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PubMed1997

[Partial nucleotide sequencing of hepatitis E virus isolated from sera of patients with acute sporadic hepatitis E in China].

28 hepatitis E virus (HEV) cDNA isolates were obtained from 41 sera of patients with acute sporadic hepatitis E (HE) in Shenzhen, Changchun and Hangzhou by a reverse transcription nested polymerase chain reaction (RT-nPCR) and 3 of the 28 RT-nPCR products of HEV cDNA ORF2 region were sequenced. The nucleotide homology of these three HEV isolates was 80.2%, 79.9% and 79.4%, respectively, as compared with the Maxico strain of HEV (M); 93.4%, 92.3% and 93.8% with the Burma epidemic strain of HEV(B) (Ep); 95.5%, 93.9% and 95.1% with the Burma sporadic strain of HEV(B) (Sp); 97.0%, 96.5% and 95.9% with the Xinjiang epidemic strain of HEV CH 1.1. It is demonstrated that these three isolates of HEV obtained from sera of acute sporadiic hepatitis E cases have a higher degree of homology with the Xinjiang strain of HEV CH 1.1 and the Burma strain of HEV(B). The data indicate that these three HEV isolates may belong to HEV(B) subtype, as the HEV CH 1.1 does.

Amino Acid Sequence↗
PubMed2006

[Intraspecific DNA sequence polymorphism and genetic markers in the mitochondrial CO I gene from three populations of Macrobrachium rosenbergii].

The mitochondrial COI gene was PCR amplified and sequenced from 17 samples obtained from three populations of Macrobrachium rosenbergii (F1 of the Burma wildtype population, Jiangsu cultured population and F2 of the Guangxi breeding population). A 498-bp long partial gene segment was acquired and used to study the genetic diversity among the three populations. Results indicated that the COI gene locus was relatively more polymorphic in the F1 of Burma wildtype population, while the polymorphism in Jiangsu cultured population and Guangxi breeding population were very poor. A total of 10 polymorphic sites and 5 haplotypes were found in the sequences of the 17 samples. The average nucleotide divergence in the three populations was 0.88%0.07% and 0 respectively. The UPGMA phylogenetic tree suggested that F2 of the Guangxi breeding population and Jiangsu cultured population were closest genetically, and their haplotypes could be gathered together to a genetic branch while F1 of the Burma wildtype population diverged and could form another relatively independent branch. For these distinct nucleotide differences, COI gene could be suitable as a genetic marker for distinguishing these two branches of the Macrobrachium rosenbergii population.

Animals↗
PubMed1998

Identification of a novel strain of hepatitis E virus responsible for sporadic acute hepatitis in Taiwan.

Hepatitis caused by the hepatitis E virus (HEV) is a self-limited disease and occurs most frequently as epidemic or sporadic hepatitis in developing countries. The role of HEV in sporadic acute hepatitis in areas without a history of hepatitis E epidemics is obscure. Recently, it was found that more than 10% of the patients with acute non-A, non-B, non-C hepatitis in Taiwan were associated with an acute HEV infection. Nucleotide sequences of the regions within the first open reading frame of HEV were determined in four cases and were 96.7-100% identical to each other. As compared to the isolates from China, Pakistan, Burma, India, Africa, and Mexico, the similarities were, however, only 71.7-79.3%. Phylogenetic analysis revealed that the four Taiwan isolates were categorized as a novel HEV group (the Taiwan strain), which was distinct from all of the strains isolated from other parts of the world. In addition, the isolates from China, Burma, India, and Pakistan were catalogued as the second genotype of HEV (the Asian strain), and the Mexican isolate as the third (the Mexican strain). The African isolate was more related to the Asian type and might be a subtype of the Asian strain. A simple genotyping method by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) is described. The findings also support the hypothesis that HEV may be responsible for some sporadic acute non-A, non-B, non-C hepatitis in other developed countries.

Base Sequence↗
PubMed2005

Mitochondrial DNA variation in Chinese and Indian rhesus macaques (Macaca mulatta).

