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Primers and Probes

Last updated: 2021 Jun 14

Total hit(s): 64

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Primer and Probe sequence specific for N gene of SARS-CoV-2 used in wastewater RT- ddPCR assay.

Amplicon Length: 95
Genomic Location of forward primer: 20131-29150,
Genomic Location of reverse primer: 29225-29206,
Genomic location of probe sequence: 29185-29204 ✍

Pre-print (medRXiv)

Title	Redesigning SARS-CoV-2 clinical RT-qPCR assays for wastewater RT-ddPCR
Author(s) name	-
Impact factor	N/A
Date of Entry	2021 Jun 14

Primer and Probe sequence specific for E gene of SARS-CoV-2 used in wastewater RT- ddPCR assay.

Amplicon Length: 100
Genomic Location of forward primer: 26260-26279,
Genomic Location of reverse primer: 26359-26340,
Genomic location of probe sequence: 26290-26317 ✍

Pre-print (medRXiv)

Title	Redesigning SARS-CoV-2 clinical RT-qPCR assays for wastewater RT-ddPCR
Author(s) name	-
Impact factor	N/A
Date of Entry	2021 Jun 14

Outer primer pairs for an RT-LAMP Cas12a assay specific for the N gene of SARS-CoV-2.

✍

33238709
(Anal Chem)

PMID	33238709 Date of Publishing: 2020 Dec 15
Title	Isothermal Amplification and Ambient Visualization in a Single Tube for the Detection of SARS-CoV-2 Using Loop-Mediated Amplification and CRISPR technology
Author(s) name	Pang B, Xu J et al.
Journal	Anal Chem
Impact factor	6.37 Citation count: 41

NLM format
Pang B, Xu J, Liu Y, Peng H, Feng W, Cao Y, Wu J, Xiao H, Pabbaraju K, Tipples G, Joyce MA, Saffran HA, Tyrrell DL, Zhang H, Le XC. Isothermal Amplification and Ambient Visualization in a Single Tube for the Detection of SARS-CoV-2 Using Loop-Mediated Amplification and CRISPR technology. Anal Chem. 2020 Dec 15;92(24):16204-16212. PMID:33238709

Inner primer pairs (FIP, BIP) for an RT-LAMP Cas12a assay specific for the N gene of SARS-CoV-2.

✍

33238709
(Anal Chem)

PMID	33238709 Date of Publishing: 2020 Dec 15
Title	Isothermal Amplification and Ambient Visualization in a Single Tube for the Detection of SARS-CoV-2 Using Loop-Mediated Amplification and CRISPR technology
Author(s) name	Pang B, Xu J et al.
Journal	Anal Chem
Impact factor	6.37 Citation count: 41

NLM format
Pang B, Xu J, Liu Y, Peng H, Feng W, Cao Y, Wu J, Xiao H, Pabbaraju K, Tipples G, Joyce MA, Saffran HA, Tyrrell DL, Zhang H, Le XC. Isothermal Amplification and Ambient Visualization in a Single Tube for the Detection of SARS-CoV-2 Using Loop-Mediated Amplification and CRISPR technology. Anal Chem. 2020 Dec 15;92(24):16204-16212. PMID:33238709

Loop primer pairs (LF and LB) for an RT-LAMP Cas12a assay specific for the N gene of SARS-CoV-2.

✍

33238709
(Anal Chem)

PMID	33238709 Date of Publishing: 2020 Dec 15
Title	Isothermal Amplification and Ambient Visualization in a Single Tube for the Detection of SARS-CoV-2 Using Loop-Mediated Amplification and CRISPR technology
Author(s) name	Pang B, Xu J et al.
Journal	Anal Chem
Impact factor	6.37 Citation count: 41

NLM format
Pang B, Xu J, Liu Y, Peng H, Feng W, Cao Y, Wu J, Xiao H, Pabbaraju K, Tipples G, Joyce MA, Saffran HA, Tyrrell DL, Zhang H, Le XC. Isothermal Amplification and Ambient Visualization in a Single Tube for the Detection of SARS-CoV-2 Using Loop-Mediated Amplification and CRISPR technology. Anal Chem. 2020 Dec 15;92(24):16204-16212. PMID:33238709

Outer primer pairs for an RT-LAMP Cas12a assay specific for the E gene of SARS-CoV-2.

