Sequence features downstream of the primer-binding site of HIV type 1 subtype E shared by subtype G and a subset of subtype A.

Two distinct sequence features downstream of the primer-binding site (PBS) were identified in a full-length HIV-1 subtype E clone amplified in this study. Both features are frequently found in HIV-1 subtypes A and G and in more than half of the full-length intersubtype recombinant clones. One of these is the absence of a trinucleotide sequence, which is located 14 nucleotides downstream of the PBS and found only in subtypes B, C, D, F, and H. The other is an insertion of 24 nucleotides immediately downstream of the PBS, which was previously reported as a sequence feature shared by subtypes A, E, and G. The analysis conducted here revealed that this 24-nucleotide insertion contained two sequence motifs duplicated in adjacent regions and was not found in all HIV-1 subtype A clones. Furthermore, our finding suggests that the PBS region of all known full-length subtype E clones, which are A/E intersubtype recombinants, is derived from the group of HIV-1 subtype A, which contains a similar insertion.

Differential stability of the mRNA secondary structures in the frameshift site of various HIV type 1 viruses.

For many retroviruses, one or more ribosomal frameshift events are required for translation of the Gag-Pol precursor protein, which is subsequently processed into the structural and enzymatic proteins found in mature virions. A specific nucleotide motif, the slippery sequence, as well as a downstream mRNA secondary structure are generally believed to have roles in the frameshift event. In HIV-1, a particular stem-loop mRNA secondary structure has been proposed for subtype B. On the basis of this model, HIV-1 subtypes A, E, and F were found in this study to share a similar stem-loop structure predicted to have a lower thermodynamic stability as compared with HIV-1 subtypes B, C, and D. The potential impact of this differential thermodynamic stability on HIV-1 replication remains to be determined.

Seroprevalence and subtype distribution of hepatitis C virus among blood donors and intravenous drug users in northern/northeastern Thailand.

The prevalence of antibodies against hepatitis C virus (HCV) and the distribution pattern of HCV subtypes were analyzed among healthy blood donors and intravenous drug users (IVDUs) in northern/northeastern Thailand. The prevalence of anti-HCV antibodies was 3.2% (26/820) among blood donors in Khon Kaen, while it was 90% (71/79) among IVDUs in Chiang Rai. HCV RNA was detected in all anti-HCV-positive sera collected from blood donors and IVDUs tested, as determined by reverse transcription-PCR analysis. Sequence analyses of amplified fragments of the HCV genome revealed that in Khon Kaen and Chiang Rai, Thailand, HCV-3a (50-60%) was the most common HCV subtype, followed by HCV-1a, HCV-1b, and subtypes of clade 6, each at 10-20%.

Differential distribution of hepatitis C virus subtypes in Asia: comparative study among Thailand, Indonesia, the Philippines and Japan.

Hepatitis C virus (HCV) is currently classified into at least six major genotypes, each of which is further divided into a number of subtypes. It has been reported that prevalence of each subtype varies among different geographical regions of the world and that severity of liver disease and sensitivity to interferon treatment varies with different subtypes. The purpose of this study was to determine and compare the prevalence of each subtype among HCV isolates in different areas in Asia such as southern (Hat Yai) and northern (Chiang Mai) parts of Thailand, Indonesia (Surabaya), the Philippines (Manila) and Japan (Kobe). Sera were obtained from various groups of patients and tested for antibodies against HCV using second and/or third generation ELISA kits. RNA was extracted from anti-HCV-positive sera and reverse-transcribed into cDNA. The cDNA-preparations were subjected to nested PCR to amplify NS5B and 5'-untranslated region (5'UTR) sequences. Amplified fragments were sequenced and subtypes of the isolates were determined based on sequence similarities with reported sequences. In Chiang Mai and Hat Yai, Thailand, HCV-3a, HCV-1a and HCV-1b were common in various populations. HCV type 6 variants were commonly found among blood donors and drug addicts in Chiang Mai, but not in Hat Yai. In Surabaya, Indonesia, HCV-2a was frequently detected in blood donors, but less frequently in patients with chronic liver disease. In blood donors, HCV-1a, HCV-1b and HCV-1d were more strongly associated with elevation of serum aminotransferase levels than HCV-2a. HCV-1a was significantly more common in patients on maintenance hemodialysis than in blood donors or patients with chronic liver disease. HCV-1d was detected exclusively in Indonesia. Another unique subtype HCV-3g was found also in Indonesia, though less frequently than HCV-1d. In the Philippines, a vast majority of the isolates were either HCV-1a or HCV-1b. Thus, HCV subtype prevalence varies among different regions of Asia.

GB virus C/hepatitis G virus (GBV-C/HGV) infection in Chiang Mai, Thailand, and identification of variants on the basis of 5'-untranslated region sequences.

