DOI: 10.5061/dryad.nk98sf7r6
title: RNA sequences for Aedes species, Dengue, and Chikungunya viruses

description: There are arthropod-borne disease outbreaks as a result of pathogen influx
 including arboviruses which are transmitted by strains of Aedes species
 that occur periodically in varying spots on the globe. The aim of this
 study was to determine phylogenetic relationship of Aedes mosquitoes,
 Dengue, and Chikungunya viruses along the Coastline of Kenya based on
 sequences of: mitochondria nicotinamide adenine dehydrogenase sub unit 4
 gene for Aedes species. non-structural protein 5 gene for Dengue
 virus non-structural protein 1 gene for Chikungunya virus
description: <strong>Sample
 collection:</strong> Indoor and outdoor sampling of adults
 <em>Aedes </em>mosquitoes was done using Biogent Sentinel trap
 baited with solid carbon dioxide and Prokopack aspiration
 technique. <strong>RNA
 extraction</strong><strong> and cDNA synthesis
 </strong> Pools of <em>Aedes
 </em>mosquitoes (20 mosquitoes per pool) were homogenized by a
 mortar and pestle and RNA extracted using 1 ml of Trizol® as earlier
 described. Only the unfed and gravid mosquitoes were utilised in this
 analysis. The female blood-fed were excluded to avoid contamination of the
 virus which could be in the blood meal. cDNA synthesis was done on 10 μl
 of the extracted RNA to generate cDNA by using EcoDry Premix (Random
 hexamers) (Clontech laboratories, Inc., Mountain view, CA, USA) in a
 procedure described earlier. <strong>Molecular
 Identification and sequencing of <em>Aedes</em> mosquitoes and
 Viruses  </strong> The mtNAD4 gene was utilised for
 identification of <em>Aedes</em> mosquitoes using primers
 listed (Table 1) as earlier described. Identification of serotypes of
 Dengue virus in the <em>Aedes</em> mosquitoes was based on
 amplification of the target viral genes (E/NS1/NS5) in RNA using multiplex
 PCR with a panel of general flavivirus family primers (Table 2) as earlier
 described. Samples tested positive for flavivirus were further tested with
 consensus primers for Dengue virus. These primers were DEN-F and DEN-CR
 and they target the E/NS1 junction of the virus genome. Only samples
 tested positive with Dengue consensus primers were further tested for the
 four Dengue serotypes using appropriate primers (Table 3) as described.
 Identification of genotypes of Chikungunya virus was based on
 amplification of the target viral gene E1 in the RNA using multiplex PCR
 with AgPath-ID One-step RT-PCR kit (Applied bio systems, Carlsbad,
 Califonia, USA) using a panel of general alphaviruses primers (Table 2).
 Samples tested positive for alphavirus were further tested with
 conventional primers for Chikungunya virus (Table 4). The amplified gene
 products were cleaned from the gel by MinElute PCR purification kit
 (Qiagen, Valencia, CA) and sequenced using Sanger high-throughput
 technique. <strong>Sequence
 analysis:</strong> Generated
 nucleotide sequences were used for phylogenetic analysis. DNAbaser v.3.0
 (http://www.dnabaser.com/articles/SNP) was used for editing bad calls in the raw chromatogram file generated from sequencing the forward and reverse strands. Deletion of the generated sequences of primers was done from the 5’ and 3’ ends. The sequences were subjected to Basic Local Alignment Tool (BLASTn) and GenBank database to compare them with available sequences and confirm the identity of the isolates. Formatting of the retrieved sequences compatible with alignment programs and identification of correct reading frame for each sequence was done using the translation program at http://us.expasy.org/tools/dna.html. The sequences were aligned for identification and removal of duplicate