Droplet microfluidic analysis of the human B cell immune repertoire over the course of SARS CoV-2 infection. Link-Seq

Here, we present Link-Seq, a highly efficient droplet microfluidic method for combined sequencing of antibody encoding genes and the transcriptome of individual B-cells at large scale. The method is based on 3’-barcoding of the transcriptome and subsequent single molecule PCR in droplets, enabling to freely shift the barcode along specific gene regions, such as the antibody heavy and light chain genes. We obtain up to 91.7% correctly paired immunoglobulin heavy and light chains and show sensitivities comparable to current gold standard commercial systems, while offering full flexibility in experimental setup. Applying Link-Seq to early SARS-CoV-2 infection samples, we discovered striking changes in the expression levels of B cell homing receptors, a burst of auto-reactive IGHV-4-34 plasmablasts, and a rare subset of dendritic cell-primed B cells (dp-B). These mechanisms likely play an important role in the short-lived immune protection against SARS-CoV-2 and the divergent results seen in plasma therapy studies.