Epstein-Barr virus (EBV) type B, a less potent transformer of B lymphocytes than type A, has rarely been detected in EBV-associated neoplasms except in AIDS-related lymphomas, in which about 50% of the cases contained this sub-type. In this study we analyzed the association of EBV and the distribution of virus sub-types in Asian non-Hodgkin's lymphoma (NHL) of the upper aerodigestive tract. We studied archival material of 29 NHL cases from Malaysia. B- and T-cell associated antigens were demonstrated by immunohistochemistry, and EBV early RNA EBER-1 was demonstrated using the RNA in situ hybridization technique. EBV was detected in the majority of tumour cells in 11/13 T-NHL but in only 1/16 B-NHL. EBV was sub-typed by single-step polymerase chain reaction of the EBNA-2 gene. This was successful in 9/10 cases of EBER-1-positive tumours and all contained type-A virus only. Our results showed a preponderance of T-cell lymphoma of the upper aerodigestive tract in the ethnic Chinese group of Malaysian patients, and EBV was strongly associated with T-NHL but not with B-NHL. Our results suggest that type-A EBV is the prevalent sub-type in Asian NHL of the upper aerodigestive tract, similarly to findings in Asian nasopharyngeal carcinoma.
HBV-DNA were analysed in 330 HBsAg-positive carriers in Malaysia by dot-blot hybridization and polymerase chain reaction. Seventy-three (22.12%) were positive for the virus. Of these, 65 (89%) were males and 8 (11%) were females. Statistically, there was no significant difference (P = 0.13). No significant decline in HBV-DNA with age in the Malay and Chinese males was observed (P = 0.2). Prevalence of HBV-DNA was higher in the Chinese carriers than in the Malay carriers for most age groups in both sexes. Sixty-one HBV-DNA-positive carriers were also positive for HBeAg. However, three individuals were positive only for anti-HBe, one was positive for both HBeAg and anti-HBe, and eight were negative for both HBeAg and anti-HBe. Fifty-seven were positive for HBeAg but negative for HBV-DNA. No relation was observed between raised alanine aminotransaminase and aspartate aminotransaminase levels and the presence of HBV-DNA (P = 0.4).
Glutathione S-transferase-theta (GSTT1) is subject to a genetic polymorphism where approximately 50% of a Caucasian population are homozygous for the null allele. Because of the possible association of the polymorphism with increased cancer risk in individuals, we genotyped by polymerase chain reaction 187 normal Chinese, 167 normal Malays and 152 normal Indians from Singapore and Malaysia. The proportion of Chinese, Malays and Indians with the null genotype were 58%, 38% and 16% respectively and mirrored previously reported frequencies of the GSTM1 null genotype in these populations. The frequency of the combined GSTM1 and GSTT1 null genotypes among Chinese, Malays and Indians were 37%, 22% and 5% respectively. The similarity with predicted frequencies indicated no interaction between the two genetic polymorphisms.
It is known that alpha1-antitrypsin deficiency is associated with emphysema in adults and liver cirrhosis in neonates. The phenotypes PiZZ and PiSZ are considered to be high risk groups. alpha1-antitrypsin deficiency is one of the most common lethal congenital disorders in Europe and the USA, occurring in approximately 1 in 2,000 caucasians of North European descent. Studies in Malaysia have found that the phenotypes PiZ and PiS are present in our population. Out of 950 samples analyzed, it was found that 10 samples were shown to be apparently Z homozygous phenotype. The phenotype is determined by high resolution isoelectrofocusing on an ultra-thin polyacrylamide gel embedded with narrow range Pi phamarlyte. The isoelectrofocused bands are confirmed by immunofixation and the plasma alpha1-antitrypsin levels determined by electroimmunoassay. The abnormal phenotypes are further confirmed by polymerase chain reaction using allele specific oligonucleotides.
