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Pimentel, VF. Study of genetic diversity of HIV inter and intra-host in recent infected patients. [Ph.D thesis (Microbiology)]. São Paulo: Instituto de Ciências Biomédicas, Universidade de São Paulo; 2016. The HIV-1 epidemic in Sao Paulo is changing, with a worrying increase in the number of new infections in young men and in the Men who have Sex with Men (MSM). The epidemic is dominated by subtypes B and F1, but there’s been a recent increase in the prevalence of subtype C. The aim of this study was to identify and characterize HIV-1 transmission networks in Sao Paulo, comparing across subtype epidemics, risk factors, and HAART exposure therapy. We gathered epidemiological, clinical and viral sequence data from HIV-1 infected individuals followed in Adolfo Lutz Institute/SP-BR from Jan 2004 through Feb 2015. After quality control, 2,260 sequences of the partial pol gene were subtyped as previously reported as B, C and F1 were included on this study. 2,107 unique background control sequences were selected by blasting our sequences against Los Alamos database and the Portuguese HIV-1 database. The dataset was screened for Drug Resistance Mutations to identify transmitted drug resistance mutations (TDRM). Maximum-Likelihood phylogenetic trees were built in RaxML for each subtype separately. We used Cluster Picker to analyze transmission dynamics according the thresholds: genetic distance (0.06) and bootstrap over 90%. Statistical analyzes were performed to identify possible correlates of clustering. Categorical variables were compared using Chi-square or Fisher’s exact test and quantitative variables were analyzed using Mann-Whitney test (SPSS). 414 (18,3%) of our population were included in clusters (range: 2-12 individuals). The rate of clustering did not differ between subtypes B and F, however more subtype C sequences (40%) significantly clustered together (p<0.001). Furthermore, more clusters were significantly found in the MSM group when compared to heterosexuals for all subtypes, (p<0.001). Also, drug naïve patients were more likely to be in clusters when compared to treated patients in all subtypes (p <0.001). TDRM were more prevalent in clustering than in non-clustering in subtypes B (p <0.001) and F1 (p =0.009), and more related to MSM group. Despite the higher number of clusters, subtype C presented a lower prevalence of TDRM, although without significant difference between cluster and non-cluster. Clustering individuals were also 5 years younger than non-clustering individuals for subtypes B and C (p<0.001 and 0.02, respectively). Our results indicate that, regardless of subtype, the HIV-1 epidemic in Sao Paulo is selfsustained by treatment-naive MSM patients, who transmit the infection before starting treatment. Subtype C presents a higher proportion of patients that cluster together. However, further analyses are necessary to clarify whether this implies a higher transmission rate of this subtype in Sao Paulo.

Estudo da diversidade genética do HIV inter e intra-hospedeiro em pacientes soroconvertores recentes.