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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 10 05:32:46 2021 (UTC+2) (The service is updated weekly)

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: 345,436


SARS-CoV

StrainNumber of sequences
SARS-CoV_strain_Frankfurt_1_NC_0047181 sequence

SARS-CoV-2

CountryNumber of sequences
Algeria18 sequences
Andorra1 sequence
Antigua and Barbuda1 sequence
Argentina481 sequences
Armenia3 sequences
Aruba11 sequences
Australia16,980 sequences
Austria762 sequences
Bahrain150 sequences
Bangladesh735 sequences
Belarus10 sequences
Belgium2,942 sequences
Belize4 sequences
Benin12 sequences
Bermuda30 sequences
Bosnia and Herzegovina33 sequences
Botswana12 sequences
Brazil1,958 sequences
Brunei5 sequences
Bulgaria15 sequences
Burkina Faso85 sequences
Cambodia2 sequences
Cameroon1 sequence
Canada4,493 sequences
Chile613 sequences
China1,019 sequences
Colombia231 sequences
Costa Rica181 sequences
Crimea6 sequences
Croatia50 sequences
Cuba2 sequences
Curacao9 sequences
Cyprus8 sequences
Czech Republic283 sequences
Côte d'Ivoire65 sequences
Democratic Republic of the Congo360 sequences
Denmark22,669 sequences
Dominican Republic8 sequences
Ecuador160 sequences
Egypt158 sequences
El Salvador6 sequences
Equatorial Guinea95 sequences
Estonia20 sequences
Faroe Islands37 sequences
Finland906 sequences
France3,063 sequences
Gabon9 sequences
Gambia360 sequences
Georgia26 sequences
Germany3,074 sequences
Ghana70 sequences
Gibraltar477 sequences
Greece134 sequences
Guadeloupe26 sequences
Guam4 sequences
Guatemala10 sequences
Guinea6 sequences
Hong Kong642 sequences
Hungary273 sequences
Iceland601 sequences
India4,334 sequences
Indonesia214 sequences
Iran232 sequences
Iraq53 sequences
Ireland1,577 sequences
Israel696 sequences
Italy1,791 sequences
Jamaica13 sequences
Japan9,840 sequences
Jordan539 sequences
Kazakhstan56 sequences
Kenya290 sequences
Kuwait11 sequences
Latvia229 sequences
Lebanon23 sequences
Lithuania213 sequences
Luxembourg2,325 sequences
Madagascar6 sequences
Malaysia295 sequences
Mali22 sequences
Malta16 sequences
Mexico381 sequences
Moldova9 sequences
Mongolia7 sequences
Montenegro12 sequences
Morocco122 sequences
Mozambique7 sequences
Myanmar2 sequences
Nepal15 sequences
Netherlands5,337 sequences
New Zealand1,063 sequences
Nigeria224 sequences
North Macedonia82 sequences
Norway1,104 sequences
Oman205 sequences
Pakistan63 sequences
Palestine77 sequences
Panama314 sequences
Papua New Guinea13 sequences
Peru355 sequences
Philippines30 sequences
Poland350 sequences
Portugal2,268 sequences
Qatar16 sequences
Republic of Congo11 sequences
Reunion4 sequences
Romania149 sequences
Russia1,652 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
Serbia126 sequences
Sierra Leone11 sequences
Singapore1,594 sequences
Slovakia59 sequences
Slovenia109 sequences
South Africa2,882 sequences
South Korea1,286 sequences
Spain5,907 sequences
Sri Lanka36 sequences
St Eustatius4 sequences
Suriname71 sequences
Sweden1,321 sequences
Switzerland5,356 sequences
Taiwan140 sequences
Thailand628 sequences
Timor-Leste19 sequences
Trinidad16 sequences
Tunisia57 sequences
Turkey345 sequences
USA68,760 sequences
Uganda133 sequences
Ukraine61 sequences
United Arab Emirates1,312 sequences
United Kingdom151,859 sequences
Uruguay129 sequences
Uzbekistan2 sequences
Venezuela12 sequences
Viet Nam25 sequences
Vietnam116 sequences
Zambia1 sequence
Zimbabwe100 sequences

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