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Status of SARS-CoV-2 detection systems (RT-PCR)
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Update: Sun Oct 25 07:18:47 2020 (UTC+2)

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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Ghana

Number of isolates sequences available: 53

Method

When the target sequence of amplification systems is available the primers and probe are aligned against the target sequence using the Smith-Waterman local sequence alignment algorithm and the alignments are classified in 3 categories:
             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 The sequence is not available warning is shown.
Please note that the reverse primer sequence is shown reverted-complemented in the alignments.

Results

Move the mouse cursor over elements to see the details.

Virus name / Accession IDRegionCollection date2019-nCoV_N12019-nCoV_N22019-nCoV_N3E-SarbecoRdRP
EPI_ISL_515082
EPI_ISL_515083
EPI_ISL_515084
EPI_ISL_515085
EPI_ISL_515086
EPI_ISL_515087
EPI_ISL_515088
EPI_ISL_515089
EPI_ISL_515090
EPI_ISL_515091
EPI_ISL_515092
EPI_ISL_515093
EPI_ISL_515094
EPI_ISL_515095
EPI_ISL_515096
EPI_ISL_515097
EPI_ISL_515098
EPI_ISL_515099
EPI_ISL_515100
EPI_ISL_515101
EPI_ISL_515102
EPI_ISL_515103
EPI_ISL_515104
EPI_ISL_515105
EPI_ISL_515106
EPI_ISL_515107
EPI_ISL_515108
EPI_ISL_515109
EPI_ISL_515110
EPI_ISL_515111
EPI_ISL_515112
EPI_ISL_515181
EPI_ISL_515182
EPI_ISL_515183
EPI_ISL_515184
EPI_ISL_515247
EPI_ISL_515248
EPI_ISL_515249The sequence is not available
Ghana/1513_S1/2020 EPI_ISL_422382Greater Accra2020-03-24
Ghana/1622_S2/2020 EPI_ISL_422384Greater Accra2020-03-24
Ghana/1651_S3/2020 EPI_ISL_422387Greater Accra2020-03-25
Ghana/2230_S4/2020 EPI_ISL_422390Greater Accra2020-03-25
Ghana/2333_S5/2020 EPI_ISL_422394Greater Accra2020-03-27
Ghana/2828_S6/2020 EPI_ISL_422397Greater Accra2020-03-29
Ghana/2853_S7/2020 EPI_ISL_422398Greater Accra2020-03-29
Ghana/2914_S8/2020 EPI_ISL_422399Greater Accra2020-03-30
Ghana/2944_S9/2020 EPI_ISL_422400Greater Accra2020-03-30
Ghana/2986_S10/2020 EPI_ISL_422401Greater Accra2020-03-31
Ghana/3176_S11/2020 EPI_ISL_422402Greater Accra2020-03-30
Ghana/3177_S12/2020 EPI_ISL_422403Greater Accra2020-03-30
Ghana/1565_S13/2020 EPI_ISL_422404Greater Accra2020-03-24
Ghana/1659_S14/2020 EPI_ISL_422405Greater Accra2020-03-25
Ghana/2850_S15/2020 EPI_ISL_422406Greater Accra2020-03-29

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