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. HIV1 HIV (HIV-1 subtypes HIV- form CRFBC CRF CRF_BC CRF146BC CRF146 RDP pattern work URFs, URFs , (URFs) sequence gene level strains Sul states Thus regions South Northeast (HIV- CRF14 (URFs (HIV CRF1

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. 1 F subsubtype sub HIV1 HIV (HIV- continents Africa America cocirculates co forms variants HIV- fulllength full length POL671 POL (POL67 NFLG53 NFLG performed worldwide F1.I F1I FI I (F1.I 75% 75 (75% F1.II F1II FII II (F1.II 62% 62 (62% isolates 1970 France, France (France Finland Belgium, Belgium , Belgium) Moreover 1998 (199 CI 19942003 1994 2003 1994-2003 Spain UK observed Interestingly ancestor progenies (HIV POL67 (POL6 NFLG5 7 (75 6 (62 197 199 (19 1994200 200 1994-200 POL6 (POL (7 (6 19 (1 199420 20 1994-20 ( 19942 2 1994-2 1994-

In Brazil, detection of the HIV-1 sub-subtype F1 has decreased with a simultaneous increase in detection of the recombinant FB and FC forms. In previous HIV-1 env molecular epidemiology studies in Rio de Janeiro, 11.4% of the detected sequences were of the F1 sub-subtype. With the goal of re-estimating the prevalence of the HIV-1 F1 sub-subtype, we performed extended analyses of these samples by examining five genomic regions, resulting in 3.3% being confirmed as F1. Moreover, genomic analysis of 11 of the 21 samples identified as F1 confirmed that nine were F1 and two were BF1. Considering the number of samples assayed, the prevalence of F1 was quite low, which supports the use of different genomic regions for the assessment of HIV-1 classification in countries where several subtypes and recombinant forms co-circulate.

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% (19/3.446): 0,8% para os homens e 0,36% para as mulheres. A seroprevalência foi mais alta no grupo de 31-45 anos (1%) e entre as pessoas com renda familiar inferior a dois salários mínimos (0,78%). A sífilis foi diagnosticada em 37% 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.

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% (19/3,446): 0.8% for men and 0.36% for women. Seroprevalence was higher in the 31-45-year age group (1%) and among persons with family income less than twice the minimum wage (0.78%) as compared to 0.33% for the higher income group. Syphilis was detected in 37% 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% (19/3.446): 0,8% para os homens e 0,36% para as mulheres. A seroprevalência foi mais alta no grupo de 31-45 anos (1%) e entre as pessoas com renda familiar inferior a dois salários mínimos (0,78%). A sífilis foi diagnosticada em 37% 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.

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% (19/3,446): 0.8% for men and 0.36% for women. Seroprevalence was higher in the 31-45-year age group (1%) and among persons with family income less than twice the minimum wage (0.78%) as compared to 0.33% for the higher income group. Syphilis was detected in 37% 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.