Genetic Diversity of Hepatitis B and C Viruses Revealed by Continuous Surveillance from 2015 to 2021 in Gabon, Central Africa
Abstract
:1. Introduction
2. Materials and Methods
2.1. Sample Collection
2.2. Ethics Statement
2.3. Viral Genome Extraction and Reverse Transcription Quantitative PCR (RT-qPCR)
2.4. Genotyping of Hepatitis Virus Strains
2.5. Whole-Genome Sequencing
2.6. Phylogenetic Analysis
2.7. Statistical Analysis
2.8. Sequence Data Availability
3. Results
3.1. HBV and HCV Detection via RT-qPCR and Demographic Information of Patients with HBV or HCV Infections
3.2. Phylogenetic Analysis and Genetic Diversity of the HBV Strains Detected in Gabon
3.3. Unusual Fusion of the HBV X (HBx) and PreC/C Proteins Caused by Rare Insertions in HBV Genomes
3.4. Phylogenetic Analysis of the HCV Strains Detected in Gabon
3.5. Potential DAA Resistance of HCV-4e Strains
4. Discussion
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
- World Health Organization. Hepatitis B. Available online: https://www.who.int/news-room/fact-sheets/detail/hepatitis-b (accessed on 11 June 2023).
- GBD 2019 Hepatitis B Collaborators; Sheena, B.S.; Hiebert, L.; Han, H.; Ippolito, H.; Abbasi-Kangevari, M.; Abbasi-Kangevari, Z.; Abbastabar, H.; Abdoli, A.; Ali, H.A.; et al. Global, regional, and national burden of hepatitis B, 1990–2019: A systematic analysis for the Global Burden of Disease Study 2019. Lancet Gastroenterol. Hepatol. 2022, 7, 796–829. [Google Scholar] [CrossRef]
- Devarbhavi, H.; Asrani, S.K.; Arab, J.P.; Nartey, Y.A.; Pose, E.; Kamath, P.S. Global burden of Liver Disease: 2023 Update. J. Hepatol. 2023, 79, 516–537. [Google Scholar] [CrossRef]
- Cooke, G.S.; Andrieux-Meyer, I.; Applegate, T.L.; Atun, R.; Burry, J.R.; Cheinquer, H.; Dusheiko, G.; Feld, J.J.; Gore, C.; Griswold, M.G.; et al. Accelerating the elimination of viral hepatitis: A Lancet Gastroenterology & Hepatology Commission. Lancet Gastroenterol. Hepatol. 2019, 4, 135–184. [Google Scholar] [CrossRef] [Green Version]
- Tabata, K.; Neufeldt, C.J.; Bartenschlager, R. Hepatitis C virus replication. Cold Spring Harb. Perspect. Med. 2020, 10, a037093. [Google Scholar] [CrossRef]
- Revill, P.A.; Tu, T.; Netter, H.J.; Yuen, L.K.W.; Locarnini, S.A.; Littlejohn, M. The evolution and clinical impact of hepatitis B virus genome diversity. Nat. Rev. Gastroenterol. Hepatol. 2020, 17, 618–634. [Google Scholar] [CrossRef] [PubMed]
- Kao, J.H.; Chen, P.J.; Lai, M.Y.; Chen, D.S. Hepatitis B genotypes correlate with clinical outcomes in patients with chronic hepatitis B. Gastroenterology 2000, 118, 554–559. [Google Scholar] [CrossRef]
- Ducancelle, A.; Pivert, A.; Bertrais, S.; Boursier, J.; Balan, V.; Veillon, P.; le Guillou-Guillemette, H.; Thibault, V.; Castelain, S.; Roquebert, B.; et al. Different precore/core mutations of hepatitis B interact with, limit, or favor liver fibrosis severity. J. Gastroenterol. Hepatol. 2016, 31, 1750–1756. [Google Scholar] [CrossRef] [PubMed]
- Kim, H.; Lee, S.A.; Kim, B.J. X region mutations of hepatitis B virus related to clinical severity. World J. Gastroenterol. 2016, 22, 5467–5478. [Google Scholar] [CrossRef]
