Genotypic subtyping of the HIV-1 polymerase gene in 30 naåve patients from Thailand.

To investigate the subtype classification of the circulating virus strains among infected Thai patients with human immunodeficiency virus type 1 (HIV-1). A random population of patients who were HIV-1 antibody positive after two independent screening assays was selected. HIV RNA from plasma samples was reverse-transcribed and amplified with specific primers that annealed to conserve regions of the HIV-1 pol gene. Amplified products were sequenced directly by using an automated sequencer. The sequencing products represent about 1.2 kb of the pol gene from each patient and they were phylogenetically analyzed and compared to the corresponding pol sequences of the published HIV-1 sequences of known genotypes. Genotype E was found in 25 of 30 patients (83.3%), and 5 patients (16.7%) were HIV-1 genotype B. The result confirmed that HIV-1 subtype E is still predominant in Thailand. Genotype B is found frequently, but there have been no examples of genotype A. In concordance with the serotypic assay, which was previously reported using the V3-peptide enzyme immunoassay (V3-PEIA), the genotypic assay of subtype E was high, at 80% and 83.3% in serotyping and genotyping, respectively. These findings of two subtypes with low heterogeneity indicate that Thailand may be a desirable site for evaluating candidate HIV-1 antiretroviral drugs and vaccines. The mixture of subtype E and B' strains also offers the opportunity to study phenotypic differences between the two subtypes.

Preliminary report for the application of nucleic acid sequence-based amplification in detection of human cytomegalovirus (HCMV) late pp67 mRNA for diagnosis of HCMV infection.

Human cytomegalovirus (HCMV) late pp67 mRNA expression by nucleic acid sequence-based amplification (NASBA) in patients, clinically diagnosed as possible HCMV, probable HCMV disease, and no disease, was evaluated. The RNAs were isolated from 11 whole-blood samples of 11 patients for the specific amplification of the pp67 mRNA. NASBA results were compared to results from PCR assay and serological assay. The HCMV pp67 mRNA could be found in 3 of 11 patients, whereas, HCMV-DNA PCR was positive in 6 of 11 patients. PCR assay for HCMV-DNA in plasma has proved to correlate with clinical diagnosis of HCMV infection. Only 2 patient samples of NASBA positive results coincided with HCMV-DNA PCR. However, the diagnosis of clinically relevant HCMV infection by NASBA was seen. Anti-CMV IgG titers of 1:1,600 or over 1:1,600 were found in 2 of 3 NASBA positive cases and 5 of 6 HCMV-DNA positive cases, whereas, anti-CMV IgM were all negative. These results showed the correlation of HCMV infection detected by NASBA, PCR assay and anti-CMV IgG of the titers up to 1:1,600. Additionally, a low antibody titer of the HIV patient could be diagnosed by NASBA or PCR. In conclusion, pp67 mRNA NASBA appears to be a promising diagnostic tool in analysis of HCMV infection and/or disease. Its diagnostic value should be defined in the specific group for the follow-up of immunocompromised patients, such as organ transplant recipients in future prospective studies.

Forensic identification by DNA fingerprinting and mitochondrial DNA typing.

Short tandem repeats (STRs), that represent an important source of highly polymorphic markers in human genome, and mitochondrial DNA (mtDNA) typing, that its sequences were conserved within the same maternal lineage, facilitated by use of the polymerase chain reaction (PCR) provide a powerful tool for forensic identification. We report the analysis of 9 STR loci and mtDNA typing of a muscle biopsied sample with 2 months postmortem by comparison with the genotype of the relative. The DNA profile showed common alleles with that of the relative but only 12 from 20 alleles (60%) were identifiable. Then, we performed mt DNA sequencing of the hypervariable region I (HV I) and obtained 100 per cent homology with that of the relative. In conclusion, personal identification can be performed precisely by the data of DNA profile and mtDNA typing compared to the genotype of the relative.

Comparison of DNA extraction from blood stain and decomposed muscle in STR polymorphism analysis.

Forensic samples that are often degraded and limited in quality cause DNA typing analysis by conventional methods unsuitable. We performed a single tube-multiplex PCR on 9 STR loci (D3S1358, vWA, FGA, TH01, TPOX, CSF1PO, D5S818, D13S317, and D7S820) and the X-Y homologous gene amelogenin of DNA extracted from six week postmortem blood stain and decomposed muscle by using QIAGEN QIAamp blood or tissue procedure. An automated genetic analyzer based on fluorescent dye technology was used to detect STR allele patterns. The DNA profile of blood stain sample obtained a complete and unambiguous pattern, whereas, that of muscle DNA extracted from QIAamp tissue and Chelex plus QIAamp blood protocols showed detected STR alleles for 70 per cent and 50 per cent of all tested alleles, respectively. The degraded muscle DNA could not yield amplified products of large size STR alleles; CSF1PO, D13S317 and D7S820. However, the analysis which relied upon the PCR-based STR polymorphism analysis and automated genetic analyzer system offers an ideal strategy for forensic identification.

Paternity testing by PCR-based STR analysis.

We present application of polymerase chain reaction (PCR)-based short tandem repeat (STR) system for use in paternity testing. The process involves a single tube multiplex PCR of 9 STR loci on different chromosomes, in conjunction with Amelogenin sex test and internal size standards, followed by using an automated DNA sequencer to detect amplified products. The results showed that this system provided unambiguously reliable results. In addition, the method is useful for routine use in that it is robust and reproducible and provides a reliable means of paternity testing.

p53 status and human papillomavirus infection in Thai women with cervical carcinoma.

