Distance thresholds guidance for various pathogens

The distance threshold (either SNPs or TN93)cut-off in MicrobeTrace is an important factor in determining the composition of the molecular network. This value should be based on _apriori _knowledge of the pathogen, its mutation rate, as well as the question being asked about the outbreak. The table below is a compilation of suggested starting thresholds for various pathogens based on SME knowledge. These are only guidelines and users should establish the correct threshold based on your specific use-case.

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Pathogen	Distance metric	Cut-off
SARS-CoV-2	SNP	6-16
MPOX	SNP	0-1
HIV	TN93	0.005-0.015
HCV	TN93	0.052
Cyclospora	TN93	0.11
N. Gonorrhoea	SNP	16
HAV	SNP	0
Acinetobacter (CRAB)	SNP	2
N. meningitidis	SNP	35
Group A streptococcus	SNP	20