Assignment Sample on A Systematic Review Of Epstein- Barr Virus
Introduction
The “EBV virus” which is even known as human herpes virus is a causative component and agent of “infectious mononucleosis”. As stated by Tan (2023), “EBV virus” with a latency phase, it can infect the epithelial cells and therefore enters onto the “B lymphocytes”. Furthermore, the “EBV virus” has been estimated to be positive in approximately 90% of adults’ population. The two phases of EBV are “Latency” and “Lytic”, active replication of the virtual genome of EBV results in lytic infection and releases virus particles as new progeny. Latency period can be defined as the time for development of an exposure or a disease to the pathogen. The primary aim of this study has been developed to understand the genetic diversity of “EBV virus”. By using Phylogeny software and MSA the classification of viral strain can be determined.
The two objectives developed in this study will help to state the genetic variation of EBV gene which causes infectious disease in human beings. Besides that, the developed hypothesis for this research will help to derive the alteration of T cells which cause the EBV infection for the “B cell proliferation” and survival memory. On the other hand, in the latency phase, the virus does not replicate. Additionally, the Type 2 virus of EBV acquired the type 1 which is the “EBNA-2A gene” and enhances the transformation ability of the Type 2 virus (Tan, 2023). The “EBV strains” are of two types such as Type 1 which is the main type and prevalent worldwide.
Furthermore, the genetic variability within different EBV genes occurs in the EBV life cycle and within the lymphocytes. However, currently EBV strains can be divided into “Type 1” and “Type 2” which do not genetically appear and are linked with other types of virus sequences. On the other hand, the inactivation of the “EBNA-3B” gene has resulted in higher transforming activity of the B cell in the EBV virus (Wongwiwat et al. 2022). The replication cycle of the EBV virus is mainly in two types such as infected B cell proliferation and virus production in the lytic cycle. As stated by Chen et al. (2021), DNA replication of the lytic phase for the EBV cycle remains in uncoupled form whereas the latent phase remains in independent form. Moreover, the Type 1 and 2 of EBV genetic variations has remained as the large systematic variation in the “241 genetic sequences”. On the other hand, the principal variation of EBV has appeared in the classification of type 1 and 2 which can be determined by “EBNA2” and “EBNA3” (Farrell & White, 2021). By studying the EBV virus, it can develop ideas about various neurological disorders even though the absence of acute infectious “mononucleosis”. The antivirus therapeutics of EBV strains are various types such as “ganciclovir”, “interferon-gamma”, “acyclovir” and “phosphonoacetic acid”.
The MSA of all EBV genome has been developed using the “MAFT version” software which helped to visualize the gene alignment. On the other hand, the “Phylogenetic analysis” of the EBV genome can be performed by using “Molecular evolutionary genetic analysis” (Marawanet al. 2021). As per the views of Wongwiwat et al. (2022), phylogeny software helps to develop large scale sequences of EBV genome which help to focus the recombination frequency for EBV lineages. The vaccine designs for the EBV virus is powerful “multi-epitope peptide” vaccines that are developed with “silico analysis”. There are approximately 250 strains of EBV and the infection due to EBV is related to various lymphomas such as “Hodgkin lymphoma” and “Burkitt’s lymphoma”. The geographical distribution effect of EBV is prevalent in the population mainly in Europe, China, South Asia and America.
Furthermore, the MSA and through gene-by-gene analysis of EBV genomes has suggested the EBV genome map which develops an effective representation of EBV genomes. As per the views of Farrell & White, (2021), the genetic variability of EBV strains occurred due to the EBV life cycle’s nature within the lymphocytes. On the other hand, Type 2 EBV strains are less in these populations and are mainly found in Africa and New Guinean populations. Moreover, Wongwiwat et al. (2022) stated that genetic variations develop the high risk of subtypes of EBV strains in the small RNA locus and the single nucleotide variant profiles. In China, the strains of the EBV virus are causing “Nasopharyngeal cancer”, particularly in Men.
Similarly, the EBV can develop several errors at the time of replication and develop more genetic variability within EBV. The genetic variability of EBV furthermore can be identified within three genetic regions such as “BZLF-1”, “EBNA-1” and “LMP-1” (Liao et al. 2022). Within these three regions, the LMP-1 is responsible for playing a significant role in tumor genesis. The EBC virus develops latent lytic infection that can target the BZLF-1 for the evolution of latent lytic cycle. Similarly, EBNA-1 is required to maintain the EBV and its latent form, which is expressed in EBV related tumors.
