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Enzyme polymorphism of the malaria vector, An. balabacensis (Diptera: Culicidae) revisited--why sample natural populations?

Hii JL, Chew M, Vun YS, Nasir M, Chang MS

Southeast Asian J. Trop. Med. Public Health, 1988 Dec;19(4):689-701.
PMID: 3238482

Two separate observations from recent electrophoretic studies of the systematics and population genetics of laboratory-reared populations which had a long history of colonization in various laboratories, were found to be inconsistent with the present study which used wild-caught populations from East Malaysia. Reanalysis of the two data sets generally indicated a low amount of genetic variation in laboratory colonies. The latter is characterized by higher frequency of monomorphic loci, low average heterozygosity values and, in one extreme case, no variability at two loci. However, natural populations of An. balabacensis and An. leucosphyrus showed more protein variability by the use of polyacrylamide gel electrophoresis. Since laboratory-maintained mosquitoes are genetically and phenotypically different from those in the field, results of laboratory studies on the systematics and population genetics of Anopheles species complexes may be biased.

Matched MeSH terms: Genetic Variation
Fulltext A review on induced mutagenesis of Stevia rebaudiana Bertoni

Chiew, Miao Si, Lai, Kok Song, Sobri Hussein, Janna Ong Abdullah

The Pertanika Journal of Scholarly Research Reviews, 2016;2(3):77-85.
MyJurnal

Stevia rebaudiana Bertoni in the Asteraceae family is commercially valuable and cultivated throughout the world due to the great demand for its steviol glycosides (SGs) contents particularly rebaudioside A. Previous studies confirmed that maximal content of SGs in stevia was achieved at or just before flowering, and delayed flowering with long days provide longer duration for steviol glycosides accumulation. However, there is no suitable stevia variety to be cultivated in Malaysia due to her short day length. Mutation induction, including gamma irradiation, had been shown to be useful for generating genetic variations as well as developing new plant varieties from which desired mutants were successfully selected. The use of mutagens, both physical and chemical, has helped in creating mutants that expressed the selected desirable traits. This paper presents some selected essential data available in extant scientific studies on stevia with the focus on application of gamma irradiation on stevia. Both established achievements and recent publications of gamma radiation on stevia were reviewed. Emphasis is on the exceptional potential of stevia through induced mutation approach especially by using gamma rays.

Matched MeSH terms: Genetic Variation
Fulltext Breast Cancer Risk Genes - Association Analysis in More than 113,000 Women

Breast Cancer Association Consortium, Dorling L, Carvalho S, Allen J, González-Neira A, Luccarini C, et al.

N Engl J Med, 2021 02 04;384(5):428-439.
PMID: 33471991 DOI: 10.1056/NEJMoa1913948

BACKGROUND: Genetic testing for breast cancer susceptibility is widely used, but for many genes, evidence of an association with breast cancer is weak, underlying risk estimates are imprecise, and reliable subtype-specific risk estimates are lacking.
METHODS: We used a panel of 34 putative susceptibility genes to perform sequencing on samples from 60,466 women with breast cancer and 53,461 controls. In separate analyses for protein-truncating variants and rare missense variants in these genes, we estimated odds ratios for breast cancer overall and tumor subtypes. We evaluated missense-variant associations according to domain and classification of pathogenicity.
RESULTS: Protein-truncating variants in 5 genes (ATM, BRCA1, BRCA2, CHEK2, and PALB2) were associated with a risk of breast cancer overall with a P value of less than 0.0001. Protein-truncating variants in 4 other genes (BARD1, RAD51C, RAD51D, and TP53) were associated with a risk of breast cancer overall with a P value of less than 0.05 and a Bayesian false-discovery probability of less than 0.05. For protein-truncating variants in 19 of the remaining 25 genes, the upper limit of the 95% confidence interval of the odds ratio for breast cancer overall was less than 2.0. For protein-truncating variants in ATM and CHEK2, odds ratios were higher for estrogen receptor (ER)-positive disease than for ER-negative disease; for protein-truncating variants in BARD1, BRCA1, BRCA2, PALB2, RAD51C, and RAD51D, odds ratios were higher for ER-negative disease than for ER-positive disease. Rare missense variants (in aggregate) in ATM, CHEK2, and TP53 were associated with a risk of breast cancer overall with a P value of less than 0.001. For BRCA1, BRCA2, and TP53, missense variants (in aggregate) that would be classified as pathogenic according to standard criteria were associated with a risk of breast cancer overall, with the risk being similar to that of protein-truncating variants.
CONCLUSIONS: The results of this study define the genes that are most clinically useful for inclusion on panels for the prediction of breast cancer risk, as well as provide estimates of the risks associated with protein-truncating variants, to guide genetic counseling. (Funded by European Union Horizon 2020 programs and others.).

