Compositions, methods and systems for processing or analyzing multi-species nucleic acid samples

A method for processing a biological sample of a human subject, comprising:

• (a) providing said biological sample from said human subject, wherein said biological sample of said human subject comprises (i) human nucleic acid molecules derived from said human subject, and (ii) non-human nucleic acid molecules derived from one or more viruses;
• (b) enriching said human nucleic acid molecules and said non-human nucleic acid molecules derived from said biological sample using a set of nucleic acid capture probes, to yield an enriched set of nucleic acid molecules comprising (i) a subset of said human nucleic acids derived from said human subject and (ii) a subset of said non-human nucleic acids derived from one or more viruses, wherein said set of nucleic acid capture probes comprises (i) a first plurality of nucleic acid probes configured to target elements of a human genome and (ii) a second plurality of nucleic acid probes configured to target elements of one or more viral genomes;
• and
• (c) sequencing said enriched set of nucleic acid molecules to yield sequence information comprising sequences of said enriched set of nucleic acid molecules, where said sequences of said enriched set of nucleic acid molecules comprise sequences of (i) human nucleic acids from said biological sample from said human subject and (ii) non-human nucleic acids from said biological sample of said human subject.