The only safe way to store you alts is to store them in a hardware wallet such as Ledger or Trezor. When you generate a seed using a hardware wallet it is not shared with the computer system and hence even if your computer is having any kind of malware or virus, the seed can never be compromised
It would be too hassle though when you are an active trading or just holding it for few weeks or days. And some of these coins have either very expensive transaction fees or very very slow in sending and receiving. An updated anti virus and extra careful on our pc/laptops/cellphones can help.