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Sequence and phylogenetic analysis of the VP2 gene of very virulent infectious bursal disease virus isolates

Hoque MM, Omar AR, Hair-Bejo M, Aini I

J. Biochem. Mol. Biol. Biophys., 2002 Apr;6(2):93-9.
PMID: 12186763

Previously we have shown that very virulent infectious bursal disease viruses (vvIBDV) that are SspI, TaqI and StyI positive (92/04, 97/61 and 94/B551) but not SspI and TaqI positive and StyI negative (94/273) cause high mortality, up to 80% in specific-pathogen-free chickens with significant damage of the bursal as well as nonbursal tissues. In this study, we sequenced the VP2 gene (1351 bp) of the 92/04, 94/273 and 94/B551 and compared them with other IBDV strains. All the isolates have the unique amino acid residues at positions 222A, 256I, 294I and 299S found in other vvIBDV strains. The deduced VP2 amino acids encoded by 92/04 is identical to the vvIBDV strains from Israel (IBDVKS), Japan (OKYM) and Europe (UK661), whereas the 94/273 and 94/B551 isolates have one to three amino acid substitutions. The 94/273 has two amino acid substitutions at positions 254 G to S and at 270 A to E that have not been reported before from vvIBDV strains. The 94/B551 also has one amino acid substitution at position 300 E to S, which is uncommon among other vvIBDV strains. However, phylogenetic analysis suggested that the isolates are very close to each other and all of them may have derived from the same origin as vvIBDV strains isolated from China, Japan and Europe. Even though antigenic index analysis of the 94/273 and 94/B551 indicated that the isolates are unique compared to other IBDV strains, their antigenic variation remain to be determined by monoclonal antibody study.

Matched MeSH terms: DNA, Viral/genetics
Genomic variations among wildtype and mutant strains of pseudorabies virus

Zeenathul NA, Mohd-Azmi ML, Ali AS, Aini I, Sheik-Omar AR, Abdul-Rahim AM, et al.

Rev. Argent. Microbiol., 2002 Jan-Mar;34(1):7-14.
PMID: 11942085

Both wild-type virulent and mutant strains of pseudorabies virus (PrV) were used in this study. Mutants used were derived from the plaque purified strain PrVmAIP. A total of six drug resistant mutants, three bromodeoxyuridine (BUdR) resistant and three iododeoxyuridine (IUdR) resistant, respectively, were isolated and passaged in chicken embryo fibroblast (CEF) cells. The DNA of these PrVs were compared with the wild-type isolates by means of the restriction fragment pattern (RFP) findings produced with Bam HI, Kpn I, Hind III and Bgl II restriction enzymes (RE). Compared to the wild-type PrVs (PrV-VBA1-parental strain of PrVmAIP; PrV-VBA2; PrV-VBA3), the RFP of PrVmAIP showed the presence of mutations within the RE sites studied. Both PrV-VBA1 and PrV-VBA2 appeared to be closely related but their RFPs differed from PrV-VBA3. Significant differences either in the number, size or migrations of the DNA fragments could also be detected in the BUdR resistant strains. Even though different features of cytopathic effect (GPE) were observed in the IUdR resistant PrVs, the RFP findings remained identical. The PrVs studied showed considerable differences from the reference PrV (PrV-CD).

Matched MeSH terms: DNA, Viral/genetics*
Iridovirus disease in two ornamental tropical freshwater fishes: African lampeye and dwarf gourami

