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Choga WT, Gobe I, Seru K, Maruapula D, Ndlovu NS, Zuze BJL, Motshosi P, Matsuru T, Sabone P, Yu X, Blackard JT, San JE, Makhema J, Gaseitsiwe S, Moyo S. Genomic epidemiology and immune escape of SARS-CoV-2 recombinant strains circulating in Botswana. IJID REGIONS 2024; 13:100484. [PMID: 39670194 PMCID: PMC11636131 DOI: 10.1016/j.ijregi.2024.100484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2024] [Revised: 10/28/2024] [Accepted: 10/28/2024] [Indexed: 12/14/2024]
Abstract
Objectives We characterized the molecular and mutational landscape of SARS-CoV-2 recombinant strains in Botswana. Methods We performed genomic, phylogenetic, and immunoinformatic analyses of 5254 near-complete genomes from 2020 to 2023. We assessed the presence of mutations of interested (MutOI) that may be associated with immune escape in silico. Results We observed a few recombinant strains in Botswana, with the majority being descendants of Omicron (XBB*), except for XV and XM. Most recombinant sequences corresponded to transmission clusters. Most recombination events occurred within the receptor-binding domain (RDB) of the spike (S) protein. We identified 16 MutOI among different proteins, with the majority occurring at a very low global prevalence (<4.8 × 10-⁵). We also observed S:Q474K, a MutOI in the RBD, that was predicted to escape human leukocyte antigen class I-mediated immune responses. Molecular surveillance is vital to inform early detection and response to potential variants with heightened immune and vaccine breakthrough properties. Conclusions These results underscore the need for continued molecular surveillance to map the evolutionary landscape of SARS-CoV-2.
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Affiliation(s)
- Wonderful T. Choga
- Botswana Harvard Health Partnership, Gaborone, Botswana
- School of Allied Health Sciences, Faculty of Health Sciences, Gaborone, Botswana
| | - Irene Gobe
- School of Allied Health Sciences, Faculty of Health Sciences, Gaborone, Botswana
| | | | | | | | | | | | - Teko Matsuru
- Botswana Harvard Health Partnership, Gaborone, Botswana
| | - Phenyo Sabone
- Botswana Harvard Health Partnership, Gaborone, Botswana
| | - Xiaoyu Yu
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, Scotland, UK
| | | | - James E. San
- Duke Human Vaccine Institute (DHVI), Durham, USA
- University of KwaZulu-Natal (UKZN), Durban, South Africa
| | | | - Simani Gaseitsiwe
- Botswana Harvard Health Partnership, Gaborone, Botswana
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, Scotland, UK
| | - Sikhulile Moyo
- Botswana Harvard Health Partnership, Gaborone, Botswana
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, USA
- School of Health Systems and Public Health, University of Pretoria, Pretoria, South Africa
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
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Choga WT, Bareng OT, Moraka NO, Maruapula D, Gobe I, Ndlovu NS, Zuze BJL, Motshosi PC, Seru KB, Matsuru T, Boitswarelo M, Matshaba M, Gaolathe T, Mosepele M, Makhema J, Tamura TJM, Li JZ, Shapiro R, Lockman S, Gaseitsiwe S, Moyo S. Low Prevalence of Nirmatrelvir-Ritonavir Resistance-Associated Mutations in SARS-CoV-2 Lineages From Botswana. Open Forum Infect Dis 2024; 11:ofae344. [PMID: 39015352 PMCID: PMC11250512 DOI: 10.1093/ofid/ofae344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Accepted: 06/20/2024] [Indexed: 07/18/2024] Open
Abstract
