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 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
| Strain | Number of sequences |
|---|---|
| SARS-CoV_strain_Frankfurt_1_NC_004718 | 1 sequence |
SARS-CoV-2
| Country | Number of sequences |
|---|---|
| Algeria | 3 sequences |
| Andorra | 1 sequence |
| Argentina | 50 sequences |
| Aruba | 11 sequences |
| Australia | 15,471 sequences |
| Austria | 762 sequences |
| Bahrain | 83 sequences |
| Bangladesh | 521 sequences |
| Belarus | 3 sequences |
| Belgium | 1,509 sequences |
| Belize | 4 sequences |
| Benin | 12 sequences |
| Bosnia and Herzegovina | 31 sequences |
| Botswana | 6 sequences |
| Brazil | 1,186 sequences |
| Brunei | 5 sequences |
| Bulgaria | 15 sequences |
| Burkina Faso | 85 sequences |
| Cambodia | 1 sequence |
| Cameroon | 1 sequence |
| Canada | 3,305 sequences |
| Chile | 228 sequences |
| China | 1,018 sequences |
| Colombia | 198 sequences |
| Costa Rica | 91 sequences |
| CotedIvoire | 49 sequences |
| Crimea | 1 sequence |
| Croatia | 22 sequences |
| Cuba | 2 sequences |
| Curacao | 9 sequences |
| Cyprus | 8 sequences |
| Czech Repubic | 1 sequence |
| Czech Republic | 217 sequences |
| Democratic Republic of the Congo | 360 sequences |
| Denmark | 9,125 sequences |
| Dominican Republic | 8 sequences |
| Ecuador | 103 sequences |
| Egypt | 158 sequences |
| Equatorial Guinea | 95 sequences |
| Estonia | 20 sequences |
| Faroe Islands | 37 sequences |
| Finland | 267 sequences |
| France | 2,145 sequences |
| Gabon | 9 sequences |
| Gambia | 360 sequences |
| Georgia | 22 sequences |
| Germany | 808 sequences |
| Ghana | 70 sequences |
| Gibraltar | 241 sequences |
| Greece | 133 sequences |
| Guadeloupe | 26 sequences |
| Guam | 4 sequences |
| Guatemala | 10 sequences |
| Hong Kong | 550 sequences |
| Hungary | 85 sequences |
| Iceland | 601 sequences |
| India | 3,442 sequences |
| Indonesia | 120 sequences |
| Iran | 186 sequences |
| Iraq | 50 sequences |
| Ireland | 733 sequences |
| Israel | 458 sequences |
| Italy | 959 sequences |
| Jamaica | 8 sequences |
| Japan | 914 sequences |
| Jordan | 226 sequences |
| Kazakhstan | 56 sequences |
| Kenya | 290 sequences |
| Kuwait | 8 sequences |
| Latvia | 199 sequences |
| Lebanon | 19 sequences |
| Lithuania | 160 sequences |
| Luxembourg | 271 sequences |
| Madagascar | 3 sequences |
| Malaysia | 125 sequences |
| Mali | 21 sequences |
| Malta | 10 sequences |
| Mexico | 309 sequences |
| Moldova | 9 sequences |
| Mongolia | 7 sequences |
| Montenegro | 12 sequences |
| Morocco | 48 sequences |
| Mozambique | 7 sequences |
| Myanmar | 2 sequences |
| Nepal | 1 sequence |
| Netherlands | 3,492 sequences |
| New Zealand | 990 sequences |
| Nigeria | 88 sequences |
| North Macedonia | 32 sequences |
| Norway | 573 sequences |
| Oman | 203 sequences |
| Pakistan | 21 sequences |
| Palestine | 70 sequences |
| Panama | 314 sequences |
| Peru | 384 sequences |
| Philippines | 30 sequences |
| Poland | 227 sequences |
| Portugal | 1,662 sequences |
| Qatar | 16 sequences |
| Republic of Congo | 11 sequences |
| Reunion | 4 sequences |
| Romania | 113 sequences |
| Russia | 953 sequences |
| Rwanda | 10 sequences |
| Saint Barthélemy | 2 sequences |
| Saint Martin | 10 sequences |
| Saudi Arabia | 572 sequences |
| Senegal | 136 sequences |
| Serbia | 88 sequences |
| Sierra Leone | 11 sequences |
| Singapore | 1,495 sequences |
| Slovakia | 25 sequences |
| Slovenia | 108 sequences |
| South Africa | 2,316 sequences |
| South Korea | 848 sequences |
| Spain | 5,192 sequences |
| Sri Lanka | 27 sequences |
| St Eustatius | 4 sequences |
| Suriname | 71 sequences |
| Sweden | 970 sequences |
| Switzerland | 3,347 sequences |
| Taiwan | 129 sequences |
| Thailand | 459 sequences |
| Timor-Leste | 19 sequences |
| Tunisia | 25 sequences |
| Turkey | 201 sequences |
| USA | 43,588 sequences |
| Uganda | 20 sequences |
| Ukraine | 61 sequences |
| United Arab Emirates | 245 sequences |
| United Kingdom | 106,416 sequences |
| Uruguay | 75 sequences |
| Uzbekistan | 2 sequences |
| Venezuela | 12 sequences |
| Viet Nam | 25 sequences |
| Vietnam | 89 sequences |
| Zambia | 1 sequence |
| Zimbabwe | 100 sequences |
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