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. 2023 Jun 13;21(6):e3002151. doi: 10.1371/journal.pbio.3002151

Fig 6. Percent genome coverage at 10× read depth for clinical specimens sequenced with the amplicon-based sequencing approach.

Fig 6

(A) Lesion swabs (n = 10) sequenced by the DPHL. Data are fitted with a logistic function and the dashed line corresponds to 80% genome coverage at a threshold of Ct 28.9. (B) Dry vesicle swabs (n = 56) from various anatomical sites and sequenced by the RIDOH RISHL. Data are fitted with a logistic function and the dashed line corresponds to 80% genome coverage at a threshold of Ct 31.2. (C) Lesion swabs (n = 6) sequenced by the FDH. Data are fitted with a logistic function and the dashed line corresponds to 80% genome coverage at a threshold of Ct 30.6. (D) Lesion swabs (n = 9) sequenced by IBL. Data are fitted with a logistic function. (E) Lesion swabs (n = 27) sequenced by the LACPHL. Data are fitted with a logistic function. (F) Lesion swabs (n = 25) from various anatomical sites and sequenced by the MDH. Data are fitted with a logistic function. (G) Clinical specimens (n = 19) consisting of lesion swabs and crusts of healing lesions sequenced by the CEVS. Data are fitted with a logistic function. (H) Clinical specimens (n = 78) consisting of lesion swabs from various anatomical sites as well as oropharyngeal swabs sequenced by INSA. (I) Vesicle swabs (n = 34) from various anatomical sites tested in parallel on Illumina and ONT sequencing platforms by the NHS. Data from both sequencing platforms are fitted with logistic function and the dashed lines correspond to 80% genome coverage at a threshold of Ct 25.6 on the Illumina platform and Ct 24.7 on the ONT platform. (J) Lesion swabs (n = 8) sequenced on the ONT platform by JHMI. Source data can be found in S5 Data. CEVS, Centro Estadual de Vigilância em Saúde; Ct, cycle threshold; DPHL, Delaware Public Health Lab; FDH, Florida Department of Health; IBL, Idaho Bureau of Laboratories; INSA, National Institute of Health Dr. Ricardo Jorge; JHMI, Johns Hopkins Medical Institutions; LACPHL, Los Angeles County Public Health Lab; MDH, Minnesota Department of Health; NHS, National Health Service; ONT, Oxford Nanopore Technology; RIDOH RISHL, Rhode Island Department of Health/Rhode Island State Health Laboratory.