DRAFT GENOME SEQUENCE OF HUMAN HERPES VIRUS-4 VRF_EBV_01, AN EPSTEIN BARR VIRUS OBTAINED FROM A PEDIATRIC POST TRANSPLANT LYMPHOPROLIFERATIVE DISORDER (PTLD) PATIENT
Objectives: To decode the sequence of Epstein-barr virus (EBV) genome isolated from a pediatric patient with post transplant lymphoproliferative disorder (PTLD).
Methods: EBV culture harvested from the blood sample of a 4-year-old patient with post liver transplant lymphoproliferative disorder prior to treatment was subjected to whole genome sequencing using Illumina platform. Generated data were subjected to various quality analysis and the filtered sequences were submitted to NCBI and published under accession number KM269735-KM269744.
Results: Annotation results of VRF_ EBV01 genome using Prokka tool and manual blast search infers 48 hypothetical proteins, each 3 genes coding for Epstein-Barr nuclear antigen 3A and 3B and each one gene coding for Epstein-Barr nuclear antigens 1, 4, 4B and DNA primase UL70 protein. Single copy of genes coding for each variant of Tegument protein BSRF1, BLRF2, BGLF2 mir-BART 1,2,3,5,7,12,15,17,20 and two copies of gene coding for primary envelopment factor BFRF1 gene was also found.
Conclusion: To date, only eight EBV genome sequences have been reported worldwide and there is no genome sequence reported from India. This study is the first of its kind to report on EBV genome from a postâ€“transplant lymphoproliferative disorder to the scientific community for the welfare of research against EBV diagnostic markers and drug discovery.
2. Zur Hausen H, Schulte-Holthausen H, Klein G, Henle W, Henle G, Clifford P, et al. EBV DNA in biopsies of Burkitt tumours and anaplastic carcinomas of the nasopharynx. Nature 1970;228:1056-8.
3. Weiss LM, Movahed LA, Warnke RA, Sklar JN. Detection of epstein-barr viral genomes in reed-sternberg cells of hodgkin's disease. Engl J Med 1989;320:502-6.
4. Klein G, Giovanella BC, Lindahl T, Fialkow PJ, Singh S, Stehlin JS. Direct evidence for the presence of Epstein-Barr virus DNA and nuclear antigen in malignant epithelial cells from patients with poorly differentiated carcinoma of the nasopharynx. Proc Natl Acad Sci U S A 1974;71:4737-41.
5. Imai S, Koizumi S, Sugiura M, Tokunaga M, Uemura Y, Yamamoto N, et al. Gastric carcinoma: monoclonal epithelial malignant cells expressing Epstein-Barr virus latent infection protein. Proc Natl Acad Sci U S A 1994;91:9131-5.
6. Hamilton-Dutoit SJ, Pallesen G, Franzmann MB, Karkov J, Black F, SkinhÃ¸j P, et al. AIDS-related lymphoma. Histopathology, immunophenotype, and association with Epstein-Barr virus as demonstrated by in situ nucleic acid hybridization. Am J Pathol 1991;1381:149-63.
7. Baer R, Bankier AT, Biggin MD, Deininger PL, Farrell PJ, Gibson TJ. DNA sequence and expression of the B95-8 epstein-barr virus genome. Nature 1984;310:207-11.
8. de Jesus O, Smith PR, Spender LC, Elgueta KC, Niller HH, Huang D. Updated Epstein-Barr virus (EBV) DNA sequence and analysis of a promoter for the BART (CST, BARF0) RNAs of EBV. J Gen Virol 2003;84:1443-50.
9. Dolan A, Addison C, Gatherer D, Davison AJ, McGeoch DJ. The genome of epstein-barr virus type 2 strain AG876. Virology 2006;350:164-70.
10. Lin Z, Wang X, Strong MJ, Concha M, Baddoo M, Xu G. Whole-genome sequencing of the Akata and Mutu Epstein-Barr virus strains. J Virol 2013;87:1172-82.
11. Kwok H, Tong AH, Lin CH, Lok S, Farrell PJ, Kwong DL, et al. Genomic sequencing and comparative analysis of Epstein-Barr virus genome isolated from primary nasopharyngeal carcinoma biopsy. PLoS One 2012;7. doi:10.1371/journal.pone.0036939. [Article in Press]
12. Liu P, Fang X, Feng Z, Guo YM, Peng RJ, Liu T. Direct sequencing and characterization of a clinical isolate of Epstein-Barr virus from nasopharyngeal carcinoma tissue by using next-generation sequencing technology. J Virol 2011;85:11291-9.
13. Zeng MS, Li DJ, Liu QL, Song LB, Li MZ, Zhang RH. Genomic sequence analysis of Epstein-Barr virus strain GD1 from a nasopharyngeal carcinoma patient. J Virol 2005;79:15323-30.
14. Murugan N, Malathi J, Umashankar V, Madhavan HN. Comparative genomic analysis of multidrug-resistant Pseudomonas aeruginosa clinical isolates VRFPA06 and VRFPA08 with VRFPA07. Genome Announcements 2014;2. doi: 10.1128/genomeA.00140-14. [Article in Press]
15. Aaron E Darling, Bob Mau, Nicole T Perna. Progressive mauve: multiple genome alignment with gene gain, Loss, and Rearrangement. PLoS One 2010;5. doi:10.1371/journal.pone.0011147. [Article in Press]
16. T Seemann. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014;30:2068-9.