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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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Bahrain

Number of isolates sequences available: 150

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_483542
EPI_ISL_483543
EPI_ISL_483544
EPI_ISL_483545
EPI_ISL_483546
EPI_ISL_483547
EPI_ISL_483548
EPI_ISL_483549
EPI_ISL_483550
EPI_ISL_483551
EPI_ISL_483552
EPI_ISL_483553
EPI_ISL_483554
EPI_ISL_483555
EPI_ISL_483556
EPI_ISL_483557
EPI_ISL_483558
EPI_ISL_483559
EPI_ISL_483560
EPI_ISL_483561
EPI_ISL_483562
EPI_ISL_483563
EPI_ISL_483564
EPI_ISL_483565
EPI_ISL_483638
EPI_ISL_483639
EPI_ISL_483640
EPI_ISL_486887
EPI_ISL_486888
EPI_ISL_486889
EPI_ISL_487270
EPI_ISL_487272
EPI_ISL_487273
EPI_ISL_487274
EPI_ISL_632250
EPI_ISL_632251
EPI_ISL_632252
EPI_ISL_632253
EPI_ISL_632254
EPI_ISL_632255
EPI_ISL_632256
EPI_ISL_632257
EPI_ISL_632258
EPI_ISL_632259
EPI_ISL_632260
EPI_ISL_632261
EPI_ISL_632262
EPI_ISL_632263
EPI_ISL_632264
EPI_ISL_632265
EPI_ISL_632266
EPI_ISL_632267
EPI_ISL_632268
EPI_ISL_632269
EPI_ISL_632270
EPI_ISL_632271
EPI_ISL_632272
EPI_ISL_632273
EPI_ISL_632274
EPI_ISL_632275
EPI_ISL_632276
EPI_ISL_632277
EPI_ISL_632278
EPI_ISL_632279
EPI_ISL_632280
EPI_ISL_632281
EPI_ISL_632282
EPI_ISL_632283
EPI_ISL_632284
EPI_ISL_632285
EPI_ISL_632899
EPI_ISL_632900
EPI_ISL_632901
EPI_ISL_632902
EPI_ISL_632903
EPI_ISL_632904
EPI_ISL_632905
EPI_ISL_632906
EPI_ISL_632907
EPI_ISL_636973
EPI_ISL_678261
EPI_ISL_678262
EPI_ISL_678263
EPI_ISL_678264
EPI_ISL_678265
EPI_ISL_678266
EPI_ISL_678267
EPI_ISL_678268
EPI_ISL_678269
EPI_ISL_678270
EPI_ISL_678271
EPI_ISL_678272
EPI_ISL_681298
EPI_ISL_681299
EPI_ISL_681300
EPI_ISL_681301
EPI_ISL_681302
EPI_ISL_681303
EPI_ISL_681304
EPI_ISL_681305
EPI_ISL_681306
EPI_ISL_681307
EPI_ISL_681308
EPI_ISL_681309
EPI_ISL_681310
EPI_ISL_681311
EPI_ISL_681312
EPI_ISL_681313
EPI_ISL_681314
EPI_ISL_681315
EPI_ISL_681316
EPI_ISL_681317
EPI_ISL_681318
EPI_ISL_681319
EPI_ISL_682299
EPI_ISL_682300
EPI_ISL_682301
EPI_ISL_682302
EPI_ISL_682303
EPI_ISL_682304
EPI_ISL_682305
EPI_ISL_682306
EPI_ISL_682307
EPI_ISL_682308
EPI_ISL_682309
EPI_ISL_682310
EPI_ISL_682311
EPI_ISL_682312
EPI_ISL_682313
EPI_ISL_682314
EPI_ISL_682315
EPI_ISL_682316
EPI_ISL_682317
EPI_ISL_682318
EPI_ISL_682319
EPI_ISL_682320
EPI_ISL_682321
EPI_ISL_682322
EPI_ISL_684028
EPI_ISL_684029
EPI_ISL_684030
EPI_ISL_684031
EPI_ISL_684032
EPI_ISL_684033
EPI_ISL_684034
EPI_ISL_684035
EPI_ISL_684036
EPI_ISL_485401Manama
EPI_ISL_510528Manama
EPI_ISL_510531Manama

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