Genetic Characterization of a New HIV-1 Sub-Subtype A in Cabo Verde, Denominated A8

Overview

Journal Viruses

Publisher MDPI

Specialty Microbiology

Date 2021 Jul 2

PMID 34201179

Citations 9

Authors

Rayana Katylin Mendes Da Silva

Isabel Ines Monteiro de Pina Araujo

Karine Venegas Maciera

Mariza Goncalves Morgado

Monick Lindenmeyer Guimaraes

Affiliations

Soon will be listed here.

Abstract

Previous molecular characterization of Human immunodeficiency virus (HIV-1) samples from Cabo Verde pointed out a vast HIV-1 diversity, with several subtypes and recombinant forms, being 5.2% classified as AU-. Thus, the aim of the present study was to improve the characterization of these AU sequences. The genomic DNA of seven HIV-1 AU -infected individuals were submitted to four overlapping nested-PCR fragments aiming to compose the full-length HIV-1 genome. The final classification was based on phylogenetic trees that were generated using the maximum likelihood and bootscan analysis. The genetic distances were calculated using Mega 7.0 software. Complete genome amplification was possible for two samples, and partial genomes were obtained for the other five. These two samples grouped together with a high support value, in a separate branch from the other sub-subtypes A and CRF26_A5U. No recombination was verified at bootscan, leading to the classification of a new sub-subtype A. The intragroup genetic distance from the new sub-subtype A at a complete genome was 5.2%, and the intergroup genetic varied from 8.1% to 19.0% in the analyzed fragments. Our study describes a new HIV-1 sub-subtype A and highlights the importance of continued molecular surveillance studies, mainly in countries with high HIV molecular diversity.

Citing Articles

Intra- and inter-subtype HIV diversity between 1994 and 2018 in southern Uganda: a longitudinal population-based study.

Kim S, Kigozi G, Martin M, Galiwango R, Quinn T, Redd A Virus Evol. 2024; 10(1):veae065.

PMID: 39399152 PMC: 11468842. DOI: 10.1093/ve/veae065.

Rev Protein Diversity in HIV-1 Group M Clades.

Lebedev A, Kim K, Ozhmegova E, Antonova A, Kazennova E, Tumanov A Viruses. 2024; 16(5).

PMID: 38793640 PMC: 11125641. DOI: 10.3390/v16050759.

Increasing intra- and inter-subtype HIV diversity despite declining HIV incidence in Uganda.

Kim S, Kigozi G, Martin M, Galiwango R, Quinn T, Redd A medRxiv. 2024; .

PMID: 38558994 PMC: 10980117. DOI: 10.1101/2024.03.14.24303990.

Criteria for classification, nomenclature, and reference sequence selection for HIV sub-subtypes of CRF01_AE and CRF07_BC strains in China.

Wang D, Feng Y, Ruan Y, Liao L, Hao J, Song C AIDS. 2024; 38(3):427-430.

PMID: 38300161 PMC: 10842659. DOI: 10.1097/QAD.0000000000003756.

Female Sex Hormones Upregulate the Replication Activity of HIV-1 Sub-Subtype A6 and CRF02_AG but Not HIV-1 Subtype B.

Nosik M, Berezhnya E, Bystritskaya E, Kiseleva I, Lobach O, Kireev D Pathogens. 2023; 12(7).

PMID: 37513727 PMC: 10383583. DOI: 10.3390/pathogens12070880.

References

Desire N, Cerutti L, Le Hingrat Q, Perrier M, Emler S, Calvez V . Characterization update of HIV-1 M subtypes diversity and proposal for subtypes A and D sub-subtypes reclassification. Retrovirology. 2018; 15(1):80. PMC: 6303845. DOI: 10.1186/s12977-018-0461-y. View

Simon F, Mauclere P, Roques P, Muller-Trutwin M, Saragosti S, Georges-Courbot M . Identification of a new human immunodeficiency virus type 1 distinct from group M and group O. Nat Med. 1998; 4(9):1032-7. DOI: 10.1038/2017. View

Lole K, Bollinger R, Paranjape R, Gadkari D, Kulkarni S, Novak N . Full-length human immunodeficiency virus type 1 genomes from subtype C-infected seroconverters in India, with evidence of intersubtype recombination. J Virol. 1998; 73(1):152-60. PMC: 103818. DOI: 10.1128/JVI.73.1.152-160.1999. View

Gao F, Vidal N, Li Y, Trask S, Chen Y, Kostrikis L . Evidence of two distinct subsubtypes within the HIV-1 subtype A radiation. AIDS Res Hum Retroviruses. 2001; 17(8):675-88. DOI: 10.1089/088922201750236951. View