Sudthongkong C, Miyata M, Miyazaki T

Dis Aquat Organ, 2002 Apr 5;48(3):163-73.
PMID: 12033703

Many species of ornamental freshwater fishes are imported into Japan from all over the world. We found African lampeye Aplocheilichthys normani and dwarf gourami Colisa lalia suffering from an iridovirus infection just after being imported by tropical fish wholesalers from Singapore. African lampeye were cultured on the Indonesian Island of Sumatra and dwarf gourami were cultured in Malaysia before export. Diseased fishes displayed distinct histopathological signs of iridovirus infection: systemic appearance of inclusion body-bearing cells, and necrosis of splenocytes and hematopoietic cells. Electron microscopy revealed viral particles (African lampeye:180 to 200 nm in edge to edge diameter; dwarf gourami: 140 to 150 nm in diameter) in an inclusion body within the cytoplasm of inclusion body-bearing cells as well as in the cytoplasm of necrotized cells. Experimental infection with an iridovirus isolate from African lampeye (ALIV) revealed pathogenicity of ALIV to African lampeye and pearl gourami Trichogaster leeri. Polymerase chain reaction (PCR) products from ALIV and an iridovirus isolate from dwarf gourami (DGIV) using iridovirus-specific primers were indistinguishable. The nucleotide sequence of PCR products derived from ALIV (696 base pairs) and DGIV (701 base pairs) had 95.3% identity. These results indicate that ALIV and DGIV have a single origin.

Matched MeSH terms: DNA, Viral/chemistry
Feline leukemia virus in owned cats in Southeast Asia and Taiwan

Capozza P, Lorusso E, Colella V, Thibault JC, Tan DY, Tronel JP, et al.

Vet Microbiol, 2021 Mar;254:109008.
PMID: 33582484 DOI: 10.1016/j.vetmic.2021.109008

Feline leukaemia virus (FeLV) is a retrovirus associated with fatal disease in cats with infection in its progressive form. Although there are numerous reports on the occurrence of FeLV in the feline population worldwide, there is a paucity of data in Asia. In this study, we assessed the circulation of FeLV by ELISA and nested PCR in cats from different countries in Southeast Asia (i.e., Thailand, Malaysia, Singapore, Philippines, Indonesia and Vietnam) and Taiwan during 2017-2018. Forty-seven cats were positive to FeLV by antigen or provirus detection, but 32 samples were considered truly positive on the basis of positive molecular testing. Frequency of occurrence of FeLV proviral DNA ranged from 0% (0/43 positive samples) in Indonesia to 18.5% (22/119 positive samples) in Thailand. A statistically significant association (p < 0.05) was found between country of cats origin, age, lifestyle, abnormal oral mucosa, and FeLV molecular positive results. In-depth studies are needed in other countries in Southeast Asia to elucidate the mosaic of knowledge about FeLV epidemiology.

Matched MeSH terms: DNA, Viral/genetics
Clinical significance of plasma Epstein-Barr Virus DNA loads in a large cohort of Malaysian patients with nasopharyngeal carcinoma

Chai SJ, Pua KC, Saleh A, Yap YY, Lim PV, Subramaniam SK, et al.

J Clin Virol, 2012 Sep;55(1):34-9.
PMID: 22739102 DOI: 10.1016/j.jcv.2012.05.017

Nasopharyngeal carcinoma (NPC) is an Epstein-Barr Virus (EBV)-associated cancer that is the fifth most common cancer in Malaysia. Early and accurate diagnoses are critical for patient prognosis. Unfortunately, early detection of NPC is still a challenge and the cost of more accurate imaging protocols is prohibitive in developing countries like Malaysia.

Matched MeSH terms: DNA, Viral/blood*
Fulltext Prevalence and viral load of oncogenic human papillomavirus (HPV) in pterygia in multi-ethnic patients in the Malay Peninsula

Chong PP, Tung CH, Rahman NA, Yajima M, Chin FW, Yeng CL, et al.

Acta Ophthalmol, 2014 Nov;92(7):e569-79.
PMID: 25043991 DOI: 10.1111/aos.12427

The aim of the study was to determine the prevalence of human papillomavirus (HPV) in primary and recurrent pterygia samples collected from different ethnic groups in the equatorial Malay Peninsula.

Matched MeSH terms: DNA, Viral/analysis
Detection of human papillomavirus DNA in routine cervical scraping samples: use for a national cervical cancer screening program in a developing nation