✍

33238709
(Anal Chem)

PMID	33238709 Date of Publishing: 2020 Dec 15
Title	Isothermal Amplification and Ambient Visualization in a Single Tube for the Detection of SARS-CoV-2 Using Loop-Mediated Amplification and CRISPR technology
Author(s) name	Pang B, Xu J et al.
Journal	Anal Chem
Impact factor	6.37 Citation count: 41

NLM format
Pang B, Xu J, Liu Y, Peng H, Feng W, Cao Y, Wu J, Xiao H, Pabbaraju K, Tipples G, Joyce MA, Saffran HA, Tyrrell DL, Zhang H, Le XC. Isothermal Amplification and Ambient Visualization in a Single Tube for the Detection of SARS-CoV-2 Using Loop-Mediated Amplification and CRISPR technology. Anal Chem. 2020 Dec 15;92(24):16204-16212. PMID:33238709

Inner primer pairs (FIP, BIP) for an RT-LAMP Cas12a assay specific for the E gene of SARS-CoV-2

✍

33238709
(Anal Chem)

PMID	33238709 Date of Publishing: 2020 Dec 15
Title	Isothermal Amplification and Ambient Visualization in a Single Tube for the Detection of SARS-CoV-2 Using Loop-Mediated Amplification and CRISPR technology
Author(s) name	Pang B, Xu J et al.
Journal	Anal Chem
Impact factor	6.37 Citation count: 41

NLM format
Pang B, Xu J, Liu Y, Peng H, Feng W, Cao Y, Wu J, Xiao H, Pabbaraju K, Tipples G, Joyce MA, Saffran HA, Tyrrell DL, Zhang H, Le XC. Isothermal Amplification and Ambient Visualization in a Single Tube for the Detection of SARS-CoV-2 Using Loop-Mediated Amplification and CRISPR technology. Anal Chem. 2020 Dec 15;92(24):16204-16212. PMID:33238709

Loop primer pairs (LF and LB) for an RT-LAMP Cas12a assay specific for the E gene of SARS-CoV-2.

✍

33238709
(Anal Chem)

PMID	33238709 Date of Publishing: 2020 Dec 15
Title	Isothermal Amplification and Ambient Visualization in a Single Tube for the Detection of SARS-CoV-2 Using Loop-Mediated Amplification and CRISPR technology
Author(s) name	Pang B, Xu J et al.
Journal	Anal Chem
Impact factor	6.37 Citation count: 41

NLM format
Pang B, Xu J, Liu Y, Peng H, Feng W, Cao Y, Wu J, Xiao H, Pabbaraju K, Tipples G, Joyce MA, Saffran HA, Tyrrell DL, Zhang H, Le XC. Isothermal Amplification and Ambient Visualization in a Single Tube for the Detection of SARS-CoV-2 Using Loop-Mediated Amplification and CRISPR technology. Anal Chem. 2020 Dec 15;92(24):16204-16212. PMID:33238709

Reporter labeled with fluorophore and quencher specific for the purpose of fluorescence detection carried out by Cas12a-mediated RT-LAMP assay.

✍

33238709
(Anal Chem)

PMID	33238709 Date of Publishing: 2020 Dec 15
Title	Isothermal Amplification and Ambient Visualization in a Single Tube for the Detection of SARS-CoV-2 Using Loop-Mediated Amplification and CRISPR technology
Author(s) name	Pang B, Xu J et al.
Journal	Anal Chem
Impact factor	6.37 Citation count: 41

NLM format
Pang B, Xu J, Liu Y, Peng H, Feng W, Cao Y, Wu J, Xiao H, Pabbaraju K, Tipples G, Joyce MA, Saffran HA, Tyrrell DL, Zhang H, Le XC. Isothermal Amplification and Ambient Visualization in a Single Tube for the Detection of SARS-CoV-2 Using Loop-Mediated Amplification and CRISPR technology. Anal Chem. 2020 Dec 15;92(24):16204-16212. PMID:33238709

Sequences of the DNA probes used in the HC-FIA assay specific for binding with the N region of the SARS-CoV-2 genome.

The software Primer Premier 5.0, was used for designing the primer ✍

33273714
(Nat Biomed Eng)

PMID	33273714 Date of Publishing: 2020 Dec
Title	Rapid lateral flow immunoassay for the fluorescence detection of SARS-CoV-2 RNA
Author(s) name	Wang D, He S et al.
Journal	Nat Biomed Eng
Impact factor	31.8 Citation count: 49

NLM format
Wang D, He S, Wang X, Yan Y, Liu J, Wu S, Liu S, Lei Y, Chen M, Li L, Zhang J, Zhang L, Hu X, Zheng X, Bai J, Zhang Y, Zhang Y, Song M, Tang Y. Rapid lateral flow immunoassay for the fluorescence detection of SARS-CoV-2 RNA. Nat Biomed Eng. 2020 Dec;4(12):1150-1158. PMID:33273714

Sequences of the DNA probes used in the HC-FIA assay specific for binding with the ORF1ab region of the SARS-CoV-2 genome.

