REFERENCES

01. Ioachim HL. Immunopathogenesis of human immunodeficiency virus infection. Cancer Res. 1990; 50: 5612-7.

02. Robertson DL, Anderson JP, Bradac JA, Karr JK, Foley B, Funkhouser RK, et al. HIV-1 nomenclature proposal. Science. 2011; 288(5463): 55-6.

03. Yamaguchi J, Vallari A, McArthur C, Sthreshley L, Cloherty GA, Berg MG, et al. Brief report: complete genome sequence of CG- 0018a-01 establishes HIV-1 subtype L. J Acquir Immune Defic Syndr. 2020; 83(3): 319-22.

04. Hemelaar J, Loganathan S, Elangovan R, Yun J, Dickson-Tetteh L, Fleminger I, et al. Global and regional molecular epidemiology of HIV-1, 1990–2015: a systematic review, global survey, and trend analysis. Lancet Infect Dis 2019; 19(2): 143-55.

05. Santoro MM, Perno CF. HIV-1 genetic variability and clinical implications. ISRN Microbiol. 2013; 17: 481314.

06. Su L, Graf M, Zhang Y, von-Briesen H, Kostler J, Melzl H, et al. Characterization of a virtually full-length human immunodeficiency virus type 1 genome of a prevalent intersubtype (C/B′) recombinant strain in China. J Virol. 2000; 74(23): 11367-76.

07. Santos AF, Sousa TM, Soares EA, Sanabani S, Martinez AM, Silveira J, et al. Characterization of a new circulating recombinant form comprising HIV-1 subtypes C and B in southern Brazil. AIDS. 2006; 20(16): 2011-9.

08. Simonetti FR, Lai A, Monno L, Binda F, Brindicci G, Punzi G, et al. Identification of a new HIV-1 BC circulating recombinant form (CRF60_BC) in Italian young men having sex with men. Infect Genet Evol. 2014; 23: 176-181.

09. Gao Q, Feng Y, Gao L, Zhang M, Liu Y, Xiao M, et al. Genetic characteristics of a new HIV-1 subtype B/C intersubtype circulating recombinant form (CRF118_BC) identified in Yunnan, China. J Infect. 2021; 83(2): 237-79.

10. Arruda MB, Boullosa LT, Cardoso CC, Costa CM, Alves CRB, Lima STS, et al. Brazilian network for HIV drug resistence surveillance (HIV-BrasNet): a survey of treatment-naive individuals. J Int AIDS Soc. 2018; 21: e25032.

11. Gräf T, Bello G, Andrade P, Arantes I, Pereira JM, da Silva ABP, et al. HIV-1 molecular diversity in Brazil unveiled by 10 years of sampling by the national genotyping network. Sci Rep. 2021; 11(1): 15842.

12. Reis MNG, Bello G, Guimarães ML, Stefani MMA. Characterization of HIV-1 CRF90_BF1 and putative novel CRFs_BF1 in Central West, North and Northeast Brazilian regions. PLoS One. 2017; 12(6): e0178578.

13. Martin DP, Varsani A, Roumagnac P, Botha G, Suresh M, Schwab KZ, et al. RDP5: a computer program for analyzing recombination in, and removing signals of recombination from, nucleotide sequence datasets. Virus Evol. 2021; 7(1): veaa087.

14. Schultz AK, Zang M, Bulla I, Leitner T, Korber B, Morgenstern B, et al jpHMM: improving the reliability of recombination prediction in HIV-1. Nucleic Acids Res. 2009; 37(Web Server issue): W647-51.

15. Salminen MO, Johansson B, Sonnerborg A, Ayehunie S, Gotte D, Leinikki P, et al. Full-length sequence of an Ethiopian human immunodeficiency virus type-1 (HIV-1) isolate of genetic subtype C. AIDS Res Hum Retroviruses. 1996; 12(14): 1329-39.

16. Passaes CPB, Guimarães ML, Bello G, Morgado MG. Near full-length genome characterization of HIV type 1 unique BC recombinant forms from southern Brazil. AIDS Res Hum Retroviruses. 2009; 25: 12.

17. Pessôa R, Loureiro P, Lopes ME, Carneiro-Proietti ABF, Sabino EC, Busch MP, et al. Ultra-deep sequencing of HIV-1 near fulllength and partial proviral genomes reveals high genetic diversity among Brazilian blood donors. PLoS One. 2016; 11(3): e0152499.

18. Hall T. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser. 1999; 41: 95-8.

19. Katoh K, Kuma K, Toh H, Miyata T. MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res. 2005; 33(2): 511-8.

20. Trifinopoulos J, Nguyen LT, Haeseler AV, Minh BQ. W-IQ-TREE: a fast-online phylogenetic tool for maximum likelihood analysis. Nucleic Acids Res. 2016; 44: W232-5.

21. Anisimova M, Gascuela O. Approximate likelihood-ratio test for branches: a fast, accurate, and powerful alternative. Syst Biol. 2006; 55(4): 539-52.

22. Csillag C. HIV-1 subtype C in Brazil. Lancet. 1994; 344: 1354.

Mem Inst Oswaldo Cruz, Rio de Janeiro, VOLUME 119 | 2024

Research Articles

Description of the new HIV-1 intersubtype B/C circulating recombinant form (CRF146_BC) detected in Brazil

Rodrigo Cunha Oliveira¹, Darren Martin², Juliana Sacramento Mota de Souza¹, Luiz Carlos Júnior Alcântara³, Monick Lindenmeyer Guimarães⁴, Carlos Brites⁵, Joana Paixão Monteiro-Cunha^1,+

¹Universidade Federal da Bahia, Departamento de Bioquímica e Biofísica, Núcleo de Bioinformática, Salvador, BA, Brasil
²University of Cape Town, Institute of Infectious Disease and Molecular Medicine, Department of Integrative Biomedical Sciences, Computational Biology Group, Cape Town, South Africa
³Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório de Flavivírus, Rio de Janeiro, RJ, Brasil
⁴Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório de AIDS e Imunologia Molecular, Rio de Janeiro, RJ, Brasil
⁵Universidade Federal da Bahia, Complexo Hospitalar Prof Edgard Santos, Laboratório de Pesquisa em Infectologia, Salvador, BA, Brasil

DOI: 10.1590/0074-02760230214

1286 views 379 downloads

Print PDF Supplementary data

ABSTRACT

BACKGROUND The human immunodeficiency virus 1 (HIV-1) infections in Brazil are predominantly caused by two subtypes, B and C.
OBJECTIVES Here we present the characterisation of a novel HIV-1 recombinant form, indicating a new Brazilian CRF BC, named CRF146 BC.
METHODS RDP, JphMM and Simplot recombination tools were used to evaluate the mosaic pattern.
FINDINGS In this work, we identified three HIV-1 nucleotide sequences previously classified as unique recombinant forms (URFs), plus one new partial genome sharing the same BC recombination pattern. The mosaic genome is almost entirely represented by the subtype C sequence, with a small subtype B recombination region in the pol gene, at the Integrase level. The phylogenetic analyses strongly indicate a common origin between the strains, which were isolated in Rio Grande do Sul, Rio de Janeiro and Bahia states.
MAIN CONCLUSIONS Thus, the new HIV-1 CRF146 BC is circulating in three different Brazilian regions: South, Southeast and Northeast.

key words: CRF146_BC HIV-1 recombination Brazil

REFERENCES