Optimization and validation of RT-LAMP assay for diagnosis of SARS-CoV2 including the globally dominant Delta variant

Jamwal, Vijay Lakshmi; Kumar, Natish; Bhat, Rahul; Jamwal, Piyush Singh; Singh, Kaurab; Dogra, Sandeep; Kulkarni, Abhishek; Bhadra, Bhaskar; Shukla, Manish R.; Saran, Saurabh; Dasgupta, Santanu; Vishwakarma, Ram A.; Gandhi, Sumit G.

doi:10.1186/s12985-021-01642-9

Virology Journal

Table 1 LAMP primer sequences

From: Optimization and validation of RT-LAMP assay for diagnosis of SARS-CoV2 including the globally dominant Delta variant

Gene	Protein	Genomic coordinates		Length of region	Name of primer set	Name of primer	Sequence
Gene	Protein	Start	End	Length of region	Name of primer set	Name of primer	Sequence
ORF1AB	NSP1	498	722	225	L1	L1-F3	CTGCACCTCATGGTCATG
						L1-B3	GATCAGTGCCAAGCTCG
						L1-FI	GAGGGACAAGGACACCAAGTGTGGTAGCAGAACTCGAAG
						L1-C-BI	CAGTGGCTTACCGCAAGGTTTTAGATCGGCGCCGTAAC
						L1-LF	CACTACGACCGTACTGAAT
						L1-LB	CGTAAGAACGGTAATAAAGGAG
ORF1AB	RdRP	14,224	14,452	229	RdRp	rdrp1F3	ACAAAGCCTTACATTAAGTGG
						rdrp1B3	CACCATCAACAAATATTTTTCTCAC
						rdrp1FIP	TGGGTGGTATGTCTGATCCCAATAGATTTGTTAAAATATGACTTCACGG
						rdrp1BIP	TGTGTTAACTGTTTGGATGACAGATGTAGGTGGGAACACTGT
						rdrp1LF	CGGTCAAAGAGTTTTAACCTCTCTT
						rdrp1LB	TGCATTCTGCATTGTGCAAACT
E	E	26,251	26,457	207	E1	e1F3	TCATTCGTTTCGGAAGAGA
						e1B3	AGGAACTCTAGAAGAATTCAGAT
						e1FIP	TGTAACTAGCAAGAATACCACGAAACAGGTACGTTAATAGTTAATAGCG
						e1BIP	GCTTCGATTGTGTGCGTACTCGAGAGTAAACGTAAAAAGAAGG
						e1LB	GCTGCAATATTGTTAACGTGAGTC
E	E	26,258	26,468	211	E2	e2F3	TTTCGGAAGAGACAGGTAC
						e2B3	ACCAGAAGATCAGGAACTCT
						e2FIP	GCGCAGTAAGGATGGCTAGTGGTACTTCTTTTTCTTGCTTTCG
						e2BIP	TGCGTACTGCTGCAATATTGTTAACGAAGAATTCAGATTTTTAACACGAG
N	N	28,354	28,569	216	N2	n2F3	CCAGAATGGAGAACGCAGTG
						n2B3	CCGTCACCACCACGAATT
						n2FIP	AGCGGTGAACCAAGACGCAGGGCGCGATCAAAACAACG
						n2BIP	AATTCCCTCGAGGACAAGGCGAGCTCTTCGGTAGTAGCCAA
						n2LF	TTATTGGGTAAACCTTGGGGC
						n2LB	TTCCAATTAACACCAATAGCAGTCC
N	N	28,526	28,740	215	L2	L2-F3	GGCTACTACCGAAGAGC
						L2-B3	GCAGCATTGTTAGCAGG
						L2-FI	CTGGCCCAGTTCCTAGGTAGTCCAGACGAATTCGTGGTG
						L2-BI	GACGGCATCATATGGGTTGCACGGGTGCCAATGTGATC
						L2-LF	GACTGAGATCTTTCATTTTACC
						L2-LB	CTGAGGGAGCCTTGAATAC
N	N	28,702	28,914	213	N1	n1F3	AGATCACATTGGCACCCG
						n1B3	CCATTGCCAGCCATTCTAGC
						n1FIP	TGCTCCCTTCTGCGTAGAAGCCAATGCTGCAATCGTGCTAC
						n1BIP	GGCGGCAGTCAAGCCTCTTCCCTACTGCTGCCTGGAGTT
						n1LF	GCAATGTTGTTCCTTGAGGAAGTT
						n1LB	GTTCCTCATCACGTAGTCGCAACA
Human β-actin	Human β-actin	585	787	203	ACTB1	hACTBF3	GCGCGGCTACAGCTTCA
						hACTBB3	GGAAGAGTGCCTCAGGGC
						hACTBFIP	AAGTCCAGGGCGACGTAGCACCGGCCGAGCGGGAAAT
						hACTBBIP	GAGATGGCCACGGCTGCTTCCATTGCCAATGGTGATGACCT
						hACTBLF	TTCTCCTTAATGTCACGCACG
						hACTBLB	CCCTGGAGAAGAGCTACGAG
Human β-actin	Human β-actin	197	390	194	ACTB2	hACTB2F3	CCCTGAAGTACCCCATCGA
						hACTB2B3	TGGGGTGTTGAAGGTCTCAA
						hACTB2FIP	AGCCACACGCAGCTCATTGTAGCACGGCATCGTCACCAAC
						hACTB2BIP	AGCACCCCGTGCTGCTGAGTCATCTTCTCGCGGTTGG
						hACTB2LF	AGATTTTCTCCATGTCGTCCCA

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ISSN: 1743-422X

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