The software Primer Premier 5.0, was used for designing the primer ✍

33273714
(Nat Biomed Eng)

PMID	33273714 Date of Publishing: 2020 Dec
Title	Rapid lateral flow immunoassay for the fluorescence detection of SARS-CoV-2 RNA
Author(s) name	Wang D, He S et al.
Journal	Nat Biomed Eng
Impact factor	31.8 Citation count: 49

NLM format
Wang D, He S, Wang X, Yan Y, Liu J, Wu S, Liu S, Lei Y, Chen M, Li L, Zhang J, Zhang L, Hu X, Zheng X, Bai J, Zhang Y, Zhang Y, Song M, Tang Y. Rapid lateral flow immunoassay for the fluorescence detection of SARS-CoV-2 RNA. Nat Biomed Eng. 2020 Dec;4(12):1150-1158. PMID:33273714

The eight specific primer sequences used in RT-LAMP assay for the detection of SARS-CoV-2.

✍

33098286
(Am J Trop Med Hyg)

PMID	33098286 Date of Publishing: 2020 Dec
Title	A sensitive reverse transcription loop mediated isothermal amplification assay for direct visual detection of SARS-CoV-2
Author(s) name	Lau YL, Ismail IB et al.
Journal	Am J Trop Med Hyg
Impact factor	2.25 Citation count: 4

NLM format
Lau YL, Ismail IB, Izati Binti Mustapa N, Lai MY, Tuan Soh TS, Hassan AH, Peariasamy KM, Lee YL, Goh PP. A sensitive reverse transcription loop mediated isothermal amplification assay for direct visual detection of SARS-CoV-2. Am J Trop Med Hyg. 2020 Dec;103(6):2350-2352. PMID:33098286

Sequences of the DNA probes used in the HC-FIA assay specific for binding with the E region of the SARS-CoV-2 genome.

The software Primer Premier 5.0, was used for designing the primer ✍

33273714
(Nat Biomed Eng)

PMID	33273714 Date of Publishing: 2020 Dec
Title	Rapid lateral flow immunoassay for the fluorescence detection of SARS-CoV-2 RNA
Author(s) name	Wang D, He S et al.
Journal	Nat Biomed Eng
Impact factor	31.8 Citation count: 49

NLM format
Wang D, He S, Wang X, Yan Y, Liu J, Wu S, Liu S, Lei Y, Chen M, Li L, Zhang J, Zhang L, Hu X, Zheng X, Bai J, Zhang Y, Zhang Y, Song M, Tang Y. Rapid lateral flow immunoassay for the fluorescence detection of SARS-CoV-2 RNA. Nat Biomed Eng. 2020 Dec;4(12):1150-1158. PMID:33273714

Primers sequence specific for the RdRp gene used in RT-LAMP assay to detect SARS-CoV-2.

Primers were designed by using PrimerExplorer version 5 (http://primerexplorer.jp/e/) ✍

33165486
(Analyst)

PMID	33165486 Date of Publishing: 2020 Nov 9
Title	Colorimetric reverse transcription loop-mediated isothermal amplification (RT-LAMP) as a visual diagnostic platform for the detection of the emerging coronavirus SARS-CoV-2
Author(s) name	Nawattanapaiboon K , Pasomsub E et al.
Journal	Analyst
Impact factor	3.98 Citation count: 20

NLM format

Nawattanapaiboon K , Pasomsub E , Prombun P , Wongbunmak A , Jenjitwanich A , Mahasupachai P , Vetcho P , Chayrach C , Manatjaroenlap N , Samphaongern C , Watthanachockchai T , Leedorkmai P , Manopwisedjaroen S , Akkarawongsapat R , Thitithanyanont A , Phanchana M , Panbangred W , Chauvatcharin S , Srikhirin T . Colorimetric reverse transcription loop-mediated isothermal amplification (RT-LAMP) as a visual diagnostic platform for the detection of the emerging coronavirus SARS-CoV-2. Analyst. 2021 Jan 21;146(2):471-477. PMID:33165486

Probe for a real-time RT-PCR test specific for the nsp1 gene of SARS-CoV-2.