sequences using Clustal Omega v1.2.1, scored in T-coffee (http://tcoffee.crg.cat/) and viewed in jalview http://www.jalview.org/ (Sievers and Higgins, 2014). The sequences were manually adjusted in Se-Al software according to DNA sequence alignments for preservation of codon homology. Columns with more than one percent of gaps were removed from the alignment using trimAl v1.4.rev6. Using pmodeltest v1.4, Maximum likelihood trees were inferred using Randomised Accelerated Maximum Likelihood (RAxML) version 8.1.20 ran with model GTR+GAMMA+I for selecting the best-ﬁt model for the maximum likelihood analyses and plotting of phylogenetic trees using interactive tree of life (https://itol.embl.de/). Table 1: Primers used in identification of <em>Aedes</em> mosquitoes <strong>Target</strong> <strong>Primer name</strong> <strong>Nucleotide sequences (5’ to 3’)</strong> <strong>Polarity </strong> <strong>Product (bp)</strong> Mosquito RNA marker (UP) Act-2F ATGGTCGGYATGGGNCAGAAGGACTC Forward 683   Act-8R GATTCCATACCCAGGAAGGADGG Reverse   <em>Ae. aegypti</em> s.l 18SFHIN     CP16 GTAAGCTTCCTTTGTACACACCGCCCGT GCGGGTACCATGCTTAAATTTAGGGGT Forward 550   Aeg.r1 TAACGGACACCGTTCTAGGCCCT Reverse   <em>Ae. tricholabis</em> UV TGTGAACTGCAGGACACAT Forward   <em>Ae. pembaensis</em> PEM GCATCGATGGGTTAATCATG Reverse 405 <em>Ae. ocharaceous</em> OCH CAAGCCGTTCGACCCTGATT Reverse 501 <em>Ae. albicosta</em> ALB CCTGGCCAGTGGCCAAAT Reverse   <em>Ae. fulgens</em> FUL GTGCACACCACTGAATT Reverse   <em>Ae. mcntoshi</em> MCN CTGATGCACTGGCCTCAAAG Reverse   <em>Ae. fryeri</em> FRR TCAACCGCCGTGCGTG Reverse   <em>ND4 </em> ND4sb+ TGATTGCCTAAGGCTCATGT Forward 344   ND4sb- TTCGGCTTCCTAGTCGTTCAT Reverse     Table 2: Primers and probes for identification of flaviviruses and alpha viruses   Primers and Probes Sequence Tm <sup>o</sup> Flavivirus     Flavi allS (Forward Primer) 5’-TACAACATgATggggAARAgAgARAA-3’ 53.8 Flavi all AS2 (Reverse Primer) 5’-gTgTCCCAgCCNgCKgTgTCATCWgC-3’   Flavi all AS4 (Reserve Primer) 5’-gTgTCCCAGCCNgCKgTRTCRTC-3’ 80.4 3P<sub>i </sub>(Probe) FAM-Tg+gTWYATgT+ggYTNg+gRgC-NFQ-MGB 50.3 3P<sub>ii </sub>(Probe) FAM-CCgTgCCATATggTATATgTggCTgggAgC-NFQ-MGB   3P<sub>iii</sub> (Probe) FAM-TTTCTggAATTTgAAgCCCTgggTTT-NFQ-MGB   Pan-alphavirus     F2A (Forward Primer) 5’- ATGATGAARTCIGGIATGTTYYT-3’   R2A (Reverse Primer) 5’-ATYTTIACTTCCATGTTCATCCA-3’   R3A (Reverse Primer) 5’-ATYTTIACTTCCATRTTCARCCA-3’   R4A (Reverse Primer) 5’-ATYTTIACTTCCATGTTGACCCA-3’   ATTO425 (Probe) - AT+GTT+GTC+GT+CIC+CIAT-BHQ1/LNA                                                       Table 3: Primers for identification of serotypes of Dengue virus <strong>Primer</strong> <strong>Gene/ protein target</strong> <strong>Primer sequence (5’ to 3’)</strong> <strong>Position </strong> FU1 NSP5 TACAACATGATGGGAAAGAGAGAGAA 9007-9032 CFD3 NSP5 GTGTCCCAGCCGGCGGTGTCATCAGC 9308-9283 DEN-F E/NS1 TCAATATGCTGAAACGCGCGAGAAACCG 38-65 DEN-CR E/ NS1 TTGCACCAACAGTCAATGTCTTCAGGTTC 455-483 TS1-R NSP5 CGTCTCAGTGATCCGGGGG (DEN-F and TS1)   TS2-R NSP5 CGCCACAAGGGCCATGAACAG (DEN-F and TS2)   TS3-R NSP5 TAACATCATCATGAGACAGAGC(DEN-F and TS3)   TS4-R NSP5 CTCTGTTGTCTTAAACAAGAGA(DEN-F and TS4)   D5-F NSP5 TCAATATGCTGAAACGCGHGAG 132-153 D5-R NSP5 GCGCCTTCNGNNGACATCCA 764-783     Table 4: Primers for identification of Chikungunya virus <strong>Primer</strong> <strong>Gene/ protein target</strong> <strong>Primer sequence (5’ to 3’)</strong> <strong>Position </strong> VIR 2052 F NSP4 TGGCGCTATGATGAAATCTGGAATGTT 6971-6997 VIR 2052R NSP4 TACGATGTTGTCGTCGCCGATGAA 7086–7109 CHIKV-F E1 CGTGGTGTACAAAGGTGACG 10524 CHIKV-R CHIKWa CHIKAs CHIKECSa E1 NSP1 NSP1 NSP1 ACG CCG GGTAGTTGACTATG GGCAAACGCAGTGGTACTTCCT GGCAGACGCAGTGGTACTTCCT TGATCCCGACTCAACCATCCT 11170 295-316 295-316 234-254