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Khan N, Kakakhel S, Malik A, Nigar K, Akhtar S, Khan AA, Khan A. Genetic substructure and host-specific natural selection trend across vaccine-candidate ORF-2 capsid protein of hepatitis-E virus. J Viral Hepat 2024; 31:524-534. [PMID: 38804127 DOI: 10.1111/jvh.13959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 05/03/2024] [Accepted: 05/13/2024] [Indexed: 05/29/2024]
Abstract
Hepatitis E virus is a primary cause of acute hepatitis worldwide. The present study attempts to assess the genetic variability and evolutionary divergence among HEV genotypes. A vaccine promising capsid-protein coding ORF-2 gene sequences of HEV was evaluated using phylogenetics, model-based population genetic methods and principal component analysis. The analyses unveiled nine distinct clusters as subpopulations for six HEV genotypes. HEV-3 genotype samples stratified into four different subgroups, while HEV-4 stratified into three additional subclusters. Rabbit-infectious HEV-3ra samples constitute a distinct cluster. Pairwise analysis identified marked genetic distinction of HEV-4c and HEV-4i subgenotypes compared to other genotypes. Numerous admixed, inter and intragenotype recombinant strains were detected. The MEME method identified several ORF-2 codon sites under positive selection. Some selection signatures lead to amino acid substitutions within ORF-2, resulting in altered physicochemical features. Moreover, a pattern of host-specific adaptive signatures was identified among HEV genotypes. The analyses conclusively depict that recombination and episodic positive selection events have shaped the observed genetic diversity among different HEV genotypes. The significant genetic diversity and stratification of HEV-3 and HEV-4 genotypes into subgroups, as identified in the current study, are noteworthy and may have implications for the efficacy of anti-HEV vaccines.
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Affiliation(s)
- Nasir Khan
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, 23200, Pakistan
| | - Sehrish Kakakhel
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, 23200, Pakistan
| | - Abdul Malik
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Kiran Nigar
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, 23200, Pakistan
| | - Suhail Akhtar
- Department of Biochemistry, A.T. Still University of Health Sciences, Kirksville, Missouri, USA
| | - Azmat Ali Khan
- Pharmaceutical Biotechnology Laboratory, Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Asifullah Khan
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, 23200, Pakistan
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Liu Z, Zhang Z, Yang L, Zhang Y, Li D, Zhang Q, Niu C, Zhang B, Zhai Y, Wang Z. Effect and mechanism of C-terminal cysteine on the properties of HEV p222 protein. Virology 2024; 595:110091. [PMID: 38718446 DOI: 10.1016/j.virol.2024.110091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Revised: 04/07/2024] [Accepted: 04/18/2024] [Indexed: 05/18/2024]
Abstract
Preliminary investigations have demonstrated that the cysteines located at the C-terminus of HEV ORF2 protein exhibits disulfide bonding capability during virus-like particles (VLPs) assembly. However, the effect and mechanism underlying the pairing of disulfide bonds formed by C627, C630, and C638 remains unclear. The p222 protein encompasses C-terminus and serves as a representative of HEV ORF2 to investigate the specific impacts of C627, C630, and C638. The three cysteines were subjected to site-directed mutagenesis and expressed in prokaryotes; Both the mutated proteins and p222 underwent polymerization except for p222A; Surprisingly, only p222 was observed as abundant spherical particles under transmission electron microscope (TEM); Stability and immunogenicity of the p222 exhibited higher than other mutated proteins; LC/MS/MS analysis identified four disulfide bonds in the p222. The novel findings suggest that the three cysteines contribute to structural and functional properties of ORF2 protein, highlighting the indispensability of each cysteine.