Othman N, Othman NH

Asian Pac J Cancer Prev, 2014;15(5):2245-9.
PMID: 24716964

BACKGROUND: Human papillomavirus is a well-established cause of the development of a variety of epithelial lesions in the cervix. However, as yet, incorporation of HPV testing into cervical cancer screening either as an adjunct or stand alone test is limited due to its cost. We therefore here ascertained the presence and type specificity of human papilloma virus (HPV) DNA in routine cervical scrapings.
MATERIALS AND METHODS: Cervical scrapings were collected from women attending clinics for routine Pap smear screening. HPV-DNA was detected by PCR using MY09/11 and GP5+/GP6+ primer sets and genotyping was accomplished by cycle-sequencing.
RESULTS: A total of 635 women were recruited into the study with mean ± SD age of 43 ± 10.5 years. Of these 92.6% (588/635) were reported as within normal limits (WNL) on cytology. The presence of HPV infection detected by nested MY/GP+-PCR was 4.4% (28/635). The overall prevalence of high-risk HPV (HR-HPV) in abnormal Pap smears was 53.8% (7/13). HPVs were also seen in 3.1% (18/588) of smears reported as WNL by cytology and 5.9% (2/34) in smears unsatisfactory for evaluation.
CONCLUSIONS: The overall percentage of HPV positivity in routine cervical screening samples is comparable with abnormal findings in cytology. Conventional Pap smear 'missed' a few samples. Since HPV testing is expensive, our results may provide valuable information for strategising implementation of effective cervical cancer screening in a country with limited resources like Malaysia. If Pap smear coverage could be improved, HPV testing could be used as an adjunct method on cases with ambiguous diagnoses.

Matched MeSH terms: DNA, Viral/genetics*
Fulltext Detection and characterization of chicken anemia virus from commercial broiler breeder chickens

Hailemariam Z, Omar AR, Hair-Bejo M, Giap TC

Virol J, 2008;5:128.
PMID: 18954433 DOI: 10.1186/1743-422X-5-128

Chicken anemia virus (CAV) is the causative agent of chicken infectious anemia (CIA). Study on the type of CAV isolates present and their genetic diversity, transmission to their progeny and level of protection afforded in the breeder farms is lacking in Malaysia. Hence, the present study was aimed to detect CAV from commercial broiler breeder farms and characterize CAV positive samples based on sequence and phylogenetic analysis of partial VP1 gene.

Matched MeSH terms: DNA, Viral/genetics
The prevalence and significance of high-risk human papillomavirus DNA test in southern Malaysia and Singapore

Tay SK, Tay YK

Aust N Z J Obstet Gynaecol, 2009 Jun;49(3):323-7.
PMID: 19566569 DOI: 10.1111/j.1479-828X.2009.01000.x

To investigate the prevalence of high-risk human papillomavirus (HPV) and its associated cytological abnormalities among women attending cervical screening clinics in southern Malaysia and Singapore.

Matched MeSH terms: DNA, Viral/analysis*
Feline parvovirus infection in an Asian palm civet (Paradoxurus hermaphroditus)

Demeter Z, Gál J, Palade EA, Rusvai M

Vet Rec, 2009 Feb 14;164(7):213-6.
PMID: 19218594
Matched MeSH terms: DNA, Viral/chemistry
Detection of Epstein-Barr virus in lower gastrointestinal tract lymphomas: a study in Malaysian patients

Yunos AM, Jaafar H, Idris FM, Kaur G, Mabruk MJ

Mol Diagn Ther, 2006;10(4):251-6.
PMID: 16884329

Many studies in the literature have shown that Epstein-Barr virus (EBV) is associated with several human lymphoid and epithelial malignancies. However, the prevalence of EBV in non-Hodgkin lymphoma (NHL) of the lower gastrointestinal (GI) tract has not been fully elucidated.

Matched MeSH terms: DNA, Viral/analysis
Fulltext Evaluation of plasma Epstein-Barr virus DNA load as a prognostic marker for nasopharyngeal carcinoma

Tan EL, Looi LM, Sam CK

Singapore Med J, 2006 Sep;47(9):803-7.
PMID: 16924363

Nasopharyngeal carcinoma (NPC) is an important cancer in Malaysia and is one of the major causes of cancer mortality in this country. This study evaluates the diagnostic and prognostic values in the quantitative relationship between the cell-free Epstein-Barr virus (EBV) deoxyribonucleic acid (DNA) load and the tumour burden.

