Displaying publications 21 - 40 of 176 in total

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  1. Electrochemical DNA detection of hepatitis E virus genotype 3 using PbS quantum dot labelling
    Ngo DB, Chaibun T, Yin LS, Lertanantawong B, Surareungchai W
    Anal Bioanal Chem, 2021 Feb;413(4):1027-1037.
    PMID: 33236225 DOI: 10.1007/s00216-020-03061-1
    The aim of this study was to develop a highly specific electrochemical DNA sensor using functionalized lead sulphide (PbS) quantum dots for hepatitis E virus genotype 3 (HEV3) DNA target detection. Functionalized-PbS quantum dots (QDs) were used as an electrochemical label for the detection of HEV3-DNA target by the technique of square wave anodic stripping voltammetry (SWASV). The functionalized-PbS quantum dots were characterized by UV-vis, FTIR, XRD, TEM and zeta potential techniques. As-prepared, functionalized-PbS quantum dots have an average size of 4.15 ± 1.35 nm. The detection platform exhibited LOD and LOQ values of 1.23 fM and 2.11 fM, respectively. HEV3-DNA target spiked serum is also reported.Graphical abstract.
    Matched MeSH terms: DNA, Viral/blood*; DNA, Viral/genetics
  2. The distribution of hepatitis B virus genotypes in Thailand
    Louisirirotchanakul S, Olinger CM, Arunkaewchaemsri P, Poovorawan Y, Kanoksinsombat C, Thongme C, et al.
    J Med Virol, 2012 Oct;84(10):1541-7.
    PMID: 22930500 DOI: 10.1002/jmv.23363
    Phylogenetic analysis was performed on hepatitis B virus (HBV) strains obtained from 86 hepatitis B surface antigen (HBsAg) positive donors from Thailand originating throughout the country. Based on the S gene, 87.5% of strains were of genotype C while 10.5% were of genotype B, with all genotype B strains obtained from patients originating from the central or the south Thailand. No genotype B strains were found in the north of Thailand. Surprisingly, one patient was infected with a genotype H strain while another patient was infected with a genotype G strain. Complete genome sequencing and recombination analysis identified the latter as being a genotype G and C2 recombinant with the breakpoint around nucleotide position 700. The origin of the genotype G fragment was not identifiable while the genotype C2 fragment most likely came from strains circulating in Laos or Malaysia. The performance of different HBsAg diagnostic kits and HBV nucleic acid amplification technology (NAT) was evaluated. The genotype H and G/C2 recombination did not interfere with HBV detection.
    Matched MeSH terms: DNA, Viral/genetics; DNA, Viral/chemistry
  3. Fulltext Prevalence of human papillomavirus in abnormal cervical smears in Malaysian patients
    Sharifah NA, Seeni A, Nurismah MI, Clarence-Ko CH, Hatta AZ, Ho NP, et al.
    Asian Pac J Cancer Prev, 2009 Apr-Jun;10(2):303-6.
    PMID: 19537900
    Cervical cancer is the second most common female malignancy in Malaysia. Despite advances in treatment, the overall survival for this disease has not changed in the last decade. Infection by certain types of HPV is recognized as a causal and necessary factor for its development. This study was carried out to determine the prevalence of HPV infection in abnormal cervical smears in Malaysian patients using archival cervical smears retrieved from the Cytopathology Unit, Universiti Kebangsaan Malaysia Medical Centre (UKMMC) between the years 1992-1995. DNA was extracted from 38 abnormal smears comprising 25 intraepithelial lesions and 13 cervical carcinomas and 10 normal smears. Amplification of HPV genes was carried out using the polymerase chain reaction (PCR) technique. HPV genotypes were determined using direct sequencing and the results were compared to the database from Genebank. DNA was successfully extracted from all 48 cervical smears. High-risk HPV (HR-HPV) genotypes were detected in 95% of the abnormal smears. Eight high-risk oncogenic types were identified: 16, 18, 31, 51, 52, 56, 58 and 66. All (100%) cervical cancer smears showed presence of HR-HPV compared to 92% of the cervical intraepithelial lesions. Among the eight HR-HPV genotypes identified, HPV 16 and 52 were the commonest (23.7% each) HPV genotypes encountered and among the CIN lesions, HPV 16 (28%) was the most frequent. We conclude that HPV 16 is the most prevalent HPV genotype present in abnormal cervical smears in Malaysian patients, and that the use of archival material to assess the presence of HPV is potentially worthwhile, and can be utilized for longitudinal studies of HPV presence and persistence.
