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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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Nigeria

Number of isolates sequences available: 87

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_450507The sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_462992
EPI_ISL_527883Akwa-Ibom
EPI_ISL_527881Delta
EPI_ISL_527872Ebonyi
EPI_ISL_527873Edo
EPI_ISL_527875Edo
EPI_ISL_527878Edo
EPI_ISL_527879Edo
EPI_ISL_527880Edo
EPI_ISL_527882Edo
EPI_ISL_527884Edo
EPI_ISL_527885Edo
EPI_ISL_527886Edo
EPI_ISL_527887Ekiti
EPI_ISL_487096Ekiti State
EPI_ISL_487097Ekiti State
EPI_ISL_487098Ekiti State
EPI_ISL_487102Ekiti State
EPI_ISL_487105Ekiti State
EPI_ISL_487108Ekiti State
EPI_ISL_527876Enugu
EPI_ISL_527877Enugu
EPI_ISL_455362Kwara State
EPI_ISL_487092Kwara State
EPI_ISL_487095Kwara State
EPI_ISL_487103Kwara State
EPI_ISL_487107Kwara State
Nigeria/Lagos01/2020 EPI_ISL_413550Lagos2020-02-27
EPI_ISL_455412Ogun State
EPI_ISL_527888Ondo
EPI_ISL_527889Ondo
EPI_ISL_527890Ondo
EPI_ISL_527891Ondo
EPI_ISL_527892Ondo
EPI_ISL_487087Ondo State
EPI_ISL_487089Ondo State
EPI_ISL_487100Ondo State
EPI_ISL_487106Ondo State
EPI_ISL_487111Ondo State
EPI_ISL_487112Ondo State
EPI_ISL_527893Osun
EPI_ISL_527894Osun
EPI_ISL_527895Osun
EPI_ISL_527896Osun
EPI_ISL_455413Osun State
EPI_ISL_455414Osun State
EPI_ISL_455415Osun State
EPI_ISL_455418Osun State
EPI_ISL_455419Osun State
EPI_ISL_455422Osun State
EPI_ISL_455423Osun State
EPI_ISL_455424Osun State
EPI_ISL_455425Osun State
EPI_ISL_455426Osun State
EPI_ISL_455427Osun State
EPI_ISL_487109Osun State
EPI_ISL_487110Osun State
EPI_ISL_487113Osun State
EPI_ISL_527897Oyo
EPI_ISL_527898Oyo
EPI_ISL_527899Oyo
EPI_ISL_527900Oyo
EPI_ISL_527901Oyo
EPI_ISL_527902Oyo
EPI_ISL_527903Oyo
EPI_ISL_527904Oyo
EPI_ISL_527905Oyo
EPI_ISL_527906Oyo
EPI_ISL_527907Oyo
EPI_ISL_527908Oyo
EPI_ISL_527909Oyo
EPI_ISL_527910Oyo
EPI_ISL_527911Oyo
EPI_ISL_527912Oyo
EPI_ISL_527913Oyo
EPI_ISL_527914Oyo
EPI_ISL_527915Oyo
EPI_ISL_455429Oyo State
EPI_ISL_455430Oyo State
EPI_ISL_455431Oyo State
EPI_ISL_487090Oyo State
EPI_ISL_487091Oyo State
EPI_ISL_487099Oyo State
EPI_ISL_487101Oyo State
EPI_ISL_487104Oyo State
EPI_ISL_527874Rivers

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