Whole genome sequencing and phylogenetic analysis of six SARS-CoV-2 strains isolated during COVID-19 pandemic in Tunisia, North Africa

Fares, Wasfi; Chouikha, Anissa; Ghedira, Kais; Gdoura, Meriam; Rezig, Dorra; Boubaker, Sondes Haddad; Dhifallah, Imen Ben; Touzi, Henda; Hammami, Walid; Meddeb, Zina; Sadraoui, Amel; Hogga, Nahed; Abouda, Imen; Kwasiborski, Aurélia; Hourdel, Véronique; Mikaty, Guillain; Caro, Valérie; Manuguerra, Jean-Claude; Alaya, Nissaf Ben; Triki, Henda

doi:10.1186/s12864-021-07870-1

Table 1 Single nt polymorphisms (SNPs) deduced by comparison of six Tunisian whole genome SARS-CoV-2 sequences with reference SARS-CoV-2 NC045512

From: Whole genome sequencing and phylogenetic analysis of six SARS-CoV-2 strains isolated during COVID-19 pandemic in Tunisia, North Africa

Gene		nsp2					nsp 3						nsp4				nsp6	nsp7	nsp8	nsp12
Nucleotide position		1059	1397	1666	2113	2416	3037	3896	4288	5557	7420	8371	8782	9479	9514	10,046	11,083	11,935	12,555	13,495	14,408	15,324	16,178
Cov0010	SNPs mutations									T > C			C > T							C > T
Cov0010	Proteins mutations									G946G			S75S							L19F
Cov0880	SNPs mutations		G > A						G > T					G > T	A > G	G > A	G > T		A > C
Cov0880	Proteins mutations		V198I						E523D					G309C	L320L	V498I	L37F		E155A
Cov1339	SNPs mutations				C > T		C > T														C > T		C > T
Cov1339	Proteins mutations				L436L		F105F														P323L		S913L
Cov1663	SNPs mutations						C > T	G > T			C > T							A > C			C > T	C > T
Cov1663	Proteins mutations						F105F	V393F			I1567I							Q31H			P323L	N628N
Cov0425	SNPs mutations					C > T	C > T					G > T									C > T
Cov0425	Proteins mutations					Y537Y	F105F					Q1884H									P323L
Cov1482	SNPs mutations	C > T		T > C			C > T														C > T
Cov1482	Proteins mutations	T85I		F/287F			F105F														P323L
Gene		nsp13	nsp14			nsp15	S								Orf3a		Orf8		N
Nucleotide position		17,690	18,523	18,877	19,525	20,032	21,648	22,210	22,397	22,424	22,435	22,468	22,503	23,403	25,411	25,563	27,896	28,144	28,346	28,347	28,835	28,878
Cov0010	SNPs mutations											G > T						T > C				G > A
Cov0010	Proteins mutations											T302T						L84S				S202N
Cov0880	SNPs mutations								T > A						A > C		G > T				T > C
Cov0880	Proteins mutations								Y279N						I7L		M1I				S188P
Cov1339	SNPs mutations	C > T		C > T	G > T			C > T		G > A	T > C		A > G	A > G		G > T
Cov1339	Proteins mutations	S485L		L280L	D496Y			P216L		A288T	C291C		Q314R	D614G		Q57H
Cov1663	SNPs mutations		G > T			C > T	C > T							A > G
Cov1663	Proteins mutations		V162L			R138C	T29I							D614G
Cov0425	SNPs mutations													A > G		G > T
Cov0425	Proteins mutations													D614G		Q57H
Cov1482	SNPs mutations													A > G		G > T			G > T	G > T
Cov1482	Proteins mutations													D614G		Q57H			G25F	G25F

(In bold and underlined: confirmed mutations with more than 2500 reads. In italics: validated mutations with less than 2500 reads)

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ISSN: 1471-2164

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