- Spearman, C.W.; Afihene, M.; Ally, R.; Apica, B.; Awuku, Y.; Cunha, L.; Dusheiko, G.; Gogela, N.; Kassianides, C.; Kew, M.; et al. Hepatitis B in sub-Saharan Africa: Strategies to achieve the 2030 elimination targets. Lancet Gastroenterol. Hepatol. 2017, 2, 900–909. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Pourkarim, M.R.; Amini-Bavil-Olyaee, S.; Kurbanov, F.; Van Ranst, M.; Tacke, F. Molecular identification of hepatitis B virus genotypes/subgenotypes: Revised classification hurdles and updated resolutions. World J. Gastroenterol. 2014, 20, 7152–7168. [Google Scholar] [CrossRef] [PubMed]
- Cai, Q.; Zhu, H.; Zhang, Y.; Li, X.; Zhang, Z. Hepatitis B virus genotype A: Design of reference sequences for sub-genotypes. Virus Genes 2016, 52, 325–333. [Google Scholar] [CrossRef]
- Tong, S.; Kim, K.H.; Chante, C.; Wands, J.; Li, J. Hepatitis B virus e antigen variants. Int. J. Med. Sci. 2005, 2, 2–7. [Google Scholar] [CrossRef] [Green Version]
- Simmonds, P.; Alberti, A.; Alter, H.J.; Bonino, F.; Bradley, D.W.; Brechot, C.; Brouwer, J.T.; Chan, S.W.; Chayama, K.; Chen, D.S. A proposed system for the nomenclature of hepatitis C viral genotypes. Hepatology 1994, 19, 1321–1324. [Google Scholar] [CrossRef]
- Simmonds, P. Genetic diversity and evolution of hepatitis C virus−15 years on. J. Gen. Virol. 2004, 85, 3173–3188. [Google Scholar] [CrossRef]
- Smith, D.B.; Bukh, J.; Kuiken, C.; Muerhoff, A.S.; Rice, C.M.; Stapleton, J.T.; Simmonds, P. Expanded classification of hepatitis C virus into 7 genotypes and 67 subtypes: Updated criteria and genotype assignment web resource. Hepatology 2014, 59, 318–327. [Google Scholar] [CrossRef] [Green Version]
- Martinez, M.A.; Franco, S. Therapy implications of hepatitis C virus genetic diversity. Viruses 2020, 13, 41. [Google Scholar] [CrossRef]
- Dietz, J.; Susser, S.; Vermehren, J.; Peiffer, K.H.; Grammatikos, G.; Berger, A.; Ferenci, P.; Buti, M.; Müllhaupt, B.; Hunyady, B.; et al. Patterns of resistance-associated substitutions in patients with chronic HCV infection following treatment with direct-acting antivirals. Gastroenterology 2018, 154, 976–988.e4. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Pawlotsky, J.M. Hepatitis C virus resistance to direct-acting antiviral drugs in interferon-free regimens. Gastroenterology 2016, 151, 70–86. [Google Scholar] [CrossRef] [Green Version]
- Sarrazin, C. The importance of resistance to direct antiviral drugs in HCV infection in clinical practice. J. Hepatol. 2016, 64, 486–504. [Google Scholar] [CrossRef] [PubMed]
- Shah, R.; Ahovegbe, L.; Niebel, M.; Shepherd, J.; Thomson, E.C. Non-epidemic HCV genotypes in low- and middle-income countries and the risk of resistance to current direct-acting antiviral regimens. J. Hepatol. 2021, 75, 462–473. [Google Scholar] [CrossRef] [PubMed]
- Schweitzer, A.; Horn, J.; Mikolajczyk, R.T.; Krause, G.; Ott, J.J. Estimations of worldwide prevalence of chronic hepatitis B virus infection: A systematic review of data published between 1965 and 2013. Lancet 2015, 386, 1546–1555. [Google Scholar] [CrossRef] [PubMed]
