Mem Inst Oswaldo Cruz, Rio de Janeiro, VOLUME 118 | 2023
Research Articles

Unique synapomorphies and high diversity in South American Raji-related Epstein-Barr virus genomes

Paula Alves1,3,+, Vanessa Emmel1, Gustavo Stefanoff1,2, Flavia Krsticevic1,3, Joaquín Ezpeleta3,Javier Murillo3, Elizabeth Tapia3, Edson Delatorre4, Eliana Abdelhay1, Rocio Hassan1,†

1Instituto Nacional de Câncer, Centro de Transplante de Medula Óssea, Rio de Janeiro, RJ, Brasil
2Instituto Nacional de Câncer, Coordenação de Pesquisa Clínica, Rio de Janeiro, RJ, Brasil
3Universidad Nacional de Rosario, Centro Internacional Franco Argentino de Ciencias de la Información y de Sistemas, Rosario, Argentina
4Universidade Federal do Espírito Santo, Centro de Ciências da Saúde, Departamento de Patologia, Laboratório de Genômica e Ecologia Viral, Vitória, ES, Brasil

DOI: 10.1590/0074-02760230122
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ABSTRACT

BACKGROUND Epstein-Barr virus (EBV) is a human gammaherpesvirus etiologically linked to several benign and malignant diseases. EBV-associated malignancies exhibit an unusual global distribution that might be partly attributed to virus and host genetic backgrounds.
OBJECTIVES To assemble a new genome of EBV (CEMO3) from a paediatric Burkitt’s lymphoma from Rio de Janeiro State (Southeast Brazil). In addition, to perform global phylogenetic analysis using complete EBV genomes, including CEMO3, and investigate the genetic relationship of some South American (SA) genomes through EBV subgenomic targets.
METHODS CEMO3 was sequenced through next generation sequencing and its coverage and gaps were corrected through the Sanger method. CEMO3 and 67 EBV genomes representing diverse geographic regions were evaluated through maximum likelihood phylogenetic analysis. Further, the polymorphism of subgenomic regions of some SA EBV genomes were assessed.
FINDINGS The whole bulk tumour sequencing yielded 23,217 reads related to EBV, which 172,713 base pairs of the newly EBV genome CEMO3 was assembled. The CEMO3 and most SA EBV genomes clustered within the SA subclade closely related to the African Raji strain, forming the South American/Raji clade. Notably, these Raji-related genomes exhibit significant genetic diversity, characterised by distinctive synapomorphies at some gene levels absent in the original Raji strain.
CONCLUSION The CEMO3 represents a new South American EBV genome assembled. Albeit the majority of EBV genomes from SA are Raji-related, it harbours a high diversity different from the original Raji strain.

key words: Epstein-Barr virus oncovirus genome diversity South America
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Financial support: CNPq (Grant 475969/2013-8), Instituto Nacional de Ciência e Tecnologia para o Controle do Câncer (Grant CNPq 573806/2008-0).
PA is post-doctorate researcher supported by Oncology Research Fellowship Program from Brazilian National Cancer Institute (INCA) from Ministry of Health of Brazil.
† In memoriam
+ Corresponding author: pdsa.science@gmail.com
ORCID https://orcid.org/0000-0002-4341-2027
Received 12 July 2023
Accepted 06 October 2023

HOW TO CITE
Alves P, Emmel V, Stefanoff G, Krsticevic F, Ezpeleta J, Murillo J, et al. Unique synapomorphies and high diversity in South American Raji-related Epstein-Barr virus genomes. Mem Inst Oswaldo Cruz. 2023; 118: e230122.

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