Matched MeSH terms: Genetic Variation*
Fulltext Prevalence of melanocortin receptor 4 (MC4R) V103I gene variant and its association with obesity among the Kampar Health Clinic cohort, Perak, Malaysia

Chua HN, Fan SH, Say YH

Med J Malaysia, 2012 Apr;67(2):234-5.
PMID: 22822657 MyJurnal

This study investigated the prevalence of the Melanocortin receptor 4 (MC4R) V1031 gene variant and its association with obesity among a cohort of 254 patients (101 males; 118 obese) attending the Kampar Health Clinic. Genotyping revealed the mutated I allele frequency of 0.02, no homozygous mutated (II), and similar distribution of V and I alleles across BMI groups, genders and ethnic groups. No significant difference was found for the means of anthropometric measurements between alleles. Prevalence of this gene variant among the Malaysian cohort was similar with previous populations (2-4% of mutated allele carrier), but was not associated with obesity.

Matched MeSH terms: Genetic Variation
25S rDNA genotyping and multi-locus sequence typing of Candida albicans of pathogenic and commensal origins in the Klang Valley, Malaysia

Illyaaseen Z, Ngeow YF, Yap SF, Ng HF

Malays J Pathol, 2021 Apr;43(1):55-61.
PMID: 33903306

Candida albicans is an important opportunistic fungal pathogen capable of causing fatal systemic infections in humans. Presently in Malaysia, there is little information available on the genetic diversity of this organism and trends in behavioural characteristics. In this project, three genotyping methods: 25S rDNA genotyping, Alternative Lengthening of Telomerase (ALT) sequence typing and Multi-Locus Sequence Typing (MLST) were applied to study the genetic diversity of strains from infected hospital in-patients and asymptomatic individuals in the community. The results showed that, with the 25S rDNA genotyping, as in other parts of the world, the most common genotype was type A which accounted for approximately 70% of the 111 isolates tested. Further typing with the ALT sequence showed type 3 to be the most common in the isolates tested. MLST analysis revealed many possibly novel sequence types, as well as a statistically significant association between pathogenicity and a group of closely related isolates, most of which were from hospital samples. Further work on genotypes associated with enhanced virulence will help to clarify the value of genotyping for clinical and epidemiological investigations.

Matched MeSH terms: Genetic Variation
Fulltext High Genetic Diversity among Stenotrophomonas maltophilia Isolates from Single Hospital: Nosocomial Outbreaks or Genotypic Profile Changes during Subcultures

Güvenir M, Otlu B, Tunc E, Aktas E, Suer K

Malays J Med Sci, 2018 Mar;25(2):40-49.
PMID: 30918454 DOI: 10.21315/mjms2018.25.2.5

