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


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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Latvia

Number of isolates sequences available: 135

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
Latvia/0001/2020 EPI_ISL_4216532020-03-25
Latvia/0002/2020 EPI_ISL_4216542020-03-25
Latvia/0003/2020 EPI_ISL_4216552020-03-25
Latvia/0004/2020 EPI_ISL_4216562020-03-25
Latvia/0005/2020 EPI_ISL_4262852020-03-30
Latvia/0006/2020 EPI_ISL_4262862020-03-30
Latvia/0007/2020 EPI_ISL_4262872020-03-30
Latvia/0008/2020 EPI_ISL_4262882020-03-30
Latvia/0009/2020 EPI_ISL_4262892020-03-30
EPI_ISL_437089
EPI_ISL_437090
EPI_ISL_437091
EPI_ISL_437092
EPI_ISL_437093
EPI_ISL_437094
EPI_ISL_437095
EPI_ISL_437096
EPI_ISL_450518
EPI_ISL_450519
EPI_ISL_450520
EPI_ISL_450521
EPI_ISL_450522
EPI_ISL_450523
EPI_ISL_450524
EPI_ISL_486390
EPI_ISL_486391
EPI_ISL_486411
EPI_ISL_486412
EPI_ISL_486413
EPI_ISL_486414
EPI_ISL_486415
EPI_ISL_486416
EPI_ISL_486418
EPI_ISL_486419
EPI_ISL_486420
EPI_ISL_486421
EPI_ISL_486422
EPI_ISL_486423
EPI_ISL_486424
EPI_ISL_486425
EPI_ISL_486426
EPI_ISL_486428
EPI_ISL_486430
EPI_ISL_486431
EPI_ISL_486432
EPI_ISL_486433
EPI_ISL_486434
EPI_ISL_486435
EPI_ISL_486436
EPI_ISL_486437
EPI_ISL_486438
EPI_ISL_492988
EPI_ISL_492989
EPI_ISL_492990
EPI_ISL_492991
EPI_ISL_492992
EPI_ISL_492993
EPI_ISL_492994
EPI_ISL_492995
EPI_ISL_492996
EPI_ISL_492997
EPI_ISL_492998
EPI_ISL_492999
EPI_ISL_493000
EPI_ISL_498226
EPI_ISL_501275
EPI_ISL_501284
EPI_ISL_501285
EPI_ISL_501286
EPI_ISL_501287
EPI_ISL_501288
EPI_ISL_501289
EPI_ISL_501808
EPI_ISL_501817
EPI_ISL_501823
EPI_ISL_501829
EPI_ISL_501833
EPI_ISL_501839
EPI_ISL_501849
EPI_ISL_501894
EPI_ISL_501895
EPI_ISL_501896
EPI_ISL_501915
EPI_ISL_501922
EPI_ISL_501929
EPI_ISL_501936
EPI_ISL_512313
EPI_ISL_512314
EPI_ISL_512645
EPI_ISL_512646
EPI_ISL_512647
EPI_ISL_512648
EPI_ISL_512649
EPI_ISL_512650
EPI_ISL_512651
EPI_ISL_512652
EPI_ISL_515185
EPI_ISL_515186
EPI_ISL_515187
EPI_ISL_515188
EPI_ISL_515189
EPI_ISL_515190
EPI_ISL_515191
EPI_ISL_515192
EPI_ISL_515193
EPI_ISL_515194
EPI_ISL_515195
EPI_ISL_515196
EPI_ISL_534199
EPI_ISL_534200
EPI_ISL_534201
EPI_ISL_534202
EPI_ISL_534203
EPI_ISL_534204
EPI_ISL_534205
EPI_ISL_534206
EPI_ISL_534207
EPI_ISL_534208
EPI_ISL_534209
EPI_ISL_534210
EPI_ISL_534211
EPI_ISL_534212
EPI_ISL_534213
EPI_ISL_534214
EPI_ISL_534215
EPI_ISL_534216
EPI_ISL_534218
EPI_ISL_534219
EPI_ISL_534220
EPI_ISL_534221
EPI_ISL_534222
EPI_ISL_534223
Latvia/ChVir2025/2020 EPI_ISL_419691Riga2020-03
EPI_ISL_486410Riga
EPI_ISL_486417Riga

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