Background We evaluated naturally occurring nirmatrelvir-ritonavir (NTV/r) resistance-associated mutations (RAMs) among severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strains from Botswana, a country with no NTV/r use to date, in order to recommend the usage of the agent for high-risk patients with coronavirus disease 2019 (COVID-19). Methods We conducted a retrospective analysis using 5254 complete SARS-CoV-2 sequences from Botswana (September 2020-September 2023). We evaluated the mutational landscape of SARS-CoV-2 3-Chymotrypsin-like protease (3CLpro) relative to the highlighted list of RAMs granted Food and Drug Administration Emergency Use Authorization in 2023. Results The sequenced 5254 samples included Beta variants of concerns (VOCs; n = 323), Delta VOCs (n = 1314), and Omicron VOCs (n = 3354). Overall, 77.8% of the sequences exhibited at least 1 polymorphism within 76/306 amino acid positions in the nsp5 gene. NTV/rRAMs were identified in 34/5254 (0.65%; 95% CI, 0.43%-0.87%) and occurred at 5 distinct positions. Among the NTV/r RAMS detected, A191V was the most prevalent (24/34; 70.6%). Notably, T21I mutation had a prevalence of 20.6% (7/34) and coexisted with either K90R (n = 3) polymorphism in Beta sequences with RAMs or P132H (n = 3) polymorphism for Omicron sequences with RAMs. Other NTV/r RAMs detected included P108S, with a prevalence of 5.88% (2/34), and L50F, with a prevalence of 2.94% (1/34). NTV/r RAMs were significantly higher (P < .001) in Delta (24/35) compared with Beta (4/34) and Omicron (6/34) sequences. Conclusions The frequency of NTV/r RAMs in Botswana was low. Higher rates were observed in Delta VOCs compared to Omicron and Beta VOCs. As NTV/r use expands globally, continuous surveillance for drug-resistant variants is essential, given the RAMs identified in our study.
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Affiliation(s)
- Wonderful T Choga
- Botswana Harvard Health Partnership, Gaborone, Botswana
- School of Applied Health Sciences, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana
| | - Ontlametse T Bareng
- Botswana Harvard Health Partnership, Gaborone, Botswana
- School of Applied Health Sciences, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana
| | - Natasha O Moraka
- Botswana Harvard Health Partnership, Gaborone, Botswana
- School of Applied Health Sciences, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana
| | | | - Irene Gobe
- School of Applied Health Sciences, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana
| | - Nokuthula S Ndlovu
- Botswana Harvard Health Partnership, Gaborone, Botswana
- Department of Biological Sciences and Biotechnology, Faculty of Sciences, Botswana International University of Science and Technology, Palapye, Botswana
| | | | | | | | - Teko Matsuru
- Botswana Harvard Health Partnership, Gaborone, Botswana
| | - Matshwenyego Boitswarelo
- Department of Health Systems Management, Clinical Services, Ministry of Health Botswana, Gaborone, Botswana
| | - Mogomotsi Matshaba
- Botswana-Baylor Children's Clinical Centre of Excellence, Gaborone, Botswana
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
| | - Tendani Gaolathe
- Botswana Harvard Health Partnership, Gaborone, Botswana
- Department of Internal Medicine, Faculty of Medicine, University of Botswana, Gaborone, Botswana
| | - Mosepele Mosepele
- Botswana Harvard Health Partnership, Gaborone, Botswana
- Department of Internal Medicine, Faculty of Medicine, University of Botswana, Gaborone, Botswana
| | - Joseph Makhema
- Botswana Harvard Health Partnership, Gaborone, Botswana
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Trevor J M Tamura
- Division of Infectious Diseases, Brigham & Women's Hospital, Boston, Massachusetts, USA
| | - Jonathan Z Li
- Division of Infectious Diseases, Brigham & Women's Hospital, Boston, Massachusetts, USA
| | - Roger Shapiro
- Botswana Harvard Health Partnership, Gaborone, Botswana
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Shahin Lockman
- Botswana Harvard Health Partnership, Gaborone, Botswana
