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

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.

Detection of the B"-GWGR variant in the southernmost region of Brazil: unveiling the complexity of the human immunodeficiency virus-1 subtype B epidemic

Typical human immunodeficiency virus-1 subtype B (HIV-1B) sequences present a GPGR signature at the tip of the variable region 3 (V3) loop; however, unusual motifs harbouring a GWGR signature have also been isolated. Although epidemiological studies have detected this variant in approximately 17-50% of the total infections in Brazil, the prevalence of B"-GWGR in the southernmost region of Brazil is not yet clear. This study aimed to investigate the C2-V3 molecular diversity of the HIV-1B epidemic in southernmost Brazil. HIV-1 seropositive patients were ana-lysed at two distinct time points in the state of Rio Grande do Sul (RS98 and RS08) and at one time point in the state of Santa Catarina (SC08). Phylogenetic analysis classified 46 individuals in the RS98 group as HIV-1B and their molecular signatures were as follows: 26% B"-GWGR, 54% B-GPGR and 20% other motifs. In the RS08 group, HIV-1B was present in 32 samples: 22% B"-GWGR, 59% B-GPGR and 19% other motifs. In the SC08 group, 32 HIV-1B samples were found: 28% B"-GWGR, 59% B-GPGR and 13% other motifs. No association could be established between the HIV-1B V3 signatures and exposure categories in the HIV-1B epidemic in RS. However, B-GPGR seemed to be related to heterosexual individuals in the SC08 group. Our results suggest that the established B"-GWGR epidemics in both cities have similar patterns, which is likely due to their geographical proximity and cultural relationship.

HIV-1 seroprevalence in the general population of Salvador, Bahia State, Northeast Brazil / Soroprevalência do HIV-1 na população geral de Salvador, Bahia, Brasil

To estimate HIV-1 seroprevalence in the general population of Salvador, Bahia, Brazil, we conducted a cross-sectional survey of 3,437 residents from 1998 to 2000. Subjects were drawn from 30 sentinel areas representing a wide range of living conditions. Plasma samples were screened for HIV-1 antibodies by ELISA and confirmed by immunofluorescent assay. Subtype determination by HMA was performed after proviral DNA amplification. Phylogenetic analysis using parsimony was performed with the neighbor-joining method. Overall HIV-1 seroprevalence was 0.55 percent (19/3,446): 0.8 percent for men and 0.36 percent for women. Seroprevalence was higher in the 31-45-year age group (1 percent) and among persons with family income less than twice the minimum wage (0.78 percent) as compared to 0.33 percent for the higher income group. Syphilis was detected in 37 percent of HIV seropositive individuals. Phylogenetic inferences identified 10 samples as subtype B in the env region and 2 samples with Benv/Fgag/Fpol and Fenv/Bgag. Age > 30 years, male gender, and income < 2 times the minimum wage were identified as risk factors for HIV-1 infection. Extrapolating the proportion of seropositive individuals to Salvador, the number of HIV-1 infected individuals was estimated at 13,750.

A seroprevalência do HIV-1 na população geral de Salvador, Bahia, Brasil, foi estimada em estudo de corte transversal com 3.437 indivíduos entre 1998-2000, residentes de 30 áreas sentinelas com ampla va-riedade de condições de vida. Realizou-se uma triagem para anticorpos anti-HIV-1 por ELISA e confirmados por imunofluorescência. A determinação do subtipo foi realizada por HMA, após amplificação do DNA proviral. As análises filogenéticas foram realizadas com PAUP utilizando os algoritmos neighbor-joining. A seroprevalência do HIV-1 foi de 0,55 por cento (19/3.446): 0,8 por cento para os homens e 0,36 por cento para as mulheres. A seroprevalência foi mais alta no grupo de 31-45 anos (1 por cento) e entre as pessoas com renda familiar inferior a dois salários mínimos (0,78 por cento). A sífilis foi diagnosticada em 37 por cento dos participantes HIV soropositivos. A análise filogenética identificou 10 amostras como subtipo B na região env, e duas amostras Benv/Fgag/Fpol e Fenv/Bgag. Idade > 30 anos, sexo masculino, renda < 2 salários mínimos se comportaram como fatores de riscos para a infecção por HIV-1. Se extrapolarmos a proporção de soropositivos para Salvador, o número de infectados pelo HIV seria 13.750.

Epidemiologia molecular do HIV-1: polimorfismo e recombinação em subtipos virais prevalentes no Brasil / Molecular epidemiology of the HIV-1: polymorphism and recombination in subtypes you capsize prevalent in Brazil

A complexa biologia e genética do vírus HIV tornam o desenvolvimento de uma vacina preventiva um enorme desafio. Entretanto, essa ainda é a melhor estratégia para o controle da epidemia pelo HIV. Assim, o objetivo deste trabalho era descrever a presença dos subtipos de HIV-1 em sítios brasileiros selecionados, assim como avaliar o polimorfismo de regiões genômicas relevantes para o desenvolvimento de vacinas em subtipos prevalentes de HIV-1 e vírus recombinantes no Brasil. Nossos resultados nos permitiram constatar a predominância do subtipo B, assim como a detecção de amostras dos subtipos F, C, D, A, além da variante B” do subtipo B, na região C2-V3 env HMA. Nenhuma associação estatisticamente significante, entretanto, pode ser detectada entre os subtipos de HIV-1 e modos de transmissão, as categorias de exposição e o gênero em amostras da cidade do Rio de Janeiro; embora um aumento do subtipo F pudesse ser detectado em usuários de drogas intravenosas (UDIs). As associação entre o subtipo C e UDIs foi detectada em amostras de Porto Alegre, RS. A introdução descontínua dos subtipos no Brasil foi sugerida pelas análises filogenética e distância. Baseados neste dado, nós inferimos que o subtipo B e a variante B” estão circulando desde o início da epidemia de Aids no Brasil e uma introdução mais recente dos subtipos F e C. A análise fiologenética das regiões env (C2-V3 e gp41), gag (p17) e nef confirmou a presença de 9 (26,5 por cento) de 34 amostras de HIV-1 potencialmente recombinantes envolvendo os subtipos B e C ou B e F, como a seguir: Bgag/Cenv/Bnef, Bgag/Cenv/Cnef, Cgag/Benv/Cnef, Bgag/Fenv/Bnef, Bgag/Fgp120/Bgp41/Bnef, Fgag/Fenv/Bnef, Bgag/Fgp120/Bgp41 e Bgag/Fgp120...