Hey,
So, I think you would be a good candidate for the programs that you listed as long as you get a good GRE score. A lot of the times GRE scores can be overlooked but some schools screen based on numbers too so I'd say just try the best you can to get the highest score. I don't think you should be discouraged by your MCAT score. You can get a high score on the GRE if you put in a good deal of work. Personally, I worked on the math section the most because that was what I knew I could do the best on as long as I don't make mistakes. As for the reading section, I memorized around 200-300 words from the most common list that Magoosh published, which helped a lot. For writing, I'd say, it's helpful to just look through a couple of the writing prompts and practice coming up with suitable examples. It can really wear you down to have to write the whole essay so this is what I'd suggest.
In terms of what you are doing during your gap year, have you also thought of applying for the NIH postbac position? A lot of grad schools really like NIH postbacs. When I interviewed at UPenn and Stanford, there were a lot of NIH postbacs there and when talking to faculty members, it was definitely helpful to mention my experiences at NIH. Also, at NIH, they give you a lot of resources to help you through the application cycle as well as providing you the platform for being introduced to different types of research since there's tons of seminars/ lectures going on all the time. I also was able to present at conferences that NIH hosted and there's opportunities to boost your resume by signing up for best poster/travel awards etc. If you want tips for getting into the NIH postbac program, after submitting your application, contact individual PIs that you're interested in and also join ClubPCR since open positions will be advertised in this group occasionally. I think it helps to also just visit NIH and just go around labs asking for openings. Alot of postbacs have gotten in this way too. In terms of the fact that you are not doing research that you hope to do in the future, you need to just come up with your own story and the reasoning behind why you pursued certain interests/ research and why you hope to go into a certain field that's not related. You don't necessarily need to be doing the research you're interested in at the moment although it will help. You can perhaps explain why you choice the neuro lab and then what made you take interest in the field of virology...and how you actively pursued it by.....gap year stuff etc.
I hope this helped. I've also been through the same/similar situation as you are going through right now and I'd say my advice is just to put in as much as you can and it'll pay off in the end. I think you are a very well qualified applicant and just make sure to highlight your uniqueness and strengths of your application in the essay and how that would make you a great scientist. I wanted to also point out that everyone is going to have different opinions about what I've suggested so take my advice with a grain of salt.
Wish you the best of luck.