Matched MeSH terms: DNA, Viral/blood*
High-titred neutralizing antibodies to human enterovirus 71 preferentially bind to the N-terminal portion of the capsid protein VP1

Tan CS, Cardosa MJ

Arch Virol, 2007;152(6):1069-73.
PMID: 17318736

Human enterovirus 71 has emerged as an important pathogen of children in the Asia Pacific region, and it may be important to consider the development of a vaccine against this virus. Human cord serum was used as a source of neutralizing antibodies to determine whether the N- or C-terminal half of the VP1 capsid protein was more likely to harbour neutralizing determinants. Cord sera from 205 individuals were tested for neutralizing antibodies against human enterovirus 71 in an indirect ELISA against recombinant VP1 antigen as well as the N- and C-terminal portions of VP1 antigen. High-titred human neutralizing antibodies were significantly more reactive with the N-terminal half of VP1 than weak or negative sera. The N-terminal half of human enterovirus 71 is likely to have important neutralizing antibody determinants and should be investigated further in vaccine development efforts.

Matched MeSH terms: DNA, Viral/genetics
Molecular characterization of infectious bursal disease virus isolates from Nepal based on hypervariable region of VP2 gene

Sharma K, Hair-Bejo M, Omar AR, Aini I

Acta Virol., 2005;49(1):59-64.
PMID: 15929400

Two Infectious bursal disease virus (IBDV) isolates, NP1SSH and NP2K were obtained from a severe infectious bursal disease (IBD) outbreak in Nepal in 2002. The hypervariable (HV) region of VP2 gene (1326 bp) of the isolates was generated by RT-PCR and sequenced. The obtained nucleotide sequences were compared with those of twenty other IBDV isolates/strains. Phylogenetic analysis based on this comparison revealed that NP1SSH and NP2K clustered with very virulent (vv) IBDV strains of serotype 1. In contrast, classical, Australian classical and attenuated strains of serotype 1 and avirulent IBDV strains of serotype 2 formed a different cluster. The deduced amino acid sequences of the two isolates showed a 98.3% identity with each other and 97.1% and 98.3% identities, respectively with very virulent IBDV (vvIBDV) isolates/strains. Three amino acids substitutions at positions 300 (E-->A), 308 (I-->F) and 334 (A-->P) within the HV region were common for both the isolates. The amino acids substitutions at positions 27 (S-->T), 28 (I-->T), 31 (D-->A), 36 (H-->Y), 135 (E-->G), 223 (G-->S), 225 (V-->I), 351 (L-->I), 352 (V-->E) and 399 (I-->S) for NP1SSH and at position 438 (I-->S) for NP2K were unique and differed from other IBDV isolates/strains. NP1SSH and NP2K showed highest similarity (97.8%) with the BD399 strain from Bangladesh as compared with other vvIBDV isolates/strains. We conclude that the NP1SSH and NP2K isolates of IBDV from Nepal represent vvIBDV of serotype 1.

Matched MeSH terms: DNA, Viral/chemistry
White spot syndrome virus isolates of tiger shrimp Penaeus monodon (Fabricious) in India are similar to exotic isolates as revealed by polymerase chain reaction and electron microscopy

Mishra SS, Shekhar MS

Indian J Exp Biol, 2005 Jul;43(7):654-61.
PMID: 16053274

Microbiological analysis of samples collected from cases of white spot disease outbreaks in cultured shrimp in different farms located in three regions along East Coast of India viz. Chidambram (Tamil Nadu), Nellore (Andhra Pradesh) and Balasore (Orissa), revealed presence of Vibrio alginolyticus, Vibrio parahaemolyticus, and Aeromonas spp. but experimental infection trials in Penaeus monodon with these isolates did not induce any acute mortality or formation of white spots on carapace. Infection trials using filtered tissue extracts by oral and injection method induced mortality in healthy P. monodon with all samples and 100% mortality was noted by the end of 7 day post-inoculation. Histopathological analysis demonstrated degenerated cells characterized by hypertrophied nuclei in gills, hepatopancreas and lymphoid organ with presence of intranuclear basophilic or eosino-basophilic bodies in tubular cells and intercellular spaces. Analysis of samples using 3 different primer sets as used by other for detection of white spot syndrome virus (WSSV) generated 643, 1447 and 520bp amplified DNA products in all samples except in one instance. Variable size virions with mean size in the range of 110 x 320 +/- 20 nm were observed under electron microscope. It could be concluded that the viral isolates in India involved with white spot syndrome in cultured shrimp are similar to RV-PJ and SEMBV in Japan, WSBV in Taiwan and WSSV in Malaysia, Indonesia, Thailand, China and Japan.