By using reverse transcription and PCR for NS3 and 5'-untranslated regions (5'UTR) of the viral genome, prevalence of GB virus C/hepatitis G virus (GBV-C/HGV) infection in Chiang Mai, Thailand, was studied. High prevalence of GBV-C/HGV infection was observed among intravenous drug users (32%) and hemodialyzed patients (25%). The prevalence was also considerably high among patients with chronic liver disease, such as chronic hepatitis (9%), liver cirrhosis (12%) and hepatocellular carcinoma (10%). On the other hand, the prevalence among healthy blood donors (1%) was significantly lower than that of the above high-risk groups. GBV-C/HGV RNA positivity was significantly higher in individuals with antibodies against hepatitis C virus (24%) than in those without (5%). Phylogenetic analysis of the 5'UTR sequences classified Thai GBV-C/HGV isolates into three groups; (i) a group of isolates that are commonly found in the United States and Europe, (ii) a group of isolates that are commonly found in Asia, and (iii) a group of novel sequence variants.

Hepatitis C virus (HCV) subtype prevalence in Chiang Mai, Thailand, and identification of novel subtypes of HCV major type 6.

Subtype analysis of hepatitis C viruses (HCVs) obtained from patients with chronic liver disease in Chiang Mai, Thailand, was performed. Of 46 HCV isolates, 13 (28%) were shown to belong to HCV subtype 3a (HCV-3a), 10 (22%) to belong to HCV-1a, 7 (15%) to belong to HCV-1b, 1 (2%) to belong to HCV-3b, and 1 (2%) to belong to a variant group, as determined from partial nucleotide sequences of the NS5B region of the viral genome. Analysis of 5' untranslated region sequences identified five other isolates (11%) of HCV type 1 and two other isolates (4%) of type 3. Detailed phylogenetic positions for the variant described above and those previously obtained from blood donors and drug addicts in Chiang Mai were determined by a six-parameter neighbor-joining method on the basis of core, E1, and NS5B region sequences. The results revealed that those sequence variants represent novel subtypes of HCV type 6. The HCV type 6 isolates appear to be antigenically different from isolates of HCV types 1 and 2, as determined by a serotyping method that utilizes recombinant peptides corresponding to a portion of the NS4 protein. The significance of subtype analysis around this area is discussed.

HIV-1 Langerhans' cell tropism associated with heterosexual transmission of HIV.

Heterosexual transmission by vaginal intercourse accounts for most transmission of human immunodeficiency virus-type 1 (HIV-1) in Africa and Asia but is less important in the HIV-1 epidemics of the United States and Western Europe. Epithelial Langerhans' cells (LCs) represent a possible source of initial cell contact for vaginal infection. Fifteen primary isolates of HIV-1 from U.S. homosexuals and 18 HIV-1 isolates from Thailand heterosexuals were evaluated for growth in LCs of U.S. origin. All the viruses from the Thai heterosexuals, which were subtype E, grew more efficiently in the LCs than any of the viruses from the U.S. homosexuals, which are subtype B. These results suggest that LC tropism is associated with the efficiency of heterosexual transmission of HIV.

Frequent detection of hepatitis C virus subtype 3a (HCV-3a) isolates in Thailand by PCR using subtype-specific primers.

By means of a polymerase chain reaction (PCR) method using subtype-specific primers for hepatitis C virus (HCV) subtypes 1a, 1b, 2a, 2b and 3a, the prevalence of each subtype among HCV isolates in Chiang Mai, Thailand, was determined. HCV-3a appeared to be the most common subtype in blood donors, and was also frequently found in patients with liver disease. HCV-1b, but not HCV-2a or -2b, was also commonly found in this area, while a considerable percentage of the total HCV isolates still remained unclassifiable by the above methods. Serotype analysis of the HCV isolates using C14-1 and C14-2 recombinant peptides revealed that HCV-3a was likely to carry an antigenic determinant(s) different from those of the major types 1 (HCV-1a and -1b) and 2 (HCV-2a and -2b).

Analysis of hepatitis C virus isolates among healthy blood donors and drug addicts in Chiang Mai, Thailand.

Hepatitis C virus (HCV) isolates obtained from 25 anti-HCV antibody-positive healthy blood donors and 29 drug addicts in Chiang Mai, Thailand, were analyzed. HCV RNA was detected in 23 blood donor samples (92%) and 24 drug addict blood samples (83%) by PCR for a portion of the NS5 region. Subtype analysis revealed that HCV type 3a (HCV-3a) was the prevailing subtype (30%), which was followed in prevalence by HCV-1a (21%), -1b (13%), -3b (13%), and -6a (2%). Six (13%) of the 47 isolates showed low sequence similarities with known types and subtypes. The sequence variants could be grouped into four branches in a molecular evolutionary phylogenetic tree.