HIV-1 Diversity, Transmission Dynamics and Primary Drug Resistance in Angola

Abstract

ObjectivesTo assess HIV-1 diversity, transmission dynamics and prevalence of transmitted drug resistance (TDR) in Angola, five years after ART scale-up.MethodsPopulation 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.Results47.1% 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.ConclusionsTransmission 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.

An analysis of drug resistance among people living with HIV/AIDS in Shanghai, China

“…Previous studies reported that HIV-1 strains with decreased sensitivity to ART drugs also showed decreased replication, indicated by lower HIV-1 virus load [ 25 , 26 ]. Age, gender, and infection route were not significantly different in the DR and non-DR groups, as reported previously [ 27 – 29 ]. In addition, duration of treatment was not related to DR rate.…”

Origin and Population Dynamics of a Novel HIV-1 Subtype G Clade Circulating in Cape Verde and Portugal

“…Subtype G is the sixth most prevalent HIV-1 clade in the world accounting for nearly 5% of all global infections [ 2 ]. This subtype reaches the highest prevalence in some African countries, comprising 30–50% of HIV-1 infections in Cape Verde [ 3 , 4 ] and Nigeria [ 5 – 12 ], and 5–15% of HIV-1 infections in Angola [ 13 – 15 ], Benin [ 16 ], Niger [ 17 , 18 ] and Togo [ 19 , 20 ]. A recent study conducted by our group suggests that subtype G most probably emerged in Central Africa around the late 1960s and was rapidly disseminated into the West and West Central African regions [ 21 ].…”

“…Notably, about two-thirds of the subtype G viruses previously described in Portugal were found in individuals from Angola and Cape Verde [ 23 ]. These countries are two former Portuguese African colonies that have strong historic links and maintain ongoing relationships with Portugal and displayed a relatively high prevalence of subtype G [ 3 , 4 , 13 – 15 ]. The high numbers of immigrants from Angola and Cape Verde who enter Portugal and also those Portuguese returning after living in the former Portuguese African colonies from the 1970s onwards [ 28 ], supposes a potential risk for introduction of HIV-1 subtype G strains in Portugal.…”

HIV Risks in Sexual Networks of Heterosexual Men in South Africa

“…Phylogenetic studies have long been used to understand the evolution of HIV and to study specific HIV transmission events but with limitations on individual transmission HIV events (Pillay & Fisher, 2007). Phylogenetic analysis has been used to understand HIV diversity and drug resistance (Bártolo et al, 2014), to understand seroconversion events (Eshleman et al, 2011), duration and concurrency of sexual partnerships in HIV transmission (Kim, Riolo, & Koopman, 2010) and to identify HIV transmissions amongst local communities and factors that may contribute to sustained transmission of the virus (Wilkinson, Engelbrecht, & de Oliveira, 2014). Understanding structural features of risks of HIV transmission, particularly in sexual networks is important as there exist minimal work focusing on characterizing these structures in South African heterosexual men.…”