How to use the CoVrimer app:

CoVrimer is a Shiny R based application that allows searching for published/novel primer pairs targeting the SARS-CoV-2 genome and visualizing their alignment to the reference genome.

CoVrimer shows the amplicon and any variation found in the amplicon as well as in the primer binding regions. CoVrimer also provides a list of in-house designed conserved and degenerate primer pairs across the viral genome and presents information on occurrence and lineage of mutations with the degenerate codes, alignment to the genome, and conservation of the binding site among other bat genomes.

Note: CoVrimer will not be updated unless total sequence number increases by 1,000,000 more than the current one.



Data and code are also available on the github repository.

Files of old versions can be found on the github.

Version 7. Variation data were taken from CNCN-NGDC on Dec 15, 2022. Variation annotation computing was performed based on 6,854,423 high quality human sequences of 29,769 variation sites.

New features;
  20 new primer pairs were added to 'published primer pair table'.
  Mutation information of published primer pairs were updated with the latest mutation data .

Version 6. Variation data were taken from CNCN-NGDC on Sept 14, 2022. Variation annotation computing was performed based on 6,380,687 high quality SARS-CoV-2 sequences of 29,762 variation sites.

Version 5. Variation data were taken from CNCN-NGDC on May 21, 2022. Variation annotation computing was performed based on 5,345,994 high quality SARS-CoV-2 sequences of 29,742 variation sites.

Version 4. Variation data were taken from CNCN-NGDC on Feb 10, 2022. Variation annotation computing was performed based on 4,073,491 high quality SARS-CoV-2 sequences of 29650 variation sites.

New features;
  Probe search in 'Get Degenerate Primer Pairs' tab.
  Download button for each table.
  Lineage information for each variation.

Version 3. Variation data were taken from CNCN-NGDC on Nov 27, 2021. Variation annotation computing was performed based on 3,117,485 high quality SARS-CoV-2 sequences of 29451 variation sites.

Version 2. Variation data were taken from CNCN-NGDC on Aug 25, 2021. Variation annotation computing was performed based on 1,797,460 high quality SARS-CoV-2 sequences.

Version 1. Variation data were taken from CNCN-NGDC on May 12, 2021. Variation annotation computing was performed based on 954,725 high quality SARS-CoV-2 sequences.

In our analysis, positions exhibiting less than 0.1% mutation frequency were considered conserved.

Please cite our app:

Vural-Ozdeniz, M., Akturk, A., Demirdizen, M., Leka, R., Acar, R., & Konu, O. (2021). CoVrimer: A tool for aligning SARS-CoV-2 primer sequences and selection of conserved/degenerate primers. Genomics, 113(5), 3174–3184. https://doi.org/10.1016/j.ygeno.2021.07.020

Acknowledgements:

We would like to thank our researchers and interns for testing the app and giving feedback; Ayşe Gökçe Keşküş, Hilal Öksüz, Eda Aytekin, Fikri Kerem Kınal and Kayra Canpolat.

Table of published primer sets

Please select a primer pair to display mutation and conservation plots for the amplicon and alignment to the reference genome

Download

Detailed Variation Information

Red dots (above the mutation percentage threshold (0.1%)) and orange dots (below the threshold (0.1%)) represent mutations in nucleotides.

Blue and green letters refer to the nucleotides in the reference genome (NC_045512) and indicate primer binding sites and the region between primers, respectively.

Next to the points are the degenerate IUPAC codes for each alteration.

PhyloP values (44 Bat virus strains Basewise Conservation) were obtained from UCSC. Positive values are given to sites that are predicted to be conserved, while negative values are assigned to sites that are predicted to be rapidly changing.

*Select the area and double-click for zoomed version.

*Before selecting the new primer pair, please double-click on the empty place to reset the zoom.

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Select the primer pair to display mutation and Phylop plots for the amplicon and alignment to the reference genome

Download Table


Detailed Variation Information

Red dots (above the mutation percentage threshold (0.1%)) and orange dots (below the threshold (0.1%)) represent mutations in nucleotides.

Blue and green letters refer to the nucleotides in the reference genome (NC_045512) and indicate primer binding sites and the region between primers, respectively.

Next to the points are the degenerate IUPAC codes for each alteration.

PhyloP values (44 Bat virus strains Basewise Conservation) were obtained from UCSC. Positive values are given to sites that are predicted to be conserved, while negative values are assigned to sites that are predicted to be rapidly changing.

*Select the area and double-click for zoomed version.

*Before selecting the new primer pair, please double-click on the empty place to reset the zoom.

Loading...
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Select the primer pair to display mutation and PhyloP plots for the amplicon and alignment to the reference genome

*Degenerate primer pairs that exhibit mutations found in different SARS-CoV-2 Lineages
Download Table

Detailed Variation Information

Red dots (above the mutation percentage threshold (0.1%)) and orange dots (below the threshold (0.1%)) represent mutations in nucleotides.

Blue and green letters refer to the nucleotides in the reference genome (NC_045512) and indicate primer binding sites and the region between primers, respectively.

Next to the points are the degenerate IUPAC codes for each alteration.

PhyloP values (44 Bat virus strains Basewise Conservation) were obtained from UCSC. Positive values are given to sites that are predicted to be conserved, while negative values are assigned to sites that are predicted to be rapidly changing.

*Select the area and double-click for zoomed version.

*Before selecting the new primer pair, please double-click on the empty place to reset the zoom.

Loading...
Loading...

Select the primer pair to display mutation and PhyloP plots for the amplicon and alignment to the reference genome

*Conserved primers flanking highly variable regions
Download Table

Detailed Variation Information

Red dots (above the mutation percentage threshold (0.1%)) and orange dots (below the threshold (0.1%)) represent mutations in nucleotides.

Blue and green letters refer to the nucleotides in the reference genome (NC_045512) and indicate primer binding sites and the region between primers, respectively.

Next to the points are the degenerate IUPAC codes for each alteration.

PhyloP values (44 Bat virus strains Basewise Conservation) were obtained from UCSC. Positive values are given to sites that are predicted to be conserved, while negative values are assigned to sites that are predicted to be rapidly changing.

*Select the area and double-click for zoomed version.

*Before selecting the new primer pair, please double-click on the empty place to reset the zoom.

Loading...
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Search your primers in reference genome

Do not include these letters in your primers and probes: “E”, “F”, “I”, “J”, “L”, “O”, “P”, “Q”, “U”, “V”, “X”, “Z”

Detailed Variation Information

Red dots (above the mutation percentage threshold (0.1%)) and orange dots (below the threshold (0.1%)) represent mutations in nucleotides.

Blue and green letters refer to the nucleotides in the reference genome (NC_045512) and indicate primer binding sites and the probe binding sites, respectively.

Next to the points are the degenerate IUPAC codes for each alteration.

PhyloP values (44 Bat virus strains Basewise Conservation) were obtained from UCSC. Positive values are given to sites that are predicted to be conserved, while negative values are assigned to sites that are predicted to be rapidly changing.

*Select the area and double-click for zoomed version.

*Before selecting the new primer pair, please double-click on the empty place to reset the zoom.

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