Hepatitis C virus genotyping based on Core and NS5B regions in Cameroonian patients
Abstract 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 det...
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| Format: | Article |
| Language: | English |
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BMC
2019-08-01
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| Series: | Virology Journal |
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| Online Access: | http://link.springer.com/article/10.1186/s12985-019-1214-9 |
| _version_ | 1818508963399860224 |
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| author | Paul Alain Tagnouokam-Ngoupo Marie Nicole Ngoufack Sebastien Kenmoe Simon Frédéric Lissock Marie Amougou-Atsama Robert Banai Laure Ngono Richard Njouom |
| author_facet | Paul Alain Tagnouokam-Ngoupo Marie Nicole Ngoufack Sebastien Kenmoe Simon Frédéric Lissock Marie Amougou-Atsama Robert Banai Laure Ngono Richard Njouom |
| author_sort | Paul Alain Tagnouokam-Ngoupo |
| collection | DOAJ |
| description | Abstract 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. |
| first_indexed | 2024-12-10T22:39:04Z |
| format | Article |
| id | doaj.art-edd3091ffcb944c2b1c42feba3cd6158 |
| institution | Directory Open Access Journal |
| issn | 1743-422X |
| language | English |
| last_indexed | 2024-12-10T22:39:04Z |
| publishDate | 2019-08-01 |
| publisher | BMC |
| record_format | Article |
| series | Virology Journal |
| spelling | doaj.art-edd3091ffcb944c2b1c42feba3cd61582022-12-22T01:30:45ZengBMCVirology Journal1743-422X2019-08-011611710.1186/s12985-019-1214-9Hepatitis C virus genotyping based on Core and NS5B regions in Cameroonian patientsPaul Alain Tagnouokam-Ngoupo0Marie Nicole Ngoufack1Sebastien Kenmoe2Simon Frédéric Lissock3Marie Amougou-Atsama4Robert Banai5Laure Ngono6Richard Njouom7Virology Department, Centre Pasteur of CameroonVirology Department, Centre Pasteur of CameroonVirology Department, Centre Pasteur of CameroonVirology Department, Centre Pasteur of CameroonVirology Department, Centre Pasteur of CameroonVirology Department, Centre Pasteur of CameroonVirology Department, Centre Pasteur of CameroonVirology Department, Centre Pasteur of CameroonAbstract 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.http://link.springer.com/article/10.1186/s12985-019-1214-9HCVGenotypingCoreNS5BGenotypesSubtypes |
| spellingShingle | Paul Alain Tagnouokam-Ngoupo Marie Nicole Ngoufack Sebastien Kenmoe Simon Frédéric Lissock Marie Amougou-Atsama Robert Banai Laure Ngono Richard Njouom Hepatitis C virus genotyping based on Core and NS5B regions in Cameroonian patients Virology Journal HCV Genotyping Core NS5B Genotypes Subtypes |
| title | Hepatitis C virus genotyping based on Core and NS5B regions in Cameroonian patients |
| title_full | Hepatitis C virus genotyping based on Core and NS5B regions in Cameroonian patients |
| title_fullStr | Hepatitis C virus genotyping based on Core and NS5B regions in Cameroonian patients |
| title_full_unstemmed | Hepatitis C virus genotyping based on Core and NS5B regions in Cameroonian patients |
| title_short | Hepatitis C virus genotyping based on Core and NS5B regions in Cameroonian patients |
| title_sort | hepatitis c virus genotyping based on core and ns5b regions in cameroonian patients |
| topic | HCV Genotyping Core NS5B Genotypes Subtypes |
| url | http://link.springer.com/article/10.1186/s12985-019-1214-9 |
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