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Simani Gaseitsiwe
- Botswana Harvard Health Partnership, Gaborone, Botswana
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Sikhulile Moyo
- Botswana Harvard Health Partnership, Gaborone, Botswana
- School of Applied Health Sciences, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
- School of Health Systems and Public Health, University of Pretoria, Pretoria, South Africa
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
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Anderson M, Mangogola T, Phinius BB, Mpebe G, Aimakhu CO, Choga WT, Phakedi B, Bhebhe LN, Ditshwanelo D, Baruti K, Mpofu-Dobo L, Othusitse L, Ratsoma T, Gaolathe T, Makhema J, Shapiro R, Lockman S, Moyo S, Gaseitsiwe S. Hepatitis B Virus Prevalence among HIV-Uninfected People Living in Rural and Peri-Urban Areas in Botswana. Microorganisms 2024; 12:1207. [PMID: 38930589 PMCID: PMC11205512 DOI: 10.3390/microorganisms12061207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 06/10/2024] [Accepted: 06/12/2024] [Indexed: 06/28/2024] Open
Abstract
(1) Background: we determined the prevalence of the hepatitis B virus (HBV) amongst people without human immunodeficiency virus (HIV) in rural and peri-urban areas in Botswana. (2) Methods: We screened for the hepatitis B surface antigen (HBsAg) from archived plasma samples of people without HIV (n = 2135) randomly selected from the Botswana Combination Prevention Program (BCPP) (2013-2018). We sequenced 415 bp of the surface region using BigDye sequencing chemistry. (3) Results: The median age of participants was 31 (IQR: 24-46) and 64% (1360/2135) were female. HBV prevalence was 4.0% (86/2135) [95% CI: 3.3-4.9]) and ranged between 0-9.2%. Older participants (>35 years) had increased odds of HBV positivity (OR: 1.94; 95% CI: [1.32-2.86]; p = 0.001). Thirteen samples were sequenced and seven (53.8%) were genotype A, three (23.1%) were genotype D and genotype E each. Clinically significant mutations were identified in the surface region, but no classic drug resistance mutations were identified. (4) Conclusions: We report an HBV prevalence of 4.0% (95% CI 3.3-4.9) among people without HIV in rural and peri-urban communities in Botswana with varying rates in different communities. A comprehensive national HBV program is required in Botswana to guide HBV prevention, testing and management.
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Affiliation(s)
- Motswedi Anderson
- Botswana Harvard Health Partnership, Private Bag BO320, Gaborone, Botswana; (M.A.); (T.M.); (B.B.P.); (G.M.); (W.T.C.); (B.P.); (L.N.B.); (D.D.); (K.B.); (L.M.-D.); (L.O.); (T.R.); (T.G.); (J.M.); (R.S.); (S.L.); (S.M.)
- Africa Health Research Institute, Durban 4013, South Africa
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Thabo Mangogola
- Botswana Harvard Health Partnership, Private Bag BO320, Gaborone, Botswana; (M.A.); (T.M.); (B.B.P.); (G.M.); (W.T.C.); (B.P.); (L.N.B.); (D.D.); (K.B.); (L.M.-D.); (L.O.); (T.R.); (T.G.); (J.M.); (R.S.); (S.L.); (S.M.)
- Pan-African University (Life and Earth Sciences Institute), University of Ibadan, Ibadan 200132, Nigeria;
| | - Bonolo B. Phinius
- Botswana Harvard Health Partnership, Private Bag BO320, Gaborone, Botswana; (M.A.); (T.M.); (B.B.P.); (G.M.); (W.T.C.); (B.P.); (L.N.B.); (D.D.); (K.B.); (L.M.-D.); (L.O.); (T.R.); (T.G.); (J.M.); (R.S.); (S.L.); (S.M.)
- School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Private Bag UB 0022, Gaborone, Botswana
| | - Gorata Mpebe
- Botswana Harvard Health Partnership, Private Bag BO320, Gaborone, Botswana; (M.A.); (T.M.); (B.B.P.); (G.M.); (W.T.C.); (B.P.); (L.N.B.); (D.D.); (K.B.); (L.M.-D.); (L.O.); (T.R.); (T.G.); (J.M.); (R.S.); (S.L.); (S.M.)
