Abstract
The inability to perform forward genetics has been a major barrier to human papillomavirus (HPV) research. Here, we report a platform for phenotypic selection of HPV mutants. Our method relies on large “concordant” virus libraries, where each mutant virus particle encapsidates the mutant plasmid that encodes it, thereby directly linking viral genotype to phenotype. This platform can achieve a ∼2500-fold enrichment of an L1 capsid protein mutant from an excess of wild-type virus. To demonstrate that this system could select rare mutants from complex libraries, we selected and validated antibody escape mutants and showed that two neutralizing antibodies that recognize overlapping epitopes in L1 display distinct patterns of HPV recognition. This genetics approach unlocks previously inaccessible avenues of investigation into the HPV life cycle and provides a powerful engine to develop improved vaccines and novel antiviral strategies.