Status of SARS-CoV-2 detection systems (RT-PCR)
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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 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: 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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