Robertson D, Anderson J, Bradac J, Carr J, Foley B, FUNKHOUSER R . HIV-1 nomenclature proposal. Science. 2000; 288(5463):55-6. DOI: 10.1126/science.288.5463.55d. View

Roques P, Robertson D, Souquiere S, Apetrei C, Nerrienet E, Barre-Sinoussi F . Phylogenetic characteristics of three new HIV-1 N strains and implications for the origin of group N. AIDS. 2004; 18(10):1371-81. DOI: 10.1097/01.aids.0000125990.86904.28. View

Foley B, Leitner T, Paraskevis D, Peeters M . Primate immunodeficiency virus classification and nomenclature: Review. Infect Genet Evol. 2016; 46:150-158. PMC: 5136504. DOI: 10.1016/j.meegid.2016.10.018. View

Reis M, Bello G, Guimaraes M, Stefani M . 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. PMC: 5476242. DOI: 10.1371/journal.pone.0178578. View

Kumar S, Stecher G, Tamura K . MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets. Mol Biol Evol. 2016; 33(7):1870-4. PMC: 8210823. DOI: 10.1093/molbev/msw054. View

10.

Tongo M, Harkins G, Dorfman J, Billings E, Tovanabutra S, de Oliveira T . Unravelling the complicated evolutionary and dissemination history of HIV-1M subtype A lineages. Virus Evol. 2018; 4(1):vey003. PMC: 5819727. DOI: 10.1093/ve/vey003. View

11.

Liu T, Shafer R . Web resources for HIV type 1 genotypic-resistance test interpretation. Clin Infect Dis. 2006; 42(11):1608-18. PMC: 2547473. DOI: 10.1086/503914. View

12.

Guindon S, Dufayard J, Lefort V, Anisimova M, Hordijk W, Gascuel O . New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol. 2010; 59(3):307-21. DOI: 10.1093/sysbio/syq010. View

13.

Hemelaar J, Elangovan R, Yun J, Dickson-Tetteh L, Kirtley S, Gouws-Williams E . Global and regional epidemiology of HIV-1 recombinants in 1990-2015: a systematic review and global survey. Lancet HIV. 2020; 7(11):e772-e781. DOI: 10.1016/S2352-3018(20)30252-6. View

14.

Gifford R, Liu T, Rhee S, Kiuchi M, Hue S, Pillay D . The calibrated population resistance tool: standardized genotypic estimation of transmitted HIV-1 drug resistance. Bioinformatics. 2009; 25(9):1197-8. PMC: 2672634. DOI: 10.1093/bioinformatics/btp134. View

15.

Plantier J, Leoz M, Dickerson J, De Oliveira F, Cordonnier F, Lemee V . A new human immunodeficiency virus derived from gorillas. Nat Med. 2009; 15(8):871-2. DOI: 10.1038/nm.2016. View

16.

Schlosser M, Kartashev V, Mikkola V, Shemshura A, Saukhat S, Kolpakov D . HIV-1 Sub-Subtype A6: Settings for Normalised Identification and Molecular Epidemiology in the Southern Federal District, Russia. Viruses. 2020; 12(4). PMC: 7232409. DOI: 10.3390/v12040475. View

17.

Vidal N, Bazepeo S, Mulanga C, Delaporte E, Peeters M . Genetic characterization of eight full-length HIV type 1 genomes from the Democratic Republic of Congo (DRC) reveal a new subsubtype, A5, in the A radiation that predominates in the recombinant structure of CRF26_A5U. AIDS Res Hum Retroviruses. 2009; 25(8):823-32. DOI: 10.1089/aid.2008.0283. View

18.

de Pina-Araujo I, Delatorre E, Guimaraes M, Morgado M, Bello G . Origin and Population Dynamics of a Novel HIV-1 Subtype G Clade Circulating in Cape Verde and Portugal. PLoS One. 2015; 10(5):e0127384. PMC: 4439163. DOI: 10.1371/journal.pone.0127384. View

19.

Yamaguchi J, Vallari A, McArthur C, Sthreshley L, Cloherty G, Berg M . Brief Report: Complete Genome Sequence of CG-0018a-01 Establishes HIV-1 Subtype L. J Acquir Immune Defic Syndr. 2019; 83(3):319-322. PMC: 7012332. DOI: 10.1097/QAI.0000000000002246. View

20.

de Pina-Araujo I, Guimaraes M, Bello G, Vicente A, Morgado M . Profile of the HIV epidemic in Cape Verde: molecular epidemiology and drug resistance mutations among HIV-1 and HIV-2 infected patients from distinct islands of the archipelago. PLoS One. 2014; 9(4):e96201. PMC: 3999145. DOI: 10.1371/journal.pone.0096201. View