Characterization of the anti-spike IgG immune response to COVID-19 vaccines in people with a wide variety of immunodeficiencies

Participants submitted saliva using the OME-505 collection device (OMNIgene Oral, Ottawa, Canada) every two weeks from vaccination through six months post-dose 3 to detect breakthrough SARS-CoV-2 infections. Viral RNA was extracted using the NucliSENS easyMag automated extraction system from 200ul of saliva in stabilizing solution and eluted in a total volume of 50ul. First strand cDNA synthesis was performed from 5ul of eluted RNA using SuperScript IV VILO Master Mix (Thermo Fisher). Positive specimens were then sequenced. Multiplex tiled amplicon libraries were prepared using the Midnight panel and Rapid barcoding kit RBK-004 (Oxford Nanopore technologies) using previously published protocol. Twelve sample pooled libraries were sequenced on a GridION X5 nanopore sequencer using Flongle adapters. After sequencing, raw data were processed using interARTIC to generate consensus sequences and variant calls. SARS-CoV-2 lineages were determined using these consensus sequences and the NextClade and Pangolin platforms.