{"about":{"site":"https://codewithpapers.app","non_affiliation":"Code with Papers and Syntology are not affiliated with, endorsed by, or sponsored by Papers with Code, Meta, or the pwc-archive mirror.","licence":"CC BY-SA 4.0","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","attribution":"https://codewithpapers.app/attribution","modified":"archive material modified by Syntology; see the attribution page"},"url":"/paper/host-pathogen-coevolution-and-the-emergence","title":"Host-pathogen coevolution and the emergence of broadly neutralizing antibodies in chronic infections","arxiv_id":"1512.06296","date":"2016-06-20","proceeding":null,"authors":[],"abstract":"The vertebrate adaptive immune system provides a flexible and diverse set of\nmolecules to neutralize pathogens. Yet, viruses such as HIV can cause chronic\ninfections by evolving as quickly as the adaptive immune system, forming an\nevolutionary arms race. Here we introduce a mathematical framework to study the\ncoevolutionary dynamics of antibodies with antigens within a host. We focus on\nchanges in the binding interactions between the antibody and antigen\npopulations, which result from the underlying stochastic evolution of genotype\nfrequencies driven by mutation, selection, and drift. We identify the critical\nviral and immune parameters that determine the distribution of antibody-antigen\nbinding affinities. We also identify definitive signatures of coevolution that\nmeasure the reciprocal response between antibodies and viruses, and we\nintroduce experimentally measurable quantities that quantify the extent of\nadaptation during continual coevolution of the two opposing populations. Using\nthis analytical framework, we infer rates of viral and immune adaptation based\non time-shifted neutralization assays in two HIV-infected patients. Finally, we\nanalyze competition between clonal lineages of antibodies and characterize the\nfate of a given lineage in terms of the state of the antibody and viral\npopulations. In particular, we derive the conditions that favor the emergence\nof broadly neutralizing antibodies, which may be useful in designing a vaccine\nagainst HIV.","url_abs":"http://arxiv.org/abs/1512.06296v2","url_pdf":"http://arxiv.org/pdf/1512.06296v2.pdf","source":{"archive":"pwc-archive (Hugging Face), CC BY-SA 4.0","snapshot":"2025-07-28","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","row_kind":"abstracts"},"code_links":[{"paper_slug":"host-pathogen-coevolution-and-the-emergence","repo_url":"https://github.com/jotwin/coevolution","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":0,"framework":"none","reach":null}],"tasks":[],"methods":[],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"syntology_url":null,"atlas_url":null,"mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}