RT-PCR Primers Track Settings
 
RT-PCR Detection Kit Primer Sets   (All Mapping and Sequencing tracks)

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Data last updated: 2020-04-14

Description

This track shows the locations of those primers in detection kits that match the reference sequence. The primers were copied from a spreadsheet created by the project OpenCovid19. The initial version of the track used the FASTA file from Design Flaws in COVID-19 Primers from Multiple International Labs.

Most are RT-qPCR primer sets, sequencing primers have the prefix Seq1- or Seq2-. RT-qPCR sets consists of one forward, one reverse and one internal probe, as indicated by the names.

As expected, the three control primers were not found at all: US-CDC-Control_RP-P, US-CDC-Control_RP-R, US-CDC-Control_RP-F.

Here is a quick overview of the origin of the primers, please see the website and spreadsheet linked above for more details:

Prefix Institution Overview Manual
CN-CDC- China CDC
NIID- Nat. Inst. of Infect. Dis., Japan
WH- National Inst. of Health (Thailand)
HKU- The University of Hong King Detects N gene and Orf1b. Not specific for SARS-Cov2, but other Sarbecovirus species are not in circulation WHO Peiris Protocol
US-CDC- CDC, USA Three reactions, target: N gene. One primer/probe set detects all betacoronaviruses, two sets are specific for SARS-CoV-2. All 3 assays must be positive Instructions
EU-Drosten Drosten Lab, Charite Berlin, Germany Set 1: run E and RdRp primers (designed for SARS-CoV, SARS-CoV-2, and bat-associated betacoronaviruses), if Set 1 is positive, use SARS-Cov-2 specific detection primer Instructions

The sequences and the identifiers for these primers were obtained from the following sources, among others:

More details can be found in the spreadsheet linked above.

Methods

The primers were mapped with the following command:
blat ../../wuhCor1.2bit primers.fa stdout -stepSize=3 -tileSize=6 -minScore=10 -oneOff=1 -noHead -fine | pslReps stdin stdout /dev/null -minNearTopSize=10 -minCover=0.8 -nohead > primers.psl

Data Access

You can download the PSL file underlying this track (primers) from our Download Server. The data can be explored interactively with the Table Browser or the Data Integrator. The data can also be accessed from scripts through our API.

Credits

This data annotation track was made by Maximilian Haeussler, with assistance from Daniel Schmelter. Fasta data collected by Tomer Altman (Biome Bioinformatics), prepared by Jason Fernandes (UCSC), updated by Darach Miller (Stanford) and the OpenCovid19 project.