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

Gunadi; Wibawa, Hendra; Hakim, Mohamad Saifudin; Marcellus; Trisnawati, Ika; Khair, Riat El; Triasih, Rina; Irene; Afiahayati; Iskandar, Kristy; Siswanto; Anggorowati, Nungki; Daniwijaya, Edwin Widyanto; Supriyati, Endah; Nugrahaningsih, Dwi Aris Agung; Budiono, Eko; Retnowulan, Heni; Puspadewi, Yunika; Puspitawati, Ira; Sianipar, Osman; Afandy, Dwiki; Simanjaya, Susan; Widitjiarso, William; Puspitarani, Dyah Ayu; Fahri, Fadil; Riawan, Untung; Fauzi, Aditya Rifqi; Kalim, Alvin Santoso; Ananda, Nur Rahmi; Setyati, Amalia; Setyowireni, Dwikisworo; Laksanawati, Ida Safitri; Arguni, Eggi; Nuryastuti, Titik; Wibawa, Tri

doi:10.1186/s12920-021-00990-3

BMC Medical Genomics

Table 1 Nucleic acid and amino acid mutations observed in seventeen SARS-CoV-2 virus genomes collected from Yogyakarta and Central Java provinces between June and September 2020

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

No.	NA position*	Gene/ Region	Number of SNP	NA change (SNP)	Type of base change	Entropy values	Frequency	Type of mutation	AA changes (position)^#
1	1154	NSP2	7	C → T	Transition	0.21456	2	Missense	A205V
2	1280			C → T	Transition	0.34883	2	Missense	V247A
3	1307			C → T	Transition	0.45056	3	Missense	T256I
4	1501			C → A	Transversion	0.34883	2	Missense	Q321K
5	1845			C → T	Transition	0.21456	1	Synonymous	N435N
6	1998			C → T	Transition	0.21456	1	Synonymous	T486T
7	2247			A → G	Transition	0.21456	1	Synonymous	R569R
8	2772	NSP3	13	C → T	Transition	0.45056	15	Synonymous	F106F
9	3264			T → C	Transition	0.21456	1	Synonymous	D270D
10	3350			T → C	Transition	0.21456	1	Synonymous	V299A
11	3819			C → T	Transition	0.52971	4	Synonymous	G443G
12	4489			C → T	Transition	0.21456	1	Missense	P679S
13	4919			C → T	Transition	0.66825	13	Missense	P822L
14	5519			C → T	Transition	0.21456	1	Missense	T1022I
15	5541			C → T	Transition	0.34883	2	Synonymous	C1029C
16	5990			C → T	Transition	0.21456	1	Missense	A1179V
17	6047			C → A	Transversion	0.21456	1	Missense	T1198K
18	6515			T → G	Transversion	0.21456	1	Missense	F1354C
19	7374			C → T	Transition	0.21456	1	Synonymous	F1640F
20	7448			C → T	Transition	0.21456	1	Missense	P1665L
21	8981	NSP4	1	C → T	Transition	0.21456	1	Missense	A231V
22	9824	NSP5	4	A → G	Transition	0.52971	4	Missense	K12R
23	9936			G → T	Transversion	0.21456	1	Missense	M49I
24	10242			C → T	Transition	0.68696	8	Synonymous	N151N
25	10339			C → T	Transition	0.21456	1	Missense	P184S
26	10818	NSP6	1	G → T	Transversion	0.21456	1	Missense	L37F
27	11887	NSP8	2	G → A	Transition	0.21456	1	Missense	A21T
28	12174			C → T	Transition	0.21456	1	Synonymous	P116P
29	12544	NSP9	1	C → T	Transition	0.21456	1	Missense	L42F
30	13465	NSP12 (RdRp)	12	C → T	Transition	0.21456	1	Missense	A97V
31	13790			G → T	Transversion	0.21456	1	Synonymous	L205L
32	13855			C → T	Transition	0.21456	1	Missense	P227L
33	13918			C → T	Transition	0.52971	3	Missense	T248I
34	14027			C → T	Transition	0.21456	1	Synonymous	D284D
35	14143			C → T	Transition	0.45056	15	Missense	P323L
36	14429			C → T	Transition	0.21456	1	Synonymous	D418D
37	15141			G → T	Transversion	0.21456	1	Missense	A656S
38	15278			G → T	Transversion	0.21456	1	Synonymous	T701T
39	15500			A → G	Transition	0.21456	1	Synonymous	L775L
40	15849			C → T	Transition	0.34883	2	Missense	H892Y