Loss of p53 function has been implicated in a wide variety of human malignacies. Many studies suggest that in cervical carcinoma p53 function is inactivated either by gene mutation or by complex formation with E6 oncoprotein product of high-risk human papillomavirus (HPV). The aim of this study was to determine the status of HPV infection and p53 gene mutation as well as their correlation in cervical carcinomas. Formalin-fixed paraffin-embedded tissues of 12 cervicitis, 21 cervical intraepithelial neoplasia grade 3 (CIN 3) and 17 squamous cell carcinomas were determined for the presence of HPV using polymerase chain reaction (PCR) amplification and dot blot hybridization. The status of p53 mutations in exons 5-8 was evaluated by polymerase chain reaction single strand conformation polymorphism (PCR-SSCP) and confirmed by direct nucleotide sequencing. HPV infections were detected in all CIN 3 and squamous cell carcinomas (100%). Mutations of p53 were present in 3 of 38 HPV-positive samples: one with an ATG-->TTG transversion (Met-->Leu) in codon 237 of exon 7; and the others with a TGC-->TGG transversion (Cys-->Trp) in codon 242 of exon 7, and a CGT-->CCT transversion (Arg-->Pro) in codon 273 of exon 8, respectively. Our findings show that the frequency of p53 mutation is low in primary cervical carcinoma and that the p53 gene mutation and HPV infection are not mutually exclusive events in the development of cervical cancer. Thus, other genetic events independent of p53 inactivation may also significantly contribute to the carcinogenesis of the uterine cervix.

Detection of various types of human papillomaviruses in premalignant and malignant cervical lesions using DNA-DNA in situ hybridization.

Detection of human papillomavirus (HPV) in formalin-fixed paraffin embedded tissue sections by in situ hybridization technique employing biotinylated (HPV) DNA probe 6/11, 16/18 and 31/33/35 was done retrospectively in 25 cases of cervical dysplasia, 32 cases of cervical squamous cell carcinoma in situ, 52 cases of invasive cervical squamous cell carcinoma and 7 cases of adenocarcinoma. HPV could be demonstrated in 10 cases (40.00%) of cervical dysplasia, 8 cases (25.00%) of cervical squamous cell carcinoma in situ and 31 cases (59.61%) of invasive cervical squamous cell carcinoma and 4 cases (57.14%) of adenocarcinoma. Among the dysplastic cases, 4 cases showed HPV 31/33/35, 4 cases showed HPV 16/18 together with HPV 31/33/35, 1 case showed mixed typing of HPV 6/11 and 31/33/35, and 1 case showed mixed typing of HPV 6/11, 16/18 and 31/33/35. In 32 cases of squamous cell carcinoma in situ, 1 case of HPV 6/11; 3 cases of HPV 16/18, 3 cases of HPV 31/33/35 and 1 case of mixed typing of HPV 16/18 and 31/33/35 were present. A case of HPV 6/11, 10 cases of HPV 16/18 and 9 cases of HPV 31/33/35 could be detected among the cases of invasive squamous cell carcinoma. Mixed typing of HPV 6/11 and 16/18; HPV 6/11 and 31/33/35; HPV 16/18 and 31/33/35; HPV 6/11, 16/18 and 31/33/35 were revealed in 2, 1, 3 and 5 cases of invasive squamous cell carcinoma, respectively. In 7 cases of adenocarcinoma, 1, 2 and 1 cases exhibited positivity for HPV 16/18; HPV 6/11 and HPV 16/18; and HPV 16/18 and HPV 31/33/35.(ABSTRACT TRUNCATED AT 250 WORDS)

Recovery frequencies of herpes simplex virus types 1 and 2 from symptomatic and asymptomatic genital herpes cases and antiviral sensitivities of isolates.

Herpes simplex viruses were isolated from 40.8 to 56.0 per cent of the patients with genital herpes. The frequency of recovery seemed to be higher in females than in males, particularly during the first episode of infection. Asymptomatic shedding of the virus from female genitalias was approximately 0.7 per cent. Herpes simplex virus type 2 represented 98.4 per cent of all isolates and the remaining isolates were type 1. These isolates exhibited a wide range of sensitiveness to 9-(2-hydroxyethoxymethyl) guanine (acyclovir) as demonstrated by antiviral inhibition assay and no single strain exhibited high in vitro drug ID50 value.

Evaluation of biotin-streptavidin enzyme-linked immunosorbent assay for detection of genital herpes simplex virus infection.

A biotin-streptavidin enzyme-linked immunosorbent assay (B-SA ELISA) was evaluated for detection of herpes simplex virus (HSV) in clinical specimens which were cervico-vaginal swabs from 205 asymptomatic women and swabs from the genital lesions of 163 suspected patients. All specimens were also subjected to a conventional virus isolation in cell culture. A blocking B-SA ELISA had 100% specificity and 98% sensitivity compared with viral isolation from patients, but had only 40% sensitivity using specimens from asymptomatics. The conventional B-SA ELISA might also be used; it gave results corresponding to B-SA ELISA blocking test except for a single specimen which was considered a false positive.