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Affiliation(s)
- Zhenzhen Liu
- College of Medicine, Henan Polytechnic University, Jiaozuo, 454000, Henan, China
| | - Zhenzhen Zhang
- College of Medicine, Henan Polytechnic University, Jiaozuo, 454000, Henan, China
| | - Lanping Yang
- College of Medicine, Henan Polytechnic University, Jiaozuo, 454000, Henan, China
| | - Yongwen Zhang
- College of Medicine, Henan Polytechnic University, Jiaozuo, 454000, Henan, China
| | - Dong Li
- College of Medicine, Henan Polytechnic University, Jiaozuo, 454000, Henan, China
| | - Qingling Zhang
- College of Medicine, Henan Polytechnic University, Jiaozuo, 454000, Henan, China
| | - Chao Niu
- College of Medicine, Henan Polytechnic University, Jiaozuo, 454000, Henan, China
| | - Baobao Zhang
- College of Medicine, Henan Polytechnic University, Jiaozuo, 454000, Henan, China
| | - Yangyang Zhai
- College of Medicine, Henan Polytechnic University, Jiaozuo, 454000, Henan, China
| | - Zhenhui Wang
- College of Medicine, Henan Polytechnic University, Jiaozuo, 454000, Henan, China.
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Orosz L, Sárvári KP, Dernovics Á, Rosztóczy A, Megyeri K. Pathogenesis and clinical features of severe hepatitis E virus infection. World J Virol 2024; 13:91580. [PMID: 38984076 PMCID: PMC11229844 DOI: 10.5501/wjv.v13.i2.91580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 02/08/2024] [Accepted: 04/15/2024] [Indexed: 06/24/2024] Open
Abstract
The hepatitis E virus (HEV), a member of the Hepeviridae family, is a small, non-enveloped icosahedral virus divided into eight distinct genotypes (HEV-1 to HEV-8). Only genotypes 1 to 4 are known to cause diseases in humans. Genotypes 1 and 2 commonly spread via fecal-oral transmission, often through the consumption of contaminated water. Genotypes 3 and 4 are known to infect pigs, deer, and wild boars, often transferring to humans through inadequately cooked meat. Acute hepatitis caused by HEV in healthy individuals is mostly asymptomatic or associated with minor symptoms, such as jaundice. However, in immunosuppressed individuals, the disease can progress to chronic hepatitis and even escalate to cirrhosis. For pregnant women, an HEV infection can cause fulminant liver failure, with a potential mortality rate of 25%. Mortality rates also rise amongst cirrhotic patients when they contract an acute HEV infection, which can even trigger acute-on-chronic liver failure if layered onto pre-existing chronic liver disease. As the prevalence of HEV infection continues to rise worldwide, highlighting the particular risks associated with severe HEV infection is of major medical interest. This text offers a brief summary of the characteristics of hepatitis developed by patient groups at an elevated risk of severe HEV infection.
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Affiliation(s)
- László Orosz
- Department of Medical Microbiology, University of Szeged, Szeged 6720, Csongrád-Csanád, Hungary
| | - Károly Péter Sárvári
- Department of Medical Microbiology, University of Szeged, Szeged 6720, Csongrád-Csanád, Hungary
| | - Áron Dernovics
- Department of Medical Microbiology, University of Szeged, Szeged 6720, Csongrád-Csanád, Hungary
| | - András Rosztóczy
- Department of Internal Medicine, Division of Gastroenterology, University of Szeged, Szeged 6725, Csongrád-Csanád, Hungary
| | - Klára Megyeri
- Department of Medical Microbiology, University of Szeged, Szeged 6720, Csongrád-Csanád, Hungary
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Arce LP, Pavan MF, Bok M, Gutiérrez SE, Estein SM, Santos AT, Condorí WE, Uhart MM, Parreño V, Vizoso-Pinto MG, Ibañez LI. A multispecies competitive nanobody-based ELISA for the detection of antibodies against hepatitis E virus. Sci Rep 2023; 13:15448. [PMID: 37723180 PMCID: PMC10507121 DOI: 10.1038/s41598-023-41955-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 09/04/2023] [Indexed: 09/20/2023] Open