Beta-thalassemia mutations in 282 alleles of 253 unrelated individuals originating from various provinces in the south of Thailand were characterized by dot blot hybridization, specific PCR-amplification and direct DNA sequencing. It was possible to characterize the mutations in 274 (97.2%) of alleles studied. Twelve different point mutations and two different large deletions of the beta-globin gene were identified. Seven common mutations, namely 4 bp deletion at codons 41/42. IVS1 position 5 (G-C), codon 19 (AAC-AGC), codon 17 (AAG-TAG), IVS1 position 1 (G-T), position -28 (A-G) and 3.5 kb deletion, accounted for about 91.5%. The mutations at mRNA cap site + 1 (A-C) and IVS1 position 1 (G-A), previously undescribed in Thailand, were found in 1 and 2 individuals, respectively. A novel mutation of 105 bp deletion at the 5' end of beta-globin gene was detected in a family originating from this area. The knowledge from this study should be useful for planning of genetic counseling and prenatal diagnosis programs for patients with beta-thalassemia in the south of Thailand.
The nucleotide sequence of the haemagglutinin-neuraminidase (HN) gene of Newcastle disease virus (NDV) viscerotropic-velogenic strain AF2240 was determined by direct RNA sequencing and by sequencing RT-PCR products. It encodes a single open reading frame of 581 amino acids with a calculated Mr of 63.8 kDa. The predicted sequence contains five asparagine glycosylation sites. Comparison of the AF2240 HN protein sequence with 13 other previously published sequences showed 88% homology. This HN protein is unique because it lacked the Arg 403 residue which is present in all of the other strains and cannot be grouped under the proposed three size classes of HN proteins in NDV.
The beta-thalassaemia mutations in 20 Malaysian children with beta-thalassaemia major were characterised by using a multi-modal approach, consisting of a slot-blot hybridisation with selected allele-specific oligonucleotides (ASO), followed by reverse dot-blot assay (RDB), amplification refractory mutation system (ARMS) and genomic sequencing. This strategy yielded a 94.4% mutation detection rate. The 6 most common mutations were codons 41/42 (-TTCT), IVS II nt 654(C --> T), IVS I nt 5(G --> C), IVS I nt 1(G -->T), codon 35 (-C) and codon 19 (A --> G), which accounted for 83.3% of all mutations detected. A strategy of initial screening with the above 6 selected ASOs for slot-blot hybridisation followed by RDB assay for the less common Asian mutations would give a mutation identification of 91.7%. Another feasible approach would be to analyse alleles from a particular racial group, by a judicious selection of 4 ASOs common to that particular subpopulation and then supplement this with RDB assay. This could yield a 100% coverage for the Chinese subpopulation in Malaysia. With these strategies, a practical approach has been identified to overcome the pitfalls posed by the molecular heterogeneity of beta-thalassaemia to enable prenatal diagnosis and carrier screening to be carried out. Regional collaborative studies are to be encouraged as an indispensable tool in providing better health care services to our patients.
We describe here a reverse transcriptase-polymerase chain reaction method for the detection of malaria parasites. Ten in vitro-cultured isolates of Plasmodium falciparum and 16 specimens from patients infected with P. falciparum were used to examine the specificity and sensitivity of the test. The sensitivity of the test was 0.3 parasites per microliter of blood. Specificity was determined by matching the sequences of the specimens' DNA to published sequences of 18S ribosomal RNA genes in the species-specific region. The test proved to be very sensitive and specific for the detection of P. falciparum infection.
Involvement of the central nervous system in dengue fever and dengue hemorrhagic fever has always been thought to be secondary to vasculitis with resultant fluid extravasation, cerebral edema, hypoperfusion, hyponatremia, liver failure, and/or renal failure. Thus, the condition has been referred to as dengue encephalopathy. Encephalitis or direct involvement of the brain by the virus was thought to be unlikely. This paper reports on six children who were seen over a period of two years presenting on the second or third day of illness with dengue encephalitis. The diagnosis was based upon a clinical picture of encephalitis and confirmed by cerebrospinal fluid (CSF) microscopy and electroencephalography changes. All six cases were confirmed dengue infections. Dengue 3 virus was isolated from the CSF of four cases and in one case, dengue 2 was detected by the polymerase chain reaction in both the CSF and blood. In the sixth case, virologic evidence was negative but dengue immunoglobulin M was detected in the CSF and blood. Since the onset of encephalitis appears early in the course of illness coinciding with the viremic phase, we postulate that the virus crosses the blood-brain barrier and directly invades the brain causing encephalitis. This study provides strong evidence that dengue 2 and 3 viruses have neurovirulent properties and behave similarly to other members of the Flaviviridae.
