Virus whole genome sequencing

Do you have a diagnostic sample or a cell culture grown viral stock that you want to characterise in-depth? Then we have a fast methodologies to perform viral whole genome sequencing and to deliver the complete genome to you: 

• Ad-random sequencing approaches are applicable on virus stocks grown in culture (eg. cells or eggs) or clinical samples with a high viral load (eg. low Cq value). 
• In targeted approaches, we use primer-enrichment strategies to increase the number of genetic reads for the viral species of your interest. In this way, the virus can be detected in clinical samples with high to even moderate viral loads. 

We also take care of more advanced viral genome data-analyses using our (veterinary) pathogen genomics expertise:

> Phylogenetic analysis

We use phylogenetic analysis methods (eg. Maximum likelihood) to analyse the genetic relatedness & evolutionary relationship between different strains. Phylogenetic trees can be enriched with strains sequenced at PathoSense, vaccine strains and publicly available genomes from GenBank.  Analyses can be conducted on whole genome sequences and can also target specific genes of interest.

> Variant analysis

In some areas of research, it is important to dig deeper into the nucleotide sequences and see how they affect the translation into protein sequences. For genes of interest, nucleotide and amino acid comparisons can be made against certain reference strains. 

> Recombination analysis

Some viruses have the possibility to exchange genes between genomes of different strains. This process is called recombination, a common phenomenon in coronaviruses and porcine reproductive & respiratory syndrome virus. Having the full sequence, it is possible to analyse the occurrence of recombination events and to deduce possible parental strains.