay for Detection of Drug Resistance Associated Mutations in the Human Immunodeficiency Virus Type 2 pol Gene

equipment and technical expertise. Excluding the PCR costs necessary for both methods, OLA costs ⬃ $1 for the two mu- tations per sample, whereas sequencing costs at least $10. Like all ligation assays, the potential disadvantage of OLA is that the presence of other mutations around the ligation site may result in failure of the assay (indeterminate result). The occur- rence of indeterminate results with OLA is related to the high level of genetic variability in HIV, such that the HIV-1 OLA has been modified for some non-B subtypes (33). For HIV-2, only two subtypes, A and B, are of epidemiological importance. In the HIV-2 RT enzyme, as is the case for HIV-1, the Q151M mutation is a multi-NRTI resistance mutation associ- ated with phenotypic resistance to zidovudine, didanosine, zal- citabine, abacavir, and stavudine, while the M184V mutation is associated with phenotypic resistance to lamivudine (3TC) and emtricitabine (1) in HIV-2. We report the development and evaluation of an OLA for detection of the Q151M and M184V mutations associated with high-level resistance to NRTIs in HIV-2.
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Analysis of a Local HIV 1 Epidemic in Portugal Highlights Established Transmission of Non B and Non G Subtypes

Analysis of a Local HIV 1 Epidemic in Portugal Highlights Established Transmission of Non B and Non G Subtypes

ern Europe in its distribution of HIV-1 subtypes (18, 21). It is important to gain a further understanding on the causes underly- ing this difference, also in light of the evidence supporting a recent increase in infections with non-B HIV-1 subtypes in several west- ern European countries (15–17, 44). In this study, we analyzed 289 HIV-1-infected individuals from Minho province, Portugal. Col- lectively, the results obtained are consistent with previous studies in Portugal showing a high prevalence of non-B subtypes (73.0%), mainly viruses of the G subtype (29.4%), followed by those of the C (14.5%) subtype. In our study population, the heterogeneity of HIV-1 subtypes is attributable to Portuguese-born individuals presumed to be infected in the region, with only 3.8% of the cases occurring in immigrants or individuals from Portugal presumed to be infected elsewhere. Contrarily, the rising prevalence of non-B HIV-1 subtypes in western Europe has been attributed to the growing number of immigrants from sub-Saharan Africa and South America, where these variants are prevalent. As an example, 27% of the HIV-1 cases diagnosed in 2007 in Spain were of non-B subtypes, and 90% of these cases were African and South Ameri- can immigrants (45). A phylogenetic analysis of our study popu- lation indicates high interindividual genetic distances for the most prevalent subtypes, B and G, suggesting old and multiple intro- ductions of viruses of these subtypes in the region. This observa- tion is in accordance with the predominance of the B subtype in western Europe, having probably been introduced on several oc- casions in the late 1970s and early 1980s (46). As for the G sub- types, it is possible that the intense human migrations between Portugal and its former African colonies in the 1970s and 1980s, due mostly to the independence wars (47), contributed to its early introduction in Portugal. These intense human migrations may have also contributed to the early introduction of other HIV-1 subtypes, namely in the case of the migration connection with Angola, where there is a large HIV-1 genetic diversity (48). The distribution of clustered sequences per subtype showed that the vast majority of the F1, C, A1, and CRF14_BG sequences were incorporated in clusters. Contrarily, the B and G subtype clusters TABLE 3 Characterization of the 17 HIV-1 transmission clusters identified in the study population of the Portuguese region of Minho
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Genetic and phylogenetic evolution of HIV 1 in a low subtype heterogeneity epidemic: the Italian example

Genetic and phylogenetic evolution of HIV 1 in a low subtype heterogeneity epidemic: the Italian example

Injecting drug users (IDUs) have been the most affected risk group during the first phase of the HIV epidemic in Italy and the HIV-1 B subtype, in accordance with other Western Countries, is the molecular form circulating among IDUs [10]. However, the annual percentages of AIDS cases reported in IDUs have gradually decreased to 32.3% in 2004 [11], in part as consequence of prevention programs [12,13]. In parallel, the AIDS cases reported in heterosexual individuals has continuously increased dur- ing the epidemic, becoming in 2004 the most prevalent risk factor for AIDS (40.4%) (Fig. 3) [10]. Similarly, in 2005 heterosexual contact accounts for over half (55%) of HIV infections newly diagnosed in the EU, nearly half (46%) of them were diagnosed in immigrants/migrants, primarily from sub-Saharan Africa, and most of these infections were acquired outside the EU (EuroHIV, 2006). More than 10% of heterosexual individuals diagnosed with AIDS in Italy are either immigrants from endemic regions for HIV-1 (6.87%) or their Italian partners (3.03%). This epidemiological evidence, not considering all the HIV-1 infections derived also from traveling abroad, suggests that at least 10% of the viruses transmit- ted through heterosexual contacts could potentially belong to non-B subtypes and CRFs. This has been recently reported in other European Countries, with a higher prevalence due to an older tradition of immigra- tion waves and much tighter historical as well as eco- nomic links with countries endemic for HIV-1 infection [14-22]
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HIV 1 subtype distribution and its demographic determinants in newly diagnosed patients in Europe suggest highly compartmentalized epidemics