The spectrum of beta-thalassemia mutations in Malays in Singapore and Kelantan (Northeast Malaysia) was studied. Allele specific priming was used to determine the mutations in beta-carriers at -28, Codon 17, IVSI #1, IVSI #5, Codon 41-42 and IVSII #654 along the beta-globin gene. The most common structural hemoglobin variant in Southeast Asia, Hb E, was detected by DNA amplification with restriction enzyme (Mnl1) analysis. Direct genomic sequencing was carried out to detect the beta-mutations uncharacterized by allele-specific priming. The most prevalent beta-mutations in Singaporean Malays were IVSI #5 (45.83%) followed by Hb E (20.83%), codon 15 (12.5%) and IVSI #1 and IVSII #654 at 4.17% each. In contrast, the distribution of the beta-mutations in Kelantan Malays differed, with Hb E as the most common mutation (39.29%) followed by IVSI #5 (17.86%), codon 41-42 (14.29%), codon 19 (10.71%) and codon 17 (3.57%). The beta-mutations in Kelantan Malays follow closely the distribution of beta-mutations in Thais and Malays of Southern Thailand and Malays of West Malaysia. The AAC-->AGC base substitution in codon 19 has been detected only in these populations. The spectrum of beta-mutations in the Singaporean Malays is more similar to those reported in Indonesia with the beta-mutation at codon 15 (TGG-->TAG) present in both populations. The characterization of beta-mutations in Singaporean and Kelantan Malays will facilitate the establishment of effective prenatal diagnosis programs for beta-thalassemia major in this ethnic group.
The DNA genomes of isolates of rice tungro bacilliform virus from Bangladesh, India, Indonesia, Malaysia and Thailand were cloned and compared with that of the type isolate from the Philippines. Restriction endonuclease maps revealed differences between the isolates and cross-hybridization showed that they fell into two groups, those from the Indian subcontinent and those from south-east Asian countries. The genomes of isolates from the Indian subcontinent contained a deletion of 64 bp when compared with those from south-east Asia. The implications of this variation are discussed.
A study was initiated to amplify by polymerase chain reaction (PCR), a short factor VIII gene fragment containing the Bcl I restriction site from hemophilia patients using published primer sequences. Preliminary findings indicated that the resulting fragment is 142 bp long. This fragment, when digested with Bcl I restriction enzyme produced two fragments, 99 bp and 43 bp in length. Polymorphism in the Bcl I region can be used to detect carrier state in the family members of the hemophiliacs.
A rapid diagnostic system for scrub typhus using nested polymerase chain reaction (PCR) was applied to clinical samples from Malaysian Aborigines. Whole blood from twenty-four patients suspected of scrub typhus infection were tested using nested polymerase chain reaction and sera were evaluated by the indirect immunoperoxidase test. Antibody responses towards Rickettsia tsutsugamushi were observed in seventeen patients with the majority having high titers of IgG antibodies. Seven patients were seronegative. The nested PCR amplified R. tsutsugamushi DNA from six patients, of which two were negative serologically and four had high titers of IgG antibodies. Second samples collected seven days after treatment were negative by PCR testing. Nested PCR is highly sensitive and specific and may be used to provide rapid confirmation of scrub typhus cases in endemic region.
A modified nested polymerase chain reaction (PCR) method for detection of Plasmodium falciparum, P. vivax and P. malariae was combined with a simple blood collection and deoxyribonucleic acid (DNA) extraction method and evaluated in Malaysia. Finger-prick blood samples from 46 hospital patients and 120 individuals living in malaria endemic areas were spotted on filter papers and dried. The simple Chelex method was used to prepare DNA templates for the nested PCR assay. Higher malaria prevalence rates for both clinical (78.2%) and field samples (30.8%) were obtained with the nested PCR method than by microscopy (76.1% and 27.5%, respectively). Nested PCR was more sensitive than microscopy in detecting mixed P. falciparum and P. vivax infections, detected 5 more malaria samples than microscopy on the first round of microscopical examination, and detected malaria in 3 microscopically negative samples. Nested PCR failed to detect parasite DNA in 2 microscopically positive samples, an overall sensitivity of 97.4% compared to microscopy. The nested PCR method, when coupled with simple dried blood spot sampling, is a useful tool for collecting accurate malaria epidemiological data, particularly in remote regions of the world.
