HÁBITOS ALIMENTARIOS

Single genome amplification followed by direct amplicon sequencing (SGS) made possible the inference and enumeration of transmitted variants (52, 93). The unambiguous description of the viral genome that initiated and founded clinical infection, allowed the comparison of genetic features of TF and non-transmitted variants. As Env is the first viral protein to interact with host cells, many early studies focused on this protein (118, 188-193). A functional Env is a trimer of heterodimers. Each heterodimer is made up of a surface unit (gp120) and a transmembrane portion (gp41). Surface unit gp120 is made up of both constant regions and variable loops, and is a heavily glycosylated protein (49). Env sequences from individuals with acute subtype C infections have been reported to have fewer potential N-linked glycosylation sites (PNLGs) and shorter variable loops when compared to Env sequences from respective donors or unmatched random chronically infected individuals (118, 190). However, many of the findings are not reproducible across cohorts or viral subtypes. Indeed, in studies of subtype B viruses, researchers have often found no differences in either the length of the variable loops or PNLGs (188, 192, 194, 195) or found differences in only the PNLGs (196). In studies of subtype A and D viruses, recipient viruses have been reported to have shorter variable loops (191, 192), but either the same (191) or fewer PNLGs (192). Comparisons of Env sequences from acutely infected individuals to all sequences in the Los Alamos National Laboratory HIV sequence database yielded shorter variable loops and fewer PNLGs for subtype A but not subtype B (192). Thus, while these Env genotypic features appear to be selected in certain cohorts and subtypes, they are not easily generalizable. Additionally, some of these differences can be attributed to differences in the populations and cohorts studied.

TF viruses have been shown to be more closely related to minor variants in the donor quasispecies (121). A large signature analysis study of subtype B Env sequences identified transmitted signatures in the signal peptide and in gp120, the latter involved the loss of a glycan which has been shown to be associated with immune escape (197). A recent study comparing

18

sequences from 137 transmission pair donors and recipients and found that recipient sequences were closer to the subtype consensus sequence than the matched donor sequences (31). The transmission of more ‘ancestral’ forms has been described previously (198-201) and is interpreted to indicate the transmission of more ‘fit’ viruses. In fact, in chronically infected individuals, viruses with immune escape mutations often infer a fitness cost (181, 184, 202-207). Upon transmission to a naïve recipient, these mutations often revert to consensus amino acid residues (208). The suggestion that more ancestral genomes were indicative of higher fitness merited an investigation into the biological properties of TF viruses.

The most widely observed, robust finding is that transmitted variants use CCR5 as a coreceptor for entry (52, 53, 118, 188, 189, 193). Multiple studies have interrogated the efficiency of receptor and coreceptor usage, hypothesizing that efficient viral replication might require enhanced receptor binding. However, no differences between TF and chronic Envs have been reported in the efficiency and speed of fusion of viral Envs with CD4 (188, 189), and TF viruses have been reported to require high levels of CD4 to mediate entry (118). Additionally, subtype B and C TF Envs were indistinguishable from chronic Envs in their entry into different primary CD4+ T-cell subsets (188, 189). While some reports have identified the integrin a4b7 as a molecule preferentially bound by TF Envs (209)(Arthos), a subsequent study looked at a larger panel of Envs and failed to see these differences (189). We and others have observed that TF Envs are more sensitive to inhibition by maraviroc, a drug that blocks Env- CCR5 interactions, and this is observed for both subtypes B and C (118, 193).

These previous studies have focused on Env in isolation, and to more thoroughly study TF biology, the interrogation of other viral proteins is important. A comprehensive study of full- length replication competent viruses from subtypes B and C found TF viruses have more Env per particle, were more infectious, interacted more efficiently with DC, were transferred more

efficiently from DC to CD4+ T-cells and were more resistant to IFN-α (54). The caveat to this

19

agreement with the results from Parrish and colleages, Fenton-May et al., found that transmitted

viruses were resistant to IFN-α, and that this resistance declined six months after transmission

(210). In this study, the authors compared the IFN-α resistance of the TF from an infected subject

to the consensus virus six months later. To determine if these properties were observed in viruses from linked donors and recipients, subsequent studies used known transmission pairs (195, 201). Surprisingly, these studies did not reproduce Parrish and colleagues’ findings. They found that recipient viruses were equally infectious and have similar replicative capacity (195,

201). Deymier et al found that recipient viruses were equally resistant to IFN-α, while Oberle and

colleagues found recipient viruses to be slightly more sensitive to IFN-α. Limited sampling of the

donor and the source of the donor viruses were caveats in these studies that might have resulted in their findings. Thus, while there are hints that transmitted viruses are distinguished by genetic and biological properties, a more thorough investigation, with larger panels of viruses are warranted.

20