Genetic Characterization of Pakistani HBV Isolates


Familial fluctuations of Hepatitis B Virus ( HBV ) are closely associated with viral pathogenesis. The coevals of discrepancies of Hepatitis B virus ( HBV ) with altered functional belongingss and increased pathogenesis are the consequence of mutational events that can impact the disease forms and response to antiviral interventions. Due to high rate mutational alterations in viral genomic construction the ensuing variables become immune to antiviral drugs hence doing it imperative to develop curative options by placing quickly happening discrepancies. This survey describes familial variableness of Pakistani HBV isolates based upon DNA sequences of cloned PreS1/PreS2/S part or PreS/S Open Reading Frame ( ORF ) . HBV DNA was isolated from blood samples of 10 unrelated patients and PreS/S ORF of HBV was amplified through PCR from these isolates. The Deoxyribonucleic acid fragments were cloned and sequenced utilizing standard methodological analysiss.

The surface cistrons from HBV isolates showed 96-99 % homology with reported HBV genotype D but Pakistani isolates demonstrated sequence freshnesss ne’er reported elsewhere. Phylogenetic analysis of the sequences revealed that these isolates clustered within the genotype D group reported in different parts of the universe nevertheless. This is the first study of HBV genotype D from Pakistan based on DNA sequence of cloned PreS/S ORF.

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Hepatitis B infection comes out to be a major wellness concern in Pakistani urban and semi-urban population. More than 350 million people suffer from chronic Hepatitis B Virus ( HBV ) worldwide and it is estimated that more than two billion people are at hazard. ( McMahon, 2005 ) . Carrier variableness rate for Hepatitis B infection has been estimated to be 0.1 % to 20 % throughout the universe ( Sali et al. 2005 ) .

An estimated 8 % of the population of South Asia is infected at least one time in their life-time with HBV ( Lindh et al. 1999 ) .Eight genotypes of HBV have been reported so far in the universe holding distinguishable geographical distribution forms. Genotype A has been reported in Northwest Europe, North America, Philippines ( Norder et Al. 1993b ; Kidd-Ljunggren et Al. 1995 ) , Hong Kong ( Lok et al. 1994 ) and South and Eastern Africa ( Bowyer et al. 1997 ) .

Similarly Genotype B and C are preponderantly found in Southeast Asia ( Okamoto et al. 1988 ; Kidd-Ljunggren et Al. 1995 ; Theamboonlers et Al. 1999 ) .

Genotype D is nevertheless the most extensively distributed and has been reported throughout the universe. It is largely found in the part stretching from South Europe and North Africa ( Norder et Al. 1993b ; Borchani-Chabchoub et Al. 2000 ) to India, in the West and South Africa ( Bowyer et al. 1997 ) . Genotype E was foremost described as a subset of genotype D ( Kidd-Ljunggren et al. 1995 ) but this subgroup was subsequently classified as an independent genotype largely found in West and South Africa ( Norder et Al. 1993a, B, 1994 ) .

Genotype F is the most divergent of all other 1s and is found in cardinal and South America ( Norder et Al. 1993a ; Arauz-Ruiz et Al. 1997a, B ; Blitz et Al. 1998 ; Mbayed et Al. 1998 ; Nakano et Al.

2001 ) . The genotype G has merely been reported in USA and France ( Stuyver et al. 2000 ) . While Arauz-Ruiz et Al. ( 2002 ) reported a new genotype H, holding profound similarity to genotype F, and known to be an Amerindian genotype. This genotype is likely a disconnected fragment of F genotype within the new universe by early division of the primogenitor HBV strains of the first colonists ( Arauz-Ruiz et al.

2002 ) .The standards for grouping the HBV isolates into different genotypes comprises of at least 92 % homology between sequences of S-gene or a minimal inter-genotypic mark of 4.1 % ( Mizkomi et al. 1999 ; Bowyer & A ; Sim, 2000 ; Stuyer et Al. 2000 ) .