The Plan of Investigation
i. Details of types of controls used with number of replicates and the result analysis
The types of controls used in EBV virus helps to restrict the lytic cycle replication as well as latent EBV antigen expression. In this aspect, “NK (Natural Killer) cells” and “Innate lymphocytes” can be used to control the EBV infection. There are two types of replicas that can be controlled by Lytic and Latency replication. As stated by Wongwiwat et al. (2022), EBV infections occurring in NK or T cells have been recognized to get involved in various additional EBV positive NK lymph proliferative ailments. Thus, by using the controls, replicas can be controlled by stimulating the host cell proliferation and DNA replication of the cells.
ii. Literature Review
EBV virus has already infected about 95% population in the world and disease cause by this virus mostly includes the human cancer. The possible impact of the changing genomic sequence for the virulence factor is affecting human capabilities. 71 various EBV strains have been identified from geographical locations and the genomic analysis have been done accordingly. The samples were collected were different types of primary tumor, as well as blood samples of patients. Some novel detection from the genomic sequence has been identified that were even present in the viral genomes. As stated by (Wongwiwat et al. 2022), EBV strain has defined with a discrete viral life cycle for primary infection such as lytic and latency reactivation phases. There are two peaks of EBV infection can be identified that can be measured among children. However, for vast majority of the individuals the latent EBV infection does not observe to have any serious health conditions. Thus, the deregulation of inability or latency has the ability to control lytic infection.
Analysis
After the extraction of total DNA, the library needs to be prepared using the EBV and DNA viruses. After that, captured libraries need to be tagged by PCR and “Misequencing” method. The scaffolding and joining operations then can be preceded by evaluating the pair-wise alignment of the EBV genome. Tabatabaie et al. (2023) stated that the products of EBV genome extraction methods need to be purified by using a gel extraction kit. The Sanger sequencing can be performed to extract the EBV genome by using “BigDye terminator”. After the extraction of the EBV genome, the hetero-genetic analysis and annotation has been performed with the genome. The hetero-genetic analysis needs to be performed with recombination analysis and the annotation can be performed with phylogenetics.
iv. a. Table for detailing the specific sources of consumables’ for fulfilling the research project in non-laboratory-based format
| Consumables | Databases Used to gather information | Use | Protection |
| Centrifuge tubes | PubMed | These are used for containing liquids during the centrifugation processes | After autoclaving They are need to be closed and covered for at least 30 minutes for reducing hazardous materials (Coppola et al. 2019) |
| Microcentrifuge tubes | PubMed | These are used to store samples such as immiscible liquids which needs to be isolated (Holt et al. 2021) | Tubes needs to be autoclaved for minimum 20 minutes to reduce the contamination |
| Petri dishes | Google Scholar | Used for Cultures and different types of viruses, bacteria, and moulds (Zuparovet al. 2020) | Needs to be autoclaved before use which can minimize the risk of contamination from airborne spores |
| Pipette and Pipette tips | PubMed | For measuring the small volumes of a liquid and to transfer them in a tube (Grau et al. 2022) | Placing them in a bio-safety cabinet and using with aerosol barrier tips to prevent the contamination caused by aerosols |
Table 1: Specific Consumables’ for Research
(Source: Developed by Author)
b. The way project adoption in a non-laboratory-based format due to disruption of COVID-19
The project has been conducted in order to understand the diversity of EBV virus, due to the disruption of COVID-19, and has collected secondary data from reliable and valid databases. As stated by Singh et al. (2022), virtual frameworks such as video recordings, publicly available webcams can be used to develop a project with the use of computer generated softwares. Due to global pandemic disruption, an overall understanding regarding the EBV virus and its impact in virus biology can be gathered by using Bioinformatics tools such as genomic databases.
Furthermore, a secondary data collection can be adopted to gather effective ideas regarding this project by using PubMed and Google scholar database. By using the key words related to this research project can be used to generate the search operations in Google scholar, as well as PubMed. A systematic review can be undertaken for this research which helps to develop an overall review of this literature. As stated by Padhyet al. (2020), systematic review along with a meta-analysis has been used widely in clinical trials and health sciences. In this aspect, this research without using the laboratory can be conducted with the help of systematic review by gathering relevant and accurate journals from the Google scholar and Pub Med databases.
Ethical considerations and COSHH
This research will evaluate the overall ethical considerations which will protect the data sources from where the research data will be gathered. The UK Data Protection Act of 2018 will be adhered to maintain the ethical work practices in this research. Furthermore, the COSHH (“Control Substances Hazardous to Health”) 2002 assessment will be followed which will help to evaluate the health risks if associated with this research. Appropriate control measures need to be used to eliminate the risks related to this project.
