Table 2.

Sequencing Primers for Sanger Sequencing

Region	Part	Primer name	Sequence
1	1	CoV-2 S_Seq1-F1a	5′-CAAATCCAATTCAGTTGTCTTCC-3′
		CoV-2 S_Seq1-F1b	5′-TGGAGGAATACAAATCCAATTCA-3′
		CoV-2 S_Seq1-R1a	5′-TAAAGCCGAAAAACCCTGAG-3′
		CoV-2 S_Seq1-R1b	5′-TGAGGGAGATCACGCACTAA-3′
	2	CoV-2 S_Seq1-F2a	5′-GGACCTTGAAGGAAAACAGG-3′
		CoV-2 S_Seq1-F2b	5′-TGCGAATAATTGCACTTTTGA-3′
		CoV-2 S_Seq1-R2a	5′-CTTTCCAGTTTGCCCTGGAG-3′
		CoV-2 S_Amp-R1b∗	5′-AACGCAGCCTGTAAAATCATC-3′
2	1	CoV-2 S_Seq2-F1a	5′-TGCAGATTCATTTGTAATTAGAGG-3′
		CoV-2 S_Amp-F2b∗	5′-CCGCATCATTTTCCACTTTT-3′
		CoV-2 S_Seq2-R1a	5′-TGCACCAATGGGTATGTCAC-3′
		CoV-2 S_Seq2-R1b	5′-CGCATATACCTGCACCAATG-3′
	2	CoV-2 S_Seq2-F2a	5′-CTGCACAGAAGTCCCTGTTG-3′
		CoV-2 S_Seq2-F2b	5′-CCCTGTTGCTATTCATGCAG-3′
		CoV-2 S_Seq2-R2a	5′-TGTACCCGCTAACAGTGCAG-3′
		CoV-2 S_Seq2-R2b	5′-GGTTGGCAATCAATTTTTGG-3′
3	1	CoV-2 S_Seq3-F1a	5′-ACTGTTTTGCCACCTTTGCT-3′
		CoV-2 S_Seq3-F1b	5′-TTAACGGCCTTACTGTTTTGC-3′
		CoV-2 S_Seq3-R1a	5′-AACCAGTGTGTGCCATTTGA-3′
		CoV-2 S_Seq3-R1b	5′-GACAAATGGCAGGAGCAGTT-3′
	2	CoV-2 S_Seq3-F2a	5′-CTTCCCTCAGTCAGCACCTC-3′
		CoV-2 S_Seq3-F2b	5′-GAGGCTGAAGTGCAAATTGA-3′
		CoV-2 S_Seq3-R2a	5′-TAGCGCGAACAAAATCTGAA-3′
		CoV-2 S_Seq3-R2b	5′-AGGGAGTGAGGCTTGTATCG-3′

Each amplicon was designed to be sequenced in two overlapping parts, with two forward and reverse primers for each part. The primers used for most samples are in bold; the other primers were used if these primers did not yield usable Sanger sequences.

^∗Two amplification primers were used as sequencing primers if not used to generate the amplicons.