Shine: A novel strategy to extract specific, sensitive and well-conserved biomarkers from massive microbial genomic datasets

Table 1 Final sets of primers and probes obtained by our strategy for different species or subspecies of Coronaviridae

Species/subspecies	Gene	Forward primer sequence	Reference ID	Forward primer position	Forward primer conservation (%)	Reverse primer sequence	Reference ID	Reverse primer position	Reverse primer conservation (%)	Probe sequence	Reference ID	Probe position	Probe conservation (%)
HKU1	ORF1ab	CTGTGAATTAGAACTTATTTGTGA	DQ415907	5649	33.30	CAGTCTTTGCTAATGTACCA	DQ415907	5743	100	AACAGCATCAACACCAACACGACTT	DQ415907	5715	100
OC43	S	TGGTGTTAATTTCAATGTAGA	KX344031	26,278	70.60	GCAGATCTACTGGARGC	KX344031	26,367	98.20	TACTACATTCGCTGCCTAGACAACCT	KX344031	26,348	100
NL63	Replicase polyprotein 1ab	GCTGGTTTATGTGTTGTTTG	JQ765564	15,138	81.70	GTACCAAATACATGATCATATGC	JQ765564	15,244	100.00	TAGGCTTACGCAGACAATCACCACAA	JQ765564	15,204	98.30
229E	Replicase polyprotein 1ab	TGGTGTTGTGTGYTAYA	KT253325	14,653	80.00	CACCATTCTGATAATATAAAGTRG	KT253325	14,744	56.70	ATCAGCAATGTAACCAAGTTCAGCAT	KT253325	14,704	100
MERS-CoV	S	GGCTAAAGATAAAGTCAAYGAG	MF598714	31,517	98.70	GGGCATTTACAACAAARG	MF598714	31,614	98.50	TCAAGGCACAATCCAAGCGTTCTG	MF598714	31,543	98.70
SARS-CoV	ORF1ab	CCTCAGGCTGAAGTAGA	AY394986	18,941	100	CCTCTATTTTGTAAGCTTTGTC	AY394986	19,010	100	CATGGCTGAGCATCGTAGAACTTCC	AY394986	18,984	100
SARS-CoV-2	ORF1ab	GTGTCAACCTATACTGTTACTA	EPI_ISL_402124	7959	100	GCATCAAACATTTTAACTGC	EPI_ISL_402124	8043	100	ACTTCCGCACTATCACCAACATCAGA	EPI_ISL_402124	8022	100

HKU1 represents Human coronavirus HKU1; OC43 represents Human coronavirus OC43; NL63 represents Human coronavirus NL63; 229E represents Human coronavirus 229E; MERS-CoV represents Middle East respiratory syndrome coronavirus; SARS-CoV represents severe acute respiratory syndrome coronavirus; SARS-CoV-2 represents severe acute respiratory syndrome coronavirus 2
Degenerate bases: R = A/G, Y = C/T, M = A/C, K = G/T, S = C/G, W = A/T, H = A/C/T, B = C/G/T, V = A/C/G, D = A/G /T,N = A/C/G/T

ISSN: 1471-2105