Abstract
The hepatitis E virus (HEV) is an emergent zoonotic virus causing viral hepatitis worldwide. Clinically, hepatitis E is not easily distinguished from other types of acute viral hepatitis. There is a need for HEV diagnostic assays to detect and prevent interspecies transmission among susceptible populations. Nanobodies (Nbs) are expressed recombinantly in different systems, produced with high yields, and have superior physicochemical properties compared with conventional antibodies (Ab). Several Nbs against ORF2, the capsid protein and main antigen, were selected and produced in E. coli. Nb39 and Nb74 specifically recognized HEV ORF2 (genotypes 3 and 4). A competitive ELISA (cELISA) was developed and validated using a reference panel of human (n = 86) and swine sera (n = 116) tested in comparison with a commercial kit. The optimal cutoff values determined by ROC analysis were 69.16% (human) and 58.76% (swine); the sensitivity and specificity were high: 97.4% (95% CI 86.5-99.5%) and 95.8% (95% CI 86.0-98.8%) for human vs. 100% (95% CI 93.5-100%) and 98.3% (95% CI 91.0-99.7%) for swine. Further, the cELISA detected total anti-HEV antibodies in wild boar, deer, and mice. To our knowledge, this is the first report of production of Nbs against HEV-3 ORF2 for diagnostic purposes.
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Affiliation(s)
- Lorena Paola Arce
- Infection Biology Laboratory, Faculty of Medicine and Instituto Superior de Investigaciones Biológicas (INSIBIO), CONICET-UNT, T4000ILI, Tucumán, Argentina
- Laboratorio de Ingeniería de Anticuerpos, Instituto de Química, Física de los Materiales, Medio ambiente y Energía (INQUIMAE-CONICET), C1428EGA, Ciudad Autónoma de Buenos Aires, Argentina
| | - María Florencia Pavan
- Laboratorio de Ingeniería de Anticuerpos, Instituto de Química, Física de los Materiales, Medio ambiente y Energía (INQUIMAE-CONICET), C1428EGA, Ciudad Autónoma de Buenos Aires, Argentina
| | - Marina Bok
- IncuINTA, Instituto de Virología, Instituto Nacional de Tecnología Agropecuaria (INTA), 1686, Husrlingham, Argentina
| | - Silvina Elena Gutiérrez
- Universidad Nacional del Centro de la Provincia de Buenos Aires, Facultad de Ciencias Veterinarias, Núcleo SAMP, Centro de Investigación Veterinaria de Tandil (UNCPBA-CICPBA-CONICET), B7000GHG, Tandil, Buenos Aires, Argentina
| | - Silvia Marcela Estein
- Universidad Nacional del Centro de la Provincia de Buenos Aires, Facultad de Ciencias Veterinarias, Núcleo SAMP, Centro de Investigación Veterinaria de Tandil (UNCPBA-CICPBA-CONICET), B7000GHG, Tandil, Buenos Aires, Argentina
| | - Agostina Tammone Santos
- Universidad Nacional del Centro de la Provincia de Buenos Aires, Facultad de Ciencias Veterinarias, Núcleo SAMP, Centro de Investigación Veterinaria de Tandil (UNCPBA-CICPBA-CONICET), B7000GHG, Tandil, Buenos Aires, Argentina
| | - Walter Ezequiel Condorí
- Universidad Nacional del Centro de la Provincia de Buenos Aires, Facultad de Ciencias Veterinarias, Núcleo SAMP, Centro de Investigación Veterinaria de Tandil (UNCPBA-CICPBA-CONICET), B7000GHG, Tandil, Buenos Aires, Argentina
| | - Marcela María Uhart
- One Health Institute, School of Veterinary Medicine, University of California Davis, Davis, CA, 95616, USA
| | - Viviana Parreño
- IncuINTA, Instituto de Virología, Instituto Nacional de Tecnología Agropecuaria (INTA), 1686, Husrlingham, Argentina
| | - María Guadalupe Vizoso-Pinto
- Infection Biology Laboratory, Faculty of Medicine and Instituto Superior de Investigaciones Biológicas (INSIBIO), CONICET-UNT, T4000ILI, Tucumán, Argentina.
| | - Lorena Itatí Ibañez
- Laboratorio de Ingeniería de Anticuerpos, Instituto de Química, Física de los Materiales, Medio ambiente y Energía (INQUIMAE-CONICET), C1428EGA, Ciudad Autónoma de Buenos Aires, Argentina.
