One of the sources referenced in the paper is about the work the company I co-founded is doing (https://phylum.io). We've been working closely with PyPI to not only report issues related to malware, but are also helping provide guidance around on-going work to help curb additional malware in the ecosystem. I think this is a step in the right direction, and one I hope other ecosystems will eventually take.
Though, this is likely to be a cat and mouse game for the foreseeable future. Detection will get better, and attackers will change tactics.
In the meantime, we've been open-sourcing some tooling to help protect developers from these sorts of attacks. Namely, a sandbox that locks down network/disk/env [1] and our CLI [2] that allows you to perform a `pip` install in the sandbox, after checking our API for behaviors/issues with the package. For example:
phylum pip install <pkgName>