Background: Stenotrophomonas maltophilia is a non-fermentative gram-negative bacillus which is widely recognised as an important nosocomial pathogen causing pneumonia, blood-stream, wound and urinary tract infections, particularly in immunosuppressed patients. The aim of this study was to evaluate a nosocomial outbreak of by S. maltophilia in an intensive care unit of a tertiary hospital and evaluate unexpected multiclonality.
Methods: A total of 11 isolates from respiratory cultures in intensive care unit of a 24 bed tertiary hospital obtained over a one months period and one isolate obtained from the nebuliser during environmental screening were investigated. The bacteria were identified by Phoenix 100 system. The clonal relatedness was evaluated by PFGE and semi-automated repetitive sequence-based PCR. Genotyping tests were repeated for 10 serial subcultures.
Results: PFGE and DiversiLab yielded 10 genotypic profiles for 12 isolates. Four to eight different genotypes were observed from 10 subcultures of the same isolate.
Conclusion: We conclude that, high genetic diversity and supposed multiclonal appearance of the outbreak isolates may be due to changing profiles during subcultures most probably depending on hypermutation.

Matched MeSH terms: Genetic Variation
Fulltext Different clinical outcomes of Entamoeba histolytica in Malaysia: does genetic diversity exist?

Anuar TS, Al-Mekhlafi HM, Abdul Ghani MK, Azreen SN, Salleh FM, Ghazali N, et al.

Korean J Parasitol, 2013 Apr;51(2):231-6.
PMID: 23710093 DOI: 10.3347/kjp.2013.51.2.231

The present study was conducted to investigate the clinical outcomes of Entamoeba histolytica infection in symptomatic and asymptomatic Orang Asli (aborigine) communities in Malaysia. Examination was performed on 500 stool samples obtained from Orang Asli communities in 3 different states using formalin-ether concentration, trichrome staining, and single-round PCR techniques. Out of 500 stool samples, single infection of E. histolytica, Entamoeba dispar, and Entamoeba moshkovskii was identified in 3.2%, 13.4%, and 1%, respectively. In addition, 10 samples had mixed infections with E. histolytica and E. dispar. Six samples containing E. dispar were also positive for E. moshkovskii, and only 2 samples had E. histolytica in association with E. dispar and E. moshkovskii. Seventeen E. histolytica-positive samples were from symptomatic subjects, whereas the remaining 11 samples came from asymptomatic subjects. These findings suggest a predominant distribution of pathogenic potential of E. histolytica strains in this community. Therefore, further studies on genotyping of E. histolytica is required, to find out association between E. histolytica genotype and the outcome of the infection.

Matched MeSH terms: Genetic Variation*
Fulltext Genetic Diversity and Clustering of the Rhoptry Associated Protein-1 of Plasmodium knowlesi from Peninsular Malaysia and Malaysian Borneo

Azlan UW, Lau YL, Fong MY

Korean J Parasitol, 2022 Dec;60(6):393-400.
PMID: 36588415 DOI: 10.3347/kjp.2022.60.6.393

Human infection with simian malaria Plasmodium knowlesi is a cause for concern in Southeast Asian countries, especially in Malaysia. A previous study on Peninsular Malaysia P. knowlesi rhoptry associated protein-1 (PkRAP1) gene has discovered the existence of dimorphism. In this study, genetic analysis of PkRAP1 in a larger number of P. knowlesi samples from Malaysian Borneo was conducted. The PkRAP1 of these P. knowlesi isolates was PCR-amplified and sequenced. The newly obtained PkRAP1 gene sequences (n = 34) were combined with those from the previous study (n = 26) and analysed for polymorphism and natural selection. Sequence analysis revealed a higher genetic diversity of PkRAP1 compared to the previous study. Exon II of the gene had higher diversity (π = 0.0172) than exon I (π = 0.0128). The diversity of the total coding region (π = 0.0167) was much higher than those of RAP1 orthologues such as PfRAP-1 (π = 0.0041) and PvRAP1 (π = 0.00088). Z-test results indicated that the gene was under purifying selection. Phylogenetic tree and haplotype network showed distinct clustering of Peninsular Malaysia and Malaysian Borneo PkRAP1 haplotypes. This geographical-based clustering of PkRAP1 haplotypes provides further evidence of the dimorphism of the gene and possible existence of 2 distinct P. knowlesi lineages in Malaysia.

