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 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
| Strain | Number of sequences |
|---|---|
| SARS-CoV_strain_Frankfurt_1_NC_004718 | 1 sequence |
SARS-CoV-2
| Country | Number of sequences |
|---|---|
| Albania | 1 sequence |
| Algeria | 18 sequences |
| Andorra | 1 sequence |
| Antigua and Barbuda | 1 sequence |
| Argentina | 662 sequences |
| Armenia | 3 sequences |
| Aruba | 19 sequences |
| Australia | 17,292 sequences |
| Austria | 1,344 sequences |
| Azerbaijan | 8 sequences |
| Bahrain | 150 sequences |
| Bangladesh | 818 sequences |
| Belarus | 35 sequences |
| Belgium | 3,748 sequences |
| Belize | 4 sequences |
| Benin | 12 sequences |
| Bermuda | 30 sequences |
| Bolivia | 27 sequences |
| Bosnia and Herzegovina | 33 sequences |
| Botswana | 13 sequences |
| Brazil | 2,422 sequences |
| Brunei | 5 sequences |
| Bulgaria | 15 sequences |
| Burkina Faso | 85 sequences |
| Cambodia | 4 sequences |
| Cameroon | 22 sequences |
| Canada | 8,614 sequences |
| Chile | 966 sequences |
| China | 1,041 sequences |
| Colombia | 290 sequences |
| Costa Rica | 181 sequences |
| Crimea | 6 sequences |
| Croatia | 50 sequences |
| Cuba | 2 sequences |
| Curacao | 9 sequences |
| Cyprus | 8 sequences |
| Czech Republic | 483 sequences |
| Czech republic | 119 sequences |
| Côte d'Ivoire | 65 sequences |
| Democratic Republic of the Congo | 360 sequences |
| Denmark | 34,781 sequences |
| Dominican Republic | 8 sequences |
| Ecuador | 208 sequences |
| Egypt | 366 sequences |
| El Salvador | 6 sequences |
| Equatorial Guinea | 95 sequences |
| Estonia | 20 sequences |
| Faroe Islands | 38 sequences |
| Finland | 1,154 sequences |
| France | 4,317 sequences |
| Gabon | 9 sequences |
| Gambia | 427 sequences |
| Georgia | 26 sequences |
| Germany | 4,582 sequences |
| Ghana | 114 sequences |
| Gibraltar | 477 sequences |
| Greece | 142 sequences |
| Guadeloupe | 26 sequences |
| Guam | 4 sequences |
| Guatemala | 32 sequences |
| Guinea | 6 sequences |
| Guyane Francaise | 10 sequences |
| Hong Kong | 642 sequences |
| Hungary | 278 sequences |
| Iceland | 4,180 sequences |
| India | 4,780 sequences |
| Indonesia | 334 sequences |
| Iran | 245 sequences |
| Iraq | 82 sequences |
| Ireland | 1,974 sequences |
| Israel | 1,319 sequences |
| Italy | 3,011 sequences |
| Jamaica | 13 sequences |
| Japan | 17,053 sequences |
| Jordan | 581 sequences |
| Kazakhstan | 56 sequences |
| Kenya | 514 sequences |
| Kuwait | 27 sequences |
| Latvia | 233 sequences |
| Lebanon | 23 sequences |
| Liechtenstein | 3 sequences |
| Lithuania | 258 sequences |
| Luxembourg | 2,325 sequences |
| Madagascar | 6 sequences |
| Malaysia | 321 sequences |
| Mali | 24 sequences |
| Malta | 17 sequences |
| Mayotte | 84 sequences |
| Mexico | 626 sequences |
| Moldova | 9 sequences |
| Mongolia | 7 sequences |
| Montenegro | 12 sequences |
| Morocco | 122 sequences |
| Mozambique | 94 sequences |
| Myanmar | 41 sequences |
| Nepal | 15 sequences |
| Netherlands | 7,416 sequences |
| New Zealand | 1,111 sequences |
| Nigeria | 260 sequences |
| North Macedonia | 82 sequences |
| Norway | 1,279 sequences |
| Oman | 205 sequences |
| Pakistan | 69 sequences |
| Palestine | 79 sequences |
| Panama | 314 sequences |
| Papua New Guinea | 13 sequences |
| Peru | 441 sequences |
| Philippines | 42 sequences |
| Poland | 440 sequences |
| Portugal | 2,422 sequences |
| Qatar | 16 sequences |
| Republic of Congo | 11 sequences |
| Reunion | 4 sequences |
| Romania | 191 sequences |
| Russia | 1,844 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 | 162 sequences |
| Sierra Leone | 11 sequences |
| Singapore | 1,731 sequences |
| Slovakia | 122 sequences |
| Slovenia | 148 sequences |
| South Africa | 3,064 sequences |
| South Korea | 1,633 sequences |
| Spain | 7,433 sequences |
| Sri Lanka | 60 sequences |
| St Eustatius | 4 sequences |
| St. Lucia | 4 sequences |
| Suriname | 71 sequences |
| Sweden | 1,389 sequences |
| Switzerland | 8,074 sequences |
| Taiwan | 150 sequences |
| Thailand | 697 sequences |
| Timor-Leste | 19 sequences |
| Trinidad | 16 sequences |
| Trinidad and Tobago | 1 sequence |
| Tunisia | 84 sequences |
| Turkey | 494 sequences |
| USA | 89,495 sequences |
| Uganda | 133 sequences |
| Ukraine | 61 sequences |
| United Arab Emirates | 1,843 sequences |
| United Kingdom | 192,124 sequences |
| Uruguay | 129 sequences |
| Uzbekistan | 2 sequences |
| Venezuela | 12 sequences |
| Viet Nam | 25 sequences |
| Vietnam | 117 sequences |
| Zambia | 2 sequences |
| Zimbabwe | 100 sequences |
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