A virus does not resemble an apple. A virus resembles a fruit.
If you fill a basked with a half a dozen apples, a half a dozen oranges and a dozen bananas, then I might describe that basket in more than one way: There are two dozen fruits in the basket. There are three fruits in the basket.
In the interest of comparing apples to apples, we may want to compare apple to Hepatitis. They both exist in a number of varieties, and the Granny Smith is as distinct from the Red Delicious as Hep A is from Hep B. They each happen to be a member of a broader category, fruits and viruses respectively. However, the contrast is more interesting. When we count apples, we count pieces of fruit, not cultivars. If we count Hepatitises, we count the strains, not the particles.
More importantly, in the interest of comparing apples to oranges, we have more than one countable sense of the word "fruit". A sentence like "There are three fruits in the basket" uses a sense that means something like "varieties of fruit". A sentence like "There are two dozen fruits in the basket" uses a sense that means something like "pieces of fruit".
We also have more than one countable sense for the word "virus". On the one hand, we can use the word "viruses" to count viral particles. On the other, we can use the word "viruses" to count viral strains. Language does not always clearly reflect reality. In this case, perhaps it does.
Finally, in the interest of being clear, we rarely use words like "fruit" or "virus" on their own when literally counting. I could say "three fruits", but I'm more likely to say "three types of fruit", letting the word "fruit" take its uncountable sense. Similarly, you could say "there are five Hepatitis viruses" and "the sample contains millions of Hepatitis viruses". You might prefer to say something like "there are five types Hepatitis virus" or "the sample contains millions of Hepatitis virions".