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. 2021 Jul 13;110:232–234. doi: 10.1016/j.ijid.2021.07.029

Figure 1.

Figure 1

Phylogenetic analysis and SARS-CoV-2 viral genome coverage with genetic variants of Patient A. NGS using NEBNext® ARTIC SARS-CoV-2 FS Library Prep Kit and Illumina NextSeq 550 platform resulted in 3.4 million reads (with 99% coverage of the genome at 10X depth, 4880x mean target coverage). RT-PCR (N1) prior to NGS testing resulted in the following cycle threshold (Ct) values: 31.3 (Patient A) and 25.2 (Patient B). (A) The clinical sample was identified as B.1.617.2 lineage (clade 20A). The phylogenetic tree was generated using COVID-DX and Nextclade (version 4-22-2021). (B) The plot shows the depth of sequencing that was recovered across the genome. We detected 35 mutations, including 12 ORF1ab, 9 spike protein, and 3 nucleocapsid genes in reference to the Wuhan wild-type strain (NC_045512.2). The spike protein mutations include: C21618G (T19R), ATACATG21764A (H69_V70del), TTTA21990T (Y145del), T22917G (L452R), C22995A (T478K), A23403G (D614G), C23604G (P681R), A24783G (N1074S), G25352T (V1264L). The percent of the SARS-CoV-2 genome recovered from the sample and genetic variants identified compared to the reference genome (Wuhan wild-type strain) are indicated (top) with no coverage (pink), and higher callable coverage (blue) shown. The proportion of known genetic variants of SARS-CoV-2 strains as reported in NextStrain (version 03-07-2021) from across the world are shown (bottom).