✍

32501535
(J Med Virol)

PMID	32501535 Date of Publishing: 2020 Nov
Title	Identification of nsp1 gene as the target of SARS-CoV-2 real time RT-PCR using nanopore whole genome sequencing
Author(s) name	Chan WM, Ip JD et al.
Journal	J Med Virol
Impact factor	2.07 Citation count: 20

NLM format
Chan WM, Ip JD, Chu AW, Yip CC, Lo LS, Chan KH, Ng AC, Poon RW, To WK, Tsang OT, Leung WS, Kwan MY, Chua GT, Chung TW, Hung IF, Kok KH, Cheng VC, Chan JF, Yuen KY, To KK. Identification of nsp1 gene as the target of SARS-CoV-2 real time RT-PCR using nanopore whole genome sequencing. J Med Virol. 2020 Nov;92(11):2725-2734. PMID:32501535

Primer pairs for a real-time RT-PCR test specific for the nsp1 gene of SARS-CoV-2.

✍

32501535
(J Med Virol)

PMID	32501535 Date of Publishing: 2020 Nov
Title	Identification of nsp1 gene as the target of SARS-CoV-2 real time RT-PCR using nanopore whole genome sequencing
Author(s) name	Chan WM, Ip JD et al.
Journal	J Med Virol
Impact factor	2.07 Citation count: 20

NLM format
Chan WM, Ip JD, Chu AW, Yip CC, Lo LS, Chan KH, Ng AC, Poon RW, To WK, Tsang OT, Leung WS, Kwan MY, Chua GT, Chung TW, Hung IF, Kok KH, Cheng VC, Chan JF, Yuen KY, To KK. Identification of nsp1 gene as the target of SARS-CoV-2 real time RT-PCR using nanopore whole genome sequencing. J Med Virol. 2020 Nov;92(11):2725-2734. PMID:32501535

Primer pairs, for a real-time RT-RAA assay, specific for the N gene of SARS CoV2.

✍

32758712
(Virology)

PMID	32758712 Date of Publishing: 2020 Oct
Title	A reverse-transcription recombinase-aided amplification assay for the rapid detection of N gene of severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)
Author(s) name	Wu T, Ge Y et al.
Journal	Virology
Impact factor	2.819 Citation count: 14

NLM format
Wu T, Ge Y, Zhao K, Zhu X, Chen Y, Wu B, Zhu F, Zhu B, Cui L. A reverse-transcription recombinase-aided amplification assay for the rapid detection of N gene of severe acute respiratory syndrome coronavirus 2(SARS-CoV-2). Virology. 2020 Oct;549:1-4. PMID:32758712

The second set of primer and probe sequences (YCH-N2) based on the Nucleocapsid gene developed by YCH (Yamanashi Central Hospital), used in real-time RT-PCR assay.

The assay uses double-quencher probe ✍

32650037
(J Virol Methods)

PMID	32650037 Date of Publishing: 2020 Oct
Title	Double-quencher probes improve detection sensitivity toward Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in a reverse-transcription polymerase chain reaction (RT-PCR) assay
Author(s) name	Hirotsu Y, Mochizuki H, Omata M.
Journal	J Virol Methods
Impact factor	1.76 Citation count: 29

NLM format
Hirotsu Y, Mochizuki H, Omata M. Double-quencher probes improve detection sensitivity toward Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in a reverse-transcription polymerase chain reaction (RT-PCR) assay. J Virol Methods. 2020 Oct;284:113926. PMID:32650037

The first set of primer and probe sequences (YCH-N1) based on the Nucleocapsid gene developed by YCH (Yamanashi Central Hospital), used in real-time RT-PCR assay.

The expected amplicon size is 158 bp. The assay uses double-quencher probe ✍

32650037
(J Virol Methods)

PMID	32650037 Date of Publishing: 2020 Oct
Title	Double-quencher probes improve detection sensitivity toward Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in a reverse-transcription polymerase chain reaction (RT-PCR) assay
Author(s) name	Hirotsu Y, Mochizuki H, Omata M.
Journal	J Virol Methods
Impact factor	1.76 Citation count: 29

NLM format
Hirotsu Y, Mochizuki H, Omata M. Double-quencher probes improve detection sensitivity toward Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in a reverse-transcription polymerase chain reaction (RT-PCR) assay. J Virol Methods. 2020 Oct;284:113926. PMID:32650037

The second set of primer and probe sequences (NIID-N2) based on the Nucleocapsid gene developed by NIID, used in real-time RT-PCR assay.

