I read an article by a gardener describing how a virus had transmitted a negative trait to his plants. It rather shocked me, because I hadn't realized that a virus could transform an adult plant. I was aware of dipping arabadopsis flowers in agrobacterium tumefaciens, but the concept of non-reproductive structures being transformed seems fascinating. What kind of virus is capable of that?
These are just a couple of short examples, but Witch's broom structures in trees can sometimes be caused by viruses - see Wikipedia: Witch's broom (fungi is maybe the most common cause though). In rose species you also have the similar Rose rosette disease (also called witches’-broom of rose), which is caused by a virus. The same webpage from Missouri Botanical Garden also includes a list of other plant viruses that you might find interesting.
Plant viruses that infect non-reproductive structures are common though - a overview can be found here: The American Phytopathological Society: Introduction to Plant Viruses, the Invisible Foe. More indepth information can be found in Plant Pathology (Agrios, 2012) (see ch. 12: "Plant diseases caused by viruses").
Viruses can infect just about any living thing, so that it could infect a plant is no surprise.
Your article describes how a small virus-infected part of a plant had been cloned and consequently the entire cloned plant was infected, and it infected plants grown hydroponically in the same water. No surprise there either.
Plant viruses have been known for centuries. One of the earliest recorded descriptions of a virus-infected plant can be found in a poem written by the Japanese Empress Kōken (718–770), in which she describes a plant with yellowing leaves in summer. The plant (a Eupatorium) was described as "autumnal".
The top 10 plant viruses (in one paper) in molecular plant pathology were listed as:
(1) Tobacco mosaic virus, (2) Tomato spotted wilt virus, (3) Tomato yellow leaf curl virus, (4) Cucumber mosaic virus, (5) Potato virus Y, (6) Cauliflower mosaic virus, (7) African cassava mosaic virus, (8) Plum pox virus, (9) Brome mosaic virus and (10) Potato virus X, with honourable mentions for viruses just missing out on the Top 10, including Citrus tristeza virus, Barley yellow dwarf virus, Potato leafroll virus and Tomato bushy stunt virus.
Some plant virologists even care enough to argue about it.
One paper describes how a plant was improved by a viral infection:
In all cases, virus infection delayed the appearance of drought symptoms. Beet plants infected with CMV* also exhibited significantly improved tolerance to freezing. Metabolite profiling analysis showed an increase in several osmoprotectants and antioxidants in BMV**-infected rice and CMV-infected beet plants before and after drought stress.
*Cucumber mosaic virus
**Brome mosaic virus
Aetiology: The earliest recorded plant virus disease
Top 10 plant viruses in molecular plant pathology
The REAL Top 10 for Plant Viruses
Introduction to Plant Viruses, the Invisible Foe
Virus infection improves drought tolerance