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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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Mexico

Number of isolates sequences available: 381

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_576258Aguascalientes
EPI_ISL_576261Aguascalientes
EPI_ISL_658863Aguascalientes
EPI_ISL_658865Aguascalientes
EPI_ISL_658868Aguascalientes
EPI_ISL_658870Aguascalientes
EPI_ISL_658873Aguascalientes
EPI_ISL_658875Aguascalientes
EPI_ISL_658880Aguascalientes
EPI_ISL_658883Aguascalientes
EPI_ISL_658891Aguascalientes
EPI_ISL_493347Baja California
EPI_ISL_496339Baja California
EPI_ISL_496340Baja California
EPI_ISL_496341Baja California
EPI_ISL_496342Baja California
EPI_ISL_496343Baja California
EPI_ISL_496344Baja California
EPI_ISL_496345Baja California
EPI_ISL_496346Baja California
EPI_ISL_496347Baja California
EPI_ISL_496348Baja California
EPI_ISL_496349Baja California
EPI_ISL_496350Baja California
EPI_ISL_496351Baja California
EPI_ISL_496352Baja California
EPI_ISL_496353Baja California
EPI_ISL_496354Baja California
EPI_ISL_496355Baja California
EPI_ISL_496356Baja California
EPI_ISL_496357Baja California
EPI_ISL_496358Baja California
EPI_ISL_496359Baja California
EPI_ISL_496360Baja California
EPI_ISL_496361Baja California
EPI_ISL_496362Baja California
EPI_ISL_496363Baja California
EPI_ISL_496364Baja California
EPI_ISL_496365Baja California
EPI_ISL_496366Baja California
EPI_ISL_496367Baja California
EPI_ISL_496368Baja California
EPI_ISL_496369Baja California
EPI_ISL_496370Baja California
EPI_ISL_496371Baja California
EPI_ISL_496372Baja California
EPI_ISL_496373Baja California
EPI_ISL_496374Baja California
EPI_ISL_496375Baja California
EPI_ISL_496376Baja California
EPI_ISL_516608Baja California
EPI_ISL_516609Baja California
EPI_ISL_516610Baja California
EPI_ISL_516611Baja California
EPI_ISL_516612Baja California
EPI_ISL_635479Baja California
EPI_ISL_635480Baja California
EPI_ISL_635481Baja California
EPI_ISL_635482Baja California
EPI_ISL_635483Baja California
EPI_ISL_635484Baja California
EPI_ISL_635485Baja California
EPI_ISL_635486Baja California
EPI_ISL_635487Baja California
EPI_ISL_635488Baja California
EPI_ISL_635489Baja California
EPI_ISL_635490Baja California
EPI_ISL_635491Baja California
EPI_ISL_635492Baja California
EPI_ISL_635493Baja California
EPI_ISL_635494Baja California
EPI_ISL_635495Baja California
EPI_ISL_635496Baja California
EPI_ISL_635497Baja California
EPI_ISL_635498Baja California
EPI_ISL_635499Baja California
EPI_ISL_635500Baja California
EPI_ISL_635501Baja California
EPI_ISL_635502Baja California
EPI_ISL_635503Baja California
EPI_ISL_635504Baja California
EPI_ISL_635505Baja California
EPI_ISL_635506Baja California
EPI_ISL_635507Baja California
EPI_ISL_635508Baja California
EPI_ISL_635509Baja California
EPI_ISL_635510Baja California
EPI_ISL_635511Baja California
EPI_ISL_635512Baja California
EPI_ISL_635513Baja California
EPI_ISL_635514Baja California
EPI_ISL_635515Baja California
EPI_ISL_635516Baja California
EPI_ISL_635517Baja California
EPI_ISL_635518Baja California
EPI_ISL_635519Baja California
EPI_ISL_635520Baja California
EPI_ISL_635521Baja California
EPI_ISL_635522Baja California
