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Genotyping hepatitis C virus from hemodialysis patients in Central Brazil by line probe assay and sequence analysis.
Braz J Med Biol Res. 2007 Apr; 40(4):545-50.BJ

Abstract

The present study examined the distribution of hepatitis C virus (HCV) genotypes and subtypes in a hemodialysis population in Goiás State, Central Brazil, and evaluated the efficiency of two genotyping methods: line probe assay (LiPA) based on the 5' noncoding region and nucleotide sequencing of the nonstructural 5B (NS5B) region of the genome. A total of 1095 sera were tested for HCV RNA by RT-nested PCR of the 5' noncoding region. The LiPA assay was able to genotype all 131 HCV RNA-positive samples. Genotypes 1 (92.4%) and 3 (7.6%) were found. Subtype 1a (65.7%) was the most prevalent, followed by subtypes 1b (26.7%) and 3a (7.6%). Direct nucleotide sequencing of 340 bp from the NS5B region was performed in 106 samples. The phylogenetic tree showed that 98 sequences (92.4%) were classified as genotype 1, subtypes 1a (72.6%) and 1b (19.8%), and 8 sequences (7.6%) as subtype 3a. The two genotyping methods gave concordant results within HCV genotypes and subtypes in 100 and 96.2% of cases, respectively. Only four samples presented discrepant results, with LiPA not distinguishing subtypes 1a and 1b. Therefore, HCV genotype 1 (subtype 1a) is predominant in hemodialysis patients in Central Brazil. By using sequence analysis of the NS5B region as a reference standard method for HCV genotyping, we found that LiPA was efficient at the genotype level, although some discrepant results were observed at the subtype level (sensitivity of 96.1% for subtype 1a and 95.2% for subtype 1b). Thus, analysis of the NS5B region permitted better discrimination between HCV subtypes, as required in epidemiological investigations.

Authors+Show Affiliations

Departamento de Virologia, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, RJ, Brasil.No affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info available

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

17401498

Citation

Espírito-Santo, M P., et al. "Genotyping Hepatitis C Virus From Hemodialysis Patients in Central Brazil By Line Probe Assay and Sequence Analysis." Brazilian Journal of Medical and Biological Research = Revista Brasileira De Pesquisas Medicas E Biologicas, vol. 40, no. 4, 2007, pp. 545-50.
Espírito-Santo MP, Carneiro MA, Reis NR, et al. Genotyping hepatitis C virus from hemodialysis patients in Central Brazil by line probe assay and sequence analysis. Braz J Med Biol Res. 2007;40(4):545-50.
Espírito-Santo, M. P., Carneiro, M. A., Reis, N. R., Kozlowski, A. G., Teles, S. A., Lampe, E., Yoshida, C. F., & Martins, R. M. (2007). Genotyping hepatitis C virus from hemodialysis patients in Central Brazil by line probe assay and sequence analysis. Brazilian Journal of Medical and Biological Research = Revista Brasileira De Pesquisas Medicas E Biologicas, 40(4), 545-50.
Espírito-Santo MP, et al. Genotyping Hepatitis C Virus From Hemodialysis Patients in Central Brazil By Line Probe Assay and Sequence Analysis. Braz J Med Biol Res. 2007;40(4):545-50. PubMed PMID: 17401498.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Genotyping hepatitis C virus from hemodialysis patients in Central Brazil by line probe assay and sequence analysis. AU - Espírito-Santo,M P, AU - Carneiro,M A S, AU - Reis,N R S, AU - Kozlowski,A G, AU - Teles,S A, AU - Lampe,E, AU - Yoshida,C F T, AU - Martins,R M B, PY - 2005/09/23/received PY - 2006/05/23/accepted PY - 2007/4/3/pubmed PY - 2008/2/2/medline PY - 2007/4/3/entrez SP - 545 EP - 50 JF - Brazilian journal of medical and biological research = Revista brasileira de pesquisas medicas e biologicas JO - Braz J Med Biol Res VL - 40 IS - 4 N2 - The present study examined the distribution of hepatitis C virus (HCV) genotypes and subtypes in a hemodialysis population in Goiás State, Central Brazil, and evaluated the efficiency of two genotyping methods: line probe assay (LiPA) based on the 5' noncoding region and nucleotide sequencing of the nonstructural 5B (NS5B) region of the genome. A total of 1095 sera were tested for HCV RNA by RT-nested PCR of the 5' noncoding region. The LiPA assay was able to genotype all 131 HCV RNA-positive samples. Genotypes 1 (92.4%) and 3 (7.6%) were found. Subtype 1a (65.7%) was the most prevalent, followed by subtypes 1b (26.7%) and 3a (7.6%). Direct nucleotide sequencing of 340 bp from the NS5B region was performed in 106 samples. The phylogenetic tree showed that 98 sequences (92.4%) were classified as genotype 1, subtypes 1a (72.6%) and 1b (19.8%), and 8 sequences (7.6%) as subtype 3a. The two genotyping methods gave concordant results within HCV genotypes and subtypes in 100 and 96.2% of cases, respectively. Only four samples presented discrepant results, with LiPA not distinguishing subtypes 1a and 1b. Therefore, HCV genotype 1 (subtype 1a) is predominant in hemodialysis patients in Central Brazil. By using sequence analysis of the NS5B region as a reference standard method for HCV genotyping, we found that LiPA was efficient at the genotype level, although some discrepant results were observed at the subtype level (sensitivity of 96.1% for subtype 1a and 95.2% for subtype 1b). Thus, analysis of the NS5B region permitted better discrimination between HCV subtypes, as required in epidemiological investigations. SN - 0100-879X UR - https://www.unboundmedicine.com/medline/citation/17401498/Genotyping_hepatitis_C_virus_from_hemodialysis_patients_in_Central_Brazil_by_line_probe_assay_and_sequence_analysis_ L2 - https://www.scielo.br/scielo.php?script=sci_arttext&pid=S0100-879X2007000400013&lng=en&nrm=iso&tlng=en DB - PRIME DP - Unbound Medicine ER -