The methodology has been previously described in detail

n genotype was obtained post analysis although for a small subset of subjects two genotypes were obtained. The most recent genotype was used if a subject had been allowed to rescreen for the study after failing to meet other entry criteria PubMed ID:http://www.ncbi.nlm.nih.gov/pubmed/19632476 and was assigned a new subject identification. UDS analysis was performed after the initial phylogenetic analysis of the population sequence on a subset of 350 samples, which included baseline or screen samples from all subjects identified as being in a VTC by population genotype phylogenetic analysis, all subjects with cVF and a randomly selected subset of 250 study subjects. UDS results were obtained for 325 baseline or screen samples. PubMed ID:http://www.ncbi.nlm.nih.gov/pubmed/19630074 The remaining VTC had a more complex geographic distribution with all members in different locations across the USA. All subjects in VTCs with more than 2 members were Hepatitis B/Hepatitis C negative and had similar ranges of CD4 and viral loads. Comparisons of HIV-1 Population Genotype Resistance Mutations non-clustered groups was significant. Four VTC subjects had virus with NNRTI mutations that included the variants K103N, E138A, Y181C and H221Y. In contrast, significantly more non-clustered subjects had virus with NNRTI mutations. The mutations observed included all of the previously listed variants as well as V90I, A98G, K101E, K101P, K103S, V106I, V106M, V108I, E138G, E138K, V179D, Y188L, G190A, P225H and M230I. No virus from VTC subjects had NRTI mutations, compared with 29/621 of the non-clustered population. The NRTI viral mutations observed in non-clustered subjects included M41L, D67N, K70R, V75I, Q151M, M184I/V, L210W, T215Y, and K219E/Q. There were two major PI mutation detected in two viruses from VTC subjects as compared with the subjects with non-clustered virus where 22/621 contained major PI mutations. In this latter group, most of the subjects had virus with a single major PI mutation in addition to minor variants. Within VTCs where major mutations were detected, no other subjects within the VTC had major mutations. However, minor PI mutation profiles of viruses within a VTC were relatively consistent. ART-Naive HIV-1 Phylogenetic Clustering Patterns Cluster Attributes.2 subjects Includes males Includes females Female only White only Black only $2 races within cluster $1 Hispanic subject $1 subject MSM Risk Factor Includes both heterosexual and MSM Risk Factor $1 subject with IVDU Heterosexual only Risk Factor All subjects in the VTC purchase Sutezolid treated in the same state/province All subjects in the VTC treated in the same city $2 subjects treated in the same city $2 subjects treated in the same state/province Clusters that included subjects from mainland USA and Puerto Rico or subjects from mainland USA and Canada VTC that include $1 Canadian subjectsa VTC that include $1 Puerto Rican subjects HCV co-infected HBV co-infected $1 subject CDC Class C $1 subject HIV-RNA.100,000 copies/mL $1 subject CD4.350 cells/mm3 $1 subject CD4,250 cells/mm3 Not all subjects within each cluster were Canadian. There were 18 additional NNRTI, NRTI, and major PI resistance mutation observed with UDS that were detected with a prevalence of between $1 and,6% of which 12/18 were different types of NNRTI mutations. The remaining 6/18 types of mutations detected at low prevalence were major PI mutations. The newly detected mutations that were observed in.1 viral genotype were the major PI mutations M46I and V82A, and the RT mutation V106I. A total of 16 subjects had virus with NNRTI