DNA was extracted from the buffy coats or serum of 212 rhesus macaques (Macaca mulatta) sampled throughout the species' geographic range. An 835 base pair (bp) fragment of mitochondrial DNA (mtDNA) was amplified from each sample, sequenced, aligned, and used to estimate genetic distances from which phylogenetic trees were constructed. A tree that included sequences from rhesus macaques whose exact origins in China are known was used to determine the regional origin of clusters of haplotypes, or haplogroups, defined by the trees. Indian rhesus sequences formed one large homogeneous haplogroup with very low levels of nucleotide diversity and no geographic structure, and a second much smaller haplogroup apparently derived from Burma. The sequences from Burma and eastern and western China were quite divergent from those in the major haplogroup of India. Each of these sequences formed separate clusters of haplotypes that exhibited far greater nucleotide diversity and/or population structure. Correspondingly, sequences from Indian rhesus macaques that are considered to represent different subspecies (based on morphological differences) were intermingled in the tree, while those from China reflected some, but not all, aspects of subspecific taxonomy. Regional variation contributed 72% toward the paired differences between sequences in an analysis of molecular variance (AMOVA), and the average differences between the populations of eastern and western China were also statistically significant. These results suggest that Indian and Chinese rhesus macaques were reproductively isolated during most, if not all, of the Pleistocene, during which time Indian rhesus macaques experienced a severe genetic bottleneck, and that some gene flow westward into India was subsequently reestablished. Samples from breeding centers in three different provinces of China included sequences from rhesus macaques that originated in both eastern (or southern) and western China, confirming anecdotal reports that regional breeding centers in China exchange breeding stock. Genetic differences among rhesus macaques (even those acquired from the same regional breeding center) that originate in different geographic regions and are employed as subjects in biomedical experiments can contribute to phenotypic differences in the traits under study.

Animals↗
PubMed1979

Bacteriophage typing of Salmonella weltevreden.

Salmonella weltevreden has been found to be one of the commonest Salmonella serotypes isolated from diverse sources in India and has also been isolated in a number of other countries. A phage typing scheme was developed for this serotype using a set of six typing phages. These phages had been selected out of 146 phage strains isolated and purified from stool samples of man, laboratory animals and other animals, sewage and surface water sources, and the lytic mutants of temperate phages form S. weltevreden. The phage typing scheme was applied systematically to type the 946 strains from India isolated during 1958-1974 and 148 strains originating from Australia, Burma, England, Gan Island, Holland, Hong Kong, Malaysia, New Zealand, Papua New Guinea, The Philippines, Thailand, The United States and Vietnam during 1953-1971. The scheme was particularly studied to evaluate its utility in mapping the epidemiologically related strains from various sources. The S. weltevreden strains could be classified into ten phage types. Phage types 2 and 7 were found exclusively amongst Indian strains, type 6 from Vietnam and type 8 from Burma, Thailand and Vietnam. Phage types were found to be stable and consistent with the independent epidemiological data available.

Bacteriophage Typing↗
PubMed1994

A new Chinese isolate of hepatitis E virus: comparison with strains recovered from different geographical regions.

The full-length cDNA of a new Chinese strain (KS2-87) of Hepatitis E virus (HEV) has been constructed and sequenced. The 5' noncoding region of KS2-87 is 26 nucleotides in length, which is one nucleotide shorter than that of HEV (B1) (Burma) and 23 nucleotides longer than that of HEV (Mexico). Comparison of the nucleotide and amino acid sequences of KS2-87 with all other published HEV sequences showed that KS2-87 was closer to two other Chinese strains (CHT-88, CHT-87) and SAR-55 (Pakistan) than to HEV (B1) and HEV (B2) (Burma) or HEV (Mexico). Comparisons of partial sequences of genes encoding a nonstructural and a structural protein revealed the existence of genetically related groups of HEV within geographical regions, whereas larger nucleotide differences were seen among isolates that were more geographically and epidemiologically distant.

Animals↗
PubMedDate not supplied

Molecular characterization of a hepatitis E virus isolate from Namibia.

