WGS
PathoSense specializes in whole-genome sequencing of micro-organisms, offering complete genomes and detailed genomic characterization of bacteria, yeasts, viruses, phages and plasmids. Our fast and cost-effective service encompasses nucleic acid extraction, long-read sequencing, expert bioinformatics analysis, and thorough reporting.
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.
Advanced bioinformatics analyses
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.
Bacterial whole genome sequencing
Do you have bacterial isolates that you want to characterise? Then our long-read nanopore sequencing workflow comes in handy as bacteria have larger genomes. We can reconstruct complete, circular genomes and plasmids at high sequencing depths. As a starting material, we use pure and fresh bacterial isolates.
Advanced bioinformatics analyses
We also take care of more advanced bacterial genome data-analyses using our (veterinary) pathogen genomics expertise:
> Phylogeny & MLST analysis
We use phylogenetic analysis methods to analyse the genetic relatedness & evolutionary relationship between different strains. Phylogenetic trees can be enriched with strains sequenced at PathoSense and publicly available genomes from GenBank. Analyses can be conducted on whole genome sequences and can also target specific genes of interest.
As the entire genome is at hand, multi-locus sequence (MLST) typing can also be used to classify strains according to available & internationally used MLST schedules for different types of bacteria.
> Virulence factor screening
Bacteria can harbour different types of virulence factors. Using the genetic information we can screen for the presence of virulence factors, which eventually can be used to assess the pathogenicity of some isolates.
> antimicrobial resistance screening
Antimicrobial resistance is a big challenge for animal and human health. Most analyses are conducted using phenotypic analysis methods but also the genetic code can be used to analyse potential antimicrobial resistance. This can be done by assessing the presence of genes or point mutations that are linked to antimicrobial resistance.