Molecular and geographic characterization of hiv-1 bf recombinant viruses

Souza, Juliana Sacramento Mota de; Júnior, Jailton J Silva; Brites, Carlos; Monteiro-Cunha, Joana P

doi:10.1016/j.virusres.2019.197650

Cited by 5 publications

(7 citation statements)

References 47 publications

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“…It has been shown that BF1 recombinant sequences have many distinct recombination patterns, indicating different recombination events. 36 In the present study, despite the different recombination patterns observed among the 35 BF1 representatives, the clustering of all recombinants in the same monophyletic cluster suggests a common origin for these viruses. This may indicate that the pure F1 Brazilian ancestor could have arisen from a possible evolution after adaptive advantages associated with recombinant strains.…”

Section: Discussioncontrasting

confidence: 39%

Tracing the relationship among HIV-1 sub-subtype F1 strains: a phylodynamic perspective

Silva

Oliveira

Souza

et al. 2022

Mem. Inst. Oswaldo Cruz

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BACKGROUND The human immunodeficiency virus type 1, F1 sub-subtype (HIV-1 F1) circulates in three continents: Africa, Europe, and South America. In Brazil, this sub-subtype co-circulates with subtypes B and C and several recombinant forms, mainly BF1 variants. OBJECTIVES This study aimed to reconstruct the dynamic history of HIV-1 F1 in Brazil. METHODS HIV-1 near full-length genome and pol gene nucleotide sequences available in public databases were assembled in two datasets (POL671 and NFLG53) to cover the largest number of F1 sub-subtype sequences. Phylodynamic and temporal analyses were performed. FINDINGS Two main strains of the F1 sub-subtype are circulating worldwide. The first (F1.I) was found among Brazilian samples (75%) and the second (F1.II) among Romanian (62%) and other European and African isolates. The F1 subtype epidemic in Brazil originated from a single entry into the country around 1970. This ancestral sample is related to samples isolated in European countries (France, Finland, and Belgium), which are possibly of African origin. Moreover, further migration (1998 CI: 1994-2003) of strains from Brazil to Europe (Spain and the UK) was observed. Interestingly, all different recombinant BF patterns found, even those from outside Brazil, present the same F1 lineage (F1.I) as an ancestor, which could be related to the acquisition of adaptive advantages for the recombinant progenies. MAIN CONCLUSIONS These findings are important for the understanding of the origin and dynamics of the F1 sub-subtype and a consequent better and greater understanding of the HIV-1 F1 and BF epidemic that still spreads from Brazil to other countries.

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Section: Discussioncontrasting

confidence: 39%

Tracing the relationship among HIV-1 sub-subtype F1 strains: a phylodynamic perspective

Silva

Oliveira

Souza

et al. 2022

Mem. Inst. Oswaldo Cruz

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“…3b). In comparison, among over 100 BF different patterns, recombination occurred more frequently in all structural genes (gag [69.3%], pol [84.9%] and env [51.4%]), while nef showed a lower rate of intragenic recombination (25.5%) [17]. Furthermore, among BC recombinant patterns, the subtype C was more frequent throughout the viral genome, especially in the accessory and regulatory genes, while among BF mosaics, the subtype B was predominant in those genes, except in vif [17].…”

Section: Discussionmentioning

confidence: 99%

“…In order to investigate and compare the recombination patterns, sequences were analyzed using jpHMM online tool [14], RDP5 software (RDP method) [15] and SimPlot (Bootscan method) [16], using the following parameters: 400 bp of slider window size and 40 bp steps size. The frequency of pure subtype B, pure subtype C and recombination (R) within the HIV-1 genes was investigated among distinct recombinant patterns [17]. The intervals for recombination breakpoints based on HXB2 numbering obtained for each sequence were used to identify the regions where the recombination between B and C subtypes were more frequent.…”

Section: Methodsmentioning

confidence: 99%

Genomic Characterization of HIV-1 Bc Recombinant Viruses

Oliveira

Monteiro-Cunha

2023

Preprint

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The Human Immunodeficiency Virus 1 (HIV-1) is characterized by high rates of genetic diversity, being classified into groups, subtypes and recombinant forms. To date, 14 Circulating Recombinant Forms (CRFs) of subtypes B and C have been identified, three of them in 2021: CRF108_BC in Spain, CRF110_BC and CRF118_BC in China. This study investigated the genetic diversity among circulating BC recombinant viruses. Near-Full Length Genomes (NFLG) of 225 BC strains were retrieved from the Los Alamos database. Recombination and phylogenetic analysis were conducted using bioinformatics tools. Sequences were obtained from 17 countries between 1992 and 2018. Fourteen CRFs and 82 distinct Unique Recombinant Forms (URFs) recombination patterns were identified. Preferential recombination points were found in pol (66.7%) and env (62.5%) genes, while subtype C is the predominant genetic form in gag, vif, vpr, tat, rev, tat2, rev2, nef and 3'-LTR genomic regions. Specific positions in pol and env genes maintain the B subtype, which may be related to the acquisition of adaptive advantage over subtype C.

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“…NFLG sequencing of HIV-1 strains involved in expanding transmission clusters is highly recommendable in order to identify new CRFs, which may have acquired adaptive advantages through recombination [ 49 , 50 ] even when recombination is not suspected in partial sequences, as it occurs with CRF108_BC. Genetic diversity and recombination are major obstacles to the development of an effective vaccine against HIV-1 [ 51 , 52 , 53 ].…”

Section: Discussionmentioning

confidence: 99%

Identification of a New HIV-1 BC Intersubtype Circulating Recombinant Form (CRF108_BC) in Spain

Cañada

Delgado

Gil

et al. 2021

Viruses

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The extraordinary genetic variability of human immunodeficiency virus type 1 (HIV-1) group M has led to the identification of 10 subtypes, 102 circulating recombinant forms (CRFs) and numerous unique recombinant forms. Among CRFs, 11 derived from subtypes B and C have been identified in China, Brazil, and Italy. Here we identify a new HIV-1 CRF_BC in Northern Spain. Originally, a phylogenetic cluster of 15 viruses of subtype C in protease-reverse transcriptase was identified in an HIV-1 molecular surveillance study in Spain, most of them from individuals from the Basque Country and heterosexually transmitted. Analyses of near full-length genome sequences from six viruses from three cities revealed that they were BC recombinant with coincident mosaic structures different from known CRFs. This allowed the definition of a new HIV-1 CRF designated CRF108_BC, whose genome is predominantly of subtype C, with four short subtype B fragments. Phylogenetic analyses with database sequences supported a Brazilian ancestry of the parental subtype C strain. Coalescent Bayesian analyses estimated the most recent common ancestor of CRF108_BC in the city of Vitoria, Basque Country, around 2000. CRF108_BC is the first CRF_BC identified in Spain and the second in Europe, after CRF60_BC, both phylogenetically related to Brazilian subtype C strains.

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Molecular and geographic characterization of hiv-1 bf recombinant viruses

Cited by 5 publications

References 47 publications

Tracing the relationship among HIV-1 sub-subtype F1 strains: a phylodynamic perspective

Tracing the relationship among HIV-1 sub-subtype F1 strains: a phylodynamic perspective

Genomic Characterization of HIV-1 Bc Recombinant Viruses

Identification of a New HIV-1 BC Intersubtype Circulating Recombinant Form (CRF108_BC) in Spain

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