It has besides been shown that familial analysis on the footing of S-gene is comparable to genotyping complete HBV genome ( Norder et al. 1993 ; Ohba et Al. 1995 ; Mizkomi et Al. 1999 ; Bowyer & A ; Sim, 2000 ; Stuyer et Al. 2000 ) On the footing of fluctuation analysis and homology of surface cistrons and full genome, HBV genotype has been defined as the subtype holding sequence similarity of approximately 92 % with a specific genotype ( Magnius and Norder, 1995 ) . This survey was aimed to find the genotypic group of Pakistani HBV isolates and to describe fluctuation profile to reported genotypes in other parts of the universe.

The Phylogenetic analysis revealed evolutionary association of Pakistani isolates with already reported genotype D of HBV.

Material and MethodsVector and strains

The vector incorporating 3 ‘ terminal thymidine at both terminals ( PCR2.1 vector ) and E.coli Top10F ‘ strain for plasmid use was purchased from Invitrogen Co.


Collection of blood samples and DNA extraction

Peripheral blood samples were obtained from 25 patients holding positive surface antigen markers from different infirmaries of Punjab state of Pakistan. These patients were screened for HBsAg, anti-HBs, HBeAg, anti-HBe, anti-HCV and anti-HIV and the patients with anti-HCV co-infection were excluded.

Viral Deoxyribonucleic acid from 10 patients was isolated through Proteinase K digestion method ( Persing et al. 1993 ) .

Primer Selection

Forward and Reverse Primers were designed by seeking most conserved flanking part of PreS/S ORF utilizing already reported HBV sequence ( accession no. NC_003977 ) . Web based freeware was utilized to plan accurate primers with optimum GC content and thaw temperatures.

PCR elaboration and cistron cloning

The PreS/S ORF of HBV was amplified through PCR from acquired isolates utilizing primers ( sense 5 ‘ TATTCTTGGGAACAAGAG 3 ‘ and antisense 5 ‘ GCAGCAAAGCCCAAAAG 3 ) .

PCR was optimized utilizing 50ng of templet, 10 picomole of each primer, 2 units of Taq polymerase, concentration of dNTPs and different thermo cycling plans. These Deoxyribonucleic acid fragments were cloned into a T-A cloning vector and confirmed through PCR and limitation digestion. Using Large Dye Terminator Cycle Sequencing Ready Reaction Kit on ABI-3100 DNA analyser, cloned Deoxyribonucleic acid fragments were sequenced.

Familial variableness analysis

A sum of 43 mention sequences were retrieved from GeneBank and were used for familial variableness analysis of Pakistani HBV isolates.

The accession Numberss with their several state of beginning are ; Genotype A ; AB194951 from Cameroon, AB014370 from Japan, EU410082 from Philippines, AF297621 from South Africa, AB222707 from Uzbekistan, Genotype B ; M54923 from Indonesia, AB073838 from Japan, AF121243 from Sweden, AY167098 from Taiwan, X97850 from the UK, Genotype C ; EU439009 from China, AB014393 from Japan, AB105172 from Hawaii, X75656 from Polynesia, X75665 from Sweden, AB222714 from Uzbekistan, Genotype D ; AF280817 from China, AB033558 from Japan, EF103276 from India, AY741798 and AY741797 from Iran, DQ991753 from Ireland, X65257 from Italy, AB263407 from Mongolia, AB033559 from Papua New Guinea, Z35716 from Poland, AF121240 from Sweden, X02496 from Switzerland, AY661793 from Turkey, AF121239 from Vietnam, X80924 from the UK, AB222709 from Uzbekistan, Genotype E ; AM494832 from Cardinal African Republic, AB106564 from Ghana, X75664 from Senegal, X75657 from West Africa, Genotype F ; X69798 from Brazil, X75658 from France, AB036911 from Venezuela, Genotype G ; AF160501 from Belgium, AF405706 from Germany, AB056513 from the USA, Genotype H ; AY090454 from Sweden. The HBV PreS/S ORF ( 1170bp ) and mention sequences were aligned with ClustalW freeware by utilizing BioEdit ( The BioEdit Sequence Alignment Editor package, Department of Microbiology, North California State University ) . Familial distance was calculated utilizing Kimura two-parameter matrix ( Saitou et al.

