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Status of SARS-CoV-2 detection systems (RT-PCR)
enabled by data from GISAID logo


Update: Sun Jan 10 05:32:46 2021 (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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Uganda

Number of isolates sequences available: 133

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_451183
EPI_ISL_451184
EPI_ISL_451185
EPI_ISL_451186
EPI_ISL_451187
EPI_ISL_451188
EPI_ISL_451189
EPI_ISL_451190
EPI_ISL_451191
EPI_ISL_451192
EPI_ISL_451193
EPI_ISL_451194
EPI_ISL_451195
EPI_ISL_451196
EPI_ISL_451197
EPI_ISL_451198
EPI_ISL_451199
EPI_ISL_451200
EPI_ISL_451201
EPI_ISL_451202
EPI_ISL_737931
EPI_ISL_737932
EPI_ISL_737933
EPI_ISL_737934
EPI_ISL_737935
EPI_ISL_737936
EPI_ISL_737937
EPI_ISL_737938
EPI_ISL_737939
EPI_ISL_737940
EPI_ISL_737941
EPI_ISL_737942
EPI_ISL_737943
EPI_ISL_737944
EPI_ISL_737945
EPI_ISL_737946
EPI_ISL_737947
EPI_ISL_737948
EPI_ISL_737949
EPI_ISL_737950
EPI_ISL_737951
EPI_ISL_737952
EPI_ISL_737953
EPI_ISL_737954
EPI_ISL_737955
EPI_ISL_737956
EPI_ISL_737957
EPI_ISL_737958
EPI_ISL_737959
EPI_ISL_737960
EPI_ISL_737961
EPI_ISL_737962
EPI_ISL_737963
EPI_ISL_737964
EPI_ISL_737965
EPI_ISL_737966
EPI_ISL_737967
EPI_ISL_737968
EPI_ISL_737969
EPI_ISL_737970
EPI_ISL_737971
EPI_ISL_737972
EPI_ISL_737973
EPI_ISL_737974
EPI_ISL_737975
EPI_ISL_737976
EPI_ISL_737977
EPI_ISL_737978
EPI_ISL_737979
EPI_ISL_737980
EPI_ISL_737981
EPI_ISL_737982
EPI_ISL_737983
EPI_ISL_737984
EPI_ISL_737985
EPI_ISL_737986
EPI_ISL_737987
EPI_ISL_737988
EPI_ISL_737989
EPI_ISL_737990
EPI_ISL_737991
EPI_ISL_737992
EPI_ISL_737993
EPI_ISL_737994
EPI_ISL_737995
EPI_ISL_737996
EPI_ISL_737997
EPI_ISL_737998
EPI_ISL_737999
EPI_ISL_738000
EPI_ISL_738001
EPI_ISL_738002
EPI_ISL_738003
EPI_ISL_738004
EPI_ISL_738005
EPI_ISL_738006
EPI_ISL_738007
EPI_ISL_738008
EPI_ISL_738009
EPI_ISL_738010
EPI_ISL_738011
EPI_ISL_738012
EPI_ISL_738013
EPI_ISL_738014
EPI_ISL_738015
EPI_ISL_738016
EPI_ISL_738017
EPI_ISL_738018
EPI_ISL_738019
EPI_ISL_738020
EPI_ISL_738021
EPI_ISL_738022
EPI_ISL_738023
EPI_ISL_738024
EPI_ISL_738025
EPI_ISL_738026
EPI_ISL_738027
EPI_ISL_738028
EPI_ISL_738029
EPI_ISL_738030
EPI_ISL_738031
EPI_ISL_738032
EPI_ISL_738033
EPI_ISL_738034
EPI_ISL_738035
EPI_ISL_738036
EPI_ISL_738037
EPI_ISL_738038
EPI_ISL_738039
EPI_ISL_738040
EPI_ISL_738041
EPI_ISL_738042
EPI_ISL_738043

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