- Department of Biological Sciences, Faculty of Science, University of Botswana, Private Bag UB 0022, Gaborone, Botswana
| | - Christopher O. Aimakhu
- Pan-African University (Life and Earth Sciences Institute), University of Ibadan, Ibadan 200132, Nigeria;
| | - Wonderful T. Choga
- Botswana Harvard Health Partnership, Private Bag BO320, Gaborone, Botswana; (M.A.); (T.M.); (B.B.P.); (G.M.); (W.T.C.); (B.P.); (L.N.B.); (D.D.); (K.B.); (L.M.-D.); (L.O.); (T.R.); (T.G.); (J.M.); (R.S.); (S.L.); (S.M.)
- School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Private Bag UB 0022, Gaborone, Botswana
| | - Basetsana Phakedi
- Botswana Harvard Health Partnership, Private Bag BO320, Gaborone, Botswana; (M.A.); (T.M.); (B.B.P.); (G.M.); (W.T.C.); (B.P.); (L.N.B.); (D.D.); (K.B.); (L.M.-D.); (L.O.); (T.R.); (T.G.); (J.M.); (R.S.); (S.L.); (S.M.)
| | - Lynnette N. Bhebhe
- Botswana Harvard Health Partnership, Private Bag BO320, Gaborone, Botswana; (M.A.); (T.M.); (B.B.P.); (G.M.); (W.T.C.); (B.P.); (L.N.B.); (D.D.); (K.B.); (L.M.-D.); (L.O.); (T.R.); (T.G.); (J.M.); (R.S.); (S.L.); (S.M.)
| | - Doreen Ditshwanelo
- Botswana Harvard Health Partnership, Private Bag BO320, Gaborone, Botswana; (M.A.); (T.M.); (B.B.P.); (G.M.); (W.T.C.); (B.P.); (L.N.B.); (D.D.); (K.B.); (L.M.-D.); (L.O.); (T.R.); (T.G.); (J.M.); (R.S.); (S.L.); (S.M.)
| | - Kabo Baruti
- Botswana Harvard Health Partnership, Private Bag BO320, Gaborone, Botswana; (M.A.); (T.M.); (B.B.P.); (G.M.); (W.T.C.); (B.P.); (L.N.B.); (D.D.); (K.B.); (L.M.-D.); (L.O.); (T.R.); (T.G.); (J.M.); (R.S.); (S.L.); (S.M.)
- Department of Biological Sciences, Faculty of Science, University of Botswana, Private Bag UB 0022, Gaborone, Botswana
| | - Linda Mpofu-Dobo
- Botswana Harvard Health Partnership, Private Bag BO320, Gaborone, Botswana; (M.A.); (T.M.); (B.B.P.); (G.M.); (W.T.C.); (B.P.); (L.N.B.); (D.D.); (K.B.); (L.M.-D.); (L.O.); (T.R.); (T.G.); (J.M.); (R.S.); (S.L.); (S.M.)
- Department of Biological Sciences and Biotechnology, Faculty of Sciences, Botswana International University of Science and Technology, Private Bag 16, Palapye, Botswana
| | - Lebogang Othusitse
- Botswana Harvard Health Partnership, Private Bag BO320, Gaborone, Botswana; (M.A.); (T.M.); (B.B.P.); (G.M.); (W.T.C.); (B.P.); (L.N.B.); (D.D.); (K.B.); (L.M.-D.); (L.O.); (T.R.); (T.G.); (J.M.); (R.S.); (S.L.); (S.M.)
| | - Tsholofelo Ratsoma
- Botswana Harvard Health Partnership, Private Bag BO320, Gaborone, Botswana; (M.A.); (T.M.); (B.B.P.); (G.M.); (W.T.C.); (B.P.); (L.N.B.); (D.D.); (K.B.); (L.M.-D.); (L.O.); (T.R.); (T.G.); (J.M.); (R.S.); (S.L.); (S.M.)
