Autologous Antibody Capture to Enrich Immunogenic Viruses for Viral Discovery

Oude Munnink, Bas B.; Jazaeri Farsani, Seyed Mohammad; Deijs, Martin; Jonkers, Jiri; Verhoeven, Joost T. P.; Ieven, Margareta; Goossens, Herman; de Jong, Menno D.; Berkhout, Ben; Loens, Katherine; Kellam, Paul; Bakker, Margreet; Canuti, Marta; Cotten, Matthew; van der Hoek, Lia

Serum collected a few weeks to a few months after respiratory or gastrointestinal infection generally contains a substantial amount of pathogen-specific immunoglobulin type G (IgGs) with a proportion of these antibodies binding to virus surface exposed epitopes [22] [23] [24] . These IgGs can be bound to magnetic beads and used to capture a target virus and to separate it from non-viral material (e.g. ribosomes) or non-immunogenic viruses (e.g. plant viruses in stool). After deep sequencing, comparison of reads in the captured material to reads in the input material should reveal virus-specific reads via capture by the antibodies. We tested this strategy in 13 respiratory samples, diagnosed as containing one of the following viruses: human parainfluenza virus 1, 2 and 4, human rhinovirus, human metapneumovirus virus, influenza virus A and B, human respiratory syncytial virus and human coronavirus 229E, OC43 and NL63. We also tested 6 fecal samples containing adenovirus, norovirus, enterovirus and sapovirus. Autologous convalescent sera collected one to a few months after infection was available for all samples (see table 1 ). Plant viruses and enterobacteriophages -viruses which are frequently present in feces -were used as negative control. These viruses are not known to elicit an immune response and are not expected to be captured by the antibody-bound beads.