1987 ) . Phylogenetic tree were constructed by the neighbor-joining ( NJ ) method ( Kimura 1980 ) .


The DNA sequences of PreS/S ORF ( 1170bp ) of 10 HBV isolates were submitted to NCBI GeneBank database under accession Numberss from FJ670505 to FJ67014. After alliance with 43 sequences of all HBV genotypes retrieved from the GeneBank the homology analysis showed that the local isolates had 96 % to 99 % similarity with genotype D of HBV, reported from elsewhere. The Phylogeny of isolates was analyzed utilizing DNA sequences of isolates and mention HBV genotypes to foster confirm that the Pakistani HBV isolates belonged to genotype D ( Fig 1. ) All isolates showed arginine residue at amino acerb place 122 finding subgroup “y” and a lysine residue at AA place 160 finding subgroup “w” jointly confirmed the serotype of the isolates as “ayw” .


Bing a viral infection hepatitis B specifically infects hepatic cells of the members of hominoidae including worlds.

Vast informations on HBV variableness has now been gathered nevertheless, the topical issues are geographical familial fluctuation that affect HBV manner of infection, disease form, immunisation, prophylaxes and intervention. HBV changes itself with clip due to mutants in its familial stuff in response to environmental emphasiss ( Bowyer and Sim 2000 ) . HBV genome has been shown to alter at a nucleotide exchange rate of 0.

1 base per twelvemonth ( Okamoto et al. 1988 ) . Heterogenecity among HBV strains go arounding globally is 104 clip greater than other DNA viruses which is due to the fact that members of hepadnaviridae household replicate through an RNA intermediate and RNA contrary RNA polymerase is known to hold high mistake rate ( Hourioux et al. 2000 ) . The diverseness of HBV is shown through its different genotypes and serological subtypes ( Ma et al. 2005 ) .In this survey, ORF of HBV complete surface was cloned and sequenced and the isolates analyzed for evolution.

The consequences indicated that there was no genotypic divergency amongst the isolates constellating in genotype D with 96-99 % homology. HBV genotypes A, B and C reported antecedently were determined through PCR based genotyping as against DNA sequencing of isolates ( Idrees et al. 2004 ) . In a recent survey, genotype D was reported from Pakistan based on HBV surface ORF part ( 967 bp ) of HBV ( Baig et al.

2008 ) nevertheless, the present survey was more comprehensive to include complete ORF surface including PreS1, PreS2 and S cistrons ( 1170 bp ) for genotypic word picture. The findings of ( Alam et al. 2007 ) substantiated that genotype D is the most prevailing genotype. Genotypic surveies on HBV in neighbouring states besides confirmed the laterality of genotype D in the part. It has been reported to be the individual noticeable genotype in Iran and Mediterranean parts ( Alavian et Al.

2003 ; Tahan et Al. 2003 ; Bozdayi et Al. 2005 ; Leblebicioglu and Eroglu 2004 ; Yalcin et Al.

2004 ; Amini-Bavil-Olyaee et Al. 2005 ) whereas genotypes A and D were reported in India with D as a dominant genotype in chronic liver patients ( Kar et al. 2007 ) .The possible grounds for prevalence of D Genotype in the part may due to archaeological and anthropological considerations. The ascendants of Caucasians foremost colonized the North of Caspian Sea migrating in three waies thenceforth. One group traveling to Europe, 2nd to India and the last one moving towards South of Iran which explains that due to common line of descent the ascendants carried the same HBV genome along with them, now being identified as D genotype.

It is plausible that mixture of HBV genotypes A-H had occurred in different parts of the universe due to immune force per unit area ( Jazayeri, and Carman ( 2009 ) . The Phylogram depicted in Fig1 supports the hypothesis ( Jazayeri, and Carman 2009 ) that the ancient HBV genome belonged to the familial construction closer to that of genotype D. This survey besides confirms the hypothesis ( Arauz-Ruiz et al.

2002 ) that genotype H is a divergent of genotype F due to H constellating closely with genotype F. In the Phylogram ( Fig1 ) , the genotypes A, B and C are closely clustered with each another, which helps suggesting the hypothesis of a common familial beginning of these genotypes during evolutionary divergency.