FIGURE 1 | Target capture dramatically improves genome coverage of low viral load SARS-CoV-2 infections. (A) Distribution of C t values for presumed positive specimens. Values obtained from the m 2000 ± 10 dark cycles are shown. Collaboration-sourced/purchased nasopharyngeal swab specimens sequenced in this study ( N = 194, left) are shown along with a separate panel of pre-clinical/purchased specimens for which only C t values were determined ( N = 99, right). Specimens that were confirmed qPCR negative by Abbott’s RealTime test were indicated as positive by the originating lab. (B) Stacked histogram plot indicating genome coverage (y-axis) without (mNGS; orange) or with (xGen; blue) SARS-CoV-2 xGen target capture. Libraries ( N = 106) with paired NGS and VL data are sorted from low to high C t (x-axis). (C) Sequence statistics (median ± standard deviation for genome coverage, read depth, and % “on target”) by viral load intervals comparing mNGS (orange) to xGen (blue). In each panel, a color bar illustrating the VL range in log cp/ml is included to facilitate comparison of VL to C t .