Analysis of the complete genome of HBV genotypes F and H found in Brazil and Mexico using the next generation sequencing method

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art_GIONDA_Analysis_of_the_complete_genome_of_HBV_genotypes_2022.PDF (1.32 MB)
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0
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article
Data de publicação
2022
DOI
Scopus
Web of Science
PubMed
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Título do Volume
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ELSEVIER ESPANA
Autores
SEBE, Pedro
FRANCISCO, Rodrigo Dos Santos
JOSE-ABREGO, Alexis
ROMAN, Sonia
PANDURO, Arturo
Citação
ANNALS OF HEPATOLOGY, v.27, suppl.1, Special Issue, article ID 100569, 8p, 2022
Projetos de Pesquisa
Unidades Organizacionais
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Resumo
Introduction and Objectives: Hepatitis B Virus is classified into ten different genotypes (A-J). Genotypes F and H cluster apart from others in phylogenetic trees and is particularly frequent in the Americas. The aim of this study was to sequence complete genomes of samples of HBV genotypes F and H from Brazil and Mexico using next generation sequencing (NGS) and to study relevant characteristics for the disease associated with this virus. Materials and methods: Ninety plasma samples with detectable HBV DNA belonging to the F (n=59) and H (n=31) genotypes were submitted to amplification of the complete HBV genome by three different methologies. Data analysis was developed using bioinformatics tools for quality assurance and comprehensive coverage of the genome. Sequences were aligned with reference sequences for subgenotyping and detecting variants in relevant positions. A phylogenetical tree was constructed using Bayesian methods. Results: HBV genome of 31 samples were amplified and 18 of them were sequenced (HBV/F=16 and HBV/H=2). One genotype F sample was co-infected with the F1b and F3 subgenotypes, while the other samples were all F2a subgenotype. Two genotype H samples clustered with other Mexican sequences. The main variants observed were found in preS and S genes (7/18) and mutations in the precore/core region (11/18). Conclusions: A NGS methodology was applied to F and H genotypes samples from Mexico and Brazil to fully characterize their sequences. This methodology will be relevant for clinical and epidemiological studies of hepatitis B in Latin America (C) 2021 Fundacion Clinica Medica Sur, A.C.
Palavras-chave
Hepatitis B, Sequencing, Next-generation, Latin America, Genotype
URI
https://observatorio.fm.usp.br/handle/OPI/47348
Referências
  1. Alvarado-Mora MV, 2013, ANTIVIR THER, V18, P429, DOI 10.3851/IMP2595
  2. Alvarado-Mora MV, 2013, ANTIVIR THER, V18, P459, DOI 10.3851/IMP2599
  3. Andrews S., 2020, SOIL-GERMANY
  4. Araujo NM, 2020, FRONT MICROBIOL, V11, DOI 10.3389/fmicb.2020.616023
  5. Armstrong RA, 2014, OPHTHAL PHYSL OPT, V34, P502, DOI 10.1111/opo.12131
  6. Bankevich A, 2012, J COMPUT BIOL, V19, P455, DOI 10.1089/cmb.2012.0021
  7. Chotiyaputta W, 2009, NAT REV GASTRO HEPAT, V6, P453, DOI 10.1038/nrgastro.2009.107
  8. Cingolani P, 2012, FLY, V6, P80, DOI 10.4161/fly.19695
  9. da Silva Luiz Caetano, 2000, Revista do Instituto de Medicina Tropical de Sao Paulo, V42, P189
  10. Enriquez-Navarro K, 2020, ANN HEPATOL, V19, P507, DOI 10.1016/j.aohep.2020.06.002
  11. Fragoso-Fonseca DE, 2018, ARCH VIROL, V163, P1981, DOI 10.1007/s00705-018-3813-y
  12. Garrison E., 2012, 12073907 ARXIV
  13. Gomes MMS, 2005, THESIS PROGRAMA POS
  14. GUNTHER S, 1995, J VIROL, V69, P5437
  15. Hall T., 1999, NUCL ACIDS S SER, V41, P95
  16. Kramvis A, 2014, INTERVIROLOGY, V57, P141, DOI 10.1159/000360947
  17. Lazarevic I, 2014, WORLD J GASTROENTERO, V20, P7653, DOI 10.3748/wjg.v20.i24.7653
  18. Limeres MJ, 2019, ARCH VIROL, V164, P2297, DOI 10.1007/s00705-019-04332-8
  19. Morozov V, 2000, GENE, V260, P55, DOI 10.1016/S0378-1119(00)00424-8
  20. Pujol F, 2020, CLIN RES HEPATOL GAS, V44, P825, DOI 10.1016/j.clinre.2020.04.018
  21. Purdy MA, 2008, J GEN VIROL, V89, P1179, DOI 10.1099/vir.0.83392-0
  22. Revill PA, 2020, NAT REV GASTRO HEPAT, V17, P618, DOI 10.1038/s41575-020-0296-6
  23. Roman S, 2013, WORLD J GASTROENTERO, V19, P5446, DOI 10.3748/wjg.v19.i33.5446
  24. Shaha Modhusudon, 2018, F1000Res, V7, P1023, DOI 10.12688/f1000research.15090.3
  25. Shi WF, 2013, INFECT GENET EVOL, V16, P355, DOI 10.1016/j.meegid.2013.03.021
  26. Sitnik R, 2004, J CLIN MICROBIOL, V42, P2455, DOI 10.1128/JCM.42.6.2455-2460.2004
  27. Sozzi V, 2018, VIROLOGY, V519, P190, DOI 10.1016/j.virol.2018.04.015
  28. Spitz N, 2017, ARCH VIROL, V162, P1695, DOI 10.1007/s00705-017-3269-5
  29. Stuyver L, 2000, J GEN VIROL, V81, P67, DOI 10.1099/0022-1317-81-1-67
  30. Suchard MA, 2018, VIRUS EVOL, V4, DOI 10.1093/ve/vey016
  31. Tacke F, 2007, J CLIN VIROL, V38, P353, DOI 10.1016/j.jcv.2006.12.024
  32. Wang HC, 2006, CANCER SCI, V97, P683, DOI 10.1111/j.1349-7006.2006.00235.x

Coleções
Artigos e Materiais de Revistas Científicas - HC/ICHC
Artigos e Materiais de Revistas Científicas - LIM/03
Artigos e Materiais de Revistas Científicas - LIM/07
Artigos e Materiais de Revistas Científicas - ODS/03