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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
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
Acceptability of Women Self-Sampling versus Clinician-Collected Samples for HPV DNA Testing: A Systematic Review

Morgan K, Azzani M, Khaing SL, Wong YL, Su TT

J Low Genit Tract Dis, 2019 Jul;23(3):193-199.
PMID: 30933030 DOI: 10.1097/LGT.0000000000000476

OBJECTIVES: Female self-sampling for human papillomavirus (HPV) DNA testing is an alternative screening method that can potentially increase cervical cancer screening coverage. This review addresses the acceptability of HPV DNA testing using self-sampling compared with conventional clinician-collected sampling. Barriers to and others factors associated with acceptability of either method were also examined.
METHODS: The following electronic resources were searched: Medline @EBSCOHOST(Medline), Embase, PubMed, and CINAHL databases. Manual searches were also conducted. The main outcome of interest was the acceptability of HPV DNA testing by self-sampling in comparison with clinician-collected sampling.
RESULTS: In total, 23 articles were included in this systematic review. The majority (19 studies) were quantitative intervention studies and 4 studies were qualitative observational studies. Eleven studies reported a preference for self-sampling by women compared with clinician-collected sampling (64.7%-93%). The remaining studies found that women preferred clinician-collected sampling because mainly of respondents' lack of confidence in their ability to complete self-sampling correctly. In most articles reviewed, the studied associated factors, such as demographic factors (age, marital status, and ethnicity), socioeconomic factors (income, education level), reproductive factors (condom use, number of children, current use of contraception, and number of partners), and habits (smoking status) were not found to be significantly associated with preference.
CONCLUSIONS: Both methods of sampling were found to be acceptable to women. Self-sampling is cost-effective and could increase the screening coverage among underscreened populations. However, more information about the quality, reliability, and accuracy of self-sampling is needed to increase women's confidence about using to this method.

Matched MeSH terms: DNA, Viral/isolation & purification*
Fulltext Sandwich-Type DNA Micro-Optode Based on Gold-Latex Spheres Label for Reflectance Dengue Virus Detection

Jeningsih, Tan LL, Ulianas A, Heng LY, Mazlan NF, Jamaluddin ND, et al.

Sensors (Basel), 2020 Mar 25;20(7).
PMID: 32218202 DOI: 10.3390/s20071820

A DNA micro-optode for dengue virus detection was developed based on the sandwich hybridization strategy of DNAs on succinimide-functionalized poly(n-butyl acrylate) (poly(nBA-NAS)) microspheres. Gold nanoparticles (AuNPs) with an average diameter of ~20 nm were synthesized using a centrifugation-based method and adsorbed on the submicrometer-sized polyelectrolyte-coated poly(styrene-co-acrylic acid) (PSA) latex particles via an electrostatic method. The AuNP-latex spheres were attached to the thiolated reporter probe (rDNA) by Au-thiol binding to functionalize as an optical gold-latex-rDNA label. The one-step sandwich hybridization recognition involved a pair of a DNA probe, i.e., capture probe (pDNA), and AuNP-PSA reporter label that flanked the target DNA (complementary DNA (cDNA)). The concentration of dengue virus cDNA was optically transduced by immobilized AuNP-PSA-rDNA conjugates as the DNA micro-optode exhibited a violet hue upon the DNA sandwich hybridization reaction, which could be monitored by a fiber-optic reflectance spectrophotometer at 637 nm. The optical genosensor showed a linear reflectance response over a wide cDNA concentration range from 1.0 × 10-21 M to 1.0 × 10-12 M cDNA (R2 = 0.9807) with a limit of detection (LOD) of 1 × 10-29 M. The DNA biosensor was reusable for three consecutive applications after regeneration with mild sodium hydroxide. The sandwich-type optical biosensor was well validated with a molecular reverse transcription polymerase chain reaction (RT-PCR) technique for screening of dengue virus in clinical samples, e.g., serum, urine, and saliva from dengue virus-infected patients under informed consent.

Matched MeSH terms: DNA, Viral/isolation & purification*
Encephalitis and retarded growth of chicks caused by Sitiawan virus, a new isolate belonging to the genus Flavivirus

Kono Y, Tsukamoto K, Abd Hamid M, Darus A, Lian TC, Sam LS, et al.

