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 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
| 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 | 38 sequences |
| Aruba | 5 sequences |
| Australia | 14,032 sequences |
| Austria | 761 sequences |
| Bahrain | 37 sequences |
| Bangladesh | 372 sequences |
| Belarus | 3 sequences |
| Belgium | 1,232 sequences |
| Belize | 4 sequences |
| Benin | 12 sequences |
| Bosnia and Herzegovina | 31 sequences |
| Botswana | 6 sequences |
| Brazil | 1,073 sequences |
| Brunei | 5 sequences |
| Bulgaria | 15 sequences |
| Cambodia | 1 sequence |
| Cameroon | 1 sequence |
| Canada | 3,199 sequences |
| Chile | 183 sequences |
| China | 1,005 sequences |
| Colombia | 175 sequences |
| Costa Rica | 91 sequences |
| Crimea | 1 sequence |
| Croatia | 22 sequences |
| Cuba | 2 sequences |
| Curacao | 4 sequences |
| Cyprus | 8 sequences |
| Czech Republic | 115 sequences |
| Democratic Republic of the Congo | 353 sequences |
| Denmark | 743 sequences |
| Dominican Republic | 8 sequences |
| Ecuador | 90 sequences |
| Egypt | 155 sequences |
| Estonia | 20 sequences |
| Faroe Islands | 14 sequences |
| Finland | 267 sequences |
| France | 1,484 sequences |
| Gabon | 4 sequences |
| Gambia | 360 sequences |
| Georgia | 22 sequences |
| Germany | 505 sequences |
| Ghana | 53 sequences |
| Gibraltar | 12 sequences |
| Greece | 133 sequences |
| Guam | 3 sequences |
| Guatemala | 10 sequences |
| Hong Kong | 423 sequences |
| Hungary | 85 sequences |
| Iceland | 601 sequences |
| India | 3,157 sequences |
| Indonesia | 114 sequences |
| Iran | 155 sequences |
| Iraq | 50 sequences |
| Ireland | 329 sequences |
| Israel | 402 sequences |
| Italy | 800 sequences |
| Jamaica | 8 sequences |
| Japan | 806 sequences |
| Jordan | 28 sequences |
| Kazakhstan | 56 sequences |
| Kenya | 290 sequences |
| Kuwait | 8 sequences |
| Latvia | 135 sequences |
| Lebanon | 15 sequences |
| Lithuania | 50 sequences |
| Luxembourg | 271 sequences |
| Madagascar | 2 sequences |
| Malaysia | 122 sequences |
| Mali | 21 sequences |
| Malta | 10 sequences |
| Mexico | 174 sequences |
| Moldova | 9 sequences |
| Mongolia | 1 sequence |
| Montenegro | 12 sequences |
| Morocco | 48 sequences |
| Myanmar | 2 sequences |
| Nepal | 1 sequence |
| Netherlands | 2,919 sequences |
| New Zealand | 902 sequences |
| Nigeria | 87 sequences |
| North Macedonia | 32 sequences |
| Norway | 437 sequences |
| Oman | 203 sequences |
| Pakistan | 20 sequences |
| Panama | 314 sequences |
| Peru | 384 sequences |
| Philippines | 29 sequences |
| Poland | 117 sequences |
| Portugal | 1,660 sequences |
| Qatar | 16 sequences |
| Republic of Congo | 11 sequences |
| Reunion | 4 sequences |
| Romania | 112 sequences |
| Russia | 563 sequences |
| Saudi Arabia | 562 sequences |
| Senegal | 136 sequences |
| Serbia | 47 sequences |
| Sierra Leone | 11 sequences |
| Singapore | 1,108 sequences |
| Slovakia | 25 sequences |
| Slovenia | 5 sequences |
| South Africa | 1,409 sequences |
| South Korea | 845 sequences |
| Spain | 4,469 sequences |
| Sri Lanka | 14 sequences |
| Suriname | 71 sequences |
| Sweden | 734 sequences |
| Switzerland | 2,768 sequences |
| Taiwan | 126 sequences |
| Thailand | 458 sequences |
| Timor-Leste | 19 sequences |
| Tunisia | 14 sequences |
| Turkey | 194 sequences |
| USA | 35,079 sequences |
| Uganda | 20 sequences |
| Ukraine | 58 sequences |
| United Arab Emirates | 247 sequences |
| United Kingdom | 67,731 sequences |
| Uruguay | 75 sequences |
| Uzbekistan | 2 sequences |
| Venezuela | 12 sequences |
| Vietnam | 87 sequences |
| Zambia | 1 sequence |
GISAID data provided on this website is subject to GISAID’s Terms and Conditions | Privacy policy of University of Turin.