Genome Detective publications

Read a selection of the published papers citing Genome Detective.

Genome Detective Tool

Vilsker M, Moosa Y, Nooij S, Fonseca V, Ghysens Y, Dumon K, et al. Genome Detective: an automated system for virus identification from high-throughput sequencing data. Birol I, editor. Bioinformatics. 2019;35(5):871–3. Available from:

Genome Detective and SARS-CoV-2 Related Papers

Cleemput S, Dumon W, Fonseca V, Abdool Karim W, Giovanetti M, Alcantara LC, et al. Genome Detective Coronavirus Typing Tool for rapid identification and characterization of novel coronavirus genomes. Luigi Martelli P, editor. Bioinformatics. 2020;36(11):3552–5. Available from:

Carbo EC, Sidorov IA, Zevenhoven-Dobbe JC, Snijder EJ, Claas EC, Laros JFJ, et al. Coronavirus discovery by metagenomic sequencing: a tool for pandemic preparedness. J Clin Virol. 2020 Oct 1;131:104594. Available from:

Tegally H, Wilkinson E, Lessells RJ, Giandhari J, Pillay S, Msomi N, et al. Sixteen novel lineages of SARS-CoV-2 in South Africa. Nat Med. 2021;27(3):440–6. Available from:

Tegally H, Wilkinson E, Giovanetti M, Iranzadeh A, Fonseca V, Giandhari J, et al. Detection of a SARS-CoV-2 variant of concern in South Africa. Nature. 2021;10:1–6. Available from:

Viana R, Moyo S, Amoako DG, Tegally H, Scheepers C, Althaus CL, et al. Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa. Nature. Jan 7;603(7902):679–86. Available from:

Genome Detective and Citations of Interest

López-Labrador FX, Brown JR, Fischer N, Harvala H, Van Boheemen S, Cinek O, et al. Recommendations for the introduction of metagenomic high-throughput sequencing in clinical virology, part I: Wet lab procedure. J Clin Virol. 2021;134:104691. Available from:

de Vries JJC, Brown JR, Couto N, Beer M, Le Mercier P, Sidorov I, et al. Recommendations for the introduction of metagenomic next-generation sequencing in clinical virology, part II: bioinformatic analysis and reporting. J Clin Virol. 2021;138:104812. Available from:

Boheemen S van, Rijn AL van, Pappas N, Carbo EC, Vorderman RHP, Sidorov I, et al. Retrospective Validation of a Metagenomic Sequencing Protocol for Combined Detection of RNA and DNA Viruses Using Respiratory Samples from Pediatric Patients. J Mol Diagnostics. 2020;22(2):196–207. Available from:

Fonseca V, Libin PJK, Theys K, Faria NR, Nunes MRT, Restovic MI, et al. A computational method for the identification of Dengue, Zika and Chikungunya virus species and genotypes. PLoS Negl Trop Dis. 2019;13(5):e0007231. Available from:

Chappell JG, Byaruhanga T, Tsoleridis T, Ball JK, Patrick McClure C. Identification of infectious agents in high-throughput sequencing data sets is easily achievable using free, cloud-based bioinformatics platforms. Vol. 57, Journal of Clinical Microbiology. American Society for Microbiology; 2019. Available from:

Faria NR, Kraemer MUG, Hill SC, Jesus JG de, Aguiar RS, Iani FCM, et al. Genomic and epidemiological monitoring of yellow fever virus transmission potential. Science. 2018;361(6405):894–9. Available from:

Rijn AL van, Boheemen S van, Carbo EC, Pappas N, Sidorov I, Mei H, et al. The respiratory virome and exacerbations in patients with chronic obstructive pulmonary disease. bioRxiv. 2019;509919. Available from:

Pineda-Peña AC, Faria NR, Imbrechts S, Libin P, Abecasis AB, Deforche K, et al. Automated subtyping of HIV-1 genetic sequences for clinical and surveillance purposes: Performance evaluation of the new REGA version 3 and seven other tools. Infect Genet Evol. 2013;19:337–48. Available from:

Kroneman A, Vennema H, Deforche K, Avoort H, Peñaranda S, Oberste MS, et al. An automated genotyping tool for enteroviruses and noroviruses. J Clin Virol. 2011;51(2):121–5. Available from:

Contact us for more information
or a personalised quotation