- Department of Biological Sciences, Faculty of Science, University of Botswana, Private Bag UB 0022, Gaborone, Botswana
| | - Tendani Gaolathe
- Botswana Harvard Health Partnership, Private Bag BO320, Gaborone, Botswana; (M.A.); (T.M.); (B.B.P.); (G.M.); (W.T.C.); (B.P.); (L.N.B.); (D.D.); (K.B.); (L.M.-D.); (L.O.); (T.R.); (T.G.); (J.M.); (R.S.); (S.L.); (S.M.)
- Faculty of Medicine, University of Botswana, Private Bag UB 0022, Gaborone, Botswana
| | - Joseph Makhema
- Botswana Harvard Health Partnership, Private Bag BO320, Gaborone, Botswana; (M.A.); (T.M.); (B.B.P.); (G.M.); (W.T.C.); (B.P.); (L.N.B.); (D.D.); (K.B.); (L.M.-D.); (L.O.); (T.R.); (T.G.); (J.M.); (R.S.); (S.L.); (S.M.)
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Roger Shapiro
- Botswana Harvard Health Partnership, Private Bag BO320, Gaborone, Botswana; (M.A.); (T.M.); (B.B.P.); (G.M.); (W.T.C.); (B.P.); (L.N.B.); (D.D.); (K.B.); (L.M.-D.); (L.O.); (T.R.); (T.G.); (J.M.); (R.S.); (S.L.); (S.M.)
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Shahin Lockman
- Botswana Harvard Health Partnership, Private Bag BO320, Gaborone, Botswana; (M.A.); (T.M.); (B.B.P.); (G.M.); (W.T.C.); (B.P.); (L.N.B.); (D.D.); (K.B.); (L.M.-D.); (L.O.); (T.R.); (T.G.); (J.M.); (R.S.); (S.L.); (S.M.)
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
- Division of Infectious Diseases, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Sikhulile Moyo
- Botswana Harvard Health Partnership, Private Bag BO320, Gaborone, Botswana; (M.A.); (T.M.); (B.B.P.); (G.M.); (W.T.C.); (B.P.); (L.N.B.); (D.D.); (K.B.); (L.M.-D.); (L.O.); (T.R.); (T.G.); (J.M.); (R.S.); (S.L.); (S.M.)
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
- Division of Medical Virology, Faculty of Medicine and Health Sciences, University of Stellenbosch, Stellenbosch, Private Bag X1, Matieland 7602, South Africa
- School of Health Systems and Public Health, University of Pretoria, Private Bag X20, Pretoria 0028, South Africa
| | - Simani Gaseitsiwe
- Botswana Harvard Health Partnership, Private Bag BO320, Gaborone, Botswana; (M.A.); (T.M.); (B.B.P.); (G.M.); (W.T.C.); (B.P.); (L.N.B.); (D.D.); (K.B.); (L.M.-D.); (L.O.); (T.R.); (T.G.); (J.M.); (R.S.); (S.L.); (S.M.)
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
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Salod Z, Mahomed O. Mapping Potential Vaccine Candidates Predicted by VaxiJen for Different Viral Pathogens between 2017-2021-A Scoping Review. Vaccines (Basel) 2022; 10:1785. [PMID: 36366294 PMCID: PMC9695814 DOI: 10.3390/vaccines10111785] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 10/16/2022] [Accepted: 10/18/2022] [Indexed: 09/29/2023] Open
Abstract
Reverse vaccinology (RV) is a promising alternative to traditional vaccinology. RV focuses on in silico methods to identify antigens or potential vaccine candidates (PVCs) from a pathogen's proteome. Researchers use VaxiJen, the most well-known RV tool, to predict PVCs for various pathogens. The purpose of this scoping review is to provide an overview of PVCs predicted by VaxiJen for different viruses between 2017 and 2021 using Arksey and O'Malley's framework and the Preferred Reporting Items for Systematic Reviews extension for Scoping Reviews (PRISMA-ScR) guidelines. We used the term 'vaxijen' to search PubMed, Scopus, Web of Science, EBSCOhost, and ProQuest One Academic. The protocol was registered at the Open Science Framework (OSF). We identified articles on this topic, charted them, and discussed the key findings. The database searches yielded 1033 articles, of which 275 were eligible. Most studies focused on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), published between 2020 and 2021. Only a few articles (8/275; 2.9%) conducted experimental validations to confirm the predictions as vaccine candidates, with 2.2% (6/275) articles mentioning recombinant protein expression. Researchers commonly targeted parts of the SARS-CoV-2 spike (S) protein, with the frequently predicted epitopes as PVCs being major histocompatibility complex (MHC) class I T cell epitopes WTAGAAAYY, RQIAPGQTG, IAIVMVTIM, and B cell epitope IAPGQTGKIADY, among others. The findings of this review are promising for the development of novel vaccines. We recommend that vaccinologists use these findings as a guide to performing experimental validation for various viruses, with SARS-CoV-2 as a priority, because better vaccines are needed, especially to stay ahead of the emergence of new variants. If successful, these vaccines could provide broader protection than traditional vaccines.
