Table 2.

Thermal cycling conditions, primers/probes for RT-qPCR and SNP genotyping used in the study.

Organism	Assay Cat number	Company	Target	Sequence	Cycling parameters
Real-time quantitative polymerase chain reaction (RT-qPCR) analysis
SARS-CoV-2	2019-nCoV CDC EUA kit (Cat number RV202001)	Integrated DNA Technologies, Coralville, IA, USA	N1	F 5′-GAC CCC AAA ATC AGC GAA AT-3′ R 5′-TCT GGT TAC TGC CAG TTG AAT CTG-3′ P-FAM-ACC CCG CAT TAC GTT TGG TGG ACC-BHQ1	Reverse transcription and RT-qPCR reaction: 50º for 10 min; 95º for 3 min Amplification: 95º for 15 s; 60º for 1 min (40 cycles)
	2019-nCoV CDC EUA kit (Cat number RV202002)		N2	F 5′-TTA CAA ACA TTG GCC GCA AA-3′ R 5′-GCG CGA CAT TCC GAA GAA-3′ P-FAM-ACA ATT TGC CCC CAG CGC TTC AG-BHQ1

SNP genotyping	Assay Cat number	Company	Target	TaqMan SARS-CoV-2 mutational Panel	Cycling parameters
Genotyping analysis: TaqMan SARS-CoV-2 mutational Panel
SARS-CoV-2	A15300	Thermo Fisher Scientific, Waltham, USA	Spike protein	Taq path Master Mix 10 mL	Pre-read 60º for 30 s; Reverse Transcription 50º for 10 min; Fast DNA polymerase activation 95º for 2 min; PCR(45 cycles) 95º for 3 s 60º for 30 s Post-read 60º for 30 s
	A51808			S.delH69V70
	A51814			S.K417N.AAG.AAT
	A51813			S.E484K.GAA.AAA
	A51816			S.P681H.CCT.CAT
	A51822			S.P681R.CCT.CGT
	A51819			S.L452R.CTG.CGG
	A51812			S.N501Y.AAT.TAT