Yeah, science.org is editorializing. The actual investigators say
> While viruses are a likely end-stage cause of colony death, other stressors such as nutritional stress and agrochemicals may have also played significant roles.
because their study just cannot tease apart the origin cause due to selection bias in the methodology. That isn't the point of their study. Their hypothesis was that miticide resistant varroa were killing (possibly already compromised) bees due to novel viruses and pathogens. Thus the use of current miticides won't help colony collapse.