References
Coppola, L., Smaldone, G., Cianflone, A., Baselice, S., Mirabelli, P. & Salvatore, M., (2019). Purification of viable peripheral blood mononuclear cells for biobanking using a robotized liquid handling workstation. Journal of Translational Medicine, 17(1), 1-12. https://doi.org/10.1186/s12967-019-2125-7
Farrell, P. J., & White, R. E. (2021). Do Epstein–Barr virus mutations and natural genome sequence variations contribute to disease?.Biomolecules, 12(1), 17. Retrieved on 13 July 2023, Retrieved From: https://doi.org/10.3390/biom12010017
Grau, J., Benedé, J.L., Chisvert, A. & Salvador, A., (2022). A high-throughput magnetic-based pipette tip microextraction as an alternative to conventional pipette tip strategies: Determination of testosterone in human saliva as a proof-of-concept. Analytica Chimica Acta, 1221, 340117. https://doi.org/10.1016/j.aca.2022.340117
Holt, M.V., Wang, T. & Young, N.L., (2021). Expeditious extraction of histones from limited cells or tissue samples and quantitative top‐down proteomic analysis. Current protocols, 1(2), 26. https://currentprotocols.onlinelibrary.wiley.com/doi/abs/10.1002/cpz1.26
Liao, H. M., Liu, H., Chin, P. J., Li, B., Hung, G. C., Tsai, S., …&Mbulaiteye, S. M. (2022). Epstein-Barr virus in burkitt lymphoma in Africa reveals a limited set of whole genome and LMP-1 sequence patterns: analysis of archival datasets and field samples from Uganda, Tanzania, and Kenya. Frontiers in Oncology, 12, 812224. Retrieved on 13 July 2023, Retrieved From: https://doi.org/10.3389/fonc.2022.812224
Marawan, M. A., Alouffi, A., El Tokhy, S., Badawy, S., Shirani, I., Dawood, A., …&Selim, A. (2021). Bovine leukaemia virus: Current epidemiological circumstance and future prospective. Viruses, 13(11), 2167. Retrieved on 13 July 2023, Retrieved From: https://doi.org/10.3390/v13112167
Padhy, B. M., Mohanty, R. R., Das, S., &Meher, B. R. (2020). Therapeutic potential of ivermectin as add on treatment in COVID 19: A systematic review and meta-analysis: Ivermectin in COVID-19: A meta-analysis. Journal of Pharmacy & Pharmaceutical Sciences, 23, 462-469. Retrieved on 13 July 2023, Retrieved From: https://journals.library.ualberta.ca/jpps/index.php/JPPS/article/view/31457
Singh, A., Jindal, V., Sandhu, R., & Chang, V. (2022). A scalable framework for smart COVID surveillance in the workplace using Deep Neural Networks and cloud computing. Expert Systems, 39(3), e12704. Retrieved on 13 July 2023, Retrieved From: https://doi.org/10.1111/exsy.12704
Tabatabaie, F. H., Hosseini, S. Y., Hashemi, S. M. A., Safaie, A., &Sarvari, J. (2023). A preliminary sequence analysis of the Epstein-Barr virus nuclear antigen 1 (EBNA1) carboxy-terminal region in cervical and ovarian cancers. Iranian Journal of Pathology, 18(1), 24. Retrieved on 13 July 2023, Retrieved From: doi: 10.30699/ijp.2023.551761.2872
Tan, H., Gong, Y., Liu, Y., Long, J., Luo, Q., Faleti, O. D., &Lyu, X. (2023). Advancing therapeutic strategies for Epstein-Barr virus-associated malignancies through lytic reactivation. Biomedicine & Pharmacotherapy, 164, 114916. Retrieved on 13 July 2023, Retrieved From: https://doi.org/10.1016/j.biopha.2023.114916
Wongwiwat, W., Fournier, B., Bassano, I., Bayoumy, A., ElguetaKarstegl, C., Styles, C., …& Farrell, P. J. (2022). Epstein-Barr Virus Genome Deletions in Epstein-Barr Virus-Positive T/NK Cell Lymphoproliferative Diseases. Journal of Virology, 96(12), e00394-22. Retrieved on 13 July 2023, Retrieved From: https://journals.asm.org/doi/abs/10.1128/jvi.00394-22
Zuparov, M.A., Khakimov, A.A., Mamiev, M.S. &Allayarov, A.N., (2020). In vitro efficacy testing of fungicides on Botrytis cinerea causing gray mold of tomato. International Journal on Emerging Technologies, 11(5), 50-55. https://www.researchgate.net/profile/Albert-Khakimov/publication/343686159_In_Vitro_Efficacy_Testing_of_Fungicides_on_Botrytis_cinerea_causing_Gray_Mold_of_Tomato/links/5f3990d1458515b7292757a0/In-Vitro-Efficacy-Testing-of-Fungicides-on-Botrytis-cinerea-causing-Gray-Mold-of-Tomato.pdf
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