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Sultana R, Biswas J, Uddin MG, Efaz FM, Ali MA, Hossain M, Islam MT, Shekhar HU, Hossain MW, Karim MM, Sajib AA, Halim MA, Mannoor K. Q531L mutation in the capsid protein of hepatitis E virus genotype 1 causes infections in patients with altered immunity and immunosuppressive condition: Mechanism based on wet lab and in-silico findings. GENE REPORTS 2023; 31:101779. [DOI: 10.1016/j.genrep.2023.101779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/12/2024]
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Shafat Z, Ahmed A, Parvez MK, Parveen S. Intrinsic disorder in the open reading frame 2 of hepatitis E virus: a protein with multiple functions beyond viral capsid. J Genet Eng Biotechnol 2023; 21:33. [PMID: 36929465 PMCID: PMC10018590 DOI: 10.1186/s43141-023-00477-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 01/31/2023] [Indexed: 03/18/2023]
Abstract
BACKGROUND Hepatitis E virus (HEV) is the cause of a liver disease hepatitis E. The translation product of HEV ORF2 has recently been demonstrated as a protein involved in multiple functions besides performing its major role of a viral capsid. As intrinsically disordered regions (IDRs) are linked to various essential roles in the virus's life cycle, we analyzed the disorder pattern distribution of the retrieved ORF2 protein sequences by employing different online predictors. Our findings might provide some clues on the disorder-based functions of ORF2 protein that possibly help us in understanding its behavior other than as a HEV capsid protein. RESULTS The modeled three dimensional (3D) structures of ORF2 showed the predominance of random coils or unstructured regions in addition to major secondary structure components (alpha helix and beta strand). After initial scrutinization, the predictors VLXT and VSL2 predicted ORF2 as a highly disordered protein while the predictors VL3 and DISOPRED3 predicted ORF2 as a moderately disordered protein, thus categorizing HEV-ORF2 into IDP (intrinsically disordered protein) or IDPR (intrinsically disordered protein region) respectively. Thus, our initial predicted disorderness in ORF2 protein 3D structures was in excellent agreement with their predicted disorder distribution patterns (evaluated through different predictors). The abundance of MoRFs (disorder-based protein binding sites) in ORF2 was observed that signified their interaction with binding partners which might further assist in viral infection. As IDPs/IDPRs are targets of regulation, we carried out the phosphorylation analysis to reveal the presence of post-translationally modified sites. Prevalence of several disordered-based phosphorylation sites further signified the involvement of ORF2 in diverse and significant biological processes. Furthermore, ORF2 structure-associated functions revealed its involvement in several crucial functions and biological processes like binding and catalytic activities. CONCLUSIONS The results predicted ORF2 as a protein with multiple functions besides its role as a capsid protein. Moreover, the occurrence of IDPR/IDP in ORF2 protein suggests that its disordered region might serve as novel drug targets via functioning as potential interacting domains. Our data collectively might provide significant implication in HEV vaccine search as disorderness in viral proteins is related to mechanisms involved in immune evasion.
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Affiliation(s)
- Zoya Shafat
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Anwar Ahmed
- Centre of Excellence in Biotechnology Research, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Mohammad K Parvez
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Shama Parveen
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India.