    Matched MeSH terms: DNA, Viral/analysis; DNA, Viral/genetics
  4. Molecular characterization of two distinct begomoviruses from Papaya in China
    Wang X, Xie Y, Zhou X
    Virus Genes, 2004 Dec;29(3):303-9.
    PMID: 15550769
    Six papaya samples showing downward leaf curling were collected in Guangdong and Guangxi provinces, China. The result of TAS-ELISA showed they were all infected by geminiviruses. Comparison of partial DNA-A sequences reveals that these virus isolates can be classified into two groups. Group I includes isolates G2, G4, G5, G28 and G29 from Guangxi province, while isolate GD2 from Guangdong province belongs to Group II. The complete DNA-A sequence of G2 and GD2 were characterized. Sequence comparisons showed that the DNA-A of G2 and GD2 were most closely related to that of Ageratum yellow vein China virus- [Hn2] and Ageratum yellow vein virus , respectively, with 83.4 and 75.2% nucleotide sequence identity, while DNA-A sequence between G2 and GD2 had only 73.4% sequence identity. The molecular data suggests that G2 and GD2 are two distinct begomoviruses, for which the name Papaya leaf curl China virus (PaLCuCNV) for G2 and Papaya leaf curl Guangdong virus (PaLCuGDV) for GD2 are proposed. Comparison of individual encoded proteins showed the coat protein of G2 and GD2 shared highest amino acid sequence identity (97.7 and 94.2%, respectively) with that of Pepper leaf curl virus -[Malaysia] (PepLCV-[MY]), suggesting the CP of these viruses may have identical ancestor.
    Matched MeSH terms: DNA, Viral/isolation & purification; DNA, Viral/chemistry
  5. Genetic diversity of chicken anemia virus following cell culture passaging in MSB-1 cells
    Hasmah MS, Omar AR, Wan KF, Hair-Bejo M, Aini I
    Acta Virol., 2004;48(2):85-9.
    PMID: 15462283
    It has been shown that a chicken anemia virus (CAV) isolates which had undergone 60 passages in MSB-1 cells (SMSC-1/P60, 3-1/P60) acquired 33-66 nucleotide substitutions at the coding region resulting in 13-16 amino acid changes as compared to the CAV isolates passaged only 5 times in MSB-1 cells (SMSC-1 and 3-1) (Chowdhury et al., Arch. Virol. 148, 2437-2448, 2003). In this study we found that a low CAV (BL-5) and a high CAV passage (BL-5/P90) differed by only 15 nucleotide substitutions resulting in 11 amino acid changes. Phylogenetic analysis based on VP1 also revealed that both isolates were close to each other but not to other CAV isolates from Malaysia, namely SMSC-1 and 3-1.
    Matched MeSH terms: DNA, Viral/isolation & purification; DNA, Viral/chemistry
  6. Abacá bunchy top virus, a new member of the genus Babuvirus (family Nanoviridae)
    Sharman M, Thomas JE, Skabo S, Holton TA
    Arch Virol, 2008;153(1):135-47.
    PMID: 17978886 DOI: 10.1007/s00705-007-1077-z
    Two isolates of a novel babuvirus causing "bunchy top" symptoms were characterised, one from abacá (Musa textilis) from the Philippines and one from banana (Musa sp.) from Sarawak (Malaysia). The name abacá bunchy top virus (ABTV) is proposed. Both isolates have a genome of six circular DNA components, each ca. 1.0-1.1 kb, analogous to those of isolates of Banana bunchy top virus (BBTV). However, unlike BBTV, both ABTV isolates lack an internal ORF in DNA-R, and the ORF in DNA-U3 found in some BBTV isolates is also absent. In all phylogenetic analyses of nanovirid isolates, ABTV and BBTV fall in the same clade, but on separate branches. However, ABTV and BBTV isolates shared only 79-81% amino acid sequence identity for the putative coat protein and 54-76% overall nucleotide sequence identity across all components. Stem-loop and major common regions were present in ABTV, but there was less than 60% identity with the major common region of BBTV. ABTV and BBTV were also shown to be serologically distinct, with only two out of ten BBTV-specific monoclonal antibodies reacting with ABTV. The two ABTV isolates may represent distinct strains of the species as they are less closely related to each other than are isolates of the two geographic subgroups (Asian and South Pacific) of BBTV.