HIV 1 subtype distribution and its demographic determinants in newly diagnosed patients in Europe suggest highly compartmentalized epidemics

Similar as in the UNAIDS report for Western Europe [33], we found subtype B to be the most prevalent sub- type but lower than reported before: 66.1% compared to the 85% reported by UNAIDS. In the subset of patients not only diagnosed but also originating from Europe the proportion of subtype B among newly diagnosed patients was significantly higher (79.5%) resembling the UNAIDS data. These differences are thus likely explained by the very different sampling strategies be- tween the studies: UNAIDS used country of origin of the patient, while we used country of sampling; and UNAIDS used a convenience sample of data collected from patients diagnosed at any time and we used a rep- resentative sample of newly diagnosed patients. Subtypes A1 (6.9%), C (6.8%) and CRF02_AG (4.7%) are the other most prevalent subtypes in patients diagnosed in Europe. Again here the results are not entirely consistent with the UNAIDS report, where the most prevalent non-B subtypes in Western and Central Europe were CRF02_AG (2000–2003: 2.94%; 2004–2007: 4.50%) and subtype C (2000–2003: 2.9%; 2004–2007: 1.91%). As in our study only newly diagnosed patients were included in the sample, a major advantage of our sampling strat- egy is that it maps the more recent past compared to previous studies. Our findings may therefore be more relevant for the epidemic in the near future.
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Prevalence and resistance mutations of non B HIV 1 subtypes among immigrants in Southern Spain along the decade 2000 2010

Prevalence and resistance mutations of non B HIV 1 subtypes among immigrants in Southern Spain along the decade 2000 2010

This study evaluates the prevalence of HIV-1 subtypes and PR and RT drug resistance mutations among HIV- 1-infected immigrants living in Southern Spain. Immi- gration had been gradually increasing since 2000, with a peak of 22% in 2008. Since then, it has been slowly decreasing to 11.8% in 2010. The largest immigrant group was form Central-South America (47.9%) most of them infected with the HIV-1 B subtype. However, up to 25% of immigrants were from countries where HIV-1 non-B subtypes are predominant, as Sub-Saharan Africa with 79% of HIV-1 non-B subtypes (subtypes A, G, J or CRF02_AG), or Eastern Europe with 60% (subtypes A, F, CRF02_AG or CRF01_AE). This marked increase in individuals infected with non-B HIV-1 subtype in our society may have a direct impact on the spread of these subtypes among Spanish native individuals in addition to the changes in appropriate treatment regimes due to differences in genetic sequences amongst the different HIV-1 strains. These results are similar to those found in studies conducted in other regions in Spain, Madrid and Canary Islands [19,20,22].
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Ability of Two Commercially Available Assays (Abbott RealTime HIV 1 and Roche Cobas AmpliPrep/Cobas TaqMan HIV 1 Version 2 0) To Quantify Low HIV 1 RNA Levels (  
    	 Alessandra Amendola, Patrizia Marsella, Maria Bloisi, Federica Forbici, Claudio Angele

Ability of Two Commercially Available Assays (Abbott RealTime HIV 1 and Roche Cobas AmpliPrep/Cobas TaqMan HIV 1 Version 2 0) To Quantify Low HIV 1 RNA Levels ( Alessandra Amendola, Patrizia Marsella, Maria Bloisi, Federica Forbici, Claudio Angeletti, Maria R Capobianchi A M Caliendo, Editor

Overall, our results on the performance characteristics of these two assays at LVL are aligned with similar data previously reported with clinical samples (20, 29–31) and with the 2nd international HIV-1 RNA WHO standard (19). In particular, although there is good agreement between the commonly used diagnostic assays for detecting both HIV-1 B and non-B subtypes along the common range of detection (14, 15, 18, 32–34), the interassay correlation is lower at the lower limit of quantification (16–18, 21, 30, 31, 35). Also, the concordance between the samples with detected or not detected VL is rather low (32–34), with both the clinical samples (11), the 2nd International HIV-1 RNA WHO Standard, and commercial test panels for HIV-1 (16, 19, 20). In line with a recent multicenter comparison study (31), we observed that interassay concordance for a threshold of 200 copies/ml was much higher (92.20%) than that at the threshold of the clinically relevant value of 50 copies/ml (89.81%).
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Viral Profiling Identifies Multiple Subtypes of Kaposi’s Sarcoma

Viral Profiling Identifies Multiple Subtypes of Kaposi’s Sarcoma

KSHV mRNA patterns in KS. We are confident about the ex- istence of different subtypes of KS, because the number of vari- ables, i.e., primer pairs (n ⫽ 188), exceeded the number of samples (n ⫽ 35). Independent corroboration using principal-component analysis (PCA) and analysis of normalization methods is pre- sented in Fig. S4 in the supplemental material. Identifying clusters of differentially regulated viral mRNAs was much more challeng- ing, because here the design was underpowered. Ideally, one would like to have as many samples as genes. This would require 188 biopsy specimens. We attempted to identify mRNAs that dif- fer among the KS subtypes and thus may be developed into prog- nostic and/or predictive biomarker signatures by making the as- sumption that latency locus mRNAs do not change in levels and could therefore be used to normalize all data (ddC T ) (30). This
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Nucleotide sequence of feline immunodeficiency virus: classification of Japanese isolates into two subtypes which are distinct from non-Japanese subtypes.

