TABLE 2.

Names and nucleotide sequences of primers used in this study^a

Target gene	Primer name	Sequence (5′ to 3′)	Use	Expected size of amplicon (bp)
SA11 VP4 in HR2 mutant plasmid	T7_FW VP4_559_F HDV_REV	TAATACGACTCACTATAGGG GCTAGGACAGCACATTATTC TCGTCCACTCGGATGGCTA	Sequence pT7-VP4SA11 plasmid containing SARS-CoV-2 HR2 peptide	2,517
HR2 of SARS-CoV-2 spike	FW REV	GATTCATTTAAATTTTTAGCGACCTCATTGAGGCGGTCAATTTCTCCGGAAGTTGTTTTTACGACATCAATAAATTTC ACTCATTGACCTTCAAGAATTGGGAAAATATGAGCAATATGGAGCTAGCGCAAATGGAAGTATAGGACAATATG	Site-directed mutagenesis of HR2 peptide	n/a
NTD of SARS-CoV-2 spike	FW REV	TAAATTCCTTTGTCAATCTCAAAGCTCTTTCCGGAAGTTGTTTTTACGACATCAATAAATTTC CCAGACCTCTAATTTCAGGGTTGTTGGAGCTAGCGCAAATGGAAGTATAGGACAATATG	Site-directed mutagenesis of NTD peptide	n/a
SA11 VP4	SA11_VP4_1F SA11_VP4_1193R	GGCTATAAAATGGCTTCGCTC GTCTACCAGTTGGACAATGGC	Sequence pT7-VP4SA11 plasmids containing SARS-CoV-2 spike peptides; PCR and Sanger sequencing of SA11 VP4 gene in viruses	1,192–1,275
SA11 VP4	SA11_VP4 FWD SA11_VP4 REV	CATCAGCATGGACGGATGTAT CCTCAGTTTGTGTTGCCATTTC	RT-qPCR of SA11 VP4 gene	83
SA11 VP1	SA11_VP1_448F SA11_VP1_576R	GCAGTCATGTTCTGGTTGGA GTTATGCCTTGGTACGCCAT	RT-qPCR of SA11 VP1 gene	89
RF NSP3	FW_331 HDV_REV	CGCGTTGGCCGATTCATTAAT TCGTCCACTCGGATGGCTA	Sequence RF NSP3 plasmids	1,769–2,186
	SARS_CoV2_FW SARS_CoV2_REV	GCTTTTCAGTGGTTGATGCT TCATAGAGGGTCATGTGAAG	PCR and Sanger sequencing of RF NSP3 gene in viruses	1,178–1,595
	FW_NSP3_qPCR REV_NSP3_qPCR	GATGCTCAAGATGGAGTCTAC CACCTGAATCATCCATTACGT	RT-qPCR of RF NSP3 gene	134
RF VP1	FW_RF_VP1_qPCR REV_RF_VP1_qPCR	CACAATCCGCAGTTCAAATTC CAGTGTGGCATTCTCCATAAC	RT-qPCR of RF VP1 gene	119

^aVP, viral protein; n/a, not applicable.