    Matched MeSH terms: DNA, Viral/genetics; DNA, Viral/chemistry
  7. Fulltext The complete genome sequence of EC1-UPM, a novel N4-like bacteriophage that infects Escherichia coli O78:K80
    Gan HM, Sieo CC, Tang SG, Omar AR, Ho YW
    Virol J, 2013;10:308.
    PMID: 24134834 DOI: 10.1186/1743-422X-10-308
    Bacteriophage EC1-UPM is an N4-like bacteriophage which specifically infects Escherichia coli O78:K80, an avian pathogenic strain that causes colibacillosis in poultry. The complete genome sequence of bacteriophage EC1-UPM was analysed and compared with other closely related N4-like phage groups to assess their genetic similarities and differences.
    Matched MeSH terms: DNA, Viral/genetics*; DNA, Viral/chemistry*
  8. Fulltext Molecular characterisation of grouper iridovirus isolates from Peninsular Malaysia
    Hassan, M.D., Hazeri, M., Omar, A.R., Abba, Y., Allaudin, Z.N., Soltani, M., et al.
    Jurnal Veterinar Malaysia, 2017;29(1):1-6.
    MyJurnal
    Grouper Iriovirus (GIV) is one of the most devastating viral diseases of marine and cultured groupers worldwide. In the current study, 5 presumptive Malaysian GIV isolates were characterised through PCR amplification of the major capsid protein (MCP) gene and phylogenetic analysis of the sequences. The sequences from the five GIV isolates showed 100% homology with each other and a close relationship with grouper iridovirus isolate (GIV_Tn_352), which was clustered in group 1 together with King grouper iridovirus isolate (KGIV_Cy_346), Singapore grouper iridovirus (SGIV), and Crimson snapper iridovirus isolate (CSIV). The phylogenetic tree also showed different degree of relatedness with other Ranavirus strains which were obtained from the blast of GIV MCP gene in the NCBI database. This study confirmed the GIV isolates from Malaysia are related to other isolates that were reported previously.
    Matched MeSH terms: DNA, Viral
  9. Genetic analysis of saffold virus-Penang in relation to other newly discovered saffold viruses
    Voon K, Ng QM, Yu M, Wang LF, Chua KB
    Southeast Asian J Trop Med Public Health, 2012 Jul;43(4):917-26.
    PMID: 23077814
    Viruses in the family Picornaviridae are classified into nine genera. Within the family Picornaviridae, two species: Encephalomyocarditis virus and Theilovirus, are listed under the genus Cardiovirus. A novel Theilovirus, Saffold virus (SAFV), was first reported in 2007. Since then, numerous SAFV isolates have been detected around the world and genetic recombinations have been reported among them. In 2009, SAFV-Penang was isolated from a febrile child with influenza-like illness in Malaysia. SAFV-Penang is a genotype 3 SAFV. In this study we investigated the genome features of SAFV-Penang to exclude the possibility it is a recombinant variant. SAFV-Penang was found not to be a recombinant variant but to have three unique non-synonymous substitutions, alanine [A689], lysine [K708] and isoleucine [I724] in the VP1 protein.
    Matched MeSH terms: DNA, Viral
  10. In-silico discovery of inhibitors against human papillomavirus E1 protein
    Gunasinghe J, Hwang SS, Yam WK, Rahman T, Wezen XC
    J Biomol Struct Dyn, 2023;41(12):5583-5596.
    PMID: 35751129 DOI: 10.1080/07391102.2022.2091659
    High-risk (HR) Human papillomavirus (e.g. HPV16 and HPV18) causes approximately two-thirds of all cervical cancers in women. Although the first and second-generation vaccines confer some protection against individuals, there are no approved drugs to treat HR-HPV infections to-date. The HPV E1 protein is an attractive drug target because the protein is highly conserved across all HPV types and is crucial for the regulation of viral DNA replication. Hence, we used the Random Forest algorithm to construct a Quantitative-Structure Activity Relationship (QSAR) model to predict the potential inhibitors against the HPV E1 protein. Our QSAR classification model achieved an accuracy of 87.5%, area under the receiver operating characteristic curve of 1.00, and F-measure of 0.87 when evaluated using an external test set. We conducted a drug repurposing campaign by deploying the model to screen the Drugbank database. The top three compounds, namely Cinalukast, Lobeglitazone, and Efatutazone were analyzed for their cell membrane permeability, toxicity, and carcinogenicity. Finally, these three compounds were subjected to molecular docking and 200 ns-long Molecular Dynamics (MD) simulations. The predicted binding free energies for the candidates were calculated using the MM-GBSA method. The binding free energies for Cinalukast, Lobeglitazone, and Efatutazone were -37.84 kcal/mol, -25.30 kcal/mol, and -29.89 kcal/mol respectively. Therefore, we propose their chemical scaffolds for future rational design of E1 inhibitors.Communicated by Ramaswamy H. Sarma.
