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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 Oct 25 07:18:47 2020 (UTC+2) (The service is updated daily)

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: 159,261


SARS-CoV

StrainNumber of sequences
SARS-CoV_strain_Frankfurt_1_NC_0047181 sequence

SARS-CoV-2

CountryNumber of sequences
Algeria3 sequences
Andorra1 sequence
Argentina38 sequences
Aruba5 sequences
Australia14,032 sequences
Austria761 sequences
Bahrain37 sequences
Bangladesh372 sequences
Belarus3 sequences
Belgium1,232 sequences
Belize4 sequences
Benin12 sequences
Bosnia and Herzegovina31 sequences
Botswana6 sequences
Brazil1,073 sequences
Brunei5 sequences
Bulgaria15 sequences
Cambodia1 sequence
Cameroon1 sequence
Canada3,199 sequences
Chile183 sequences
China1,005 sequences
Colombia175 sequences
Costa Rica91 sequences
Crimea1 sequence
Croatia22 sequences
Cuba2 sequences
Curacao4 sequences
Cyprus8 sequences
Czech Republic115 sequences
Democratic Republic of the Congo353 sequences
Denmark743 sequences
Dominican Republic8 sequences
Ecuador90 sequences
Egypt155 sequences
Estonia20 sequences
Faroe Islands14 sequences
Finland267 sequences
France1,484 sequences
Gabon4 sequences
Gambia360 sequences
Georgia22 sequences
Germany505 sequences
Ghana53 sequences
Gibraltar12 sequences
Greece133 sequences
Guam3 sequences
Guatemala10 sequences
Hong Kong423 sequences
Hungary85 sequences
Iceland601 sequences
India3,157 sequences
Indonesia114 sequences
Iran155 sequences
Iraq50 sequences
Ireland329 sequences
Israel402 sequences
Italy800 sequences
Jamaica8 sequences
Japan806 sequences
Jordan28 sequences
Kazakhstan56 sequences
Kenya290 sequences
Kuwait8 sequences
Latvia135 sequences
Lebanon15 sequences
Lithuania50 sequences
Luxembourg271 sequences
Madagascar2 sequences
Malaysia122 sequences
Mali21 sequences
Malta10 sequences
Mexico174 sequences
Moldova9 sequences
Mongolia1 sequence
Montenegro12 sequences
Morocco48 sequences
Myanmar2 sequences
Nepal1 sequence
Netherlands2,919 sequences
New Zealand902 sequences
Nigeria87 sequences
North Macedonia32 sequences
Norway437 sequences
Oman203 sequences
Pakistan20 sequences
Panama314 sequences
Peru384 sequences
Philippines29 sequences
Poland117 sequences
Portugal1,660 sequences
Qatar16 sequences
Republic of Congo11 sequences
Reunion4 sequences
Romania112 sequences
Russia563 sequences
Saudi Arabia562 sequences
Senegal136 sequences
Serbia47 sequences
Sierra Leone11 sequences
Singapore1,108 sequences
Slovakia25 sequences
Slovenia5 sequences
South Africa1,409 sequences
South Korea845 sequences
Spain4,469 sequences
Sri Lanka14 sequences
Suriname71 sequences
Sweden734 sequences
Switzerland2,768 sequences
Taiwan126 sequences
Thailand458 sequences
Timor-Leste19 sequences
Tunisia14 sequences
Turkey194 sequences
USA35,079 sequences
Uganda20 sequences
Ukraine58 sequences
United Arab Emirates247 sequences
United Kingdom67,731 sequences
Uruguay75 sequences
Uzbekistan2 sequences
Venezuela12 sequences
Vietnam87 sequences
Zambia1 sequence

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