Experimental characterization of the properties of authentic viruses circulating in infected individuals presents a problem when investigating RNA viruses with error-prone polymerases. The hepatitis C virus provides an extreme example of RNA virus genetic variability, as the nucleotide composition of HCV genomes can vary by more than 30% between strains. The envelope glycoproteins E1 and E2 in particular are able to tolerate a particularly high level of variation. They are under continual selection pressure from the host antibody response during chronic infection and can tolerate adaptive mutations, leading to great diversity in a single host. The diversity of E1/E2 in circulating viruses has hindered investigations of their function and development of a vaccine that will generate antibodies able to potently neutralize entry of genetically distinct strains.
Here we describe methods used in our laboratory to overcome the limitations of investigating the properties of the envelope glycoproteins representing only small numbers of HCV variants. Using a high-fidelity, limiting dilution (“endpoint”) PCR approach to amplify single E1/E2 cDNA templates, which can then generate recombinant model viral particles using retrovirus packaging/reporter constructs. These retroviral pseudoparticles (pseudotypes) facilitate investigation of the properties of authentic E1/E2 glycoproteins in a single-round infection assay. We also describe optimized methods for generation of infectious pseudoparticles from patient-isolated E1/E2 and methods for performing neutralization assays with both anti-virus and anti-host antibodies.