    Matched MeSH terms: DNA, Viral
  11. Identification and comparison of RCMV ALL 03 open reading frame (ORF) among several different strains of cytomegalovirus worldwide
    Balakrishnan KN, Abdullah AA, Bala J, Abba Y, Sarah SA, Jesse FFA, et al.
    Infect Genet Evol, 2017 10;54:81-90.
    PMID: 28642159 DOI: 10.1016/j.meegid.2017.06.020
    BACKGROUND: Rat cytomegalovirus ALL-03 (Malaysian strain) which was isolated from a placenta and uterus of a house rat, Rattus rattus diardii has the ability to cross the placenta and infecting the fetus. To further elucidate the pathogenesis of the Malaysian strain of Rat Cytomegalovirus ALL-03 (RCMV ALL-03), detailed analysis on the viral genome sequence is crucial.

    METHODS: Genome sequencing of RCMV ALL-03 was carried out in order to identify the open reading frame (ORF), homology comparison of ORF with other strains of CMV, phylogenetic analysis, classifying ORF with its corresponding conserved genes, and determination of functional proteins and grouping of gene families in order to obtain fundamental knowledge of the genome.

    RESULTS: The present study revealed a total of 123 Coding DNA sequences (CDS) from RCMV ALL-03 with 37 conserved ORF domains as with all herpesvirus genomes. All the CDS possess similar function with RCMV-England followed by RCMV-Berlin, RCMV-Maastricht, and Human CMV. The phylogenetic analysis of RCMV ALL-03 based on conserving genes of herpes virus showed that the Malaysian RCMV isolate is closest to RCMV-English and RCMV-Berlin strains, with 99% and 97% homology, respectively. Similarly, it also demonstrated an evolutionary relationship between RCMV ALL-03 and other strains of herpesviruses from all the three subfamilies. Interestingly, betaherpesvirus subfamily, which has been shown to be more closely related with gammaherpesviruses as compared to alphaherpesviruses, shares some of the functional ORFs. In addition, the arrangement of gene blocks for RCMV ALL-03, which was conserved among herpesvirus family members was also observed in the RCMV ALL-03 genome.

    CONCLUSION: Genomic analysis of RCMV ALL-03 provided an overall picture of the whole genome organization and it served as a good platform for further understanding on the divergence in the family of Herpesviridae.

    Matched MeSH terms: DNA, Viral/genetics
  12. Fulltext Real-time PCR tests to specifically detect IHHNV lineages and an IHHNV EVE integrated in the genome of Penaeus monodon
    Cowley JA, Rao M, Coman GJ
    Dis Aquat Organ, 2018 Jul 04;129(2):145-158.
    PMID: 29972375 DOI: 10.3354/dao03243
    Infectious hypodermal and hematopoietic necrosis virus (IHHNV) can cause mass mortalities in western blue shrimp Penaeus stylirostris, runt deformity syndrome in Pacific white shrimp P. vannamei and scalloped abdominal shell deformities in black tiger shrimp P. monodon. In P. monodon, however, PCR-based diagnosis of IHHNV can be complicated by the presence of a chromosome-integrated, non-replicating endogenous viral element (EVE). To facilitate high-throughput screening of P. monodon for IHHNV infection and/or EVE sequences, here we report real-time PCR tests designed to specifically detect IHHNV Lineage I, II and III but not EVE Type A sequences and vice versa. Using 108 dsDNA copies of plasmid (p)DNA controls containing either IHHNV or EVE-Type A sequences, both tests displayed absolute specificity. The IHHNV-q309 PCR reliably detected down to ≤10 copies of pDNA, at which levels a 309F/R PCR amplicon was just detectable, and the presence of an IHHNV-EVE sequence did not significantly impact its sensitivity. The IHHNV-qEVE PCR was similarly sensitive. Testing of batches of P. monodon clinical samples from Vietnam/Malaysia and Australia identified good diagnostic concordance between the IHHNV-q309 and 309F/R PCR tests. As expected for a sequence integrated into host chromosomal DNA, IHHNV-qEVE PCR Ct values were highly uniform among samples from shrimp in which an EVE was present. The highly specific and sensitive IHHNV-q309 and IHHNV-qEVE real-time PCR tests described here should prove useful for selecting broodstock free of IHHNV infection and in maintaining breeding populations of P. monodon specific pathogen free for IHHNV, and if desired, also free of IHHNV-EVE sequences.
