To discard co-infection of ZIKV with dengue and/or chikungunya viruses, we analyzed the urine, saliva samples and the viral strains isolated from Vero cell using he NAT- Dengue, Zika and Chikungunya discriminatory kit (Instituto de Biologia Molecular do Paraná and Fundação Oswaldo Cruz, Brazil). To measure genomic ZIKV load, viral RNA was reverse transcribed and amplified using the TaqMan Fast Virus 1-Step Master Mix (Applied Biosystems) in an Applied Biosystems StepOnePlus Instrument. For each reaction we used 400 nM forward primer (5’-CTTGGAGTGCTTGTGATT-3’, genome position 3451–3468), 600 nM reverse primer (5’-CTCCTCCAGTGTTCATTT-3’, genome position 3637–3620) and 250 nM probe (5’FAM- AGAAGAGAATGACCACAAAGATCA-3’TAMRA, genome position 3494–3517). The sequences of this primer set were kindly provided by Isabelle Lepark-Goffart (French National Reference Centre for Arboviruses, IRBA, Marseille, France). Samples were run in duplicate. The reverse transcription was performed at 50°C for 5 minutes. The qPCR conditions were 95°C for 20 seconds, followed by 40 amplification cycles of 95°C for 15 seconds and 60°C for 1 minute. Copy numbers of ZIKV genomic RNA were calculated by absolute quantitation using a standard curve for each run. To construct a standard curve, we cloned an amplicon comprising the genomic region 3085–4032 of the isolate Rio-U1 using pGEM-T Easy Vector (Promega) to serve as a template for in vitro transcription. The RNA transcript was made with mMessage mMachine High Yield Capped RNA Transcription Kit (Invitrogen) using T7 enzyme and purified using MEGAclear Kit (Ambion) according to manufacturer’s instructions. The purity of the transcript was verified using NanoDrop 8000 Spectrophotometer (Thermo Scientific), the integrity was analyzed using 2100 Bioanalyzer (Agilent) using the RNA 6000 Nano Kit (Agilent), and the concentration of the RNA was accessed using Qubit 2.0 Fluorometer (Invitrogen). The standard curve was generated by a ten-fold dilution (ranging from 10 to 109 copies/reaction) of the transcript. The limit of detection under standard assay conditions was approximately 40 viral RNA copies/mL.
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