Table 1.

SARS-CoV-2 spike mutation patterns used for variant typing by multiplex oligonucleotude ligation assay.

Variant	69–70del	N501Y	K417N	K417T	T478K	D215G	L452R	E484K	E484Q	T19R	T95I
Alpha	69–70del	N501Y	WT	WT	WT	WT	WT	WT	WT	WT	WT
Beta	WT	N501Y	K417N	NDET	WT	D215G	WT	E484K	NDET	WT	WT
Gamma	WT	N501Y	NDET	K417T	WT	WT	WT	E484K	NDET	WT	WT
Delta	WT	WT	WT	WT	T478K	WT	L452R	WT	WT	T19R	T95I or WT
B.1.1.529/BA.1	69–70del	N501Y	K417N	NDET	T478K	NDET	WT	NDET (A)	NDET (A)	WT	T95I
BA.2	WT	N501Y	K417N	NDET	T478K	WT	WT	NDET (A)	NDET (A)	NDET (I)	WT
BA.4	69–70del	N501Y	K417N	NDET	T478K	WT	L452R	NDET (A)	NDET (A)	NDET (I)	WT
BA.5	69–70del	N501Y	K417N	NDET	T478K	WT	L452R	NDET (A)	NDET (A)	NDET (I)	WT

WT, wild-type Wuhan reference sequence; NDET, not detected. BA.1.1.529/BA.1 contains a 3 amino acid insertion (EPE) at spike amino acid 214 such that both D215G and the WT sequences are not detected. In BA.1.1.529/BA.1, BA.2, BA.4, and BA.5, spike amino acid 484 is mutated to Alanine (A) so E484K, E484Q, and the WT sequences are not detected. In BA.2, BA.4, and BA.5, spike amino acid 19 is mutated to Isoleucine (I) so neither T19R nor WT sequences are detected.