Table 1. Characteristics of four patients with COVID-19 and SARS-CoV-2 virus samples from Yogyakarta and Central Java.
| Patient No | Sex | Age (year) | COVID-19 severity | CT value | Virus name (GISAID Accession ID) | Average coverage | Collection date | Lineage (GISAID clade) | Amino acid mutations* (no. mutation and position of proteins-encoded genes) |
|---|---|---|---|---|---|---|---|---|---|
| 1 | Female | 83 | Moderate | 16.9 | hCoV19/Indonesia/YO-UGM-781481/2020 (EPI_ISL_516829) |
3748x | 10 August 2020 | GH | 9: NSP3-ORF1ab (P679S), NSP12-ORF1ab (P323L, A656S), NSP13-ORF1ab (M576I), Spike-S (D614G), NS3-ORF3a (A54V, Q57H, A99S), NP-N (Q160R) |
| 2 | Male | 77 | Moderate | 19.7 | hCoV19/Indonesia/YO-UGM-202449/2020 (EPI_ISL_516800) |
22088x | 22 June 2020 | GH | 4: NSP3-ORF1ab (P822L), NSP12-ORF1ab (P323L), Spike-S (D614G), NS3-ORF3a (Q57H) |
| 3 | Female | 55 | Moderate | 24.7 | hCov19/Indonesia/JT-UGM-202538/2020 (EPI_ISL_525492) |
347x | 26 June 2020 | GH | 5: NSP3-ORF1ab (P822L), NSP12-ORF1ab (P323L), Spike-S (D614G), NS3-ORF3a (Q57H), NS7a-ORF7a (H73Y) |
| 4 | Male | 30 | Mild | 27.9 | hCoV19/Indonesia/YO-UGM-200927/2020 (EPI_ISL_516806) |
102x | 16 May 2020 | L | 1: NSP5-ORF1ab (M49I) |
Notes:
*
Name of SARS-CoV-2 proteins (bold) are followed by related genes (italic) and amino acid mutation indicated in bracket.
CT, cycle threshold.
Ref. sequence: hCoV-19/Wuhan/Hu-1/2019 (NC_045512.2).