Hepatitis E virus (HEV) causes sporadic and epidemic acute viral hepatitis in many developing countries. In Africa, hepatitis E has been documented by virus detection (reverse transcriptase polymerase chain reaction, RT-PCR) in Egypt, Chad, Algeria, Morocco and Tunisia. Cases of presumptive hepatitis E also have been documented by detection of antibody to HEV in the Sudan, Kenya, Ethiopia, Somalia, Djibouti and South Africa. Recently, we reported the recovery of 9 isolates of HEV from feces collected during an outbreak of jaundice in Namibia. These specimens were stored frozen for many years at the South African Institute for Medical Research awaiting new methods to determine the etiology of jaundice. HEV genomic sequences were detected by antigen-capture RT-PCR with primers that amplified 2 independent regions of the HEV genome (ORF-2 and ORF-3). To further characterize the HEV 83-Namibia isolates, we determined the nucleotide (nt) sequence of the 3' end of the capsid gene (296 of 1, 980 nt in ORF-2) and ORF-3 for 1 isolate. The capsid gene sequence shared 86% identity with the prototype Burma strain and up to 96% identity with other African strains at the (nt) level, and 99% identity with Burma or other Africa strains at the amino acid level. A 188 (nt) fragment amplified from ORF-3 was also highly homologous to other HEV but was too short for meaningful comparison. Phylogenetic analysis indicated that HEV 83-Namibia is closely related to other African isolates, and differs from Burmese, Mexican and Chinese HEV. These data link the HEV causing the 1983 Namibia outbreak to more recent HEV transmission in northern and sub-Saharan Africa, suggesting this subgenotype of HEV is firmly established throughout the continent.

Capsid↗
PubMed1990

Differences between the venoms of two sub-species of Russell's viper: Vipera russelli pulchella and Vipera russelli siamensis.

Ion exchange chromatography was carried out using venoms obtained from two sub-species of Russell's viper; V. russelli siamensis from Burma and V. russelli pulchella from Sri Lanka. Differences were observed in the elution position of venom components having haemolytic and procoagulant activity but not those causing fibrinolysis. Only the V. russelli siamensis venom exhibited any platelet aggregating activity. The Indian (Haffkine) polyspecific and the Burmese (Burma Pharmaceutical Industries) monospecific antivenoms, when used in cross immunoelectrophoresis against the two venoms, revealed differences in the number and/or intensity of the precipitin bands present. An important functional consequence of this was that the Burmese antivenom did not neutralize the haemolytic activity of the V. russelli pulchella venom in vitro and would thus probably not be effective in treating this consequence of envenoming by Russell's viper in Sri Lanka. Differences in the composition and the clinical effects of the two venoms emphasizes the importance of using venom from the local snake for antivenom production if optimal clinical efficacy is to be achieved.

Chromatography, Ion Exchange↗
PubMed1996

Two types of Russell's viper revealed by variation in phospholipases A2 from venom of the subspecies.

This study compared the phospholipases A2 (PLA2S) present in four commercially available venoms of Russell's viper subspecies by HPLC fractionation and partial sequence analysis. A potent heterodimeric PLA2 neurotoxin (designated a Russtoxin) was found in the venoms of all Russell's vipers except Daboia russelli (Sri Lanka and South India). The venom PLA2S of D. r. russelli (southern India) used in a previous study appear to be the same as those of D. r. pulchella (Sri Lanka), while the venom PLA2S of D. r. russelli (Pakistan) and D. r. siamensis (Burma and Thailand) resemble those of D. r. formosensis (Taiwan). This study provides evidence for the presence of two types of Russell's viper. Daboia russelli formosensis (Taiwan). D. r. siamensis (Thailand and Burma) and D. r. russelli (Pakistan) represent one type whose venom contains PLA2S having an Asn residue at the N-terminus, while D. r. pulchella (South India and Sri Lanka) represents the other type, whose venom contains PLA2S with a N-terminal residue Ser.

Amino Acid Sequence↗
PubMed1992

Molecular cloning and sequencing of the Mexico isolate of hepatitis E virus (HEV).