EPI_ISL_635523Baja California
EPI_ISL_635524Baja California
EPI_ISL_635525Baja California
EPI_ISL_635526Baja California
EPI_ISL_635527Baja California
EPI_ISL_635528Baja California
EPI_ISL_635529Baja California
EPI_ISL_635530Baja California
EPI_ISL_635531Baja California
EPI_ISL_635532Baja California
EPI_ISL_635533Baja California
EPI_ISL_635534Baja California
EPI_ISL_635535Baja California
EPI_ISL_635536Baja California
EPI_ISL_635537Baja California
EPI_ISL_635538Baja California
EPI_ISL_635539Baja California
EPI_ISL_635540Baja California
EPI_ISL_635541Baja California
EPI_ISL_635542Baja California
EPI_ISL_635543Baja California
EPI_ISL_635544Baja California
EPI_ISL_635545Baja California
EPI_ISL_635546Baja California
EPI_ISL_635547Baja California
EPI_ISL_635548Baja California
EPI_ISL_635549Baja California
EPI_ISL_635550Baja California
EPI_ISL_635551Baja California
EPI_ISL_635552Baja California
EPI_ISL_635553Baja California
EPI_ISL_635554Baja California
EPI_ISL_635555Baja California
EPI_ISL_635556Baja California
EPI_ISL_635557Baja California
EPI_ISL_635558Baja California
EPI_ISL_635559Baja California
EPI_ISL_635560Baja California
EPI_ISL_635561Baja California
EPI_ISL_635562Baja California
EPI_ISL_635563Baja California
EPI_ISL_635564Baja California
EPI_ISL_635565Baja California
EPI_ISL_635566Baja California
EPI_ISL_635567Baja California
EPI_ISL_635568Baja California
EPI_ISL_635569Baja California
EPI_ISL_635570Baja California
EPI_ISL_635571Baja California
EPI_ISL_635572Baja California
EPI_ISL_635573Baja California
EPI_ISL_635574Baja California
EPI_ISL_635575Baja California
EPI_ISL_635576Baja California
EPI_ISL_636113Baja California
EPI_ISL_636114Baja California
EPI_ISL_636115Baja California
EPI_ISL_636117Baja California
EPI_ISL_636118Baja California
EPI_ISL_636119Baja California
EPI_ISL_730127Baja California
EPI_ISL_730128Baja California
EPI_ISL_730129Baja California
EPI_ISL_730130Baja California
EPI_ISL_730131Baja California
EPI_ISL_730132Baja California
EPI_ISL_730133Baja California
EPI_ISL_730134Baja California
EPI_ISL_730135Baja California
EPI_ISL_730136Baja California
EPI_ISL_730197Baja California
EPI_ISL_730198Baja California
EPI_ISL_730199Baja California
EPI_ISL_730200Baja California
EPI_ISL_730201Baja California
EPI_ISL_730202Baja California
EPI_ISL_730203Baja California
EPI_ISL_730204Baja California
EPI_ISL_730205Baja California
EPI_ISL_730206Baja California
EPI_ISL_730207Baja California
EPI_ISL_730208Baja California
EPI_ISL_730209Baja California
EPI_ISL_730210Baja California
EPI_ISL_730211Baja California
EPI_ISL_730212Baja California
EPI_ISL_730213Baja California
EPI_ISL_730214Baja California
EPI_ISL_730215Baja California
EPI_ISL_730216Baja California
EPI_ISL_730217Baja California
EPI_ISL_730218Baja California
EPI_ISL_730219Baja California
EPI_ISL_730220Baja California
EPI_ISL_730221Baja California
EPI_ISL_730222Baja California
EPI_ISL_730223Baja California
EPI_ISL_730224Baja California
EPI_ISL_730225Baja California
EPI_ISL_730226Baja California
EPI_ISL_730227Baja California
EPI_ISL_730228Baja California
EPI_ISL_485587Baja California SurThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_493340Baja California Sur
