It has emerged from ISARIC4C that simultaneously characterising the genomic information of coronaviruses and the underlying nasal microbiome from a single clinical sample could help characterise infection and disease. Metatranscriptomic approaches can be used to sequence SARS-CoV-2 (and other coronaviruses) and identify mRNAs associated with active transcription in the nasal microbiome. The findings shared in this paper shed light on the performance of different enrichment strategies and their applicability in characterising the composition of the nasal microbiome. In this study, various enrichment methods were assessed to detect SARS-CoV-2, identify lineages and define the nasal microbiome. The methods were underpinned by Oxford Nanopore long-read sequencing and variations of sequence independent single primer amplification (SISPA). The utility of the method(s) was also validated on samples from patients infected with seasonal coronaviruses.