Matched MeSH terms: Genetic Variation*
Fulltext Differential prevalence of Plasmodium infections and cryptic Plasmodium knowlesi malaria in humans in Thailand

Putaporntip C, Hongsrimuang T, Seethamchai S, Kobasa T, Limkittikul K, Cui L, et al.

J Infect Dis, 2009 Apr 15;199(8):1143-50.
PMID: 19284284 DOI: 10.1086/597414

BACKGROUND: A case of human infection with Plasmodium knowlesi has been recently discovered in Thailand. To investigate the prevalence of this malaria species, a molecular-based survey was performed.
METHODS: Blood samples from 1874 patients were tested for Plasmodium species by microscopy and nested polymerase chain reaction. P. knowlesi was characterized by sequencing the merozoite surface protein 1 gene (msp-1).
RESULTS: Of all Plasmodium species identified, P. falciparum, P. vivax, P. malariae, P. ovale, and P. knowlesi contributed 43.52%, 68.08%, 1.37%, 1.03%, and 0.57%, respectively. Mixed-species infections were more common in northwestern and southwestern regions bordering Myanmar (23%-24%) than in eastern and southern areas (3%-5%). In northwestern and southwestern regions, mixed-species infections had a significantly higher prevalence in dry than in rainy seasons (P < .001). P. knowlesi was found in 10 patients, mostly from southern and southwestern areas-9 were coinfected with either P. falciparum or P. vivax. Most of the P. knowlesi Thai isolates were more closely related to isolates from macaques than to isolates from Sarawak patients. The msp-1 sequences of isolates from the same area of endemicity differed and possessed novel sequences, indicating genetic polymorphism in P. knowlesi infecting humans.
CONCLUSIONS: This survey highlights the widespread distribution of P. knowlesi in Thailand, albeit at low prevalence and mostly occurring as cryptic infections.

Matched MeSH terms: Genetic Variation
Fragmented population structure of plasmodium falciparum in a region of declining endemicity

Anthony TG, Conway DJ, Cox-Singh J, Matusop A, Ratnam S, Shamsul S, et al.

J Infect Dis, 2005 May 1;191(9):1558-64.
PMID: 15809916

The population genetic structure of Plasmodium falciparum differs between endemic regions, but the characteristics of a population recently fragmented by effective malaria control have been unknown.

Matched MeSH terms: Genetic Variation
Fulltext Phylogeographical pattern and evolutionary history of an important Peninsular Malaysian timber species, Neobalanocarpus heimii (Dipterocarpaceae)

Tnah LH, Lee SL, Ng KK, Lee CT, Bhassu S, Othman RY

J Hered, 2013 Jan-Feb;104(1):115-26.
PMID: 23132907 DOI: 10.1093/jhered/ess076

Tectonic movements, climatic oscillations, and marine transgressions during the Cenozoic have had a dramatic effect on the biota of the tropical rain forest. This study aims to reveal the phylogeography and evolutionary history of a Peninsular Malaysian endemic tropical timber species, Neobalanocarpus heimii (Dipterocarpaceae). A total of 32 natural populations of N. heimii, with 8 samples from each population were investigated. Fifteen haplotypes were identified from five noncoding chloroplast DNA (cpDNA) regions. Overall, two major genealogical cpDNA lineages of N. heimii were elucidated: a widespread southern and a northern region. The species is predicted to have survived in multiple refugia during climatic oscillations: the northwestern region (R1), the northeastern region (R2), and the southern region (R3). These putative glacial refugia exhibited higher levels of genetic diversity, population differentiation, and the presence of unique haplotypes. Recolonization of refugia R1 and R2 could have first expanded into the northern region and migrated both northeastwards and northwestwards. Meanwhile, recolonization of N. heimii throughout the southern region could have commenced from refugia R3 and migrated toward the northeast and northwest, respectively. The populations of Tersang, Pasir Raja, and Rotan Tunggal exhibited remarkably high haplotype diversity, which could have been the contact zones that have received an admixture of gene pools from the northerly and also southerly regions. As a whole, the populations of N. heimii derived from glacial refugia and contact zones should be considered in the conservation strategies in order to safeguard the long-term survival of the species.