Nucleotide sequence of feline immunodeficiency virus: classification of Japanese isolates into two subtypes which are distinct from non-Japanese subtypes.

protection against a distinctly heterologous (20% diversity) isolate of subtype D was not achieved. Further, we are studying cell tropism relating to our seven Japanese isolates and the Petaluma isolate, using various types of cells in vitro. Our major objective for the current epidemiological survey is to construct and use phylogenetic trees of the env regions of isolates worldwide as a method for identifying candidate strains for FIV vaccine development. Our current studies es- tablish the existence of a new subtype (D) in addition to the three previously reported. Hence, an FIV vaccine for world- wide use needs to be effective against all four subtypes. Addi- tional env gene sequences of isolates throughout the world combined with information on their neutralizing epitopes should help construct phylogenetic trees useful for the predic- tion of vaccine efficacy. Nevertheless, experimental vaccine trials with additional FIV isolates, for use as both a vaccine immunogen and a challenge inoculum, are needed to confirm their prophylactic value.
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Lipopolysaccharide subtypes of Haemophilus influenzae type b from an outbreak of invasive disease

Lipopolysaccharide subtypes of Haemophilus influenzae type b from an outbreak of invasive disease

influenzae isolates examined from these contacts, only 1 was type b, which was obtained from a day-care worker and had the same LPS subtype and major outer membrane protein electrophoret[r]

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Prevalence of HLA-B*27 subtypes in ethnic Tamil population of India with Ankylosing Spondylitis

Prevalence of HLA-B*27 subtypes in ethnic Tamil population of India with Ankylosing Spondylitis

There is a considerable geographic and ethnic difference in the distribution of the HLA-B*27 alleles. B*27:05 is the predominant subtype found in almost all ethnic populations and is seen among North American Indians, American Mestizos, Siberian Chukchis and Eskimos. Rare subtypes like B*27:01 is observed only in Caucasoid populations while B*27:02 is the common subtype among Jews(109). B*27:03 has been reported in West Africans population and are rarely seen outside of Africa. Almost 61% of the total B*27 positive samples from West Africa are B*27:03 subtype. Subtypes B*27:04, 06 and 07 have been reported in Orientals only and of these B*27:04 is the most common subtype among the Chinese and Japanese(110). In the Xinjiang region there was a high heterogeneity and the characteristics of genetic epidemiology were significant. Seven HLA-B*27 allele subtypes were detected in 247 cases of AS patients in Xinjiang Uygur patients with ankylosing spondylitis. In the same study five HLAB*27 allele subtypes were detected in Uygur AS patients and six HLA-B*27 allele subtypes were detected in Han patients. HLA- B*27:05 was the predominant subtype in Uygur patients with prevalence of 58.95%, which is much higher than that in Han patients in Xinjiang (31.58%) and 7 other areas of China. HLA-B*27:02/B*27:05 homozygote was identified among the Uygur AS patients. HLA-B*27:02/B*27:04 and HLA-B*27:04/B*27:05, and HLA- B*27:05/B*27:05 homozygotes were identified in 3 Han patients(111).
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The expression of endothelin type A and B receptors in the lateral wall of the mouse cochlea

The expression of endothelin type A and B receptors in the lateral wall of the mouse cochlea

Real-time PCR was used to determine the gene expression profiles of the ET receptor subtypes. cDNAs were amplified by real-time PCR using an FTC-2000 (FUNGLYN, CANADA). Each analysis was performed in a total volume of 30 µl reaction mixture containing 5 µl cDNA sample, 1 µl SYBR Green I, and 2 µl gene-specific forward and reverse primers (10 µM each). Housekeeping genes were included to normalize the data. Amplifications were performed as follows, 45 cycles at 94ºC for 2min, 94ºC for 20 sec and 54ºC for 20 sec, with a final extension at 70ºC for 30 sec and at 80ºC for 20 sec .
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TREATMENT OF CHRONIC HEPATITIS B, DELTA RELATED LIVER DISEASE AND NON-A NON-B HEPATITIS

TREATMENT OF CHRONIC HEPATITIS B, DELTA RELATED LIVER DISEASE AND NON-A NON-B HEPATITIS

The hepatitis Delta virus is an incomplete RNAvirus which produces disease inpatients who are hepatitis surface antigen positive. This is a highly pathogenic virus and is responsible for both acute and chronic liver disease 33 . Hepatitis Delta virus infection in patients with chronic hepatitis B is associatedwith a more rapid progression to cirrhosis compared with hepatitis B surface antigen carriers with chronic hepatitis and no evidence of HDV infection 34 . The incidence ofHDV infection in HBSAg positive carriers is 12.3% to 51% reported in different series from Italy 34,35 . This high degree of prevalence of HDV certainly warrants treatment programmes to eliminate the delta virus.
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