- Makuwa, M.; Caron, M.; Souquière, S.; Malonga-Mouelet, G.; Mahé, A.; Kazanji, M. Prevalence and genetic diversity of hepatitis B and delta viruses in pregnant women in Gabon: Molecular evidence that hepatitis delta virus clade 8 originates from and is endemic in central Africa. J. Clin. Microbiol. 2008, 46, 754–756. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Makuwa, M.; Mintsa-Ndong, A.; Souquière, S.; Nkoghé, D.; Leroy, E.M.; Kazanji, M. Prevalence and molecular diversity of hepatitis B virus and hepatitis delta virus in urban and rural populations in northern Gabon in Central Africa. J. Clin. Microbiol. 2009, 47, 2265–2268. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Ndong-Atome, G.R.; Makuwa, M.; Ouwe-Missi-Oukem-Boyer, O.; Pybus, O.G.; Branger, M.; Le Hello, S.; Boye-Cheik, S.B.; Brun-Vezinet, F.; Kazanji, M.; Roques, P.; et al. High prevalence of hepatitis C virus infection and predominance of genotype 4 in rural Gabon. J. Med. Virol. 2008, 80, 1581–1587. [Google Scholar] [CrossRef]
- Ndong-Atome, G.R.; Njouom, R.; Padilla, C.; Bisvigou, U.; Makuwa, M.; Kazanji, M. Absence of intrafamilial transmission of hepatitis C virus and low risk for sexual transmission in rural central Africa indicate a cohort effect. J. Clin. Virol. 2009, 45, 349–353. [Google Scholar] [CrossRef]
- Abe, H.; Ushijima, Y.; Loembe, M.M.; Bikangui, R.; Nguema-Ondo, G.; Mpingabo, P.I.; Zadeh, V.R.; Pemba, C.M.; Kurosaki, Y.; Igasaki, Y.; et al. Re-emergence of dengue virus serotype 3 infections in Gabon in 2016–2017, and evidence for the risk of repeated dengue virus infections. Int. J. Infect. Dis. 2020, 91, 129–136. [Google Scholar] [CrossRef]
- Abe, H.; Ushijima, Y.; Bikangui, R.; Loembe, M.M.; Agnandji, S.T.; de Vries, S.G.; Grobusch, M.P.; Lell, B.; Yasuda, J. Ongoing evolution of hepatitis B virus during viremia in patients with febrile in Central Africa. J. Med. Virol. 2020, 92, 251–256. [Google Scholar] [CrossRef]
- Candotti, D.; Temple, J.; Sarkodie, F.; Allain, J.P. Frequent recovery and broad genotype 2 diversity characterize hepatitis C virus infection in Ghana, West Africa. J. Virol. 2003, 77, 7914–7923. [Google Scholar] [CrossRef] [Green Version]
- Abe, H.; Ushijima, Y.; Bikangui, R.; Ondo, G.N.; Zadeh, V.R.; Pemba, C.M.; Mpingabo, P.I.; Igasaki, Y.; de Vries, S.G.; Grobusch, M.P.; et al. First evidence for continuous circulation of hepatitis A virus subgenotype IIA in Central Africa. J. Viral Hepat. 2020, 27, 1234–1242. [Google Scholar] [CrossRef]
- Stuyver, L.; De Gendt, S.; Van Geyt, C.; Zoulim, F.; Fried, M.; Schinazi, R.F.; Rossau, R. A new genotype of hepatitis B virus: Complete genome and phylogenetic relatedness. J. Gen. Virol. 2000, 81, 67–74. [Google Scholar] [CrossRef]
- Enomoto, N.; Takada, A.; Nakao, T.; Date, T. There are two major types of hepatitis C virus in Japan. Biochem. Biophys. Res. Commun. 1990, 170, 1021–1025. [Google Scholar] [CrossRef]
- World Health Organization. Global Health Sector Strategies 2022–2030. Available online: https://www.who.int/teams/global-hiv-hepatitis-and-stis-programmes/strategies/global-health-sector-strategies (accessed on 8 June 2023).
- United Nations. Transforming Our World: The 2030 Agenda for Sustainable Development. Available online: https://sdgs.un.org/2030agenda (accessed on 8 June 2023).