Matched MeSH terms: Genetic Variation*
Fulltext Genetic diversity and distinctiveness of the proboscis monkeys (Nasalis larvatus) of the Klias Peninsula, Sabah, Malaysia

Munshi-South J, Bernard H

J Hered, 2011 May-Jun;102(3):342-6.
PMID: 21414965 DOI: 10.1093/jhered/esr013

In this study, we sequenced a partial segment of the mitochondrial control region from 21 proboscis monkeys of the Klias peninsula, the last large population remaining on the west coast of Sabah, Malaysia. Our results showed that this population retains substantial genetic variation, and subpopulations from different river systems in the central and southern portions of the Klias share multiple haplotypes. We also compared our data with previously generated sequences from 2 eastern populations of proboscis monkeys in Sabah and found little evidence of regional genetic structure. Based on these results, we argue that conservation efforts should focus on restoring connectivity between central and southern Klias peninsula proboscis monkeys and discuss future analyses needed to better understand the mitochondrial structure of proboscis monkeys in Sabah.

Matched MeSH terms: Genetic Variation*
Genetic Structure and Diversity Among Historic and Modern Populations of the Sumatran Rhinoceros (Dicerorhinus sumatrensis)

Brandt JR, van Coeverden de Groot PJ, Witt KE, Engelbrektsson PK, Helgen KM, Malhi RS, et al.

J Hered, 2018 06 27;109(5):553-565.
PMID: 29684146 DOI: 10.1093/jhered/esy019

The Sumatran rhinoceros (Dicerorhinus sumatrensis), once widespread across Southeast Asia, now consists of as few as 30 individuals within Sumatra and Borneo. To aid in conservation planning, we sequenced 218 bp of control region mitochondrial (mt) DNA, identifying 17 distinct mitochondrial haplotypes across modern (N = 13) and museum (N = 26) samples. Museum specimens from Laos and Myanmar had divergent mtDNA, consistent with the placement of western mainland rhinos into the distinct subspecies D. s. lasiotis (presumed extinct). Haplotypes from Bornean rhinos were highly diverse, but dissimilar from those of other regions, supporting the distinctiveness of the subspecies D. s. harrissoni. Rhinos from Sumatra and Peninsular Malaysia shared mtDNA haplotypes, consistent with their traditional placement into a single subspecies D. s sumatrensis. Modern samples of D. s. sumatrensis were genotyped at 18 microsatellite loci. Rhinos within Sumatra formed 2 sub-populations, likely separated by the Barisan Mountains, though with only modest genetic differentiation between them. There are so few remaining Sumatran rhinoceros that separate management strategies for subspecies or subpopulations may not be viable, while each surviving rhino pedigree is likely to retain alleles found in no other individuals. Given the low population size and low reproductive potential of Sumatran rhinos, rapid genetic erosion is inevitable, though an under-appreciated concern is the potential for fixation of harmful genetic variants. Both concerns underscore 2 overriding priorities for the species: 1) translocation of wild rhinos to ex situ facilities, and 2) collection and storage of gametes and cell lines from every surviving captive and wild individual.

