Table 2.

List of the eight overlapping ORFs in the 3’ genome region of SARS-CoV-2 meeting all five prediction criteria of the CodScr + SeqComp method.

Overlapping ORFa	Genome positionb	Length (nt)	Within gene (genome position)	Shift of the overlapping ORF	P-value from the CodScr method	PLS-DA score	LDA score	LDA-ancestral score	LDA-novel score	Prediction criteria met
nORF1	24051–24170	120	S (24050–24172)	+1	0.0001	−0.45	−37.03	37.07	−1.54	5
nORF2*	24072–24170	99	S (24071–24172)	+1	0.0001	−0.13	−35.41	37.08	−8.74	5
nORF3	25457–25582	126	ORF3a (25456–25584)	+1	0.04	−1.46	−41.89	21.48	12.76	5
nORF4	25524–25697	174	ORF3a (25522–25698)	+2	0.02	−1.32	−40.44	−27.80	−59.59	5
nORF5	26693–26872	180	M(26691–26873)	+2	0.003	−0.02	−36.26	−17.74	−60.62	5
nORF6	28284–28577	294	N (28283–28579)	+1	0.0001	−0.52	−39.17	27.12	11.56	5
nORF7*	28305–28577	273	N (28304–28579)	+1	0.0001	−0.35	−39.29	26.88	12.29	5
nORF8*	28359–28577	219	N (28358–28579)	+1	0.0001	−0.21	−37.77	27.78	14.76	5

^aTerm “n” stands for “new” and asterisk indicates an overlapping ORF starting with an AUG codon which is in frame with respect to the previous overlapping ORF.

^bThe boundaries of the overlapping ORF are referred to the reference genome sequence of SARS-CoV-2 (NC_045512.2).