Haemoglobin Bart's hydrops fetalis is the result of complete absence of functional alpha-globin genes where the fetus is homozygous for the alpha 0-thal gene. Prenatal diagnosis can be made by analysis of fetal DNA from chorionic villus, amniotic cells and fetal blood. Earlier studies for analysing genomic DNA needed digestion with restriction enzymes and hybridisation to radiolabelled probes which took 2 weeks. We have used the polymerase chain reaction (PCR) and non-radioactive primers to identify specific target sequences with results available within 1-3 days for the diagnosis of haemoglobin Bart's syndrome. With fetal blood samples, complete absence of alpha-chain synthesis is confirmed by globin chain electrophoresis on cellulose acetate pH 6.0.
The polymorphism of the human leucocyte antigen HLA-DR2 and the heterogeneity of HLA-DR2 class II-related haplotypes (HLA-DRB1-DRB5-DQA1-DQB1) were investigated in four populations of east and south-east Asia (SEA) and five Melanesian populations using TaqI restriction fragment length polymorphism (RFLP) analysis, and the polymerase chain reaction (PCR) amplification-based techniques PCR-RFLP and sequence-specific oligonucleotide (SSO) typing. The haplotype DRB1*1502-DRB5*0101-DQA1*0102-DQB1*0601 was common in Malaysians, Javanese, Thursday Islanders, Madang, Goroka and the Australian Aborigines, while DRB1*16021-DRB5*0101-DQA1*0102-DQB1*0502 was common in the Thai and Thursday Islanders. DRB1*1501-DRB5*0101-DQA1*0102-DQB1*0602 was present at a high frequency in Northern Chinese, Goroka, Watut and Australian Aborigines. The study describes four rare or unusual haplotypes: HLA-DRB1*1501-DRB5*0101-DQA1*0101-DQB1*0601, DRB1*1502-DRB5*0101-DQA1*0101-DQB1*0502, DRB1*1502-DRB5*0102-DQA1* 0102-DQB1*0502 and DRB1*1501-DRB5*0101-DQA1*0101/2-DQB1*0503; the latter two were confirmed by segregation in two Javanese families. A new DR2 allele, initially detected by PCR-RFLP and confirmed by DNA sequencing as DRB1*16022 (previously designated DRB1*16Madang), was seen in a Madang individual. A new HLA-DR2 TaqI RFLP subtype, locally designated as DR15U, is also described. This RFLP subtype segregated in a Javanese family and correlated with a typically SEA haplotype, DRB1*1502-DRB5*0102-DQA1*0101-DQB1*0501. The allele HLA-DR16Thai, determined by TaqI DRB RFLP, was found by PCR-RFLP and SSO typing to correlate with a unique SEA haplotype, HLA-DRB1*16021-DRB5*0101-DQA1*0102-DQB1*0502, and was observed in the Thai, Malaysian, Thursday Islander, Javanese and Northern Chinese populations.
Five polymorphisms in the C6 and C7 genes have been investigated in seven ethnic groups. The allele frequencies are broadly similar in most groups except C7 M/N which is monomorphic in our group of Africans, and C6 MspI and C7 S367T where the allele frequencies in African and Cape Coloured subjects are very different from the other ethnic groups. There is very little allelic association except between C6 A/B and C6 MspI. Seventeen of the 32 possible haplotypes have been observed, suggesting that much recombination has taken place. We describe a new method for the investigation of the MspI RFLP located in intron 3 of C6 (approximately 3 kbp 3' from exon 3 and 1.5 kbp 5' from exon 4) and its molecular basis, together with an improved method for the isolation of DNA from stored serum.
Mosquito adults and larvae were collected from dengue high risk areas and transported to the laboratory for identification. Identified mosquitos were pooled according to the species, date and locality and stored at -70 degrees C. A total of 1,385 pools of Aedes albopictus and 267 pools of Ae. Aegypti were collected from major towns in 12 states in Peninsular Malaysia. Virus isolation was carried out using cell culture (C6/36 clone) of Ae. albopictus and detection of dengue virus by the peroxidase anti-peroxidase staining. All positive isolations were further re-confirmed by the reverse transcriptase-polymerase chain reaction (RT-PCR). Most of the pools were negative with PAP staining and RT-PCR. However, 11 mosquito pools were positive with PAP staining. On the other hand, samples from Terengganu, Pulau Pinang and Johor were positive using both methods.