Matched MeSH terms: Genetic Variation
Comparative Phylogeography of Forest-Dependent Mammals Reveals Paleo-Forest Corridors throughout Sundaland

Mason VC, Helgen KM, Murphy WJ

J Hered, 2019 03 05;110(2):158-172.
PMID: 30247638 DOI: 10.1093/jhered/esy046

The evolutionary history of the colugo, a gliding arboreal mammal distributed throughout Sundaland, was influenced by the location of and connections between forest habitats. By comparing colugo phylogenetic patterns, species ecology, sample distributions, and times of divergence to those of other Sundaic taxa with different life-history traits and dispersal capabilities, we inferred the probable distribution of paleo-forest corridors and their influence on observed biogeographic patterns. We identified a consistent pattern of early diversification between east and west Bornean lineages in colugos, lesser mouse deer, and Sunda pangolins, but not in greater mouse deer. This deep east-west split within Borneo has not been commonly described in mammals. Colugos on West Borneo diverged from colugos in Peninsular Malaysia and Sumatra in the late Pliocene, however most other mammalian populations distributed across these same geographic regions diverged from a common ancestor more recently in the Pleistocene. Low genetic divergence between colugos on large landmasses and their neighboring satellite islands indicated that past forest distributions were recently much larger than present refugial distributions. Our analysis of colugo evolutionary history reconstructs Borneo as the most likely ancestral area of origin for Sunda colugos, and suggests that forests present during the middle Pliocene within the Sunda Shelf were more evergreen and contiguous, while forests were more fragmented, transient, seasonal, or with lower density canopies in the Pleistocene.

Matched MeSH terms: Genetic Variation
Genetic Diversity and Demographic History of an Upper Hill Dipterocarp (Shorea platyclados): Implications for Conservation

Ng CH, Lee SL, Tnah LH, Ng KKS, Lee CT, Diway B, et al.

J Hered, 2019 12 17;110(7):844-856.
PMID: 31554011 DOI: 10.1093/jhered/esz052

Southeast Asian rainforests at upper hill elevations are increasingly vulnerable to degradation because most lowland forest areas have been converted to different land uses. As such, understanding the genetics of upper hill species is becoming more crucial for their future management and conservation. Shorea platyclados is an important, widespread upper hill dipterocarp in Malaysia. To elucidate the genetic structure of S. platyclados and ultimately provide guidelines for a conservation strategy for this species, we carried out a comprehensive study of the genetic diversity and demographic history of S. platyclados. Twenty-seven populations of S. platyclados across its range in Malaysia were genotyped at 15 polymorphic microsatellite loci and sequenced at seven noncoding chloroplast DNA (cpDNA) regions. A total of 303 alleles were derived from the microsatellite loci, and 29 haplotypes were identified based on 2892 bp of concatenated cpDNA sequences. The populations showed moderately high genetic diversity (mean HE = 0.680 for microsatellite gene diversity and HT = 0.650 for total haplotype diversity) and low genetic differentiation (FST = 0.060). Bayesian clustering divided the studied populations into two groups corresponding to western and eastern Malaysia. Bottleneck analysis did not detect any recent bottleneck events. Extended Bayesian skyline analyses showed a model of constant size for the past population history of this species. Based on our findings, priority areas for in situ and ex situ conservation and a minimum population size are recommended for the sustainable utilization of S. platyclados.

Matched MeSH terms: Genetic Variation*
Sequence changes in six variants of rice tungro bacilliform virus and their phylogenetic relationships

Cabauatan PQ, Melcher U, Ishikawa K, Omura T, Hibino H, Koganezawa H, et al.