- Makuwa, M.; Souquière, S.; Telfer, P.; Apetrei, C.; Vray, M.; Bedjabaga, I.; Mouinga-Ondeme, A.; Onanga, R.; Marx, P.A.; Kazanji, M.; et al. Identification of hepatitis B virus subgenotype A3 in rural Gabon. J. Med. Virol. 2006, 78, 1175–1184. [Google Scholar] [CrossRef]
- Hong, X.; Bianchini, E.N.; Wang, J.C.; Hu, J. Characterization of Intracellular Precore-Derived Proteins and Their Functions in Hepatitis B Virus-Infected Human Hepatocytes. mBio 2023, 14, e0350122. [Google Scholar] [CrossRef]
- Prieto, C.; Montecinos, J.; Jiménez, G.; Riquelme, C.; Garrido, D.; Hernández, S.; Loyola, A.; Villanueva, R.A. Phosphorylation of Phylogenetically Conserved Amino Acid Residues Confines HBx within Different Cell Compartments of Human Hepatocarcinoma Cells. Molecules 2021, 26, 1254. [Google Scholar] [CrossRef] [PubMed]
- Hernández, S.; Álvarez-Astudillo, F.; Garrido, D.; Prieto, C.; Loyola, A.; Villanueva, R.A. Canonical and Divergent N-Terminal HBx Isoform Proteins Unveiled: Characteristics and Roles during HBV Replication. Biomedicines 2021, 9, 1701. [Google Scholar] [CrossRef]
- Lucifora, J.; Arzberger, S.; Durantel, D.; Belloni, L.; Strubin, M.; Levrero, M.; Zoulim, F.; Hantz, O.; Protzer, U. Hepatitis B virus X protein is essential to initiate and maintain virus replication after infection. J. Hepatol. 2011, 55, 996–1003. [Google Scholar] [CrossRef]
- Simmonds, P. The origin of hepatitis C virus. Curr. Top. Microbiol. Immunol. 2013, 369, 1–15. [Google Scholar] [CrossRef] [PubMed]
- Sarrazin, C.; Dvory-Sobol, H.; Svarovskaia, E.S.; Doehle, B.P.; Pang, P.S.; Chuang, S.M.; Ma, J.; Ding, X.; Afdhal, N.H.; Kowdley, K.V.; et al. Prevalence of Resistance-Associated Substitutions in HCV NS5A, NS5B, or NS3 and Outcomes of Treatment With Ledipasvir and Sofosbuvir. Gastroenterology 2016, 151, 501–512.e1. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Gottwein, J.M.; Pham, L.V.; Mikkelsen, L.S.; Ghanem, L.; Ramirez, S.; Scheel, T.K.H.; Carlsen, T.H.R.; Bukh, J. Efficacy of NS5A Inhibitors Against Hepatitis C Virus Genotypes 1–7 and Escape Variants. Gastroenterology 2018, 154, 1435–1448. [Google Scholar] [CrossRef]
- Nguyen, D.; Smith, D.; Vaughan-Jackson, A.; Magri, A.; STOP-HCV Consortium; Barnes, E.; Simmonds, P. Efficacy of NS5A inhibitors against unusual and potentially difficult-to-treat HCV subtypes commonly found in sub-Saharan Africa and South East Asia. J. Hepatol. 2020, 73, 794–799. [Google Scholar] [CrossRef] [PubMed]
- Ushijima, Y.; Abe, H.; Mbadinga, M.J.V.M.; Ondo, G.N.; Bikangui, R.; Agnandji, S.T.; Lell, B.; Yasuda, J. Re-emergence of dengue, chikungunya, and Zika viruses in 2021 after a 10-year gap in Gabon. IJID Reg. 2022, 5, 68–71. [Google Scholar] [CrossRef]
- Ushijima, Y.; Abe, H.; Nguema Ondo, G.; Bikangui, R.; Massinga Loembé, M.; Zadeh, V.R.; Essimengane, J.G.E.; Mbouna, A.V.N.; Bache, E.B.; Agnandji, S.T.; et al. Surveillance of the major pathogenic arboviruses of public health concern in Gabon, Central Africa: Increased risk of West Nile virus and dengue virus infections. BMC Infect. Dis. 2021, 21, 265. [Google Scholar] [CrossRef]
- Abe, H.; Ushijima, Y.; Bikangui, R.; Ondo, G.N.; Lell, B.; Adegnika, A.A.; Yasuda, J. Delays in the arrival of the waves of COVID-19: A comparison between Gabon and the African continent. Lancet Microbe 2022, 3, e476. [Google Scholar] [CrossRef]
- El-Akel, W.; El-Sayed, M.H.; El Kassas, M.; El-Serafy, M.; Khairy, M.; Elsaeed, K.; Kabil, K.; Hassany, M.; Shawky, A.; Yosry, A.; et al. National treatment programme of hepatitis C in Egypt: Hepatitis C virus model of care. J. Viral Hepat. 2017, 24, 262–267. [Google Scholar] [CrossRef] [PubMed]
- El Kassas, M.; Funk, A.L.; Salaheldin, M.; Shimakawa, Y.; Eltabbakh, M.; Jean, K.; El Tahan, A.; Sweedy, A.T.; Afify, S.; Youssef, N.F.; et al. Increased recurrence rates of hepatocellular carcinoma after DAA therapy in a hepatitis C-infected Egyptian cohort: A comparative analysis. J. Viral Hepat. 2018, 25, 623–630. [Google Scholar] [CrossRef] [PubMed]
- Shoun, A.A.; Abozahra, R.; Baraka, K.; Mehrez, M.; Abdelhamid, S.M. Identifying different mutation sites leading to resistance to the direct-acting antiviral (DAA) sofosbuvir in hepatitis C virus patients from Egypt. Microorganisms 2022, 10, 679. [Google Scholar] [CrossRef] [PubMed]
