Methods of utilizing recombination for the identification of binding moieties

A method of identifying a cognate binding moiety of one or more antigens, said method comprising the steps of:

• a) providing
• 1) a population of cells, each of said cells comprising:
• i) a cell surface antigen,
• ii) a nucleic acid comprising a first recombination motif, and
• iii) a conditionally expressed infection apparatus;
• and
• 2) a plurality of virions, each of said virions comprising:
• i) one of a plurality of transgenic viral surface binding moieties and
• ii) a nucleic acid comprising a second recombination motif capable of integrating with said first motif;
• b) contacting said population of cells with said virions;
• c) incubating said cells with said virions under conditions that are not permissive for infection but are sufficient to allow binding of one or more of said cell surface antigens by one or more of said cognate binding moieties, whereby one or more of said cells are bound by one or more of said virions;
• d) emulsifying said bound cells, thereby encapsulating one or more of said cells in one or more emulsion droplets;
• e) incubating said emulsified cells under conditions permissive to expression of said conditionally expressed infection apparatus, thereby allowing infection of one or more of said emulsified cells by one or more virions present in the same emulsion droplet;
• f) incubating said cells in a manner sufficient to allow recombination between said first and second site-specific recombination motifs in infected cells, thereby generating a recombinant product;
• and
• g) identifying a cognate binding moiety of one or more of said antigens by identifying the nucleic acid sequence of said recombinant product or an identifying fragment thereof, in a cell, and identifying from said nucleic acid sequence an antigen and a cognate binding moiety.