Am J Trop Med Hyg, 2001 5 19;63(1-2):94-101.
PMID: 11358004

A new virus named Sitiawan virus (SV) was isolated from sick broiler chicks in chicken embryos. The virus replicated well with cytopathogenic effect (CPE) in the chicken B-lymphocyte cell line LSCC-BK3. The virus was an enveloped RNA virus of approximately 41 nm in size with hemagglutinating activity (HA) to goose erythrocytes. It was cross-reactive with Japanese encephalitis virus (JEV), a member of flaviviruses by HA inhibition tests but not by cross-virus neutralization tests. The cDNA fragment of NS5 gene was amplified with primers corresponding to NS5 gene of flaviviruses. The nucleotide sequences were 92% homologous to Tembusu virus, a member of the mosquito-borne virus cluster of the genus Flavivirus. In cross-neutralization tests with Tembusu virus, antiserum to SV did not neutralize Tembusu virus, and antiserum to Tembusu virus neutralized more weakly to SV than against homologous virus. These results indicate that SV is a new virus which can be differentiated serologically from Tembusu virus but is otherwise similar with respect to nucleotide sequence. The virus causes encephalitis, growth retardation, and increased blood glucose levels in inoculated chicks.

Matched MeSH terms: DNA, Viral/isolation & purification
Nucleotide sequence of precore region of hepatitis B virus DNA in HBsAg-positive carriers in Malaysia

Ton SH, Iskandar K, Noriah R, Thanaletchimy N

Scand. J. Infect. Dis., 1996;28(6):543-8.
PMID: 9060053

As most published studies on precore mutants have been carried out on isolates from patients with liver diseases, and it is unclear whether HBsAg carriers with viraemia in the absence of HBeAg are also generally infected by such mutants, it was decided to sequence the precore region in some HBV-DNA isolated from HBsAg-positive carriers. Precore sequences of HBV-DNA from 43 HBsAg carriers in Malaysia were studied. Three HBV subtypes were identified according to the nucleotide sequence of the precore region. Most of the carriers were found to be infected by the subtype adr. Mutations were detected in the precore regions. The most common conserved mutation was a silent mutation involving conversion from T to C (CCT to CCC) at position 1858 at codon 15 (proline). It was found that 4/43 (9.3%) had a mutation at the penultimate codon where TGG was changed to TAG. All 4 isolates with the TAG mutation had nt T at position 1858. Of the 4 carriers who were infected by these mutant viruses, 2 were coinfected with the wild type, 1 was infected only by a variant with the mutation at position 1896, while another was infected by a variant with mutations at positions 1896 and 1899. Three of the 4 were anti-HBe positive while 1 was HBeAg positive. Alanine aminotransaminase activities in all 4 carriers were normal. This study therefore demonstrated that variants with stop codons at the penultimate codon could be found in asymptomatic carriers in Malaysia.

Matched MeSH terms: DNA, Viral/isolation & purification
Infectiousness of HBsAg carriers in Malaysia

Ton SH, Yeoh KS, Lim WC, Noriah R, Cheong SK, Thanaletchimy N

J Trop Med Hyg, 1995 Aug;98(4):277-80.
PMID: 7636926

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).

Matched MeSH terms: DNA, Viral/isolation & purification
Analytical performance of HPV assays on vaginal self-collected vs practitioner-collected cervical samples: the SCoPE study

Saville M, Hawkes D, Keung M, Ip E, Silvers J, Sultana F, et al.