41	15891			A → G	Transition	0.21456	1	Missense	M906V
42	16130	NSP13	8	A → T	Transversion	0.45056	3	Synonymous	P53P
43	16196			C → T	Transition	0.21456	1	Synonymous	H75H
44	16351			C → T	Transition	0.21456	1	Missense	T127I
45	16382			G → T	Transversion	0.52971	4	Synonymous	T137T
46	16429			C → T	Transition	0.21456	1	Missense	T153I
47	16476			G → T	Transversion	0.21456	1	Missense	V169F
48	16745			C → T	Transition	0.21456	1	Synonymous	I258I
49	17699			G → T	Transversion	0.21456	1	Missense	M576I
50	18382	NSP14	4	C → T	Transition	0.21456	1	Missense	P203L
51	18479			C → T	Transition	0.68696	8	Synonymous	Y235Y
52	18612			C → T	Transition	0.59084	14	Synonymous	L280L
53	18737			A → G	Transition	0.21456	1	Synonymous	L321L
54	19859	NSP15	2	T → C	Transition	0.21456	1	Synonymous	I168I
55	20364			C → T	Transition	0.21456	1	Missense	H337Y
56	20843	NSP16	2	C → T	Transition	0.21456	1	Synonymous	F150F
57	21058			A → G	Transition	0.21456	2	Missense	Y222C
58	21310	Spike (S)	12	C → T	Transition	0.34883	2	Missense	L5F
59	21387			T → C	Transition	0.21456	1	Synonymous	N30N
60	21477			C → T	Transition	0.52971	4	Synonymous	S60S
61	21483			T → C	Transition	0.21456	1	Synonymous	V62V
62	21544			G → C	Transversion	0.21456	1	Missense	V83L
63	21935			T → C	Transition	0.52971	4	Missense	V213A
64	22069			T → C	Transition	0.21456	1	Missense	W258R
65	23138			A → G	Transition	0.34883	16	Missense	D614G
66	23328			G → T	Transversion	0.21456	1	Missense	Q677H
67	23664			C → T	Transition	0.21456	1	Synonymous	Y789Y
68	23729			A → T	Transversion	0.21456	1	Missense	N811I
69	23928			G → T	Transversion	0.21456	1	Synonymous	L877L
70	25288	NS3	6	C → T	Transition	0.21456	1	Missense	A54V
71	25298			G → T	Transversion	0.59084	14	Missense	Q57H
72	25349			C → T	Transition	0.34883	2	Synonymous	S74S
73	25422			G → T	Transversion	0.21456	1	Missense	A99S
74	25579			C → T	Transition	0.21456	1	Missense	T151I
75	25791			G → T	Transversion	0.21456	1	Missense	D222Y
76	26470	M	3	C → T	Transition	0.59084	14	Synonymous	Y71Y
77	26536			C → A	Transversion	0.34883	2	Synonymous	L93L
78	26602			A → G	Transition	0.66825	7	Synonymous	E115E
79	27345	NS7a	1	C → T	Transition	0.21456	1	Missense	H73Y
80	27808	NS8	1	G → A	Transition	0.21456	1	Synonymous	L60L
81	28046	N	14	C → T	Transition	0.21456	1	Missense	P13L
82	28363			G → T	Transversion	0.52971	4	Missense	A119S
83	28470			T → C	Transition	0.21456	1	Synonymous	N154N
84	28479			C → T	Transition	0.21456	1	Synonymous	I157I
85	28487			A → G	Transition	0.21456	1	Missense	Q160R
86	28586			G → T	Transversion	0.52971	4	Missense	S193I
87	28593			A → T	Transversion	0.21456	1	Missense	R195S
88	28603			C → T	Transition	0.21456	1	Missense	P199S
89	28616			G → A	Transition	0.34883	2	Missense	R203K
90	28617			G → A	Transition	0.34883	2
91	28618			G → C	Transversion	0.34883	2	Missense	G204R
92	28710			G → T	Transversion	0.21456	1	Missense	M234I
93	28944			A → G	Transition	0.21456	1	Synonymous	S312S
94	29094			A → T	Transversion	0.34883	2	Synonymous	T362T

Bold indicates non-synonymous substitutions
^*Nucleic acid numbering starting from ORF1ab start codon (ATG)
^#Amino acid numbering starting from start codon of each gene

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ISSN: 1755-8794

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