EPI_ISL_493345Baja California Sur
EPI_ISL_493346Baja California Sur
EPI_ISL_576265Campeche
EPI_ISL_576266Campeche
EPI_ISL_576267Campeche
Mexico/Chiapas-InDRE_02/2020 EPI_ISL_424666Chiapas2020-02-29
EPI_ISL_493338Chiapas
Mexico/Chihuahua-IMSS_01/2020 EPI_ISL_424731Chihuahua2020-03-13
EPI_ISL_516613Chihuahua
EPI_ISL_516614Chihuahua
EPI_ISL_516615Chihuahua
EPI_ISL_516616Chihuahua
EPI_ISL_516617Chihuahua
EPI_ISL_516618Coahuila
EPI_ISL_516619Coahuila
EPI_ISL_516620Coahuila
EPI_ISL_516621Coahuila de Zaragoza
EPI_ISL_576278Colima
EPI_ISL_576279Colima
EPI_ISL_455432Durango
EPI_ISL_493334Guanajuato
EPI_ISL_493335Guanajuato
EPI_ISL_455434Guerrero
EPI_ISL_493339Guerrero
EPI_ISL_658896Guerrero
EPI_ISL_658899Guerrero
EPI_ISL_658901Guerrero
EPI_ISL_485591HidalgoThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_485592HidalgoThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_576257Hidalgo
EPI_ISL_576268Hidalgo
EPI_ISL_455435Jalisco
EPI_ISL_455454Jalisco
Mexico/CDMX-InDRE_01/2020 EPI_ISL_412972Mexico City2020-02-27
Mexico/CDMX-INER_01/2020 EPI_ISL_424345Mexico City2020-03-12
Mexico/CDMX-INER_02/2020 EPI_ISL_424348Mexico City2020-03-13
Mexico/CDMX-INER_03/2020 EPI_ISL_424625Mexico City2020-03-13
Mexico/CDMX-INER_04/2020 EPI_ISL_424626Mexico City2020-03-15
Mexico/CDMX-INER_05/2020 EPI_ISL_424627Mexico City2020-03-16
Mexico/CDMX-InDRE_06/2020 EPI_ISL_424673Mexico City2020-03-12
Mexico/CDMX-INCMNSZ_01/2020 EPI_ISL_426361Mexico City2020-03-12
Mexico/CDMX-INCMNSZ_02/2020 EPI_ISL_426362Mexico City2020-03-10
Mexico/CDMX-INCMNSZ_03/2020 EPI_ISL_426363Mexico City2020-03-12
Mexico/CDMX-INCMNSZ_04/2020 EPI_ISL_426364Mexico City2020-03-12
Mexico/CDMX-INCMNSZ_05/2020 EPI_ISL_426365Mexico City2020-03-12
EPI_ISL_455436Mexico City
EPI_ISL_455437Mexico City
EPI_ISL_455439Mexico City
EPI_ISL_485578Mexico CityThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_485584Mexico CityThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_485585Mexico CityThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_485597Mexico CityThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_485600Mexico CityThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_485601Mexico CityThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_485602Mexico CityThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_522872Mexico City
EPI_ISL_522873Mexico City
EPI_ISL_522874Mexico City
EPI_ISL_522875Mexico City
EPI_ISL_522876Mexico City
EPI_ISL_522877Mexico City
EPI_ISL_522878Mexico City
EPI_ISL_522879Mexico City
EPI_ISL_522880Mexico City
EPI_ISL_522940Mexico City
EPI_ISL_522941Mexico City
EPI_ISL_522942Mexico City
EPI_ISL_522978Mexico City
EPI_ISL_522979Mexico City
EPI_ISL_522980Mexico City
EPI_ISL_522981Mexico City
EPI_ISL_522982Mexico City
EPI_ISL_522983Mexico City
EPI_ISL_522984Mexico City
EPI_ISL_522985Mexico City
EPI_ISL_522986Mexico City
EPI_ISL_523500Mexico City
EPI_ISL_485583MichoacanThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_576271Michoacan
EPI_ISL_576276Michoacan
EPI_ISL_576277Michoacan
EPI_ISL_485576MorelosThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_485577MorelosThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_493341Morelos
EPI_ISL_493342Nayarit
EPI_ISL_493343Nayarit