The assay uses single-quencher probe ✍

32650037
(J Virol Methods)

PMID	32650037 Date of Publishing: 2020 Oct
Title	Double-quencher probes improve detection sensitivity toward Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in a reverse-transcription polymerase chain reaction (RT-PCR) assay
Author(s) name	Hirotsu Y, Mochizuki H, Omata M.
Journal	J Virol Methods
Impact factor	1.76 Citation count: 29

NLM format
Hirotsu Y, Mochizuki H, Omata M. Double-quencher probes improve detection sensitivity toward Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in a reverse-transcription polymerase chain reaction (RT-PCR) assay. J Virol Methods. 2020 Oct;284:113926. PMID:32650037

The first set of primer and probe sequences (NIID-N1) based on the Nucleocapsid gene developed by NIID, used in real-time RT-PCR assay.

The expected amplicon size is 128 bp. The assay uses single-quencher probe ✍

32650037
(J Virol Methods)

PMID	32650037 Date of Publishing: 2020 Oct
Title	Double-quencher probes improve detection sensitivity toward Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in a reverse-transcription polymerase chain reaction (RT-PCR) assay
Author(s) name	Hirotsu Y, Mochizuki H, Omata M.
Journal	J Virol Methods
Impact factor	1.76 Citation count: 29

NLM format
Hirotsu Y, Mochizuki H, Omata M. Double-quencher probes improve detection sensitivity toward Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in a reverse-transcription polymerase chain reaction (RT-PCR) assay. J Virol Methods. 2020 Oct;284:113926. PMID:32650037

The second set of primer and probe sequences (CDC-N2) based on the Nucleocapsid gene developed by CDC, used in real-time RT-PCR assay.

The expected amplicon size is 67 bp. The assay uses single-quencher probe ✍

32650037
(J Virol Methods)

PMID	32650037 Date of Publishing: 2020 Oct
Title	Double-quencher probes improve detection sensitivity toward Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in a reverse-transcription polymerase chain reaction (RT-PCR) assay
Author(s) name	Hirotsu Y, Mochizuki H, Omata M.
Journal	J Virol Methods
Impact factor	1.76 Citation count: 29

NLM format
Hirotsu Y, Mochizuki H, Omata M. Double-quencher probes improve detection sensitivity toward Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in a reverse-transcription polymerase chain reaction (RT-PCR) assay. J Virol Methods. 2020 Oct;284:113926. PMID:32650037

Probe for a real-time RT-RAA assay specific for the N gene of SARS CoV2.

Probe Format Modifications: FAM: 6-Carboxyfluorescein; THF: tetrahydrofuran; BHQ: black hole quencher; C3 spacer: 3 phosphate blocker. ✍

32758712
(Virology)

PMID	32758712 Date of Publishing: 2020 Oct
Title	A reverse-transcription recombinase-aided amplification assay for the rapid detection of N gene of severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)
Author(s) name	Wu T, Ge Y et al.
Journal	Virology
Impact factor	2.819 Citation count: 14

NLM format
Wu T, Ge Y, Zhao K, Zhu X, Chen Y, Wu B, Zhu F, Zhu B, Cui L. A reverse-transcription recombinase-aided amplification assay for the rapid detection of N gene of severe acute respiratory syndrome coronavirus 2(SARS-CoV-2). Virology. 2020 Oct;549:1-4. PMID:32758712

The first set of primer and probe sequences (CDC-N1) based on the Nucleocapsid gene developed by CDC, used in real-time RT-PCR assay.

The expected amplicon size is 72 bp. The assay uses single-quencher probe ✍

32650037
(J Virol Methods)

PMID	32650037 Date of Publishing: 2020 Oct
Title	Double-quencher probes improve detection sensitivity toward Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in a reverse-transcription polymerase chain reaction (RT-PCR) assay
Author(s) name	Hirotsu Y, Mochizuki H, Omata M.
Journal	J Virol Methods
Impact factor	1.76 Citation count: 29

NLM format
Hirotsu Y, Mochizuki H, Omata M. Double-quencher probes improve detection sensitivity toward Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in a reverse-transcription polymerase chain reaction (RT-PCR) assay. J Virol Methods. 2020 Oct;284:113926. PMID:32650037

The primer and probe sequences of RNAse P (internal positive control) developed by CDC, used in real-time RT-PCR assay.

The assay uses single-quencher probe ✍

32650037
(J Virol Methods)

PMID	32650037 Date of Publishing: 2020 Oct
Title	Double-quencher probes improve detection sensitivity toward Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in a reverse-transcription polymerase chain reaction (RT-PCR) assay
Author(s) name	Hirotsu Y, Mochizuki H, Omata M.
Journal	J Virol Methods
Impact factor	1.76 Citation count: 29

NLM format
Hirotsu Y, Mochizuki H, Omata M. Double-quencher probes improve detection sensitivity toward Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in a reverse-transcription polymerase chain reaction (RT-PCR) assay. J Virol Methods. 2020 Oct;284:113926. PMID:32650037