Bees are considered to be threatened globally, with severe overwinter losses of the most important commercial pollinator, the Western honeybee, a major concern in the Northern Hemisphere. Emerging infectious diseases have risen to prominence due to their temporal correlation with colony losses. Among these is Deformed wing virus (DWV), which has been frequently linked to colony mortality. We now provide evidence of a strong statistical association between overwintering colony decline in the field and the presence of DWV genotype-B (DWV-B), a genetic variant of DWV that has recently been shown to be more virulent than the original DWV genotype-A. We link the prevalence of DWV-B directly to a quantitative measure of overwinter decline (workforce mortality) of honeybee colonies in the field. We demonstrate that increased prevalence of virus infection in individual bees is associated with higher overwinter mortality. We also observed a substantial reduction of infected colonies in the spring, suggesting that virus-infected individuals had died during the winter. Our findings demonstrate that DWV-B, plus possible A/B recombinants exhibiting DWV-B at PCR primer binding sites, may be a major cause of elevated overwinter honeybee loss. Its potential emergence in naïve populations of bees may have far-reaching ecological and economic impacts.Insect pollination, which is carried out mostly by bees, is required for 75% of all food crops 1 ; the global value of insect pollination in 2005 has been estimated at €153 billion 2 , although this is likely to be an underestimate 3 . In addition, 85% of wild plants are pollinated by animals 4 , chief among these being bees. Bees are therefore of considerable economic and ecological importance. The honeybee Apis mellifera is by far the most important commercial pollinator and is relied upon heavily for the successful pollination of many food crops 5 . However, over the last decade severe yearly losses of honeybees in the Northern Hemisphere 6-9 have raised concerns about food security 10 .The emergence of several infectious diseases has coincided with elevated honeybee colony losses [11][12][13] . Notable among these are positive single stranded RNA (positive ssRNA) viruses that have risen to prominence since the arrival of a novel biological vector from Asia, the ectoparasitic mite Varroa destructor. The mite feeds on the hemolymph of honey bee pupae and adults 14 . Its ability to act as a viral vector and potential incubator of several honeybee RNA viruses has given rise to a new viral transmission route, thereby aiding the spread and re-emergence of several bee viruses [15][16][17] .