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Affiliation(s)
- Zakia Salod
- Discipline of Public Health Medicine, University of KwaZulu-Natal, Durban 4051, South Africa
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Belaiba Z, Ayouni K, Gdoura M, Kammoun Rebai W, Touzi H, Sadraoui A, Hammemi W, Yacoubi L, Abdelati S, Hamzaoui L, Msaddak Azzouz M, Chouikha A, Triki H. Whole genome analysis of hepatitis B virus before and during long-term therapy in chronic infected patients: Molecular characterization, impact on treatment and liver disease progression. Front Microbiol 2022; 13:1020147. [PMID: 36325017 PMCID: PMC9618822 DOI: 10.3389/fmicb.2022.1020147] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 09/15/2022] [Indexed: 07/23/2023] Open
Abstract
Hepatitis B virus (HBV) infection remains a serious public health concern worldwide despite the availability of an efficient vaccine and the major improvements in antiviral treatments. The aim of the present study is to analyze the mutational profile of the HBV whole genome in ETV non-responder chronic HBV patients, in order to investigate antiviral drug resistance, immune escape, and liver disease progression to Liver Cirrhosis (LC) or Hepatocellular Carcinoma (HCC). Blood samples were collected from five chronic hepatitis B patients. For each patient, two plasma samples were collected, before and during the treatment. Whole genome sequencing was performed using Sanger technology. Phylogenetic analysis comparing the studied sequences with reference ones was used for genotyping. The mutational profile was analyzed by comparison with the reference sequence M32138. Genotyping showed that the studied strains belong to subgenotypes D1, D7, and D8. The mutational analysis showed high genetic variability. In the RT region of the polymerase gene, 28 amino acid (aa) mutations were detected. The most significant mutations were the pattern rtL180M + rtS202G + rtM204V, which confer treatment resistance. In the S gene, 35 mutations were detected namely sP120T, sT126S, sG130R, sY134F, sS193L, sI195M, and sL216stop were previously described to lead to vaccine, immunotherapy, and/or diagnosis escape. In the C gene, 34 mutations were found. In particular, cG1764A, cC1766G/T, cT1768A, and cC1773T in the BCP; cG1896A and cG1899A in the precore region and cT12S, cE64D, cA80T, and cP130Q in the core region were associated with disease progression to LC and/or HCC. Other mutations were associated with viral replication increase including cT1753V, cG1764A/T, cC1766G/T, cT1768A, and cC1788G in the BCP as well as cG1896A and cG1899A in the precore region. In the X gene, 30 aa substitutions were detected, of which substitutions xT36D, xP46S, xA47T, xI88F, xA102V, xI127T, xK130M, xV131I, and xF132Y were previously described to lead to LC and/or HCC disease progression. In conclusion, our results show high genetic variability in the long-term treatment of chronic HBV patients causing several effects. This could contribute to guiding national efforts to optimize relevant HBV treatment management in order to achieve the global hepatitis elimination goal by 2030.