    Matched MeSH terms: DNA, Viral/genetics*
  13. Advancements in electrochemical DNA sensor for detection of human papilloma virus - A review
    Rasouli E, Shahnavaz Z, Basirun WJ, Rezayi M, Avan A, Ghayour-Mobarhan M, et al.
    Anal Biochem, 2018 09 01;556:136-144.
    PMID: 29981317 DOI: 10.1016/j.ab.2018.07.002
    Human papillomavirus (HPV) is one of the most common sexually transmitted disease, transmitted through intimate skin contact or mucosal membrane. The HPV virus consists of a double-stranded circular DNA and the role of HPV virus in cervical cancer has been studied extensively. Thus it is critical to develop rapid identification method for early detection of the virus. A portable biosensing device could give rapid and reliable results for the identification and quantitative determination of the virus. The fabrication of electrochemical biosensors is one of the current techniques utilized to achieve this aim. In such electrochemical biosensors, a single-strand DNA is immobilized onto an electrically conducting surface and the changes in electrical parameters due to the hybridization on the electrode surface are measured. This review covers the recent developments in electrochemical DNA biosensors for the detection of HPV virus. Due to the several advantages of electrochemical DNA biosensors, their applications have witnessed an increased interest and research focus nowadays.
    Matched MeSH terms: DNA, Viral/analysis*
  14. Strategies for the Construction of Cassava Brown Streak Disease Viral Infectious Clones
    Duff-Farrier CRA, Mbanzibwa DR, Nanyiti S, Bunawan H, Pablo-Rodriguez JL, Tomlinson KR, et al.
    Mol Biotechnol, 2019 Feb;61(2):93-101.
    PMID: 30484144 DOI: 10.1007/s12033-018-0139-7
    Cassava brown streak disease (CBSD) has major impacts on yield and quality of the tuberous roots of cassava in Eastern and Central Arica. At least two Potyviridae species cause the disease: Cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV). Cloned viral genome sequences known as infectious clones (ICs) have been important in the study of other viruses, both as a means of standardising infectious material and characterising viral gene function. IC construction is often technically challenging for Potyviridae due to sequence instability in E. coli. Here, we evaluate three methods for the construction of infectious clones for CBSD. Whilst a simple IC for in vitro transcription was made for UCBSV isolate 'Kikombe', such an approach failed to deliver full-length clones for CBSV isolates 'Nampula' or 'Tanza', necessitating more complex approaches for their construction. The ICs successfully generated symptomatic infection in the model host N. benthamiana and in the natural host cassava. This shows that whilst generating ICs for CBSV is still a technical challenge, a structured approach, evaluating both in vitro and in planta transcription systems should successfully deliver ICs, allowing further study into the symptomology and virulence factors in this important disease complex.
    Matched MeSH terms: DNA, Viral/genetics
  15. A case-control study of cervix cancer in Singapore
    Cuzick J, De Stavola B, McCance D, Ho TH, Tan G, Cheng H, et al.
    Br. J. Cancer, 1989 Aug;60(2):238-43.
    PMID: 2548559
    Cervix cancer is about twice as common in Asia as in the Western world and its incidence varies among different Asian ethnic groups. A study based in Singapore, the population of which comprises Chinese, Indians and Malaysians, offers the opportunity to evaluate whether the same risk factors are important in this part of the world as in the West. A total of 135 cases and an equal number of controls were interviewed and details concerning reproductive and sexual history, smoking, hygiene, socio-economic status and education were collected. Seventy-three cases had invasive cancer while 62 had micro-invasive disease or CIN III. The most important risk factors were parity and number of sexual partners. Smoking was rare in cases and controls and did not appear to be an important determinant of risk. Of the socio-economic factors, education appeared most predictive and lowered the risk. Age at first intercourse was strongly correlated with education (positively) and parity (negatively), but not with number of sexual partners. Biopsies were available for HPV DNA analysis in 38 cases and 37% were positive, mostly for HPV type 16. All these factors gave similar risks in invasive and preinvasive disease.