Hepatitis E virus (HEV) is the major causative agent of hepatitis E or what was formerly known as enterically transmitted non-A, non-B hepatitis. The disease has a worldwide distribution but occurs principally in developing countries in any of three forms: large epidemics, smaller outbreaks, or sporadic infections. Genetic variation of different HEV strains was previously noted and it will be important to determine the extent to which this variation may pose problems in the diagnosis and treatment of HEV infection. To analyze differences at the genetic level between HEV(Mexico; M) and the previously characterized HEV(Burma; B) and HEV(Pakistan; P) isolates, overlapping cDNAs were cloned from samples obtained from an infected human and an experimentally inoculated cynomolgus macaque. These cDNA clones, representing the nearly complete (7185-bp) genome of HEV(M), confirmed an expression strategy for the virus that involves the use of 3 forward open reading frames (ORFs). The HEV(M) strain has an overall 76 and 77% nucleic acid identity with the HEV(B) strain and HEV(P) strain, respectively; however, the degree of sequence variation was not uniform throughout the viral genome. A hypervariable region was identified in ORF1 that exhibited a 58 and 54% nucleic acid sequence and 13% amino acid similarity with the Burma strain and the Pakistan strain, respectively. A large number of the nucleotide differences occurred at the third codon position, with the deduced amino acid sequences similarity of 83, 93, and 87% between HEV(M) and HEV(B) isolates in ORF1, ORF2, and ORF3, respectively, and with 84, 93, and 87% amino acid identities between HEV(M) and HEV(P) isolates in ORF1, ORF2, and ORF3, respectively. The nucleotide sequences derived from the highly conserved regions of HEV genome will be useful in developing polymerase chain reaction-based tests to confirm the viral infection. Knowledge of the extent of the sequence variation encountered with HEV will not only aid in the future development of diagnostic and vaccine reagents but also further our understanding of how HEV strain variation might impact the pathological outcome of infection.

Amino Acid Sequence↗
PubMed2005

Mitochondrial phylogeography and subspecific variation in the red panda (Ailurus fulgens): implications for conservation.

The red panda (Ailurus fulgens) is an endangered species and its present distribution is restricted to isolated mountain ranges in western China (Sichuan, Yunnan, and Tibet provinces) and the Himalayan Mountains chain of Nepal, India, Bhutan, and Burma. To examine the evolutionary history across its current range, and to assess the genetic divergence among current subspecies and population structure among different geographic locations, we sequenced mitochondrial DNA from the control region (CR) and cytochrome (cyt) b gene for 41 individuals in Sichuan, Yunnan, Tibet of China, and Burma. 25 CR haplotypes (10 for cyt b) were identified from 11 geographic locations. Only three haplotypes were shared among sample localities, including one among current subspecies. Nine haplotypes were shared with the study of Su et al. [Mol. Biol. Evol. 18 (2001) 1070]. CR haplotype diversity was high (0.95+/-0.02) and nucleotide diversity among all haplotypes was relatively low (0.018+/-0.009). Phylogenetic confirmed trees show a shallow pattern with very little structure or statistical robustness. The application of two coalescent-based tests for population growth allowed us to interpret this phylogeny as the result of a recent population expansion. Analysis of molecular variance and nested clade analysis failed to detect significant geographic structure in both data sets. The lack of significant differentiation between subspecies does not indicate the presence of evolutionary significant units. We suggest that the present population structure has resulted from habitat fragmentation and expansion from glacial refugia. Due to its habitat requirements it is likely that the red panda has undergone bottlenecks and population expansions several times in the recent past. The present population may exhibit a pattern reminiscent of a relatively recent population expansion.

Animals↗
PubMed1997

Hepatitis E virus in Nepal: similarities with the Burmese and Indian variants.

Hepatitis E has been the predominant type of acute hepatitis in Nepal both in adults and children, in sporadic and epidemic forms. We examined six hepatitis E virus (HEV) isolates obtained during an 8-year period, from 1987 to 1995, in the Kathmandu valley of Nepal. Analysis of portions of the putative helicase, polymerase and capsid genes demonstrated close genetic relatedness among themselves (> 96.4% identity) and with the Burmese (> 95.5%) and Indian (> 95.3%) isolates, and less so with the African (> 94.4%) and the Chinese (> 91%) isolates within the Asian genotype. Phylogenetic analysis placed the Nepali isolates in the Burma-India evolutionary branch and showed that the oldest isolate, TK78/87 was more similar to the Burmese isolates whereas the most recent isolates were closer to the Indian ones. Assuming no frameshifts, the Nepali isolates showed high amino acid conservation, but also unique changes when compared to other HEV isolates. Amino acid residue 614 of the capsid protein was identified as a possible marker to distinguish the Burma-Nepal-India from the China-Central Asian Republics subgenotype, and the Mexico genotype.