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Affiliation(s)
- Zeineb Belaiba
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Pasteur Institute of Tunis, University Tunis El Manar (UTM), Tunis, Tunisia
- Research Laboratory “Virus, Vectors and Hosts: One Health Approach and Technological Innovation for a Better Health,” LR20IPT02, Pasteur Institute of Tunis, University Tunis El Manar (UTM), Tunis, Tunisia
| | - Kaouther Ayouni
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Pasteur Institute of Tunis, University Tunis El Manar (UTM), Tunis, Tunisia
- Research Laboratory “Virus, Vectors and Hosts: One Health Approach and Technological Innovation for a Better Health,” LR20IPT02, Pasteur Institute of Tunis, University Tunis El Manar (UTM), Tunis, Tunisia
| | - Mariem Gdoura
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Pasteur Institute of Tunis, University Tunis El Manar (UTM), Tunis, Tunisia
- Research Laboratory “Virus, Vectors and Hosts: One Health Approach and Technological Innovation for a Better Health,” LR20IPT02, Pasteur Institute of Tunis, University Tunis El Manar (UTM), Tunis, Tunisia
| | - Wafa Kammoun Rebai
- Laboratory of Biomedical Genomics and Oncogenetics (LR16IPT05), Pasteur Institute of Tunis, University Tunis El Manar (UTM), Tunis, Tunisia
| | - Henda Touzi
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Pasteur Institute of Tunis, University Tunis El Manar (UTM), Tunis, Tunisia
| | - Amel Sadraoui
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Pasteur Institute of Tunis, University Tunis El Manar (UTM), Tunis, Tunisia
| | - Walid Hammemi
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Pasteur Institute of Tunis, University Tunis El Manar (UTM), Tunis, Tunisia
| | - Lamia Yacoubi
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Pasteur Institute of Tunis, University Tunis El Manar (UTM), Tunis, Tunisia
| | - Salwa Abdelati
- Department of Gastroenterology, Polyclinic of CNSS, Sousse, Tunisia
| | - Lamine Hamzaoui
- Department of Gastroenterology, Hospital of Tahar Maamouri, Nabeul, Tunisia
| | | | - Anissa Chouikha
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Pasteur Institute of Tunis, University Tunis El Manar (UTM), Tunis, Tunisia
- Research Laboratory “Virus, Vectors and Hosts: One Health Approach and Technological Innovation for a Better Health,” LR20IPT02, Pasteur Institute of Tunis, University Tunis El Manar (UTM), Tunis, Tunisia
| | - Henda Triki
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Pasteur Institute of Tunis, University Tunis El Manar (UTM), Tunis, Tunisia
- Research Laboratory “Virus, Vectors and Hosts: One Health Approach and Technological Innovation for a Better Health,” LR20IPT02, Pasteur Institute of Tunis, University Tunis El Manar (UTM), Tunis, Tunisia
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Zhao HJ, Hu YF, Han QJ, Zhang J. Innate and adaptive immune escape mechanisms of hepatitis B virus. World J Gastroenterol 2022; 28:881-896. [PMID: 35317051 PMCID: PMC8908287 DOI: 10.3748/wjg.v28.i9.881] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 08/09/2021] [Accepted: 01/29/2022] [Indexed: 02/06/2023] Open
Abstract
Chronic hepatitis B virus (HBV) infection is an international health problem with extremely high mortality and morbidity rates. Although current clinical chronic hepatitis B (CHB) treatment strategies can partly inhibit and eliminate HBV, viral breakthrough may result due to non-adherence to treatment, the emergence of viral resistance, and a long treatment cycle. Persistent CHB infection arises as a consequence of complex interactions between the virus and the host innate and adaptive immune systems. Therefore, understanding the immune escape mechanisms involved in persistent HBV infection is important for designing novel CHB treatment strategies to clear HBV and achieve long-lasting immune control. This review details the immunological and biological characteristics and escape mechanisms of HBV and the novel immune-based therapies that are currently used for treating HBV.
