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Molecular characterization of Hepatitis C virus 3a in Peshawar.

Gul A, Zahid N, Ahmed J, Zahir F, Khan IA, Ali I - BMC Infect. Dis. (2016)

Bottom Line: Among the 422 (82.75 %) PCR positive samples, 192 (45.5 %) were identified as having HCV genotype 3a infection.Nucleotide sequence analysis of the obtained viral genomic sequences based on partial HCV 3a Core gene sequences with reference sequences from different countries showed that our sequences clustered with some local and regional sequences with high bootstrap values.HCV 3a is highly prevalent in Peshawar, Pakistan and its phylogenetics based on Core gene sequences indicate the prevalence of different lineages of HCV 3a in Peshawar which may have consequences for disease management strategies causing more economic pressure on the impoverished population due to possible antiviral resistance.

View Article: PubMed Central - PubMed

Affiliation: Institute of Basic Medical Sciences, Khyber Medical University Peshawar, Peshawar, Pakistan.

ABSTRACT

Background: The purpose of this study was to explore molecular epidemiology of HCV genotype 3a in Peshawar based on sequencing and phylogenetic analysis of Core region of HCV genome.

Methods: Chronically infected Hepatitis C virus infected patients enrolled under the Prime Minister Hepatitis C control program at three Tertiary care units of Peshawar [Khyber Teaching Hospital Peshawar, Lady Reading Hospital Peshawar, Hayat Abad Medical Complex Peshawar] were included in this cross sectional observational study. Qualitative detection of HCV and HCV genotyping was carried out by a modified reverse transcription-polymerase chain reaction (RT-PCR) and type specific genotyping assay. The Core gene of HCV genotype 3a was amplified, cloned and sequenced. The sequences obtained were used for phylogenetic analysis using MEGA 6 software.

Results: Among the 422 (82.75 %) PCR positive samples, 192 (45.5 %) were identified as having HCV genotype 3a infection. HCV Core gene sequencing was carried out randomly for the characterization of HCV 3a. Nucleotide sequence analysis of the obtained viral genomic sequences based on partial HCV 3a Core gene sequences with reference sequences from different countries showed that our sequences clustered with some local and regional sequences with high bootstrap values.

Conclusion: HCV 3a is highly prevalent in Peshawar, Pakistan and its phylogenetics based on Core gene sequences indicate the prevalence of different lineages of HCV 3a in Peshawar which may have consequences for disease management strategies causing more economic pressure on the impoverished population due to possible antiviral resistance.

No MeSH data available.


Related in: MedlinePlus

Phylogenetic tree of HCV 3a Core gene sequences constructed by Maximum Likelihood algorithm (MEGA 6 Software) with Bootstrap values shown on the branches. Tree shows the phylogenetic relationship of twelve newly reported sequences, marked in red with 36 Core gene sequences from different geographical regions. The isolate/country/Accession no of the sequences are shown in figure
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Fig1: Phylogenetic tree of HCV 3a Core gene sequences constructed by Maximum Likelihood algorithm (MEGA 6 Software) with Bootstrap values shown on the branches. Tree shows the phylogenetic relationship of twelve newly reported sequences, marked in red with 36 Core gene sequences from different geographical regions. The isolate/country/Accession no of the sequences are shown in figure

Mentions: For identification of HCV genotype 3a infection among the actively infected HCV samples, RT PCR followed by Type specific nested PCR based genotyping assay was carried out. Genotyping analysis revealed that out of the 422 (82.75 %) samples processed. Out of 422 actively infected patients, 257 (61 %) were females and 165 (39 %) were male) HCV genotype 3a was identified as the most abundant HCV subtype 192 (45.50 %). Mean age of patients included in the study was 38 ± 11.8 (Mean ± SD. For authentication of HCV genotype 3a, Core gene amplification and sequencing was carried out by randomly selecting a representative number (58/192) of samples and it was established that the patients had HCV 3a infection. These results were also validated by an online sub-typing tool (http://www.bioafrica.net/rega-genotype/html/subtypinghcv.html). Detailed sequence and phylogenetic analysis of the obtained viral genomic sequences was carried out. Phylogenetic tree was developed with Maximum Likelihood algorithm (1000 bootstrap replicates). To analyze HCV genotype 3a of Peshawar origin, the available subtype 3a sequences of the Core gene were retrieved from NCBI and aligned with the respective subtype identified in this study. Pair wise nucleotide and deduced amino acid sequence comparison of our sequences with 36 reported sequences from different countries was performed which indicated that some of the HCV 3a isolates of Peshawar clustered together with each other and with isolates from Pakistan (KP869047, KP869048, KP869049, KP869055, KP869056, KP869057, KP869058), while others clustered closer to European, Indian, Iranian or Chinese HCV sequences with high bootstrap support (Fig. 1). Two of the representative isolates (KP869053 and KP869054) were clustered with the European isolates. Isolate KP869050 and KP869051 shared homology with both the Indian, Iranian and Chinese isolates. Moreover isolate KP869052 was found closely related to those from Iran and Pakistan.Fig. 1


Molecular characterization of Hepatitis C virus 3a in Peshawar.