Adolescent↗
PubMed2001

Shan women and girls and the sex industry in Southeast Asia; political causes and human rights implications.

The human rights abuses which occur during civil conflicts pose special threats to the health and lives of women. These can include rape, sexual violence, increased vulnerability to trafficking into prostitution, and exposure to HIV infection. The long-standing civil conflict in the Shan States of Burma is investigated as a contributing cause to the trafficking of ethnic Shan women and girls into the Southeast Asian sex industry, and to the subsequent high rates of HIV infection found among these women. The context of chronic human rights abuses in the Shan states is explored, as well as the effects of recent forced population transfers on the part of the Burmese Military Regime. Rights abuses specific to trafficked women may further increase their vulnerability to HIV and other STD. The need for a political resolution to the crisis in Burma is discussed, as are approaches aimed at preventing trafficking, empowering women already in the sex industry, and reducing the risks of HIV and other STD among these women and girls.

Female↗
PubMed1991

Surveys of human enterotoxigenic Escherichia coli from three different geographical areas for possible colonization factors.

Enterotoxigenic Escherichia coli (ETEC) from Burma, central Africa (Rwanda and Zaire) and Peru, were screened by enzyme-linked immunoassays for the colonization factor antigens (CFAs) and putative colonization factors (PCFs): CFA/I, CFA/II, which consists of three coli surface-associated (CS) antigens, CS1, CS2 and CS3, CFA/III, CFA/IV (CS4, CS5, CS6), CS7, PCFO9, PCFO159. H4, PCFO166, and CS17. The highest proportion of ETEC with identifiable colonization factors (71%) were found in the strains from Burma, which were mainly positive for CFA/I (38%), but strains producing CFA/II (4%), CFA/IV (11%), CS7 (10%), CS17 (4%), PCFO159, H4 (2%) and PCFO166 (2%) were also found. Sixty-nine percent of the ETEC from central Africa were positive for known colonization factors. While CFA/I positive strains were important (12%), a higher number of ETEC producing CFA/IV (33%) and CS17 (24%) were found. Fifty-two percent of the Peruvian strains produced identifiable colonization factors. The largest group of strains produced antigens of the CFA/IV complex (17%), while ETEC producing CFA/II (6%), CFA/III and CS6 (2%), CS7 (6%), PCFO9 (6%), PCFO166 (8%) and CS17 (7%) were also found. These surveys show that there is a considerable variation in the proportions and types of colonization factor found in different geographical areas. From 29 to 48% of the ETEC did not possess an identifiable colonization factor. These were particularly of the LT only producing type. These results have important implications for vaccine formulation.

Antigens, Bacterial↗
PubMed2001

Strong association of a tumor necrosis factor-alpha promoter allele with cerebral malaria in Myanmar.

To investigate the host genetic factors affecting the clinical course of falciparum malaria, polymorphism of the tumor necrosis factor-alpha (TNF-alpha) promoter region was analyzed in patients with cerebral malaria. Two hundred and forty-three Myanmar patients with falciparum malaria at Mae Sot Malaria clinic and Mae Sot General Hospital located at the border between Thailand and Myanmar, were included in this study. Among the patients (128 from Karen, 115 from Burma), 200 were uncomplicated and 43 had cerebral malaria. The TNF-alpha 5'- flanking region showed biallelic polymorphic sites at -238, -308, -857, -863, -1031, and there were 7 alleles (TNFP-A, B, C, D, M1, M4, M7) found in the patients from Myanmar. We found that the TNFP-D allele was significantly associated with cerebral malaria in the populations from Karen (Pc<0.0001, OR=124.86) and Burma (Pc<0.0001, OR=34.50). TNFP-D showed no significant linkage disequilibrium with any alleles of HLA-B or HLA-DRB1, suggesting that TNFP-D was primarily associated with cerebral malaria in Myanmar.

Gene Frequency↗
PubMed1996

A 38-kDa host factor interacts with functionally important motifs within the Autographa californica multinucleocapsid nuclear polyhedrosis virus homologous region (hr1) DNA sequence.