RT-qPCR-Positive Patients | RT-qPCR-Negative Patients | p-Value | ||||
---|---|---|---|---|---|---|
Virus | Age (95% CI) | M/F Ratio | Age (95% CI) | M/F Ratio | Age | M/F Ratio |
HBV | 21.55 (13.70–29.39) | 0.45 | 12.97 (12.28–13.66) | 0.48 | <0.05 | 0.83 |
HCV | 48.56 (32.61–64.50) | 0.33 | 12.90 (12.23–13.58) | 0.48 | <0.001 | 0.38 |
Protein | Position | 4a | 4b | 4c | 4d | 4e | 4f | 4g | 4k | 4l | 4m | 4n | 4o | 4p | 4q | 4r | 4s | 4t | 4v | 4w |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
NS3 | V36 | L | L | L | L | L | L | L | L | L | L | L | L | L | L | L | L | L | L | L |
Q41 | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | |
F43 | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | |
T54 | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | |
V55 | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | |
Y56 | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | |
N77 | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | |
Q80 | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | |
S122 | T | - | T | T | T | T | T | T | T | - | T | T | T | N | T | N | T | N | T | |
R155 | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | |
A156 | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | |
D168 | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | T | - | - | - | |
I/V170 | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | |
NS5A | L23 | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - |
K24 | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | |
M28 | V | L | L | L | L | L | L | L | L | L | L | - | L | L | - | L | L | L | - | |
Q30 | L | S | R | R | R | R | L | R | R | S | R | T | R | R | R | R | R | R | S | |
L31 | M | M | M | M | M | M | M | - | M | M | M | M | M | M | - | - | M | M | M | |
P32 | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | |
S38 | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | |
H54 | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | |
H58 | P | P | P | T | P | P | P | P | P | R | T | P | P | P | P | P | P | P | P | |
E62 | D | - | Q | - | - | - | S | - | - | R | - | - | - | - | S | - | - | - | - | |
A92 | - | T | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | |
Y93 | - | H | - | - | - | - | R | - | - | - | - | - | - | - | - | - | - | - | S | |
NS5B | S96 | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - |
N142 | - | - | - | - | - | - | - | - | - | - | - | - | S | - | - | - | - | - | S | |
L159 | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | |
S282 | T | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | |
C/F/M289 | - | - | - | - | - | - | - | - | - | - | - | - | - | L | - | - | - | L | - | |
L320 | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | |
C316 | - | - | - | - | - | N | H | - | - | - | - | - | - | - | H | - | - | - | - | |
V321 | - | - | - | - | - | - | I | - | - | - | - | - | - | - | I | - | - | - | - | |
S556 | G | G | G | G | G | G | G | G | G | G | G | G | G | G | N | G | G | G | G |
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Abe, H.; Ushijima, Y.; Bikangui, R.; Ondo, G.N.; Pemba, C.M.; Zadeh, V.R.; Mpingabo, P.I.; Ueda, H.; Agnandji, S.T.; Lell, B.; et al. Genetic Diversity of Hepatitis B and C Viruses Revealed by Continuous Surveillance from 2015 to 2021 in Gabon, Central Africa. Microorganisms 2023, 11, 2046. https://doi.org/10.3390/microorganisms11082046
Abe H, Ushijima Y, Bikangui R, Ondo GN, Pemba CM, Zadeh VR, Mpingabo PI, Ueda H, Agnandji ST, Lell B, et al. Genetic Diversity of Hepatitis B and C Viruses Revealed by Continuous Surveillance from 2015 to 2021 in Gabon, Central Africa. Microorganisms. 2023; 11(8):2046. https://doi.org/10.3390/microorganisms11082046
Chicago/Turabian StyleAbe, Haruka, Yuri Ushijima, Rodrigue Bikangui, Georgelin Nguema Ondo, Christelle M. Pemba, Vahid R. Zadeh, Patrick I. Mpingabo, Hayato Ueda, Selidji T. Agnandji, Bertrand Lell, and et al. 2023. "Genetic Diversity of Hepatitis B and C Viruses Revealed by Continuous Surveillance from 2015 to 2021 in Gabon, Central Africa" Microorganisms 11, no. 8: 2046. https://doi.org/10.3390/microorganisms11082046