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


Update: Sun Jan 31 07:00:30 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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Nigeria

Number of isolates sequences available: 260

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_654794
EPI_ISL_729921Abuja
EPI_ISL_729924Abuja
EPI_ISL_729927Abuja
EPI_ISL_729930Abuja
EPI_ISL_729931Abuja
EPI_ISL_729932Abuja
EPI_ISL_729933Abuja
EPI_ISL_729934Abuja
EPI_ISL_729935Abuja
EPI_ISL_730018Abuja
EPI_ISL_730019Abuja
EPI_ISL_730020Abuja
EPI_ISL_730021Abuja
EPI_ISL_730022Abuja
EPI_ISL_730024Abuja
EPI_ISL_730025Abuja
EPI_ISL_730026Abuja
EPI_ISL_730027Abuja
EPI_ISL_872601Abuja
EPI_ISL_872602Abuja
EPI_ISL_872603Abuja
EPI_ISL_872604Abuja
EPI_ISL_872606Abuja
EPI_ISL_872607Abuja
EPI_ISL_872608Abuja
EPI_ISL_872609Abuja
EPI_ISL_872610Abuja
EPI_ISL_872611Abuja
EPI_ISL_872612Abuja
EPI_ISL_872613Abuja
EPI_ISL_872614Abuja
EPI_ISL_872615Abuja
EPI_ISL_872616Abuja
EPI_ISL_872617Abuja
EPI_ISL_872618Abuja
EPI_ISL_872619Abuja
EPI_ISL_872620Abuja
EPI_ISL_872621Abuja
EPI_ISL_872622Abuja
EPI_ISL_872623Abuja
EPI_ISL_872624Abuja
EPI_ISL_872625Abuja
EPI_ISL_872626Abuja
EPI_ISL_872627Abuja
EPI_ISL_527883Akwa-Ibom
EPI_ISL_729951Akwa-Ibom State
EPI_ISL_729952Akwa-Ibom State
EPI_ISL_729953Akwa-Ibom State
EPI_ISL_729954Akwa-Ibom State
EPI_ISL_729955Akwa-Ibom State
EPI_ISL_729956Akwa-Ibom State
EPI_ISL_729957Akwa-Ibom State
EPI_ISL_729958Akwa-Ibom State
EPI_ISL_729986Akwa-Ibom State
EPI_ISL_729987Akwa-Ibom State
EPI_ISL_729988Akwa-Ibom State
EPI_ISL_729989Akwa-Ibom State
EPI_ISL_729990Akwa-Ibom State
EPI_ISL_729991Akwa-Ibom State
EPI_ISL_729992Akwa-Ibom State
EPI_ISL_729993Akwa-Ibom State
EPI_ISL_729994Akwa-Ibom State
EPI_ISL_729928Benue State
EPI_ISL_730017Benue State
EPI_ISL_729959Borno State
EPI_ISL_729960Borno State
EPI_ISL_729961Borno State
EPI_ISL_729962Borno State
EPI_ISL_729963Borno State
EPI_ISL_729964Borno State
EPI_ISL_729995Borno State
EPI_ISL_729996Borno State
EPI_ISL_729997Borno State
EPI_ISL_729998Borno State
EPI_ISL_729999Borno State
EPI_ISL_730000Borno State
EPI_ISL_730001Borno State
EPI_ISL_730002Borno State
EPI_ISL_730003Borno State
EPI_ISL_730004Borno State
EPI_ISL_730005Borno State
EPI_ISL_730006Borno State
EPI_ISL_730007Borno State
EPI_ISL_730008Borno State
EPI_ISL_730009Borno State
EPI_ISL_730010Borno State
EPI_ISL_730011Borno State
EPI_ISL_730012Borno State
EPI_ISL_730013Borno State
EPI_ISL_730014Borno State
EPI_ISL_730015Borno State
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_737200FCT
EPI_ISL_737201FCT
EPI_ISL_737205FCT
EPI_ISL_737206FCT
EPI_ISL_737207FCT
EPI_ISL_766049Federal Capital Territory
EPI_ISL_766051Federal Capital Territory
EPI_ISL_825385Federal Capital Territory
EPI_ISL_825437Federal Capital Territory
EPI_ISL_825617Federal Capital Territory
EPI_ISL_825632Federal Capital Territory
EPI_ISL_825633Federal Capital TerritoryThe sequence is not available
EPI_ISL_825713Federal Capital Territory
EPI_ISL_825714Federal Capital Territory
EPI_ISL_825807Federal Capital Territory
EPI_ISL_729920Kaduna State
EPI_ISL_729937Kano State
EPI_ISL_729936Katsina State
EPI_ISL_730023Katsina State
EPI_ISL_729942Kogi State
EPI_ISL_455362Kwara State
EPI_ISL_487092Kwara State
EPI_ISL_487095Kwara State
EPI_ISL_487103Kwara State
EPI_ISL_487107Kwara State
EPI_ISL_730044Kwara State
EPI_ISL_730045Kwara StateThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_730046Kwara State
EPI_ISL_730047Kwara State
EPI_ISL_730048Kwara State
Nigeria/Lagos01/2020 EPI_ISL_413550Lagos2020-02-27
EPI_ISL_729938Lagos State
EPI_ISL_729939Lagos State
EPI_ISL_729940Lagos State
EPI_ISL_729941Lagos State
EPI_ISL_729943Lagos State
EPI_ISL_729945Lagos State
EPI_ISL_729946Lagos State
EPI_ISL_729947Lagos State
EPI_ISL_729948Lagos State
EPI_ISL_729949Lagos State
EPI_ISL_729950Lagos State
EPI_ISL_730028Lagos State
EPI_ISL_730029Lagos State
EPI_ISL_730030Lagos State
EPI_ISL_730031Lagos State
EPI_ISL_730032Lagos State
EPI_ISL_730033Lagos State
EPI_ISL_730034Lagos State
EPI_ISL_730035Lagos State
EPI_ISL_730036Lagos State
EPI_ISL_730037Lagos State
EPI_ISL_730038Lagos State
EPI_ISL_730039Lagos State
EPI_ISL_730041Lagos State
EPI_ISL_730042Lagos State
EPI_ISL_730043Lagos State
EPI_ISL_872600Lagos State
EPI_ISL_729925Nasarawa State
EPI_ISL_729926Nasarawa State
EPI_ISL_730016Nasarawa State
EPI_ISL_729922Niger State
EPI_ISL_729923Niger State
EPI_ISL_729929Niger State
EPI_ISL_455412Ogun State
EPI_ISL_729944Ogun State
EPI_ISL_730040Ogun 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_729966Osun State
EPI_ISL_729967Osun State
EPI_ISL_729968Osun State
EPI_ISL_729969Osun State
EPI_ISL_729970Osun State
EPI_ISL_729971Osun State
EPI_ISL_729972Osun State
EPI_ISL_729973Osun State
EPI_ISL_729974Osun State
EPI_ISL_729975Osun State
EPI_ISL_729976Osun State
EPI_ISL_729977Osun State
EPI_ISL_729978Osun State
EPI_ISL_729979Osun State
EPI_ISL_729980Osun State
EPI_ISL_729981Osun State
EPI_ISL_729982Osun State
EPI_ISL_729983Osun State
EPI_ISL_729984Osun State
EPI_ISL_729985Osun 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_729965Oyo State
EPI_ISL_527874Rivers
EPI_ISL_872605Zamfara State

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