Research Article: Phylogenetic analysis of hepatitis C virus among HIV/ HCV co-infected patients in Nigeria

Date Published: February 6, 2019

Publisher: Public Library of Science

Author(s): Juliet A. Shenge, Georgina N. Odaibo, David O. Olaleye, Jason Blackard.


Hepatitis C virus (HCV) infection has been associated with liver disease including liver cirrhosis and hepatocellular carcinoma (HCC) in chronically-infected persons. However, in HIV/HCV co-infected patients, increased rate of progression to cirrhosis and HCC has been reported. Limited information exists regarding genetic variants of HCV circulating among co-infected patients, which could be important in the design of broadly protective vaccine and management of the disease. Here, we determined the genotypes of HCV isolates circulating among HIV/HCV co-infected patients in Ibadan, southwestern Nigeria. One hundred and twenty-five HIV/HCV IgM positive samples obtained from HIV laboratory, University of Ibadan were used for this study. HCV NS5B gene was amplified using polymerase chain reaction (PCR). The amplified NS5B gene was sequenced using gene specific primers. Twenty isolates were amplified, out of which 13 were successfully sequenced. Phylogenetic analysis of the 13 sequenced isolates showed three HCV subtypes 1a, 3a and 5a belonging to genotypes 1, 3 and 5 respectively. Ten isolates (77%) belong to subtype 5a, followed by 2 isolates (15%) subtype 1a and 1 isolate (8%) was subtype 3a. The predominant HCV genotype was 5, followed by genotype 1 (subtype 1a). The findings, as well as the observed mutations in NS5B gene, indicate the need for screening and monitoring of HIV/HCV co-infected patients. Further study to determine the phylogeny of isolates circulating in other parts of Nigeria will be carried out.

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Hepatitis C virus (HCV) still affects more than 185 million people worldwide despite availability of highly effective antiviral therapy such as direct acting antiviral agents (DAA) [1]. According to [2], an estimated 3–4 million people become infected every year, representing more than three percent of the world’s population that are chronically infected, with most of these cases occurring in Africa [2, 3]. It is also estimated that about 350, 000 people die from liver failure and liver cancer caused by hepatitis C disease each year. Furthermore, about 2.3 million people infected with HIV are actually co-infected with hepatitis C virus globally [4].

HCV NS5B gene of 20 isolates were amplified while 13 (65%) of the 20 were successfully sequenced. The sequences have percentage identity of 97%- 100% with reference sequences obtained from GenBank HCV databases. Phylogenetic analysis of the 13 isolates showed three HCV genotypes 1, 3 and 5 (subtypes 1a, 3a and 5a). Ten isolates (77%) were subtype 5a, followed by 2 isolates (15%) subtype 1a and 1 (8%) was subtype 3a. Fig 1 shows the phylogenetic tree of the NS5B gene sequences of the isolates, while Fig 2 shows the amino acid translation indicating conserved and variable sites in the NS5B region. Amino acid substitutions in NS5B gene was compared with the prototype strain H77. Major mutations observed among the genotype 1 isolates (1a) were at positions 61 (G61K) and 89 (G89E). At the other positions, all the amino acids were conserved. In the lone genotype 3, there were substitutions in the following positions: 15 (S15G), 7(T7V), 54 (S54C), 71 (T71S) 89 (G89L) and 80 (T80I). Major mutations among the genotype 5 (5a subtype) isolates were at amino acid positions 89 (G89R) and 84 (S84C).

This study has shown HCV genotype 5, (subtype 5a), as the predominant HCV strain circulating among HIV/HCV co-infected patients in the study area in Nigeria, with the other genotypes being 1 and 3. Previous studies also showed genotype 5 among HCV- infected blood donors and patients with clinical symptoms [41]. Genotype 5 has not been reported among co-infected patients before now. However, multiple genotypes including 1, 2 and 4 have been previously reported among the general population in Nigeria [42, 43], in addition to numerous reported sero-prevalence studies [44]. These reports show that even within regions in Nigeria, HCV genotypes are differentially distributed and this has serious implication for HCV vaccine development and management of infection in the country. The predominance of genotype 5 among HCV infected individuals co-infected with HIV, may represent a trend of infection with the genotype. However, a larger study may be needed in the population, to provide further information on HCV types and pathogenesis among HIV co-infected population. HCV genotype 5 is not distributed globally [45] and as such, it has not been widely studied in infected persons, making its predominance among this population an interesting information and concern with regards to treatment and management.

In conclusion, three HCV genotypes 1, 3 and 5 were found circulating among HIV/HCV co-infected persons in Ibadan, Nigeria, with the predominant strain as genotype 5 S1 Fig. Mutations observed at the NS5B gene of HCV isolates have implications for therapy and monitoring of drug resistance, especially in regions, where the use of DAAs is limited, due to costs of procurement of the drugs. The high prevalence of genotype 5 among HCV patients co-infected with HIV has implication for diagnosis and treatment of this population in Nigeria.




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