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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 Nov 29 12:36:20 2020 (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: 225,307


SARS-CoV

StrainNumber of sequences
SARS-CoV_strain_Frankfurt_1_NC_0047181 sequence

SARS-CoV-2

CountryNumber of sequences
Algeria3 sequences
Andorra1 sequence
Argentina50 sequences
Aruba11 sequences
Australia15,471 sequences
Austria762 sequences
Bahrain83 sequences
Bangladesh521 sequences
Belarus3 sequences
Belgium1,509 sequences
Belize4 sequences
Benin12 sequences
Bosnia and Herzegovina31 sequences
Botswana6 sequences
Brazil1,186 sequences
Brunei5 sequences
Bulgaria15 sequences
Burkina Faso85 sequences
Cambodia1 sequence
Cameroon1 sequence
Canada3,305 sequences
Chile228 sequences
China1,018 sequences
Colombia198 sequences
Costa Rica91 sequences
CotedIvoire49 sequences
Crimea1 sequence
Croatia22 sequences
Cuba2 sequences
Curacao9 sequences
Cyprus8 sequences
Czech Repubic1 sequence
Czech Republic217 sequences
Democratic Republic of the Congo360 sequences
Denmark9,125 sequences
Dominican Republic8 sequences
Ecuador103 sequences
Egypt158 sequences
Equatorial Guinea95 sequences
Estonia20 sequences
Faroe Islands37 sequences
Finland267 sequences
France2,145 sequences
Gabon9 sequences
Gambia360 sequences
Georgia22 sequences
Germany808 sequences
Ghana70 sequences
Gibraltar241 sequences
Greece133 sequences
Guadeloupe26 sequences
Guam4 sequences
Guatemala10 sequences
Hong Kong550 sequences
Hungary85 sequences
Iceland601 sequences
India3,442 sequences
Indonesia120 sequences
Iran186 sequences
Iraq50 sequences
Ireland733 sequences
Israel458 sequences
Italy959 sequences
Jamaica8 sequences
Japan914 sequences
Jordan226 sequences
Kazakhstan56 sequences
Kenya290 sequences
Kuwait8 sequences
Latvia199 sequences
Lebanon19 sequences
Lithuania160 sequences
Luxembourg271 sequences
Madagascar3 sequences
Malaysia125 sequences
Mali21 sequences
Malta10 sequences
Mexico309 sequences
Moldova9 sequences
Mongolia7 sequences
Montenegro12 sequences
Morocco48 sequences
Mozambique7 sequences
Myanmar2 sequences
Nepal1 sequence
Netherlands3,492 sequences
New Zealand990 sequences
Nigeria88 sequences
North Macedonia32 sequences
Norway573 sequences
Oman203 sequences
Pakistan21 sequences
Palestine70 sequences
Panama314 sequences
Peru384 sequences
Philippines30 sequences
Poland227 sequences
Portugal1,662 sequences
Qatar16 sequences
Republic of Congo11 sequences
Reunion4 sequences
Romania113 sequences
Russia953 sequences
Rwanda10 sequences
Saint Barthélemy2 sequences
Saint Martin10 sequences
Saudi Arabia572 sequences
Senegal136 sequences
Serbia88 sequences
Sierra Leone11 sequences
Singapore1,495 sequences
Slovakia25 sequences
Slovenia108 sequences
South Africa2,316 sequences
South Korea848 sequences
Spain5,192 sequences
Sri Lanka27 sequences
St Eustatius4 sequences
Suriname71 sequences
Sweden970 sequences
Switzerland3,347 sequences
Taiwan129 sequences
Thailand459 sequences
Timor-Leste19 sequences
Tunisia25 sequences
Turkey201 sequences
USA43,588 sequences
Uganda20 sequences
Ukraine61 sequences
United Arab Emirates245 sequences
United Kingdom106,416 sequences
Uruguay75 sequences
Uzbekistan2 sequences
Venezuela12 sequences
Viet Nam25 sequences
Vietnam89 sequences
Zambia1 sequence
Zimbabwe100 sequences

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