I have human genome samples and I want to find any bacterial or viral integration with my genome. But I couldnt find any nt database for virus.
follow this https://bioinf.shenwei.me/taxonkit/tutorial/
Viruses (top level including everything) have taxID: 10239.
If you need to restrict to a specific subset of viruses then use the NCBI Taxonomy browser to identify the taxID you would want to use with @shenwei's tutorial.
Is it also applicable in nt datebase?
If you are using a local copy of nt database for blast+ it is now simple to do with a new option -taxids. This allows you to limit results to only those taxID.