title: HIV-1 diversity, transmission dynamics and primary drug resistance in Angola.
abstract: OBJECTIVE
  To assess HIV-1 diversity, transmission dynamics and prevalence of transmitted drug resistance (TDR) in Angola, five years after ART scale-up.
  
  
  METHODS
  Population sequencing of the pol gene was performed on 139 plasma samples collected in 2009 from drug-naive HIV-1 infected individuals living in Luanda. HIV-1 subtypes were determined using phylogenetic analysis. Drug resistance mutations were identified using the Calibrated Population Resistance Tool (CPR). Transmission networks were determined using phylogenetic analysis of all Angolan sequences present in the databases. Evolutionary trends were determined by comparison with a similar survey performed in 2001.
  
  
  RESULTS
  47.1% of the viruses were pure subtypes (all except B), 47.1% were recombinants and 5.8% were untypable. The prevalence of subtype A decreased significantly from 2001 to 2009 (40.0% to 10.8%, P = 0.0019) while the prevalence of unique recombinant forms (URFs) increased > 2-fold (40.0% to 83.1%, P < 0.0001). The most frequent URFs comprised untypable sequences with subtypes H (U/H, n = 7, 10.8%), A (U/A, n = 6, 9.2%) and G (G/U, n = 4, 6.2%). Newly identified U/H recombinants formed a highly supported monophyletic cluster suggesting a local and common origin. TDR mutation K103N was found in one (0.7%) patient (1.6% in 2001). Out of the 364 sequences sampled for transmission network analysis, 130 (35.7%) were part of a transmission network. Forty eight transmission clusters were identified; the majority (56.3%) comprised sequences sampled in 2008-2010 in Luanda which is consistent with a locally fuelled epidemic. Very low genetic distance was found in 27 transmission pairs sampled in the same year, suggesting recent transmission events.
  
  
  CONCLUSIONS
  Transmission of drug resistant strains was still negligible in Luanda in 2009, five years after the scale-up of ART. The dominance of small and recent transmission clusters and the emergence of new URFs are consistent with a rising HIV-1 epidemics mainly driven by heterosexual transmission.
authors.affiliation: Unidade dos Retrovírus e Infecções Associadas, Centro de Patogénese Molecular e Instituto de Investigação do Medicamento (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal; Centro de Investigação Interdisciplinar Egas Moniz, Instituto Superior de Ciências da Saúde Egas Moniz, Monte de Caparica, Portugal.
authors.forename: Inês
authors.initials: I
authors.lastname: Bártolo
authors.affiliation: Centro de Investigação Interdisciplinar Egas Moniz, Instituto Superior de Ciências da Saúde Egas Moniz, Monte de Caparica, Portugal.
authors.forename: Suzana
authors.initials: S
authors.lastname: Zakovic
authors.affiliation: Unidade dos Retrovírus e Infecções Associadas, Centro de Patogénese Molecular e Instituto de Investigação do Medicamento (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal; Centro de Investigação Interdisciplinar Egas Moniz, Instituto Superior de Ciências da Saúde Egas Moniz, Monte de Caparica, Portugal.
authors.forename: Francisco
authors.initials: F
authors.lastname: Martin
authors.affiliation: Unidade dos Retrovírus e Infecções Associadas, Centro de Patogénese Molecular e Instituto de Investigação do Medicamento (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal.
authors.forename: Claudia
authors.initials: C
authors.lastname: Palladino
authors.affiliation: Laboratório de Biologia Molecular, Centro Hospitalar Lisboa Ocidental, Hospital Egas Moniz, Lisboa, Portugal.
authors.forename: Patrícia
authors.initials: P
authors.lastname: Carvalho
authors.affiliation: Laboratório de Biologia Molecular, Centro Hospitalar Lisboa Ocidental, Hospital Egas Moniz, Lisboa, Portugal; Rega Institute for Medical Research, KU Leuven, Leuven, Belgium.
authors.forename: Ricardo
authors.initials: R
authors.lastname: Camacho
authors.affiliation: Abbott GmbH & Co. KG, Wiesbaden, Germany.
authors.forename: Sven
authors.initials: S
authors.lastname: Thamm
authors.affiliation: Hospital da Divina Providência, Serviço de Doenças Infecciosas, Luanda, Angola.
authors.forename: Sofia
authors.initials: S
authors.lastname: Clemente
authors.affiliation: Unidade dos Retrovírus e Infecções Associadas, Centro de Patogénese Molecular e Instituto de Investigação do Medicamento (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal; Centro de Investigação Interdisciplinar Egas Moniz, Instituto Superior de Ciências da Saúde Egas Moniz, Monte de Caparica, Portugal.
authors.forename: Nuno
authors.initials: N
authors.lastname: Taveira
mesh_terms: D000810:Angola; D024882:Drug Resistance, Viral / Q000235:genetics; D014644:Genetic Variation; D005838:Genotype; D015658:HIV Infections / Q000188:drug therapy / Q000235:genetics* / Q000635:transmission; D015497:HIV-1 / Q000187:drug effects / Q000235:genetics* / Q000472:pathogenicity; D006801:Humans; D017720:Molecular Epidemiology; D009154:Mutation; D010802:Phylogeny; D016415:Sequence Alignment; D017421:Sequence Analysis