    Matched MeSH terms: DNA, Viral/analysis
  16. Target DNA detection of human papilloma virus-16 E7 gene by capture-target-reporter sandwich on interdigitated electrode sensor
    Lin J, Gopinath SCB, Lakshmipriya T, Chen Y, Yuan WR, Yang M
    Int J Biol Macromol, 2019 Dec 01;141:564-569.
    PMID: 31493451 DOI: 10.1016/j.ijbiomac.2019.09.012
    Human papilloma virus (HPV) affects predominantly the genital area, which includes vagina, cervix, penis, vulva scrotum, rectum and anus. Among 100 types of HPV, 14 types are considered to cause the risky cancer. The gene HPV-16 E7 is responsible for the development of cancer with the infected women. Earlier identification of this gene sequence avoids the cancer progression. The targeted HPV-16 E7 sequence was sandwiched by capture and reporter sequences on the carbodiimidazole-modified interdigitated electrode (IDE) surface. Target sequence at 100 f. was paired to the capture sequence immobilized on IDE sensing surface. To this surface, different concentrations of reporter sequence with and without gold rod (GNR) were evaluated. In both cases the detections were attained 1 aM by the reporter sequence pairing and with GNR increments in current were found. This enhancement was found to be 1000 folds, considering the condition was revealed in the absence of reporter. This sandwich detection strategy of capture-target-reporter sequences for HPV-16 detection on the IDE sensing surface helps to diagnose the association of cervical cancer.
    Matched MeSH terms: DNA, Viral/analysis*
  17. Asian consensus recommendations on optimizing the diagnosis and initiation of treatment of hepatitis B virus infection in resource-limited settings
    Gane EJ, Charlton MR, Mohamed R, Sollano JD, Tun KS, Pham TTT, et al.
    J Viral Hepat, 2020 05;27(5):466-475.
    PMID: 31785182 DOI: 10.1111/jvh.13244
    Asia has an intermediate-to-high prevalence of and high morbidity and mortality from hepatitis B virus (HBV) infection. Optimization of diagnosis and initiation of treatment is one of the crucial strategies for lowering disease burden in this region. Therefore, a panel of 24 experts from 10 Asian countries convened, and reviewed the literature, to develop consensus guidance on diagnosis and initiation of treatment of HBV infection in resource-limited Asian settings. The panel proposed 11 recommendations related to diagnosis, pre-treatment assessment, and indications of therapy of HBV infection, and management of HBV-infected patients with co-infections. In resource-limited Asian settings, testing for hepatitis B surface antigen may be considered as the primary test for diagnosis of HBV infection. Pre-treatment assessments should include tests for complete blood count, liver and renal function, hepatitis B e-antigen (HBeAg), anti-HBe, HBV DNA, co-infection markers and assessment of severity of liver disease. Noninvasive tests such as AST-to-platelet ratio index, fibrosis score 4 or transient elastography may be used as alternatives to liver biopsy for assessing disease severity. Considering the high burden of HBV infection in Asia, the panel adopted an aggressive approach, and recommended initiation of antiviral therapy in all HBV-infected, compensated or decompensated cirrhotic individuals with detectable HBV DNA levels, regardless of HBeAg status or alanine transaminase levels. The panel also developed a simple algorithm for guiding the initiation of treatment in noncirrhotic, HBV-infected individuals. The recommendations proposed herein, may help guide clinicians, to optimize the diagnosis and improvise the treatment rates for HBV infection in Asia.
    Matched MeSH terms: DNA, Viral/blood
  18. Fulltext Human papillomavirus DNA and virus-encoded antigens in cervical carcinoma
    Padmanathan A, Yadav M, Gregory AR, Kumar S, Norhanum AW
    Med J Malaysia, 1997 Jun;52(2):108-16.
