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Frequency distribution of hepatitis C virus genotypes in different geographical regions of Pakistan and their possible routes of transmission.

ABSTRACT: BACKGROUND: Information regarding hepatitis C virus genotypes and subtypes circulating in Pakistan and various risk factors for their transmission are not known well. The specific objective of this study was to find out the frequency of various HCV genotypes present in well-characterized Pakistani HCV isolates and their possible routes of transmission. METHODS: A total of 3351 serum samples were tested by type-specific genotyping assay. Out of 3351 HCV RNA positive patients, 2039 were males and 1312 were females. As regard as genotyped samples, 2165 belonged to Punjab region, 823 belonged to N.W.F.P., 239 to Sindh and 124 patients were from Balochistan. RESULTS: Out of the total 3351 tested serum samples, type-specific PCR fragments were observed in 3150 (94.00%) serum samples. The distribution of genotypes of the typeable samples as determined by this assay, was as follows: 1664 (49.05%) genotype 3a; 592 (17.66%) genotype 3b; 280 (8.35%) genotype 1a; 252 (7.52%) genotype 2a; 101 (3.01%) genotype 1b; 50 (1.49%) with genotype 4; 25 (0.75%) with 3c; 27 (0.80%) genotype 2b; 6 (0.18%) with subtype 5a; 5 (0.15%) genotype 1c; 4 (0.12%) with subtype 6a; 3 (0.09%) genotype 2c; and 161 (4.80%) patients were infected with mixed infection. Two hundred and one (5.99%) serum samples were found untypeable by the present genotyping system. More than 86% and 72% patients with genotypes 3a and 3b respectively had received multiple injections in past. For genotypes 1a and 1b the route of transmission was major/minor surgery along with unknown reasons. Majority of the cases with type 2a, 2b and indeterminate genotypes were sporadic. Mixed infections were common in thalassaemic patients. CONCLUSION: The most common HCV genotype in Pakistan is type 3a. Regional difference in genotypes was observed only in Balochistan province of Pakistan. More than 70% of the cases were acquired in hospitals through reuse of needles/syringes and major/minor surgery that is very common in this country.

SUBMITTER: Idrees M

PROVIDER: S-EPMC2409346 | biostudies-literature | 2008

REPOSITORIES: biostudies-literature

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Frequency distribution of hepatitis C virus genotypes in different geographical regions of Pakistan and their possible routes of transmission.

Idrees Muhammad M Riazuddin Sheikh S

BMC infectious diseases 20080523

<h4>Background</h4>Information regarding hepatitis C virus genotypes and subtypes circulating in Pakistan and various risk factors for their transmission are not known well. The specific objective of this study was to find out the frequency of various HCV genotypes present in well-characterized Pakistani HCV isolates and their possible routes of transmission.<h4>Methods</h4>A total of 3351 serum samples were tested by type-specific genotyping assay. Out of 3351 HCV RNA positive patients, 2039 we ...[more]

PMID: 18498666

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Project description:Background. Central intermediary metabolism (CIM) in bacteria is defined as a set of metabolic biochemical reactions within a cell, which is essential for the cell to survive in response to environmental perturbations. The genes associated with CIM are commonly found in both pathogenic and non-pathogenic strains. As these genes are involved in vital metabolic processes of bacteria, we explored the efficiency of the genes in genotypic characterization of Burkholderia pseudomallei isolates, compared with the established pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) schemes. Methods. Nine previously sequenced B. pseudomallei isolates from Malaysia were characterized by PFGE, MLST and CIM genes. The isolates were later compared to the other 39 B. pseudomallei strains, retrieved from GenBank using both MLST and sequence analysis of CIM genes. UniFrac and hierachical clustering analyses were performed using the results generated by both MLST and sequence analysis of CIM genes. Results. Genetic relatedness of nine Malaysian B. pseudomallei isolates and the other 39 strains was investigated. The nine Malaysian isolates were subtyped into six PFGE profiles, four MLST profiles and five sequence types based on CIM genes alignment. All methods demonstrated the clonality of OB and CB as well as CMS and THE. However, PFGE showed less than 70% similarity between a pair of morphology variants, OS and OB. In contrast, OS was identical to the soil isolate, MARAN. To have a better understanding of the genetic diversity of B. pseudomallei worldwide, we further aligned the sequences of genes used in MLST and genes associated with CIM for the nine Malaysian isolates and 39 B. pseudomallei strains from NCBI database. Overall, based on the CIM genes, the strains were subtyped into 33 profiles where majority of the strains from Asian countries were clustered together. On the other hand, MLST resolved the isolates into 31 profiles which formed three clusters. Hierarchical clustering using UniFrac distance suggested that the isolates from Australia were genetically distinct from the Asian isolates. Nevertheless, statistical significant differences were detected between isolates from Malaysia, Thailand and Australia. Discussion. Overall, PFGE showed higher discriminative power in clustering the nine Malaysian B. pseudomallei isolates and indicated its suitability for localized epidemiological study. Compared to MLST, CIM genes showed higher resolution in distinguishing those non-related strains and better clustering of strains from different geographical regions. A closer genetic relatedness of Malaysian isolates with all Asian strains in comparison to Australian strains was observed. This finding was supported by UniFrac analysis which resulted in geographical segregation between Australia and the Asian countries.

Project description:BACKGROUND:Childhood immunization is one of the most cost-effective interventions for child health. Still, many children are not able to receive completed immunization status. Wealth - related inequality in immunization is considered a major reason for equitable coverage of immunization in Pakistan. Therefore, we examine wealth-related inequality in completed childhood immunization and to assess achievement indices across geographical regions in Pakistan. METHODS:The analysis was based on a nationally representative demographic and health survey (DHS) of Pakistan, conducted in 2012-13. We examined completed childhood (12-23 months) immunization in the various regions of the country and we used concentration, extended concentration and achievement indices to demonstrate inequality across geographical regions in Pakistan. RESULTS:Inequality in completed childhood immunization was seen in Pakistan with concentration index (CI) of 0.181 (95% CI: 0.164-0.209). Regions with high average of complete immunization showed lower inequality except for Sindh. Despite having better average immunization coverage in Kyber Pakhtunkhwa, the relative change of 128% in concentration index (CI) from C2 (standard CI) to C5 (when poorer quantile received highest weights) shows this to be also the most inequitable regions. Four parameters of inequality aversion (v = 2, 3, 4 & 5) demonstrated that 'dis - achievement' in completed immunization is densely concentrated among the poorer regions. Balochistan, Sindh and Gilgit Baltistan exhibited broader inequality gaps (93.75%, 83.35%, and 54.93%, respectively) at higher aversion parameter. CONCLUSIONS:As hypothesized, achievement index uncovers 'penalized' immunization coverage amongst the poorest population. Thus any policy that stringently focuses on improving average immunization rate without any strategy to deal with inequality will only improve immunization rate within wealthier groups. Based on these results, it is advisable to public health policy makers to use both aspect of information: average and degree of inequality in immunization coverage.

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Frequency distribution of hepatitis C virus genotypes in different geographical regions of Pakistan and their possible routes of transmission.

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Frequency distribution of hepatitis C virus genotypes in different geographical regions of Pakistan and their possible routes of transmission.

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