Retrospective Characterisation of the 2006-07 Swine Vesicular Disease Epidemic in Northern Italy by Whole Genome Sequence Analysis

In this study, by using whole-genome sequence data in combination with epidemiological information on disease occurrences, we report a retrospective epidemiological investigation of the 2006-2007 SVD epidemic, providing new insights into the transmission dynamics and evolutionary mode of the two phases that characterised the epidemic event. Our analyses support evidence of undetected premises likely missed from the chain of observed infections, of which role as the link between the two phases is reinforced by the tempo of SVD virus evolution. These silent transmissions likely resulting from the gradual loss of a clear SVD clinical manifestation linked to sub-clinical infections, may poses a risk of failure in the early detection of new cases. This study emphasises the power of joint inference schemes based on genomic and epidemiological data integration to inform on transmission dynamics of disease epidemics, ultimately aimed at better disease control.