CoV2ID provides a complete, quality checked and regularly updated list of oligonucleotides for SARS-CoV-2. The database evaluates available therapeutic and detection protocols according to the virus genetic diversity.


What can be done in CoV2ID

SARS-CoV-2 virus
CoV2ID>> Find a brief description of the SARS-CoV-2 virus

Reference genome>> Obtain the reference SARS-CoV-2 genome sequence

Sequence alignments>> Explore the genetic diversity across SARS-CoV-2 genomes

Oligonucleotides>> Find the best targets for your SARS-CoV-2 identification system

Search>> Explore several tables with different measures of sequence conservation.

 SARS-CoV-2 virus particles




Database content

Total number of oligonucleotides: 492 PCR primers: 181 LAMP primers: 237 Target Generation: 14 Probes: 29 Detection protocols: 57
Localization of oligonucleotides (arrows) in the SARS-CoV-2 virus reference genome

What can be found in CoV2ID


Search for the best oligonucleotides according
to the degree of conservation
in specific sequence alignments
Select the most conserved/variable regions
across the SARS-CoV-2 genome
Find PCR primer pairs ordered by the average
degree of conservation
in diverse sequence alignments
Search for oligonucleotides described
in peer reviewed publications ordered
by the average degree of conservation
in diverse sequence alignments
Find information on the sequence conservation
measures used in this site
Conserved
genomic regions
Select the best alignment according to
different measure of sequence conservation
PCR primer pairs
The best oligonucleotides
Our sequence
conservation measures
The top alignments
Oligonucleotides
in specific alignments


Most conserved oligonucleotides for the SARS-CoV-2 genome

The CoV2ID score measures the level of conservation of the oligo according to the viral genetic diversity. The higher the score, the more conserved is the oligo.

Top oligonucleotides
Databasereference CoV2ID score
CoV2ID001 100
CoV2ID006 100
CoV2ID008 100
CoV2ID047 100
CoV2ID050 100
CoV2ID054 100
CoV2ID073 100
CoV2ID075 100
CoV2ID086 100
CoV2ID158 100
CoV2ID160 100
CoV2ID161 100
CoV2ID165 100
CoV2ID167 100
CoV2ID174 100
Top PCR primers
Primer1 Primer2 CoV2ID score
CoV2ID008 CoV2ID485 100
CoV2ID174 CoV2ID267 100
CoV2ID178 CoV2ID267 100
CoV2ID193 CoV2ID391 100
CoV2ID267 CoV2ID430 100
CoV2ID358 CoV2ID425 100
CoV2ID410 CoV2ID485 100
CoV2ID459 CoV2ID485 100
CoV2ID485 CoV2ID486 100
CoV2ID324 CoV2ID436 99.7
CoV2ID054 CoV2ID423 99.69
CoV2ID160 CoV2ID384 99.68
CoV2ID178 CoV2ID207 99.67
CoV2ID001 CoV2ID085 99.65
CoV2ID050 CoV2ID085 99.65


SARS-CoV-2 oligos in other human coronaviruses

Top divergent oligos in other coronaviruses

(the best ones to avoid false positives)
Oligos CoV2ID score
CoV2ID362 8.43
CoV2ID195 8.49
CoV2ID232 8.86
CoV2ID479 8.95
CoV2ID193 9.02
CoV2ID249 9.08
CoV2ID191 9.13
CoV2ID469 9.22
CoV2ID199 9.25
CoV2ID320 9.31

Top conserved oligos in other coronaviruses

(the most similar, may cause false positives)
Oligonucleotide CoV2ID score
CoV2ID102 91.43
CoV2ID280 89.33
CoV2ID331 87.54
CoV2ID330 83.6
CoV2ID272 83.08
CoV2ID333 82.4
CoV2ID332 81.74
CoV2ID455 81.12
CoV2ID058 79.05
CoV2ID105 78.1

Explore multiple sequence alignments


SARS-CoV-2 genome variation

Most conserved regions for the SARS-CoV-2 genome

The percentage of identical sites and pairwise identity level of conservation of the oligo according to genetic diversity. The higher the score, the more conserved is the oligo.

List of the most conserved genomic regions considering the PIS and PPI (100 nt windows):





Top region (PIS)
Genome Position PIS
15901-16000 100
15951-16050 100
5551-5650 99
8651-8750 99
15301-15400 99
24551-24650 99
26351-26450 99
8701-8800 98
9951-10050 98
15201-15300 98
15251-15350 98
19601-19700 98
26251-26350 98
26301-26400 98
26401-26500 98
Top region (PPI)
Genome Position PPI
1101-1200 100
2501-2600 100
2901-3000 100
2951-3050 100
3401-3500 100
3701-3800 100
3751-3850 100
3801-3900 100
3851-3950 100
4751-4850 100
5051-5150 100
5101-5200 100
5151-5250 100
5301-5400 100
5551-5650 100