Hepatitis C virus genotyping based on Core and NS5B regions in Cameroonian patients.
Cameroon
Core
Genotypes
Genotyping
HCV
NS5B
Subtypes
Journal
Virology journal
ISSN: 1743-422X
Titre abrégé: Virol J
Pays: England
ID NLM: 101231645
Informations de publication
Date de publication:
09 08 2019
09 08 2019
Historique:
received:
21
05
2019
accepted:
06
08
2019
entrez:
11
8
2019
pubmed:
11
8
2019
medline:
18
12
2019
Statut:
epublish
Résumé
Current HCV treatments are genotype specific although potential pan-genotype treatments have recently been described. Therefore, genotyping is an essential tool for the therapeutic management of HCV infection and a variety of technologies have been developed for HCV genotypes determination. Sequences analysis of HCV sub-genomic regions is considered as gold standard and is widely used for HCV genotyping. Here, we compared HCV genotyping using core and NS5B regions in routine practice in HCV-positive Cameroonian patients. All plasma samples received at Centre Pasteur of Cameroon (CPC) in 2016 for HCV genotyping were included. Viral loads were determined using the Abbott Real Time assay. Further, genotyping was based on the amplification and sequencing of core and NS5B regions following by phylogenetic analysis of corresponding sequences. A total of 369 samples were received during the study period with high viral load values (median: 930,952 IU/ml; IQR: 281,833-2,861,179). Positive amplification was obtained in at least one genomic region (core or NS5B) for all the samples with similar amplification rate in the two genomic regions (p = 0.34). Phylogenetic analysis showed that among the 369 samples, 146 (39.6%) were classified as genotype 4, 132 (35.8%) as genotype 1, 89 (24.1%) as genotype 2, in both core and NS5B regions. Interestingly, for two samples (0.54%) discordant genotypes were obtained in both regions with the core region classified as genotype 4 while the NS5B was identified as genotype 1 indicating the presence of putative HCV recombinant virus or multiple infections in these samples. Discrimination of HCV subtypes was most likely possible with NS5B compared to core region. We found high amplification rates of HCV in both core and NS5B regions, and a good concordance was obtained at genotype level using both regions except for two samples where putative 1-4 recombinants/multiple infections were detected. Therefore, HCV genotyping based on at least two genomic regions could help to identify putative recombinants and improve therapeutic management of HCV infection.
Sections du résumé
BACKGROUND
Current HCV treatments are genotype specific although potential pan-genotype treatments have recently been described. Therefore, genotyping is an essential tool for the therapeutic management of HCV infection and a variety of technologies have been developed for HCV genotypes determination. Sequences analysis of HCV sub-genomic regions is considered as gold standard and is widely used for HCV genotyping. Here, we compared HCV genotyping using core and NS5B regions in routine practice in HCV-positive Cameroonian patients.
METHODS
All plasma samples received at Centre Pasteur of Cameroon (CPC) in 2016 for HCV genotyping were included. Viral loads were determined using the Abbott Real Time assay. Further, genotyping was based on the amplification and sequencing of core and NS5B regions following by phylogenetic analysis of corresponding sequences.
RESULTS
A total of 369 samples were received during the study period with high viral load values (median: 930,952 IU/ml; IQR: 281,833-2,861,179). Positive amplification was obtained in at least one genomic region (core or NS5B) for all the samples with similar amplification rate in the two genomic regions (p = 0.34). Phylogenetic analysis showed that among the 369 samples, 146 (39.6%) were classified as genotype 4, 132 (35.8%) as genotype 1, 89 (24.1%) as genotype 2, in both core and NS5B regions. Interestingly, for two samples (0.54%) discordant genotypes were obtained in both regions with the core region classified as genotype 4 while the NS5B was identified as genotype 1 indicating the presence of putative HCV recombinant virus or multiple infections in these samples. Discrimination of HCV subtypes was most likely possible with NS5B compared to core region.
CONCLUSIONS
We found high amplification rates of HCV in both core and NS5B regions, and a good concordance was obtained at genotype level using both regions except for two samples where putative 1-4 recombinants/multiple infections were detected. Therefore, HCV genotyping based on at least two genomic regions could help to identify putative recombinants and improve therapeutic management of HCV infection.
Identifiants
pubmed: 31399103
doi: 10.1186/s12985-019-1214-9
pii: 10.1186/s12985-019-1214-9
pmc: PMC6688274
doi:
Substances chimiques
Viral Core Proteins
0
Viral Nonstructural Proteins
0
NS-5 protein, hepatitis C virus
EC 2.7.7.48
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
101Références
Intervirology. 1999;42(1):1-8
pubmed: 10393497
J Virol. 2002 Apr;76(8):4034-43
pubmed: 11907242
J Med Virol. 2003 Mar;69(3):384-90
pubmed: 12526049
J Clin Microbiol. 2003 Nov;41(11):5240-4
pubmed: 14605173
J Clin Microbiol. 2005 Feb;43(2):733-9
pubmed: 15695672
J Med Virol. 2005 Nov;77(3):390-8
pubmed: 16173014
J Virol. 2007 Apr;81(8):4357-62
pubmed: 17267503
J Clin Microbiol. 2007 Apr;45(4):1102-12
pubmed: 17287328
J Viral Hepat. 2011 Feb;18(2):77-83
pubmed: 21235686
Virol J. 2011 Oct 03;8:459
pubmed: 21967749
Viruses. 2011 Oct;3(10):2006-24
pubmed: 22069526
PLoS One. 2012;7(8):e42002
pubmed: 22870274
Int J Mol Med. 2013 Feb;31(2):347-52
pubmed: 23241873
J Med Virol. 2013 May;85(5):815-22
pubmed: 23508907
Hepatology. 2014 Jan;59(1):318-27
pubmed: 24115039
Mol Biol Evol. 2013 Dec;30(12):2725-9
pubmed: 24132122
J Clin Microbiol. 2015 Oct;53(10):3155-64
pubmed: 26202126
AIDS. 2016 Jan 2;30(1):1-8
pubmed: 26731750
Bioorg Med Chem Lett. 2016 Jul 1;26(13):3158-3162
pubmed: 27180013
World J Gastroenterol. 2016 Sep 14;22(34):7824-40
pubmed: 27678366
J Med Chem. 2017 Jan 12;60(1):290-306
pubmed: 27808515
Curr Opin Virol. 2017 Jun;24:31-37
pubmed: 28419938
Liver Int. 2018 Mar;38(3):451-457
pubmed: 28782185
Ann Gastroenterol. 2019 Jan-Feb;32(1):88-92
pubmed: 30598597
BMC Infect Dis. 2019 May 3;19(1):378
pubmed: 31053098
J Gen Virol. 1994 May;75 ( Pt 5):1053-61
pubmed: 8176367
J Gen Virol. 1993 Jun;74 ( Pt 6):1093-102
pubmed: 8389799