EPI_ISL_576262Nuevo Leon
EPI_ISL_576263Nuevo Leon
EPI_ISL_648380Nuevo Leon
EPI_ISL_648595Nuevo Leon
EPI_ISL_648597Nuevo Leon
EPI_ISL_648598Nuevo Leon
EPI_ISL_648600Nuevo Leon
EPI_ISL_648602Nuevo Leon
EPI_ISL_648603Nuevo Leon
EPI_ISL_648606Nuevo Leon
EPI_ISL_648607Nuevo Leon
EPI_ISL_648608Nuevo Leon
EPI_ISL_648609Nuevo Leon
EPI_ISL_779169Nuevo Leon
EPI_ISL_779170Nuevo Leon
EPI_ISL_779171Nuevo Leon
EPI_ISL_779172Nuevo Leon
EPI_ISL_779173Nuevo Leon
EPI_ISL_779174Nuevo Leon
EPI_ISL_779175Nuevo Leon
EPI_ISL_779176Nuevo Leon
EPI_ISL_779177Nuevo Leon
EPI_ISL_779178Nuevo Leon
EPI_ISL_779179Nuevo Leon
EPI_ISL_779180Nuevo Leon
EPI_ISL_779181Nuevo Leon
EPI_ISL_779182Nuevo Leon
EPI_ISL_779183Nuevo Leon
EPI_ISL_779184Nuevo Leon
EPI_ISL_779185Nuevo Leon
EPI_ISL_779186Nuevo Leon
EPI_ISL_779187Nuevo Leon
EPI_ISL_779188Nuevo Leon
EPI_ISL_779189Nuevo Leon
EPI_ISL_779190Nuevo Leon
EPI_ISL_779191Nuevo Leon
EPI_ISL_779192Nuevo Leon
EPI_ISL_779193Nuevo Leon
EPI_ISL_779194Nuevo Leon
EPI_ISL_779195Nuevo Leon
EPI_ISL_779196Nuevo Leon
EPI_ISL_779197Nuevo Leon
EPI_ISL_779198Nuevo Leon
EPI_ISL_485593OaxacaThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_576264Oaxaca
Mexico/Puebla-InDRE_05/2020 EPI_ISL_424672Puebla2020-03-11
EPI_ISL_455455Puebla
EPI_ISL_485590PueblaThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
Mexico/Queretaro-InDRE_04/2020 EPI_ISL_424670Queretaro2020-03-10
EPI_ISL_455456Queretaro
EPI_ISL_485580QueretaroThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_658878Queretaro
EPI_ISL_658886Queretaro
EPI_ISL_658888Queretaro
EPI_ISL_658893Queretaro
EPI_ISL_455438Quintana Roo
EPI_ISL_658904Quintana Roo
EPI_ISL_576272San Luis Potosi
EPI_ISL_660068San Luis Potosi
EPI_ISL_493336Sinaloa
EPI_ISL_493344Sonora
EPI_ISL_493349Sonora
EPI_ISL_516622Sonora
EPI_ISL_516623Sonora
EPI_ISL_636116Sonora
EPI_ISL_636120Sonora
Mexico/EdoMex-InDRE_03/2020 EPI_ISL_424667State of Mexico2020-03-04
EPI_ISL_452139State of Mexico
EPI_ISL_452141State of Mexico
EPI_ISL_485575State of MexicoThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_485579State of MexicoThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_485581State of MexicoThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_485582State of MexicoThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_485586State of MexicoThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_485588State of MexicoThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_485589State of MexicoThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_485594State of MexicoThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_485595State of MexicoThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_485596State of MexicoThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_485598State of MexicoThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_485599State of MexicoThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_493337Tabasco
EPI_ISL_516624Tamaulipas
EPI_ISL_516625Tamaulipas
EPI_ISL_576259Tlaxcala
EPI_ISL_576260Tlaxcala
EPI_ISL_576269Veracruz
EPI_ISL_576270Veracruz
EPI_ISL_493348Yucatan
EPI_ISL_576273Zacatecas
EPI_ISL_576274Zacatecas
EPI_ISL_576275Zacatecas

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