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Mustafa G, Mahrosh HS, Attique SA, Arif R, Farah MA, Al-Anazi KM, Ali S. Identification of Plant Peptides as Novel Inhibitors of Orthohepevirus A (HEV) Capsid Protein by Virtual Screening. Molecules 2023; 28:molecules28062675. [PMID: 36985647 PMCID: PMC10051542 DOI: 10.3390/molecules28062675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 03/12/2023] [Accepted: 03/14/2023] [Indexed: 03/18/2023] Open
Abstract
Hepatitis E virus (HEV) is the notable causative agent of acute and chronic hepatic, renal, pancreatic, neurological, and hematopoietic blood cell infections with high risk in immunocompromised patients. Hepatic failure is mostly documented among adults, pregnant women, and patients with preexisting liver disease. HEV is a positive sense RNA virus of 7.2 kb genome size with typically three open reading frames (ORFs) which play essential roles in viral replication, genome assembly, and transcription. The mutational substitution in the viral RNA genome makes more it difficult to understand the actual relationship in the host–virus association. ORFs of HEV encode different structural and non-structural proteins and one of them is the capsid protein which is coded by ORF2. The capsid protein mediates the encapsulation of the viral genome as well as being involved in virion assembly. In the current study, the ligand-based docking approach was employed to inhibit the active amino acids of the viral capsid protein. Depending upon S-score, ADMET profiling, and drug scanning, the top ten tetrapeptides were selected as potential drug candidates with no toxicity counter to HEV receptor protein. The S-score or docking score is a mathematical function which predicts the binding affinities of docked complexes. The binding affinity of the predicted drug–target complexes helps in the selectivity of the desired compound as a potential drug. The best two selected peptides (i.e., TDGH with S-score of −8.5 and EGDE with S-score of −8.0) interacted with the active site amino acids of the capsid protein (i.e., Arg399, Gln420, and Asp444). The molecular dynamics simulations of RMSD trajectories of TDGH–capsid protein and EDGE–capsid protein have revealed that both docked complexes were structurally stable. The study revealed that these tetrapeptides would serve as strong potential inhibitors and a starting point for the development of new drug molecules against the HEV capsid protein. In future, in vivo studies are needed to explore selected peptides as potential drug candidates.
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Affiliation(s)
- Ghulam Mustafa
- Department of Biochemistry, Government College University Faisalabad, Faisalabad 38000, Pakistan
- Correspondence:
| | - Hafiza Salaha Mahrosh
- Department of Biochemistry, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan
| | - Syed Awais Attique
- School of Interdisciplinary Engineering & Science (SINES), National University of Sciences & Technology (NUST), Islamabad 44000, Pakistan
- Agency for Science, Technology and Research (A*STAR), Bioinformatics Institute, 30 Biopolis Street, Matrix, Singapore 138671, Singapore
| | - Rawaba Arif
- Department of Biochemistry, University of Jhang, Jhang 35200, Pakistan
| | - Mohammad Abul Farah
- Department of Zoology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Khalid Mashay Al-Anazi
- Department of Zoology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Sajad Ali
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Republic of Korea
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Hepatitis E virus genotype 3 in bovine livers slaughtered in the state of Rio Grande do Sul, Brazil. Braz J Microbiol 2022; 53:1115-1120. [PMID: 35355235 PMCID: PMC9433617 DOI: 10.1007/s42770-022-00741-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 03/25/2022] [Indexed: 11/02/2022] Open
Abstract
Foodborne viruses are becoming a global concern as they overwhelm the health system and have the potential to spread globally. Among them, some genotypes of hepatitis E virus (HEV), which is one of the main causes of acute hepatitis in humans, have a zoonotic potential and can be found in foods of animal origin. Infected farm animals are a possible source of the virus, either by direct contact with animal excreta or meat. In the present study, 240 bovine liver samples from slaughter carried out in Rio Grande do Sul (RS), Brazil, were analyzed and tested for the presence of HEV. After performing PCR, 5.4% of positive samples were observed. One of the samples could be identified by molecular phylogenetic analysis as belonging to genotype 3, for which pigs are natural reservoirs, but has not been reported in bovine meat and products so far.
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