Status of SARS-CoV-2 detection systems (RT-PCR)
enabled by data from
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
| Strain | Number of sequences |
|---|---|
| SARS-CoV_strain_Frankfurt_1_NC_004718 | 1 sequence |
SARS-CoV-2
| Country | Number of sequences |
|---|---|
| Algeria | 18 sequences |
| Andorra | 1 sequence |
| Antigua and Barbuda | 1 sequence |
| Argentina | 481 sequences |
| Armenia | 3 sequences |
| Aruba | 11 sequences |
| Australia | 16,980 sequences |
| Austria | 762 sequences |
| Bahrain | 150 sequences |
| Bangladesh | 735 sequences |
| Belarus | 10 sequences |
| Belgium | 2,942 sequences |
| Belize | 4 sequences |
| Benin | 12 sequences |
| Bermuda | 30 sequences |
| Bosnia and Herzegovina | 33 sequences |
| Botswana | 12 sequences |
| Brazil | 1,958 sequences |
| Brunei | 5 sequences |
| Bulgaria | 15 sequences |
| Burkina Faso | 85 sequences |
| Cambodia | 2 sequences |
| Cameroon | 1 sequence |
| Canada | 4,493 sequences |
| Chile | 613 sequences |
| China | 1,019 sequences |
| Colombia | 231 sequences |
| Costa Rica | 181 sequences |
| Crimea | 6 sequences |
| Croatia | 50 sequences |
| Cuba | 2 sequences |
| Curacao | 9 sequences |
| Cyprus | 8 sequences |
| Czech Republic | 283 sequences |
| Côte d'Ivoire | 65 sequences |
| Democratic Republic of the Congo | 360 sequences |
| Denmark | 22,669 sequences |
| Dominican Republic | 8 sequences |
| Ecuador | 160 sequences |
| Egypt | 158 sequences |
| El Salvador | 6 sequences |
| Equatorial Guinea | 95 sequences |
| Estonia | 20 sequences |
| Faroe Islands | 37 sequences |
| Finland | 906 sequences |
| France | 3,063 sequences |
| Gabon | 9 sequences |
| Gambia | 360 sequences |
| Georgia | 26 sequences |
| Germany | 3,074 sequences |
| Ghana | 70 sequences |
| Gibraltar | 477 sequences |
| Greece | 134 sequences |
| Guadeloupe | 26 sequences |
| Guam | 4 sequences |
| Guatemala | 10 sequences |
| Guinea | 6 sequences |
| Hong Kong | 642 sequences |
| Hungary | 273 sequences |
| Iceland | 601 sequences |
| India | 4,334 sequences |
| Indonesia | 214 sequences |
| Iran | 232 sequences |
| Iraq | 53 sequences |
| Ireland | 1,577 sequences |
| Israel | 696 sequences |
| Italy | 1,791 sequences |
| Jamaica | 13 sequences |
| Japan | 9,840 sequences |
| Jordan | 539 sequences |
| Kazakhstan | 56 sequences |
| Kenya | 290 sequences |
| Kuwait | 11 sequences |
| Latvia | 229 sequences |
| Lebanon | 23 sequences |
| Lithuania | 213 sequences |
| Luxembourg | 2,325 sequences |
| Madagascar | 6 sequences |
| Malaysia | 295 sequences |
| Mali | 22 sequences |
| Malta | 16 sequences |
| Mexico | 381 sequences |
| Moldova | 9 sequences |
| Mongolia | 7 sequences |
| Montenegro | 12 sequences |
| Morocco | 122 sequences |
| Mozambique | 7 sequences |
| Myanmar | 2 sequences |
| Nepal | 15 sequences |
| Netherlands | 5,337 sequences |
| New Zealand | 1,063 sequences |
| Nigeria | 224 sequences |
| North Macedonia | 82 sequences |
| Norway | 1,104 sequences |
| Oman | 205 sequences |
| Pakistan | 63 sequences |
| Palestine | 77 sequences |
| Panama | 314 sequences |
| Papua New Guinea | 13 sequences |
| Peru | 355 sequences |
| Philippines | 30 sequences |
| Poland | 350 sequences |
| Portugal | 2,268 sequences |
| Qatar | 16 sequences |
| Republic of Congo | 11 sequences |
| Reunion | 4 sequences |
| Romania | 149 sequences |
| Russia | 1,652 sequences |
| Rwanda | 36 sequences |
| Saint Barthélemy | 2 sequences |
| Saint Kitts and Nevis | 3 sequences |
| Saint Martin | 10 sequences |
| Saint Vincent and the Grenadines | 1 sequence |
| Saudi Arabia | 953 sequences |
| Senegal | 136 sequences |
| Serbia | 126 sequences |
| Sierra Leone | 11 sequences |
| Singapore | 1,594 sequences |
| Slovakia | 59 sequences |
| Slovenia | 109 sequences |
| South Africa | 2,882 sequences |
| South Korea | 1,286 sequences |
| Spain | 5,907 sequences |
| Sri Lanka | 36 sequences |
| St Eustatius | 4 sequences |
| Suriname | 71 sequences |
| Sweden | 1,321 sequences |
| Switzerland | 5,356 sequences |
| Taiwan | 140 sequences |
| Thailand | 628 sequences |
| Timor-Leste | 19 sequences |
| Trinidad | 16 sequences |
| Tunisia | 57 sequences |
| Turkey | 345 sequences |
| USA | 68,760 sequences |
| Uganda | 133 sequences |
| Ukraine | 61 sequences |
| United Arab Emirates | 1,312 sequences |
| United Kingdom | 151,859 sequences |
| Uruguay | 129 sequences |
| Uzbekistan | 2 sequences |
| Venezuela | 12 sequences |
| Viet Nam | 25 sequences |
| Vietnam | 116 sequences |
| Zambia | 1 sequence |
| Zimbabwe | 100 sequences |
GISAID data provided on this website is subject to GISAID’s Terms and Conditions | Privacy policy of University of Turin.