P17-09. Immunization with a single HIV-1 envelope sequence can generate CD8+ T lymphocytes capable of recognizing multiple variant forms of envelope

Background: The ability of CD8+ T lymphocytes to recognize a diversity of mutant forms of an HIV epitope is of central importance in the immune containment of this virus. The present studies were pursued to determine the mechanism employed by CD8+ T lymphocytes to recognize mutant viruses. In particular, we sought to determine whether mutant sequences are recognized by distinct CD8+ T lymphocyte populations or whether individual clonal populations of CD8+ T lymphocytes recognize a diversity of mutant sequences. Methods: We employed flow cytometry, Vβ repertoire analysis, and CDR3 sequencing methodologies to characterize the clonal diversity of CD8+ T lymphocytes that recognize variant forms of the HIV-1 envelope (Env) p41A epitope generated after infection by SHIV-89.6P or elicited by HIV-1 89.6P Env immunization of Mamu-A*01+ rhesus monkeys. To evaluate the capacity of the CD8+ T lymphocytes to recognize genetically diverse isolates of HIV-1, we employed a series of tetramers constructed with variants of the p41A epitope of HIV-1 Env. To define which T cell receptor mediated the recognition of each specific variant p41A, we isolated variant p41A-specific CD8+ T lymphocyte populations and analyzed the expression of 46 Vβ families and subfamilies genes. We then determined the precise clones employed for the recognition of each variant epitope peptide through CDR3 sequencing. Results: In both the infected and the vaccinated monkeys, we observed clonotypes capable of recognizing the majority of the variant epitope peptides. Conclusion: These data show that exposure to a single HIV-1 Env sequence can generate clonotypes capable of recognizing multiple variant forms of HIV-1 Env. Such Env-specific CD8+ T lymphocytes should be able to confer potent, effective protection against a diverse spectrum of circulating viruses

Elucidation of Hepatitis C Virus Transmission and Early Diversification by Single Genome Sequencing

A precise molecular identification of transmitted hepatitis C virus (HCV) genomes could illuminate key aspects of transmission biology, immunopathogenesis and natural history. We used single genome sequencing of 2,922 half or quarter genomes from plasma viral RNA to identify transmitted/founder (T/F) viruses in 17 subjects with acute community-acquired HCV infection. Sequences from 13 of 17 acute subjects, but none of 14 chronic controls, exhibited one or more discrete low diversity viral lineages. Sequences within each lineage generally revealed a star-like phylogeny of mutations that coalesced to unambiguous T/F viral genomes. Numbers of transmitted viruses leading to productive clinical infection were estimated to range from 1 to 37 or more (median = 4). Four acutely infected subjects showed a distinctly different pattern of virus diversity that deviated from a star-like phylogeny. In these cases, empirical analysis and mathematical modeling suggested high multiplicity virus transmission from individuals who themselves were acutely infected or had experienced a virus population bottleneck due to antiviral drug therapy. These results provide new quantitative and qualitative insights into HCV transmission, revealing for the first time virus-host interactions that successful vaccines or treatment interventions will need to overcome. Our findings further suggest a novel experimental strategy for identifying full-length T/F genomes for proteome-wide analyses of HCV biology and adaptation to antiviral drug or immune pressures

Defining functional distances over Gene Ontology

<p>Abstract</p> <p>Background</p> <p>A fundamental problem when trying to define the functional relationships between proteins is the difficulty in quantifying functional similarities, even when well-structured ontologies exist regarding the activity of proteins (i.e. 'gene ontology' -GO-). However, functional metrics can overcome the problems in the comparing and evaluating functional assignments and predictions. As a reference of proximity, previous approaches to compare GO terms considered linkage in terms of ontology weighted by a probability distribution that balances the non-uniform 'richness' of different parts of the Direct Acyclic Graph. Here, we have followed a different approach to quantify functional similarities between GO terms.</p> <p>Results</p> <p>We propose a new method to derive 'functional distances' between GO terms that is based on the simultaneous occurrence of terms in the same set of Interpro entries, instead of relying on the structure of the GO. The coincidence of GO terms reveals natural biological links between the GO functions and defines a distance model <it>D</it>_{<it>f </it>}which fulfils the properties of a Metric Space. The distances obtained in this way can be represented as a hierarchical 'Functional Tree'.</p> <p>Conclusion</p> <p>The method proposed provides a new definition of distance that enables the similarity between GO terms to be quantified. Additionally, the 'Functional Tree' defines groups with biological meaning enhancing its utility for protein function comparison and prediction. Finally, this approach could be for function-based protein searches in databases, and for analysing the gene clusters produced by DNA array experiments.</p