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Update:

Author: Olivier Friard - Department of Life Sciences and Systems Biology - University of Turin - Italy

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.

The isolates collection dates are in YYYY-MM-DD format (ISO 8601).

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Full match - All primers and probe have a 100% identity with the target sequence. In case of a 2 probes system (RdRP) at least one probe must have a 100% identity.

The identities of forward/reverse primers AND probe are greater than or equal to 80% AND the length of the amplification product is comprised between the reference length plus/minus 8 bp.

The identity of one primer OR the probe are less than 80% OR the length of the amplification product is NOT comprised between reference length plus/minus 8 bp.

If the target sequence is not available the

Please note that the reverse primer sequence is shown reverted-complemented in the alignments.

Move the mouse cursor over elements to see the details.

Virus name / Accession ID | Region | Collection date | 2019-nCoV_N1 | 2019-nCoV_N2 | 2019-nCoV_N3 | E-Sarbeco | RdRP |
---|---|---|---|---|---|---|---|

The sequence is not available | The sequence is not available | The sequence is not available | The sequence is not available | The sequence is not available | |||

The sequence is not available | The sequence is not available | The sequence is not available | The sequence is not available | The sequence is not available | |||

Gilgit | 2020-03-04 | ||||||

Gilgit | The sequence is not available | The sequence is not available | The sequence is not available | The sequence is not available | The sequence is not available | ||

Gilgit | The sequence is not available | The sequence is not available | The sequence is not available | The sequence is not available | The sequence is not available | ||

Gilgit | The sequence is not available | The sequence is not available | The sequence is not available | The sequence is not available | The sequence is not available | ||

Gilgit | The sequence is not available | The sequence is not available | The sequence is not available | The sequence is not available | The sequence is not available | ||

Islamabad | |||||||

Islamabad | |||||||

Islamabad | |||||||

Islamabad | |||||||

KPK | 2020-03-12 | ||||||

Karachi | |||||||

Karachi | |||||||

Karachi | |||||||

Karachi | |||||||

Karachi | |||||||

Karachi | |||||||

Karachi | |||||||

Karachi | |||||||

Karachi | |||||||

Karachi | The sequence is not available | ||||||

Karachi | |||||||

Karachi | |||||||

Karachi | |||||||

Karachi | The sequence is not available | ||||||

Karachi | |||||||

Karachi | |||||||

Karachi | |||||||

Karachi | |||||||

Karachi | |||||||

Karachi | |||||||

Karachi | |||||||

Karachi | |||||||

Karachi | |||||||

Karachi | |||||||

Karachi | The sequence is not available | ||||||

Karachi | |||||||

Karachi | |||||||

Karachi | |||||||

Karachi | |||||||

Karachi | |||||||

Karachi | |||||||

Karachi | |||||||

Karachi | |||||||

Karachi | |||||||

Karachi | |||||||

Karachi | |||||||

Karachi | |||||||

Karachi | |||||||

Karachi | |||||||

Karachi | |||||||

Karachi | |||||||

Rawalpindi | |||||||

Rawalpindi | |||||||

Sindh |

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