We recently demonstrated that the Autographa californica multinucleocapsid nuclear polyhedrosis virus homologous region (hr1) enhances transcription from the viral polyhedrin promoter and also functions as a putative origin of replication (ori). Hr1, carrying five 28-base pair core palindrome units, has also been mapped with respect to its enhancer and ori functions (Habib, S., Pandey, S., Chatterji, U., Burma, S., Ahmad, R., Jain, A., and Hasnain, S. E. (1996) DNA Cell Biol. 15, 737-747). A 38-kDa host factor termed hr1-binding protein (hr1-BP) binds with high specificity and affinity (Kd approximately 6.5 x 10(-11) M) to functionally important motifs within hr1. The core palindrome as well as sequences immediately flanking it are required for this interaction. Divalent cations are not essential, and ionic interactions play only a minor role in complex formation. hr1-BP binds through the minor groove of the double helix to multiple sites within hr1, and binding occurs as a function of the number of modules within hr1. Phosphorylation of hr1-BP is important for host factor-hr1 interaction. Hr1-BP differs in several respects from the other host factor, polyhedrin promoter-binding protein, described previously (Burma, S., Mukherjee, B., Jain, A., Habib, S., and Hasnain, S. E. (1994) J. Biol. Chem. 269, 2750-2757). When hr1-BP was sequestered out, in vivo, by a plasmid carrying hr1 alone, the hr1-mediated enhancement of reporter expression was abolished, demonstrating that the binding of hr1-BP may be crucial for the enhancer activity of the dual function hr1 element.

Base Sequence↗
PubMed1989

Molecular genetic variation in the centromeric region of the X chromosome in three Drosophila ananassae populations. I. Contrasts between the vermilion and forked loci.

We have surveyed three natural populations of Drosophila ananassae for restriction map variation at the forked (f) and vermilion (v) loci, using 6-cutter restriction enzymes. Both loci are located in the centromeric region of the X chromosome. Two major conclusions can be drawn from the data. First, we found strong evidence for population subdivision, i.e., significant differences in the frequency distributions of polymorphisms and/or haplotypes between the Burma, India, and Brazil populations. Secondly, the pattern of DNA sequence variation between the two loci is unexpectedly different. The level of nucleotide variation in the v locus region is reduced (relative to f), especially in the Burma population. Furthermore, in contrast to v, we found no insertions/deletions larger than 700 bp and no significant linkage disequilibrium at f. The genetic differentiation among subpopulations can readily be attributed to restricted migration as the predominant evolutionary force. According to population genetics theory, the differences in DNA polymorphisms between the two loci are in qualitative agreement with the hypothesis that recombination is reduced in the v locus region ("centromere effect") but not at f. In order to test this hypothesis directly, we determined the cytogenetic positions of several loci in the centromeric region by in situ hybridization and found by comparison with the genetic map that recombination at v is indeed very low, much lower than at f.

Animals↗
PubMed1992

Reduced levels of DNA polymorphism and fixed between-population differences in the centromeric region of Drosophila ananassae.

We have estimated DNA sequence variation within and between two populations of Drosophila ananassae, using six-cutter restriction site variation at vermilion (v) and furrowed (fw). These two gene regions are located close to the centromere on the left and right X chromosome arms, respectively. In the fw region, no DNA polymorphism was detected within each population. In the v region, average heterozygosity per nucleotide was very low in both populations (pi = 0.0005 in the Burma population, and 0.0009 in the India population). These estimates are significantly lower than those from loci in more distal gene regions. The distribution of DNA polymorphisms between both populations was also striking. At fw, three fixed differences between the Burma and India populations were detected (two restriction site differences and one insertion/deletion of approximately 2 kb). At v, each DNA polymorphism in high frequency in the total sample was nearly fixed in one or the other population, although none of them reached complete fixation. The observed pattern of reduced variation within populations and fixed differences between populations appears to correlate with recombination rate. We conclude that recent hitchhiking associated with directional selection is the best explanation for this pattern. The data indicate that different selective sweeps have occurred in the two populations. The possible role of genetic hitchhiking in rapid population differentiation in gene regions of restricted recombination is discussed.

Animals↗