J Clin Virol, 2020 06;127:104375.
PMID: 32361328 DOI: 10.1016/j.jcv.2020.104375

BACKGROUND: In the last decade, human papillomavirus (HPV) testing has been evaluated extensively for cervical screening, with studies finding increased sensitivity compared to cytology. Another advantage of HPV based-screening is the ability to test vaginal samples that can be collected by women themselves. Self-collection has the potential to extend cervical screening coverage by increasing participation rates, particularly among women who are under-screened or have never screened. This could have a significant impact on cervical cancer prevention, as the majority of invasive cervical cancer cases occur among under-screened women. Both the Netherlands and Australia have transitioned their national programs from cytology to HPV as the primary screening test and both countries include a pathway for self-collection.
OBJECTIVES: We evaluated the relative sensitivity for HPV detection of self-collection compared with practitioner-collected cervical specimens in the context of the Australian National Cervical Screening Program (NCSP).
STUDY DESIGN: 303 women aged ≥18 years attending a single tertiary referral centre took their own sample using a flocked-swab, and then had a practitioner-collected sample taken at colposcopy. All samples were tested at a single laboratory on the six PCR-based HPV assays which can be utilised in the NCSP; Roche cobas 4800 and cobas, Abbott RealTime, BD Onclarity, Cepheid Xpert, and Seegene Anyplex.
RESULTS: HPV16/18 results had high observed agreement between self- and practitioner-collected samples on all assays (range: 0.94-0.99), with good agreement for non-HPV16/18 oncogenic HPV types (range: 0.64-0.73).
CONCLUSIONS: Self-collection for HPV-based cervical screening shows good concordance and relative sensitivity when compared to practitionercollected samples across assays in the NCSP.

Matched MeSH terms: DNA, Viral/isolation & purification
Significant association of high-risk human papillomavirus (HPV) but not of p53 polymorphisms with oral squamous cell carcinomas in Malaysia

Saini R, Tang TH, Zain RB, Cheong SC, Musa KI, Saini D, et al.

J Cancer Res Clin Oncol, 2011 Feb;137(2):311-20.
PMID: 20419384 DOI: 10.1007/s00432-010-0886-8

PURPOSE: The purpose of this study was to evaluate the role of HPV and p53 polymorphisms in oral squamous cell carcinomas (OSCC) affecting Malaysian population.
METHODS: We analysed frozen samples from 105 OSCC as well as 105 oral specimens derived from healthy individuals. PCR assays targeting two regions of the virus were used. PCR amplification for the analysis of p53 codon 72 arginine/proline alleles was carried out in a separate reaction.
RESULTS: HPV DNA was detected in 51.4% OSCC samples, while 24.8% controls were found to be HPV positive. HPV was found to be significantly associated with OSCC (P

Matched MeSH terms: DNA, Viral/isolation & purification
Determination of a universal nucleic acid extraction procedure for PCR detection of gastroenteritis viruses in faecal specimens

Rasool NB, Monroe SS, Glass RI

J Virol Methods, 2002 Feb;100(1-2):1-16.
PMID: 11742648

Four nucleic acid extraction protocols were examined for their suitability for extraction of the ssRNA, dsRNA and dsDNA genomes of gastroenteritis viruses, for PCR detection. Protocol (A), employed specimen lysis with guanidinium thiocyanate, extraction with phenol-chloroform-isoamyl alcohol and nucleic acid purification by size-fractionated silica particles. Protocol (B), utilised specimen lysis with guanidinium thiocyanate and nucleic acid purification by silica, followed by phenol-chloroform-isoamyl alcohol extraction. Protocol (C), employed specimen lysis with guanidinium thiocyanate and nucleic acid purification by RNAID glass powder. Protocol (D), employed specimen lysis with sodium dodecyl sulphate, proteinase K digestion and extraction with phenol-chloroform-isoamyl alcohol. Of the four protocols, (B) appeared to be a suitable candidate 'universal' nucleic acid extraction procedure for PCR detection of different viral agents of gastroenteritis in a single nucleic acid extract of a faecal specimen, irrespective of genome composition. Omission of the phenol-chloroform extraction step did not affect negatively the ability of protocol (B) to allow PCR detection of gastroenteritis viruses in faecal specimens. PCR detection of NLVs, astroviruses, rotaviruses and adenoviruses, in single nucleic acid extracts of faecal specimens obtained from the field, confirmed the universality of the modified protocol (B). We propose the modified protocol (B) as a 'universal' nucleic acid extraction procedure, for monoplex PCR detection of gastroenteritis viruses in single nucleic acid extracts of faecal specimens and for development of multiplex PCR for their simultaneous detection.

Matched MeSH terms: DNA, Viral/isolation & purification*