Matched MeSH terms: DNA, Viral/genetics
Comparative analysis of viral RNA and apoptotic cells in bursae following infection with infectious bursal disease virus

Kong LL, Omar AR, Hair-Bejo M, Aini I, Seow HF

Comp Immunol Microbiol Infect Dis, 2004 Nov;27(6):433-43.
PMID: 15325516

Specific-pathogen-free (SPF) chickens infected with very virulent (vv) infectious bursal disease virus (IBDV) UPM94/273 developed lower pathogenicity compared to UPM97/61. Sequence analysis indicated that UPM94/273 is an exceptional vvIBDV. In this study, a SYBR Green I based real-time reverse transcriptase reaction assay was developed to measure viral RNA in the bursae of SPF chickens infected with IBDV. Specificity of the amplified products was confirmed by melting temperature analysis. A linear relationship was observed between the amount of input viral RNA and the threshold values for IBDV-specific product over five log10 dilutions. The viral RNA level following infection with UPM94/273 was significantly higher at day 1 and 2 post-inoculation (p.i.) compared to UPM97/61 infected chickens. However, chickens infected with UPM97/61 had significantly higher numbers of bursal cells undergoing apoptosis compared to UPM94/273 infected chickens. In both groups, the number of apoptotic cells and viral RNA levels peak at day 3 p.i. This study indicates that UPM97/61 and UPM94/273 have different efficiency of replication and percentage of apoptotic cells in bursae during the acute phase of IBDV infection.

Matched MeSH terms: DNA, Viral/genetics
Molecular characterization of serotype A foot-and-mouth disease viruses circulating in Vietnam in 2009

Le VP, Nguyen T, Lee KN, Ko YJ, Lee HS, Nguyen VC, et al.

Vet Microbiol, 2010 Jul 29;144(1-2):58-66.
PMID: 20097490 DOI: 10.1016/j.vetmic.2009.12.033

Foot-and-mouth disease (FMD) is a major cause of endemic outbreaks in Vietnam in recent years. In this work, six serotype A foot-and-mouth disease viruses (FMDV), collected from endemic outbreaks during January and February of 2009 in four different provinces in Vietnam, were genetically characterized for their complete genome sequences. Genetic analysis based on the complete viral genome sequence indicated that they were closely related to each other and shared 99.0-99.8% amino acid (aa) identity. Genetic and deduced aa analysis of the capsid coding gene VP1 showed that the six Vietnamese strains were all classified into the genotype IX from a total of 10 major genotypes worldwide, sharing 98.1-100% aa identity each other. They were most closely related to the type A strains recently isolated in Laos (A/LAO/36/2003, A/LAO/1/2006, A/LAO/6/2006, A/LAO/7/2006, and A/LAO/8/2006), Thailand (A/TAI/2/1997 and A/TAI/118/1987), and Malaysia (A/MAY/2/2002), sharing 88.3-95.5% nucleotide (nt) identities. In contrast, Vietnamese type A strains showed low nt identities with the two old type A FMDVs, isolated in 1960 in Thailand (a15thailand iso43) and in 1975 in the Philippines (aphilippines iso50), ranging from 77.3 to 80.9% nt identity. A multiple alignment based on the deduced amino acid sequences of the capsid VP1 coding gene of type A FMDV revealed three amino acid substitutions between Vietnamese strains and the strains of other Southeast Asian countries (Laos, Thailand, Malaysia, and the Philippines). Alanine was replaced by valine at residue 24, asparagine by arginine at residue 85, and serine by threonine at residue 196. Furthermore, type A FMDV strains recently isolated in Vietnam, Laos, Thailand, and Malaysia all have one amino acid deletion at residue 140 of the capsid VP1 protein compared with the two old type A FMDV strains from Thailand and the Philippines as well as most other type A representatives worldwide. This article is the first to report on the comprehensive genetic characterization of type A FMDV circulating in Vietnam.