J Gen Virol, 1999 Aug;80 ( Pt 8):2229-37.
PMID: 10466823

The DNA of three biological variants, G1, Ic and G2, which originated from the same greenhouse isolate of rice tungro bacilliform virus (RTBV) at the International Rice Research Institute (IRRI), was cloned and sequenced. Comparison of the sequences revealed small differences in genome sizes. The variants were between 95 and 99% identical at the nucleotide and amino acid levels. Alignment of the three genome sequences with those of three published RTBV sequences (Phi-1, Phi-2 and Phi-3) revealed numerous nucleotide substitutions and some insertions and deletions. The published RTBV sequences originated from the same greenhouse isolate at IRRI 20, 11 and 9 years ago. All open reading frames (ORFs) and known functional domains were conserved across the six variants. The cysteine-rich region of ORF3 showed the greatest variation. When the six DNA sequences from IRRI were compared with that of an isolate from Malaysia (Serdang), similar changes were observed in the cysteine-rich region in addition to other nucleotide substitutions and deletions across the genome. The aligned nucleotide sequences of the IRRI variants and Serdang were used to analyse phylogenetic relationships by the bootstrapped parsimony, distance and maximum-likelihood methods. The isolates clustered in three groups: Serdang alone; Ic and G1; and Phi-1, Phi-2, Phi-3 and G2. The distribution of phylogenetically informative residues in the IRRI sequences shared with the Serdang sequence and the differing tree topologies for segments of the genome suggested that recombination, as well as substitutions and insertions or deletions, has played a role in the evolution of RTBV variants. The significance and implications of these evolutionary forces are discussed in comparison with badnaviruses and caulimoviruses.

Matched MeSH terms: Genetic Variation
Genome structure of Sagiyama virus and its relatedness to other alphaviruses

Shirako Y, Yamaguchi Y

J Gen Virol, 2000 May;81(Pt 5):1353-60.
PMID: 10769079

Sagiyama virus (SAG) is a member of the genus Alphavirus in the family Togaviridae, isolated in Japan from mosquitoes in 1956. We determined the complete nucleotide sequence of the SAG genomic RNA from the original stock virus which formed a mixture of plaques with different sizes, and that from a full-length cDNA clone, pSAG2, infectious RNA transcripts from which formed uniform large plaques on BHK-21 cells. The SAG genome was 11698 nt in length exclusive of the 3' poly(A) tail. Between the complete nucleotide sequences of the full-length cDNA clone, pSAG2, and the consensus sequence from the original stock virus, there were nine amino acid differences; two each in nsP1, nsP2 and E1, and three in E2, some of which may be responsible for plaque phenotypic variants in the original virus stock. SAG was most closely related to Ross River virus among other alphaviruses fully sequenced, with amino acid sequence identities of 86% in the nonstructural proteins and of 83% in the structural proteins. The 3' terminal 280 nt region of SAG was 82% identical to that of Barmah Forest virus, which was otherwise not closely related to SAG. Comparison of the nucleotide sequence of SAG with partial nucleotide sequences of Getah virus (GET), which was originally isolated in Malaysia in 1955 and is closely related to SAG in serology and in biology, showed near identity between the two viruses, suggesting that SAG is a strain of GET.

Matched MeSH terms: Genetic Variation
Genetic variation of Japanese encephalitis virus in nature

Chen WR, Tesh RB, Rico-Hesse R

J Gen Virol, 1990 Dec;71 ( Pt 12):2915-22.
PMID: 2273391

Forty-six strains of Japanese encephalitis (JE) virus from a variety of geographic areas in Asia were examined by primer-extension sequencing of the RNA template. A 240 nucleotide sequence from the pre-M gene region was selected for study because it provided sufficient information for determining genetic relationships among the virus isolates. Using 12% divergence as a cutoff point for virus relationships, the 46 isolates fell into three distinct genotypic groups. One genotypic group consisted of JE virus isolates from northern Thailand and Cambodia. A second group was composed of isolates from southern Thailand, Malaysia, Sarawak and Indonesia. The remainder of the isolates, from Japan, China, Taiwan, the Philippines, Sri Lanka, India and Nepal, made up a third group. The implications of these findings in relation to the epidemiology of JE are discussed. Results of this study demonstrate that the comparison of short nucleotide sequences can provide insight into JE virus evolution, transmission and, possibly, pathogenesis.

Matched MeSH terms: Genetic Variation*
Fulltext Geographical, genetic and functional diversity of antiretroviral host factor TRIMCyp in cynomolgus macaque (Macaca fascicularis)

Saito A, Kono K, Nomaguchi M, Yasutomi Y, Adachi A, Shioda T, et al.