    PMID: 10968067
    The present study was undertaken to evaluate the prevalence of HPV in formalin-fixed, paraffin-embedded cervical carcinoma tissues using PCR followed by non-radioactive Southern hybridization with type-specific oligonucleotides for HPV 16 and 18. In addition, the tissue sections were immunohistochemically screened with two monoclonal antibodies, for expression of HPV 16 L1 and HPV 18 E6 proteins. A total of 57 of 60 cervical carcinomas (95.0%) were found with HPV using both techniques. HPV 16 and HPV 18 were present in equal proportions. Results of both DNA hybridization and immunohistochemistry were in agreement for the majority of the cases. HPV 16 and 18 DNA and virus-encoded antigens, L1 and E6 were found highly prevalent in these cervical carcinomas. Due to the high prevalence of HPV with cervical carcinoma in Malaysia, the implementation of routine diagnosis for the virus in cervical biopsies would be clinically useful.
    Matched MeSH terms: DNA, Viral/analysis*
  19. Geographical distribution of the human polyomavirus JC virus type A and B and isolation of a new type from Ghana
    Guo J, Kitamura T, Ebihara H, Sugimoto C, Kunitake T, Takehisa J, et al.
    J Gen Virol, 1996 May;77 ( Pt 5):919-27.
    PMID: 8609488
    The JC polyomavirus (JCV) is ubiquitous in humans infecting children asymptomatically, then persisting in renal tissue. Since JCV DNA can be readily isolated from urine, it should be a useful tool with which to study the evolution of DNA viruses in humans. We showed that JCV DNA from the urine of Japanese, Taiwanese, Dutch and German patients can be classified into A and B types, based upon restriction fragment length polymorphisms (RFLPs). This work was extended in the present study. We established multiple JCV DNA clones from the UK, Spain, Italy, Sweden, South Korea, People's Republic of China, Malaysia, Indonesia, Mongolia, India, Sri Lanka, Saudi Arabia, Ethiopia, Kenya, Zambia, South Africa and Ghana. Using type-specific RFLPs, most clones except the four clones from Ghana were classified as either type A or B. We constructed a molecular phylogenetic tree for the Ghanaian clones and several representative type A and B clones. According to the phylogenetic tree, the Ghanaian clones constituted a major new group, tentatively named type C. From the findings presented here and elsewhere, the following conclusions were drawn: (i) type A is prevalent only in Europe; (ii) type B is found mainly in Asia and Africa; and (iii) type C is localized to part of Africa. Our findings should help to clarify how JCV evolved in humans.
    Matched MeSH terms: DNA, Viral/chemistry
  20. Fulltext Enterovirus A71 DNA-Launched Infectious Clone as a Robust Reverse Genetic Tool
    Tan CW, Tee HK, Lee MH, Sam IC, Chan YF
    PLoS One, 2016;11(9):e0162771.
    PMID: 27617744 DOI: 10.1371/journal.pone.0162771
    Enterovirus A71 (EV-A71) causes major outbreaks of hand, foot and mouth disease, and is occasionally associated with neurological complications and death in children. Reverse genetics is widely used in the field of virology for functional study of viral genes. For EV-A71, such tools are limited to clones that are transcriptionally controlled by T7/SP6 bacteriophage promoter. This is often time-consuming and expensive. Here, we describe the development of infectious plasmid DNA-based EV-A71 clones, for which EV-A71 genome expression is under transcriptional control by the CMV-intermediate early promoter and SV40 transcriptional-termination signal. Transfection of this EV-A71 infectious DNA produces good virus yield similar to in vitro-transcribed EV-A71 infectious RNA, 6.4 and 5.8 log10PFU/ml, respectively. Infectious plasmid with enhanced green fluorescence protein and Nano luciferase reporter genes also produced good virus titers, with 4.3 and 5.0 log10 PFU/ml, respectively. Another infectious plasmid with both CMV and T7 promoters was also developed for easy manipulation of in vitro transcription or direct plasmid transfection. Transfection with either dual-promoter infectious plasmid DNA or infectious RNA derived from this dual-promoter clone produced infectious viral particles. Incorporation of hepatitis delta virus ribozyme, which yields precise 3' ends of the DNA-launched EV-A71 genomic transcripts, increased infectious viral production. In contrast, the incorporation of hammerhead ribozyme in the DNA-launched EV-A71 resulted in lower virus yield, but improved the virus titers for T7 promoter-derived infectious RNA. This study describes rapid and robust reverse genetic tools for EV-A71.
    Matched MeSH terms: DNA, Viral/genetics*
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