Viral WGS & metagenomics

Viral genomic information can be deduced in different ways from samples, including random sequencing approaches and targeted sequencing approaches. These choices will depend on the prior knowledge one has about the virus of interest in the sample, and the expected viral load. PathoSense has experience with different enrichment strategies and both random and target sequencing approaches can be applied in the wet laboratory. Together with you, we will decided on the most optimal strategy for your experiments.

Downstream analyses start with proper quality control and a correct genome assembly. Our preference goes to de novo assembled genomes but we can also help customers with reference-based genome assemblies. We have a broad expertise with many viral agents but interesting to note is our particular experience with specific enrichment strategies for viruses with a large genome (eg. herpesvirus), whereas targeted workflows and assembly methods are available for others (eg. influenza A virus, PRRSV...). BRSV, BVDV, PCV2, PRRSV, PPV-1, IBV, influenza A, rotavirus, IBDV, FeCoV... or something else?

We use phylogenetic analysis methods (eg. Maximum likelihood) to analyse the genetic relatedness & evolutionary relationship between different strains. Phylogenetic trees can be enriched with sequences of interest, such as sequences available at PathoSense, at the customer or in Genbank. Moreover, analyses can be targeted to the entire genome or certain genes of interest.

In some areas of research, eg. vaccine development or drug discovery, it is important to dig deeper into the nucleotide sequences and quasispecies. Using SNP analysis or variant calling, the presence and proportion of certain nucleotide mutations can be investigated in precision. Furthermore, these nucleotide sequences can be translated into amino acid sequences, enabling researchers to link functionality and phenotypic observations to the strain of interest.

Some viruses have the possibility to exchange parts of the genome between genomes of different strains. In viruses with a linear genome this process is called recombination (eg. PRRSV, coronavirus...), whereas in viruses with a segmented genome (influenza A, rotavirus...) this is called reassortment. Having the full sequence allows to analyse the occurrence of recombination events and to deduce possible parental strains.

When developing (auto)vaccines, adventitious agents can pose a big challenge. Viral metagenomics workflows can be used effectively to screen quickly for the presence of undesired infectious agents (other than the one expected) in a sample.