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Status of SARS-CoV-2 detection systems (RT-PCR)
enabled by data from GISAID logo

This service aims to verify the systems for the diagnostic detection of 2019-nCoV by real-time RT-PCR amplification.
All oligonucleotides (primers and probes) used for each system are aligned against all the sequences from the GISAID EpiCoV™ database and the alignment identity scores are checked. A color code is finally delivered to the system in base of its ability to amplify or not the corresponding SARS-CoV-2 isolate. The details are available on the results pages.
At the moment the 3 systems published by the Centers for Disease Control and Prevention (2019-nCoV_N1, 2019-nCoV_N2 and 2019-nCoV_N3) and the 2 systems published by the Charité Hospital (Berlin, Germany - RdRP and Sarbeco) are monitored.

Author: Olivier Friard - Department of Life Sciences and Systems Biology - University of Turin - Italy

Update: Sun Jan 31 07:00:30 2021 (UTC+2)

The service is no more updated as a tool to check primers is available on the GISAID site: PrimerChecked

We gratefully acknowledge the Authors of the Originating and Submitting laboratories of the genetic sequence and metadata shared via GISAID, on which this research is based.

References

GISAID EpiCoV™ database
CDC: 2019-Novel Coronavirus (2019-nCoV) Real-time rRT-PCR Panel Primers and Probes
Berlin-Charité Diagnostic detection of 2019-nCoV by real-time RT-PCR


Number of isolates sequences: 452,787


SARS-CoV

StrainNumber of sequences
SARS-CoV_strain_Frankfurt_1_NC_0047181 sequence

SARS-CoV-2

CountryNumber of sequences
Albania1 sequence
Algeria18 sequences
Andorra1 sequence
Antigua and Barbuda1 sequence
Argentina662 sequences
Armenia3 sequences
Aruba19 sequences
Australia17,292 sequences
Austria1,344 sequences
Azerbaijan8 sequences
Bahrain150 sequences
Bangladesh818 sequences
Belarus35 sequences
Belgium3,748 sequences
Belize4 sequences
Benin12 sequences
Bermuda30 sequences
Bolivia27 sequences
Bosnia and Herzegovina33 sequences
Botswana13 sequences
Brazil2,422 sequences
Brunei5 sequences
Bulgaria15 sequences
Burkina Faso85 sequences
Cambodia4 sequences
Cameroon22 sequences
Canada8,614 sequences
Chile966 sequences
China1,041 sequences
Colombia290 sequences
Costa Rica181 sequences
Crimea6 sequences
Croatia50 sequences
Cuba2 sequences
Curacao9 sequences
Cyprus8 sequences
Czech Republic483 sequences
Czech republic119 sequences
Côte d'Ivoire65 sequences
Democratic Republic of the Congo360 sequences
Denmark34,781 sequences
Dominican Republic8 sequences
Ecuador208 sequences
Egypt366 sequences
El Salvador6 sequences
Equatorial Guinea95 sequences
Estonia20 sequences
Faroe Islands38 sequences
Finland1,154 sequences
France4,317 sequences
Gabon9 sequences
Gambia427 sequences
Georgia26 sequences
Germany4,582 sequences
Ghana114 sequences
Gibraltar477 sequences
Greece142 sequences
Guadeloupe26 sequences
Guam4 sequences
Guatemala32 sequences
Guinea6 sequences
Guyane Francaise10 sequences
Hong Kong642 sequences
Hungary278 sequences
Iceland4,180 sequences
India4,780 sequences
Indonesia334 sequences
Iran245 sequences
Iraq82 sequences
Ireland1,974 sequences
Israel1,319 sequences
Italy3,011 sequences
Jamaica13 sequences
Japan17,053 sequences
Jordan581 sequences
Kazakhstan56 sequences
Kenya514 sequences
Kuwait27 sequences
Latvia233 sequences
Lebanon23 sequences
Liechtenstein3 sequences
Lithuania258 sequences
Luxembourg2,325 sequences
Madagascar6 sequences
Malaysia321 sequences
Mali24 sequences
Malta17 sequences
Mayotte84 sequences
Mexico626 sequences
Moldova9 sequences
Mongolia7 sequences
Montenegro12 sequences
Morocco122 sequences
Mozambique94 sequences
Myanmar41 sequences
Nepal15 sequences
Netherlands7,416 sequences
New Zealand1,111 sequences
Nigeria260 sequences
North Macedonia82 sequences
Norway1,279 sequences
Oman205 sequences
Pakistan69 sequences
Palestine79 sequences
Panama314 sequences
Papua New Guinea13 sequences
Peru441 sequences
Philippines42 sequences
Poland440 sequences
Portugal2,422 sequences
Qatar16 sequences
Republic of Congo11 sequences
Reunion4 sequences
Romania191 sequences
Russia1,844 sequences
Rwanda36 sequences
Saint Barthélemy2 sequences
Saint Kitts and Nevis3 sequences
Saint Martin10 sequences
Saint Vincent and the Grenadines1 sequence
Saudi Arabia953 sequences
Senegal136 sequences
Serbia162 sequences
Sierra Leone11 sequences
Singapore1,731 sequences
Slovakia122 sequences
Slovenia148 sequences
South Africa3,064 sequences
South Korea1,633 sequences
Spain7,433 sequences
Sri Lanka60 sequences
St Eustatius4 sequences
St. Lucia4 sequences
Suriname71 sequences
Sweden1,389 sequences
Switzerland8,074 sequences
Taiwan150 sequences
Thailand697 sequences
Timor-Leste19 sequences
Trinidad16 sequences
Trinidad and Tobago1 sequence
Tunisia84 sequences
Turkey494 sequences
USA89,495 sequences
Uganda133 sequences
Ukraine61 sequences
United Arab Emirates1,843 sequences
United Kingdom192,124 sequences
Uruguay129 sequences
Uzbekistan2 sequences
Venezuela12 sequences
Viet Nam25 sequences
Vietnam117 sequences
Zambia2 sequences
Zimbabwe100 sequences

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