Towards reliable whole genome sequencing for outbreak preparedness and response

BMC Genomics

Table 1 Overview of the usability of the different sequence methods. The sequence method, platform, time to results, costs and suitability for public health decision making is indicated

Sequence method	Amplicon	Amplicon	Metagenomic	Metagenomic	Capture-based
Platform	Illumina	Nanopore	Illumina	Nanopore	Illumina
Time to result	3 days	< 24 hours	3 days	< 24 hours	8 days
Costs of the instrument^a	€200.000	€1.000	€200.000	€1.000	€200.000
Cost of the analysis^b	€100	€100	€600	€600	€600
Costs per sample	€200	€50	€200	€50	€300
Virus specific PCR required	Yes	Yes	No	No	No
Ct threshold for WGS	Ct29-33	Ct25-29	Ct29-33	Ct25-29	Ct29-33
Ct threshold for detection	Ct33	Ct33	Ct33	Ct29-33	Ct33

^aEstimated costs are laboratory and/or country dependent
^bEstimated costs are estimated based on a €100 per hour and are laboratory and/or country dependent

ISSN: 1471-2164