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Table 4 Amino acid mutations detected in SARS-CoV-2 viruses collected from two family cluster cases in Yogyakarta and Central Java provinces

From: Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters

Virus (Accession No.) NSP2 NSP3 NSP4 NSP5 NSP12 (RdRp)
Amino acid position in each gene 247 256 321 299 822 231 12 248 323 892
Wuhan/19 (NC_045512.2) V T Q V P A K T P H
YO-UGM-10001 (EPI_ISL_576113)* A T Q V L A R I L H
YO-UGM-10002 (EPI_ISL_576114)* V I Q V L A R I L H
YO-UGM-10003 (EPI_ISL_576115)* A T Q V L A R I L H
YO-UGM-10004 (EPI_ISL_576116)** V T Q A L V K T L H
YO-UGM-10005 (EPI_ISL_576128)** V I K V L A K T L Y
YO-UGM-10006 (EPI_ISL_576130)** V I K V L A K T L Y
YO-UGM-10007 (EPI_ISL_632936) V T Q V L A K T L H
YO-UGM-781481 (EPI_ISL_516829) V T Q V P A K T L H
YO-UGM-202449 (EPI_ISL_516800) V T Q V L A K T L H
JT-UGM-202538 (EPI_ISL_525492) V T Q V L A K T L H
YO-UGM-200927 (EPI_ISL_516806) V T Q V P A K T P H
JT-UGM-47906 (EPI_ISL_576383) V T Q V P A K T L H
JT-UGM-47964 (EPI_ISL_610162) V T Q V P A K T P H
JT-UGM-48660 (EPI_ISL_610161) V T Q V L A R T L H
YO-UGM-00061 (EPI_ISL_575331) V T Q V L A K T L H
YO-UGM-48651 (EPI_ISL_632937) V T Q V P A K T L H
YO-UGM-107727 (EPI_ISL_576145) V T Q V P A K T L H
Virus (Accession No.) NSP13 NSP14 Spike NS3 N   
Amino acid position in each gene    5 213 614 57 119 193   
Wuhan/19 (NC_045512.2) T P L V D Q A S   
YO-UGM-10001 (EPI_ISL_576113)* T P L A G H S I   
YO-UGM-10002 (EPI_ISL_576114)* T P L A G H S I   
YO-UGM-10003 (EPI_ISL_576115)* T P L A G H S I   
YO-UGM-10004 (EPI_ISL_576116)** I L L V G H A S   
YO-UGM-10005 (EPI_ISL_576128)** T P F V G H A S   
YO-UGM-10006 (EPI_ISL_576130)** T P F V G H A S   
YO-UGM-10007 (EPI_ISL_632936) T P L V G H A S   
YO-UGM-781481 (EPI_ISL_516829) T P L V G H A S   
YO-UGM-202449 (EPI_ISL_516800) T P L V G H A S   
JT-UGM-202538 (EPI_ISL_525492) T P L V G H A S   
YO-UGM-200927 (EPI_ISL_516806) T P L V D Q A S   
JT-UGM-47906 (EPI_ISL_576383) T P L V G Q A S   
JT-UGM-47964 (EPI_ISL_610162) T P L V G Q A S   
JT-UGM-48660 (EPI_ISL_610161) T P L A G H S I   
YO-UGM-00061 (EPI_ISL_575331) T P L V G H A S   
YO-UGM-48651 (EPI_ISL_632937) T P L V G H A S   
YO-UGM-107727 (EPI_ISL_576145) T P L V G Q A S   
  1. Family clusters are indicated in asterisks: Case-1 (*) and Case-2 (**). In family cluster-1 and 2, variations in the amino acids of the NSP2 protein (V247A and T256I, and T256I and Q321K, respectively) were noted, but not in others. The virus samples isolated from fatal disease outcomes of family cluster-1 (YO-UGM-10001|EPI_ISL_576113 and YO-UGM-10003|EPI_ISL_576115) carried V247A mutation in the NSP2 protein, while those from the recovered patient (YO-UGM-10002|EPI_ISL_576114) did not. Bold, amino acids were different from their reference (Wuhan/19 [NC_045512.2])