Towards reliable whole genome sequencing for outbreak preparedness and response

• Published in: BMC genomics Vol. 23; no. 1; pp. 1 - 9
• Main Authors: Nieuwenhuijse, David F., van der Linden, Anne, Kohl, Robert H. G., Sikkema, Reina S., Koopmans, Marion P. G., Oude Munnink, Bas B.
• Format: Journal Article
• Language: English
• Published: London BioMed Central 09.08.2022; BioMed Central Ltd; BMC
• Subjects: Animal Genetics and Genomics; Arbovirus; Arboviruses; Biomedical and Life Sciences; Communicable diseases; Control; Decision making; DNA sequencing; Epidemics; Epidemiology; Gene sequencing; Genetic aspects; Genomes; Genomics; Identification and classification; Infectious diseases; Life Sciences; Long reads; Metagenomics; Methods; Microarrays; Microbial Genetics and Genomics; Netherlands; Nucleotide sequencing; Outbreaks; Pathogens; Plant Genetics and Genomics; Platform comparison; Proteomics; Public health; Research Article; Severe acute respiratory syndrome coronavirus 2; Short reads; Technology application; Vector-borne diseases; Viruses; West Nile virus; Whole genome sequencing; Zika virus; Netherlands; Metagenomics; Long reads; Whole genome sequencing; Platform comparison; Short reads; Arbovirus; Epidemiology
• ISSN: 1471-2164; 1471-2164
• DOI: 10.1186/s12864-022-08749-5

Background To understand the dynamics of infectious diseases, genomic epidemiology is increasingly advocated, with a need for rapid generation of genetic sequences during outbreaks for public health decision making. Here, we explore the use of metagenomic sequencing compared to specific amplicon- and capture-based sequencing, both on the Nanopore and the Illumina platform for generation of whole genomes of Usutu virus, Zika virus, West Nile virus, and Yellow Fever virus. Results We show that amplicon-based Nanopore sequencing can be used to rapidly obtain whole genome sequences in samples with a viral load up to Ct 33 and capture-based Illumina is the most sensitive method for initial virus determination. Conclusions The choice of sequencing approach and platform is important for laboratories wishing to start whole genome sequencing. Depending on the purpose of genome sequencing the best choice can differ. The insights presented in this work and the shown differences in data characteristics can guide labs to make a well informed choice.