Gul A, Zahid N, Ahmed J, Zahir F, Khan IA, Ali I - BMC Infect. Dis. (2016)

Phylogenetic tree of HCV 3a Core gene sequences constructed by Maximum Likelihood algorithm (MEGA 6 Software) with Bootstrap values shown on the branches. Tree shows the phylogenetic relationship of twelve newly reported sequences, marked in red with 36 Core gene sequences from different geographical regions. The isolate/country/Accession no of the sequences are shown in figure
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4836082&req=5

Fig1: Phylogenetic tree of HCV 3a Core gene sequences constructed by Maximum Likelihood algorithm (MEGA 6 Software) with Bootstrap values shown on the branches. Tree shows the phylogenetic relationship of twelve newly reported sequences, marked in red with 36 Core gene sequences from different geographical regions. The isolate/country/Accession no of the sequences are shown in figure
Mentions: For identification of HCV genotype 3a infection among the actively infected HCV samples, RT PCR followed by Type specific nested PCR based genotyping assay was carried out. Genotyping analysis revealed that out of the 422 (82.75 %) samples processed. Out of 422 actively infected patients, 257 (61 %) were females and 165 (39 %) were male) HCV genotype 3a was identified as the most abundant HCV subtype 192 (45.50 %). Mean age of patients included in the study was 38 ± 11.8 (Mean ± SD. For authentication of HCV genotype 3a, Core gene amplification and sequencing was carried out by randomly selecting a representative number (58/192) of samples and it was established that the patients had HCV 3a infection. These results were also validated by an online sub-typing tool (http://www.bioafrica.net/rega-genotype/html/subtypinghcv.html). Detailed sequence and phylogenetic analysis of the obtained viral genomic sequences was carried out. Phylogenetic tree was developed with Maximum Likelihood algorithm (1000 bootstrap replicates). To analyze HCV genotype 3a of Peshawar origin, the available subtype 3a sequences of the Core gene were retrieved from NCBI and aligned with the respective subtype identified in this study. Pair wise nucleotide and deduced amino acid sequence comparison of our sequences with 36 reported sequences from different countries was performed which indicated that some of the HCV 3a isolates of Peshawar clustered together with each other and with isolates from Pakistan (KP869047, KP869048, KP869049, KP869055, KP869056, KP869057, KP869058), while others clustered closer to European, Indian, Iranian or Chinese HCV sequences with high bootstrap support (Fig. 1). Two of the representative isolates (KP869053 and KP869054) were clustered with the European isolates. Isolate KP869050 and KP869051 shared homology with both the Indian, Iranian and Chinese isolates. Moreover isolate KP869052 was found closely related to those from Iran and Pakistan.Fig. 1

Bottom Line: Among the 422 (82.75 %) PCR positive samples, 192 (45.5 %) were identified as having HCV genotype 3a infection.Nucleotide sequence analysis of the obtained viral genomic sequences based on partial HCV 3a Core gene sequences with reference sequences from different countries showed that our sequences clustered with some local and regional sequences with high bootstrap values.HCV 3a is highly prevalent in Peshawar, Pakistan and its phylogenetics based on Core gene sequences indicate the prevalence of different lineages of HCV 3a in Peshawar which may have consequences for disease management strategies causing more economic pressure on the impoverished population due to possible antiviral resistance.

View Article: PubMed Central - PubMed

Affiliation: Institute of Basic Medical Sciences, Khyber Medical University Peshawar, Peshawar, Pakistan.

ABSTRACT

Background: The purpose of this study was to explore molecular epidemiology of HCV genotype 3a in Peshawar based on sequencing and phylogenetic analysis of Core region of HCV genome.

Methods: Chronically infected Hepatitis C virus infected patients enrolled under the Prime Minister Hepatitis C control program at three Tertiary care units of Peshawar [Khyber Teaching Hospital Peshawar, Lady Reading Hospital Peshawar, Hayat Abad Medical Complex Peshawar] were included in this cross sectional observational study. Qualitative detection of HCV and HCV genotyping was carried out by a modified reverse transcription-polymerase chain reaction (RT-PCR) and type specific genotyping assay. The Core gene of HCV genotype 3a was amplified, cloned and sequenced. The sequences obtained were used for phylogenetic analysis using MEGA 6 software.

Results: Among the 422 (82.75 %) PCR positive samples, 192 (45.5 %) were identified as having HCV genotype 3a infection. HCV Core gene sequencing was carried out randomly for the characterization of HCV 3a. Nucleotide sequence analysis of the obtained viral genomic sequences based on partial HCV 3a Core gene sequences with reference sequences from different countries showed that our sequences clustered with some local and regional sequences with high bootstrap values.

Conclusion: HCV 3a is highly prevalent in Peshawar, Pakistan and its phylogenetics based on Core gene sequences indicate the prevalence of different lineages of HCV 3a in Peshawar which may have consequences for disease management strategies causing more economic pressure on the impoverished population due to possible antiviral resistance.

No MeSH data available.


Related in: MedlinePlus