J Gen Virol, 2012 Mar;93(Pt 3):594-602.
PMID: 22113010 DOI: 10.1099/vir.0.038075-0

The antiretroviral factor tripartite motif protein 5 (TRIM5) gene-derived isoform (TRIMCyp) has been found in at least three species of Old World monkey: rhesus (Macaca mulatta), pig-tailed (Macaca nemestrina) and cynomolgus (Macaca fascicularis) macaques. Although the frequency of TRIMCyp has been well studied in rhesus and pig-tailed macaques, the frequency and prevalence of TRIMCyp in cynomolgus macaques remain to be definitively elucidated. Here, the geographical and genetic diversity of TRIM5α/TRIMCyp in cynomolgus macaques was studied in comparison with their anti-lentiviral activity. It was found that the frequency of TRIMCyp in a population in the Philippines was significantly higher than those in Indonesian and Malaysian populations. Major and minor haplotypes of cynomolgus macaque TRIMCyp with single nucleotide polymorphisms in the cyclophilin A domain were also found. The functional significance of the polymorphism in TRIMCyp was examined, and it was demonstrated that the major haplotype of TRIMCyp suppressed human immunodeficiency virus type 1 (HIV-1) but not HIV-2, whilst the minor haplotype of TRIMCyp suppressed HIV-2 but not HIV-1. The major haplotype of TRIMCyp did not restrict a monkey-tropic HIV-1 clone, NL-DT5R, which contains a capsid with the simian immunodeficiency virus-derived loop between α-helices 4 and 5 and the entire vif gene. These results indicate that polymorphisms of TRIMCyp affect its anti-lentiviral activity. Overall, the results of this study will help our understanding of the genetic background of cynomolgus macaque TRIMCyp, as well as the host factors composing species barriers of primate lentiviruses.

Matched MeSH terms: Genetic Variation*
Comparative PCR-based fingerprinting of Vibrio cholerae isolated in Malaysia

Shuan Ju Teh C, Thong KL, Osawa R, Heng Chua K

J Gen Appl Microbiol, 2011;57(1):19-26.
PMID: 21478644

Vibrio cholerae, the causative agent of cholera, is endemic in many parts of the world, especially in countries poor in resources. Molecular subtyping of V. cholerae is useful to trace the regional spread of a clone or multidrug-resistant strains during outbreaks of cholera. Current available PCR-based fingerprinting methods such as Random Amplified Polymorphic DNA (RAPD)-PCR, Enterobacterial Repetitive Intergenic Consensus Sequence (ERIC)-PCR, and Repetitive Extragenic Palindromic (REP)-PCR were used to subtype V. cholerae. However, there are problems for inter-laboratory comparison as these PCR methods have their own limitations especially when different PCR methods have been used for molecular typing. In this study, a Vibrio cholerae Repeats-PCR (VCR-PCR) approach which targets the genetic polymorphism of the integron island of Vibrios was used and compared with other PCR-based fingerprinting methods in subtyping. Forty-three V. cholerae of different serogroups from various sources were tested. The PCR-fingerprinting approaches were evaluated on typeability, reproducibility, stability and discriminatory power. Overall, Malaysian non-O1/non-O139 V. cholerae were more diverse than O1 strains. Four non-O1/non-O139 strains were closely related with O1 strains. The O139 strain in this study shared similarity with strains of both O1 and non-O1/non-O139 serogroups. ERIC-PCR was the most discriminative approach (D value = 0.996). VCR-PCR was useful in discriminating non-O1/non-O139 strains. RAPD-PCR and REP-PCR were less suitable for efficient subtyping purposes as they were not reproducible and lacked stability. The combination of the ERIC-PCR and VCR-PCR may overcome the inadequacy of any one approach and hence provide more informative data.

Matched MeSH terms: Genetic Variation

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