DeZi-ARTIC Pan-serotype dengue primer scheme
PrimalScheme is the open-source platform for designing and sharing multiplex PCR primer schemes used in amplicon-based viral genome sequencing. It was first used to generate sequencing primers during the Ebola epidemic, and soon after during the Zika PHEIC. The ARTIC2/DeZi pan-dengue v1.0.0 scheme displayed below generates 400 bp amplicons that tile across all four DENV serotypes simultaneously, enabling whole-genome sequencing on nanopore (MinION) or Illumina platforms directly from low-titre clinical samples.
For DeZi partner labs, this scheme is the workhorse primer set behind the network's genomic surveillance pillar — the same wet-lab and bioinformatics pipeline that was first validated and used to track DENV-3 in Angola and will be used to generate whole-genome sequences from across the network and beyond.
Selected previous work from our team
Multiplex-PCR method for sequencing arboviruses directly from clinical samples
Quick J, Grubaugh ND, Pullan ST, Claro IM, Smith AD, Gangavarapu K, Oliveira G, Robles-Sikisaka R, Rogers TF, Beutler NA, Burton DR, Lewis-Ximenez LL, de Jesus JG, Giovanetti M, Hill SC, Black A, Bedford T, Carroll MW, Nunes M, Alcantara LC Jr, Sabino EC, Baylis SA, Faria NR, Loose M, Simpson JT, Pybus OG, Andersen KG, Loman NJ. Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples. Nat Protoc. 2017 Jun;12(6):1261-1276. https://doi/10.1038/nprot.2017.066.
Hill SC, Neto de Vasconcelos J, Granja BG, Thézé J, Jandondo D, Neto Z, Mirandela M, Sebastião CDS, Cândido ALM, Clemente C, Pereira da Silva S, de Oliveira T, Pybus OG, Faria NR, Afonso JM. Early Genomic Detection of Cosmopolitan Genotype of Dengue Virus Serotype 2, Angola, 2018. Emerg Infect Dis. 2019 Apr;25(4):784-787. https://doi/10.3201/eid2504.180958.
Faria NR, Kraemer MUG, Hill SC, Goes de Jesus J, Aguiar RS, Iani FCM, Xavier J, Quick J, du Plessis L, Dellicour S, Thézé J, Carvalho RDO, Baele G, Wu C‑H, Silveira PP, Arruda MB, Pereira MA, Pereira GC, Lourenço J, Obolski U, Abade L, Vasylyeva TI, Giovanetti M, Yi D, Weiss DJ, Wint GRW, Shearer FM, Funk S, Nikolay B, Fonseca V, Adelino TER, Oliveira MAA, Silva MVF, Sacchetto L, Figueiredo PO, Rezende IM, Mello EM, Said RFC, Santos DA, Ferraz ML, Brito MG, Santana LF, Menezes MT, Brindeiro RM, Tanuri A, dos Santos FCP, Cunha MS, Nogueira JS, Rocco IM, da Costa AC, Komninakis SCV, Azevedo V, Chieppe AO, Araujo ESM, Mendonça MCL, dos Santos CC, dos Santos CD, Mares‑Guia AM, Nogueira RMR, Sequeira PC, Abreu RG, Garcia MHO, Abreu AL, Okumoto O, Kroon EG, de Albuquerque CFC, Lewandowski K, Pullan ST, Carroll M, de Oliveira T, Sabino EC, Souza RP, Suchard MA, Lemey P, Trindade GS, Drumond BP, Filippis AMB, Loman NJ, Cauchemez S, Alcantara LCJ, Pybus OG. Genomic and epidemiological monitoring of yellow fever virus transmission potential. Science. 2018;361(6405):894–899. https://doi.org/10.1126/science.aat7115
Metagenomic sequencing directly from clinical samples
Claro IM, Ramundo MS, Coletti TM, da Silva CAM, Valenca IN, Candido DS, Sales FCS, Manuli ER, de Jesus JG, de Paula A, Felix AC, Andrade PDS, Pinho MC, Souza WM, Amorim MR, Proenca-Modena JL, Kallas EG, Levi JE, Faria NR, Sabino EC, Loman NJ, Quick J. Rapid viral metagenomics using SMART-9N amplification and nanopore sequencing. Wellcome Open Res. 2023 Apr 24;6:241. http://doi/10.12688/wellcomeopenres.17170.2.
Sequencing arboviruses, identifying mosquitoes and their blood meals directly from mosquito samples
Mirza JD, de Oliveira Guimarães L, Wilkinson S, Rocha EC, Bertanhe M, Helfstein VC, Telles de‑Deus J, Claro IM, Cumley N, Quick J, Faria NR, Sabino EC, Kirchgatter K, Loman NJ. Tracking arboviruses, their transmission vectors and potential hosts by nanopore sequencing of mosquitoes. Microb Genom. 2024;10(1):001184. https://doi.org/10.1099/mgen.0.001184.