Matched MeSH terms: DNA, Viral/genetics
Fulltext Peginterferon alfa-2b in the treatment of Chinese patients with HBeAg-positive chronic hepatitis B: a randomized trial

Cheng J, Wang Y, Hou J, Luo D, Xie Q, Ning Q, et al.

J Clin Virol, 2014 Dec;61(4):509-16.
PMID: 25200354 DOI: 10.1016/j.jcv.2014.08.008

In mainland China, peginterferon (PEG-IFN) alfa-2b 1.0μg/kg/wk for 24 weeks is the approved treatment for HBeAg-positive chronic hepatitis B.

Matched MeSH terms: DNA, Viral/blood
Fulltext Isolated hepatitis B core antibody positive among vaccinated cohort in Malaysia

Hudu SA, Malik YA, Niazlin MT, Harmal NS, Alshrari AS, Sekawi Z

Ann Saudi Med, 2013;33(6):591-4.
PMID: 24413864 DOI: 10.5144/0256-4947.2013.591

BACKGROUND AND OBJECTIVES: Hepatitis B core antibodies (anti-HBc) are detected in almost every patient with previous exposure to hepatitis B virus (HBV). However, with this marker alone, one cannot understand the activity of the disease; therefore, this study aimed to identify the implication of isolated hepatitis B core antibody and evaluate the effect of hepatitis B vaccine booster in isolated anti-HBc among adults who received the HBV vaccine as infants.
DESIGN AND SETTINGS: A prospective cohort study of vaccinated undergraduate students of University Putra Malaysia.
PATIENTS AND METHODS: A total of 408 undergraduate students who received infant hepatitis B vaccination volunteered for this study; 5 mL of venous blood was taken from the volunteers. Hepatitis B surface antigen (HBsAg) and core antibodies were tested using a commercially available enzyme-linked immunosorbent assay kit according to the manufacturer's instructions (DRG international Inc., USA). Molecular detection of hepatitis B viral DNA was performed using nested polymerase chain reaction.
RESULTS: The prevalence of isolated anti-HBc among the vaccinated cohort was found to be 5.0%, out of which 80% had a hepatitis B surface antibodies (anti-HBs) titer higher than 10 IU/L, while 20% had less than 10 IU/L anti-HBs titer. All the anti-HBc positivesubjects had detectable hepatitis B viral DNA in their serum. Anamnestic response was found to be 100% among isolated anti-HBc with negative antibody.
CONCLUSION: Isolated anti-HBc developed protective levels of anti-HBs after a single dose of recombinant hepatitis B vaccination. HBV DNA was detected in all isolated anti-HBc indicating occult chronic HBV infection with undetectable HBsAg.

Matched MeSH terms: DNA, Viral/blood*
Fulltext Molecular epidemiology of coxsackievirus A16: intratype and prevalent intertype recombination identified

Chen X, Tan X, Li J, Jin Y, Gong L, Hong M, et al.

PLoS One, 2013;8(12):e82861.
PMID: 24340064 DOI: 10.1371/journal.pone.0082861

Coxsackievirus A16 (CVA16) is responsible for nearly 50% of all the conﬁrmed hand, foot, and mouth disease (HFMD) cases in mainland China, sometimes it could also cause severe complications, and even death. To clarify the genetic characteristics and the epidemic patterns of CVA16 in mainland China, comprehensive bioinfomatics analyses were performed by using 35 CVA16 whole genome sequences from 1998 to 2011, 593 complete CVA16 VP1 sequences from 1981 to 2011, and prototype strains of human enterovirus species A (EV-A). Analysis on complete VP1 sequences revealed that subgenotypes B1a and B1b were prevalent strains and have been co-circulating in many Asian countries since 2000, especially in mainland China for at least 13 years. While the prevalence of subgenotype B1c (totally 20 strains) was much limited, only found in Malaysia from 2005 to 2007 and in France in 2010. Genotype B2 only caused epidemic in Japan and Malaysia from 1981 to 2000. Both subgenotypes B1a and B1b were potential recombinant viruses containing sequences from other EV-A donors in the 5'-untranslated region and P2, P3 non-structural protein encoding regions.

Matched MeSH terms: DNA, Viral/analysis*

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