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Affiliation(s)
- Hua-Jun Zhao
- Institute of Immunopharmaceutical Sciences, School of Pharmaceutical Sciences, Shandong University, Jinan 250012, Shandong Province, China
| | - Yi-Fei Hu
- Institute of Immunopharmaceutical Sciences, School of Pharmaceutical Sciences, Shandong University, Jinan 250012, Shandong Province, China
| | - Qiu-Ju Han
- Institute of Immunopharmaceutical Sciences, School of Pharmaceutical Sciences, Shandong University, Jinan 250012, Shandong Province, China
| | - Jian Zhang
- Institute of Immunopharmaceutical Sciences, School of Pharmaceutical Sciences, Shandong University, Jinan 250012, Shandong Province, China
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7
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Abstract
This review discusses peptide epitopes used as antigens in the development of vaccines in clinical trials as well as future vaccine candidates. It covers peptides used in potential immunotherapies for infectious diseases including SARS-CoV-2, influenza, hepatitis B and C, HIV, malaria, and others. In addition, peptides for cancer vaccines that target examples of overexpressed proteins are summarized, including human epidermal growth factor receptor 2 (HER-2), mucin 1 (MUC1), folate receptor, and others. The uses of peptides to target cancers caused by infective agents, for example, cervical cancer caused by human papilloma virus (HPV), are also discussed. This review also provides an overview of model peptide epitopes used to stimulate non-specific immune responses, and of self-adjuvanting peptides, as well as the influence of other adjuvants on peptide formulations. As highlighted in this review, several peptide immunotherapies are in advanced clinical trials as vaccines, and there is great potential for future therapies due the specificity of the response that can be achieved using peptide epitopes.
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Affiliation(s)
- Ian W Hamley
- Department of Chemistry, University of Reading, Whiteknights, Reading RG6 6AD, U.K
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Al-Azzam S, Ding Y, Liu J, Pandya P, Ting JP, Afshar S. Peptides to combat viral infectious diseases. Peptides 2020; 134:170402. [PMID: 32889022 PMCID: PMC7462603 DOI: 10.1016/j.peptides.2020.170402] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 08/24/2020] [Accepted: 08/28/2020] [Indexed: 12/14/2022]
Abstract
Viral infectious diseases have resulted in millions of deaths throughout history and have created a significant public healthcare burden. Tremendous efforts have been placed by the scientific communities, health officials and government organizations to detect, treat, and prevent viral infection. However, the complicated life cycle and rapid genetic mutations of viruses demand continuous development of novel medicines with high efficacy and safety profiles. Peptides provide a promising outlook as a tool to combat the spread and re-emergence of viral infection. This article provides an overview of five viral infectious diseases with high global prevalence: influenza, chronic hepatitis B, acquired immunodeficiency syndrome, severe acute respiratory syndrome, and coronavirus disease 2019. The current and potential peptide-based therapies, vaccines, and diagnostics for each disease are discussed.
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Affiliation(s)
- Shams Al-Azzam
- Professional Scientific Services, Eurofins Lancaster Laboratories, Lancaster, PA, 17605, USA
| | - Yun Ding
- Protein Engineering, Lilly Biotechnology Center, Eli Lilly and Company, San Diego, CA, 92121, USA
| | - Jinsha Liu
- Protein Engineering, Lilly Biotechnology Center, Eli Lilly and Company, San Diego, CA, 92121, USA
| | - Priyanka Pandya
- Protein Engineering, Lilly Biotechnology Center, Eli Lilly and Company, San Diego, CA, 92121, USA
| | - Joey Paolo Ting
- Protein Engineering, Lilly Biotechnology Center, Eli Lilly and Company, San Diego, CA, 92121, USA
| | - Sepideh Afshar
- Protein Engineering, Lilly Biotechnology Center, Eli Lilly and Company, San Diego, CA, 92121, USA.
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9
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Hepatitis B Virus Infection: From Diagnostics to Treatments. Viruses 2020; 12:v12121366. [PMID: 33265922 PMCID: PMC7761508 DOI: 10.3390/v12121366] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 11/28/2020] [Indexed: 02/07/2023] Open
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