PathoSense DeepDive is an extension of the PathoSense Diagnostic Assay designed for comprehensive viral genome analysis, facilitating phylogenetic studies, genetic subtyping, and strain differentiation using sequencing data from the PathoSense Diagnostic Assay.
Traditional diagnostic methods require veterinarians to specify which pathogens to test for, which can sometimes lead to missed diagnoses if the right selections aren't made. The PathoSense Diagnostic Assay overcomes this challenge by using nanopore sequencing to analyze genetic material from infectious pathogens without prior selection. This technology identifies all viruses and bacteria present in a sample, providing a comprehensive view of potential causes of disease.
DeepDive is an advanced feature of the PathoSense Diagnostic Assay that allows for subsequent in-depth viral genome analysis when sufficient data is available. It enables phylogenetic analysis, genetic subtyping, and differentiation between vaccine and wild-type strains, helping veterinarians make more informed clinical decisions.
The DeepDive report provides veterinarians with structured insights into viral genomic data, detailing information about the sample, genome quality, and phylogenetic relationships.
It features genome quality metrics like sequencing depth and completeness, which are crucial for determining the reliability of the findings. The data is considered of sufficient quality if an average coverage of at least 10X is achieved across at least 70% of the genome – or the specific portion used for typing. This approach ensures that the analysis is based on sufficiently deep and reliable sequencing data, which is essential for accurate interpretation. A sample report illustrating genome completeness is provided below (Fig. 1).
A key element of the report is the phylogenetic analysis, where viral sequences are compared with reference strains to evaluate their genetic connections. This analysis illustrates how identified strains relate to known variants, vaccine strains, and field isolates, facilitating accurate outbreak tracking and strain differentiation. Additionally, the report emphasizes subtyping results, indicating whether a detected virus belongs to a specific genotype, which is vital for epidemiological monitoring and formulating vaccine strategies.
Fig. 1: Example of Genome completeness as shown in a DeepDive report.
DeepDive can be requested if sufficient sequencing data is available directly from the PathoSense Diagnostic analysis.
Several factors should be considered as they can influence viral genomic yields:
Virus Type: Small, non-enveloped viruses are easier to sequence than large, complex genomes (e.g., herpesviruses).
Sample Purity & Viral Load: Higher viral concentrations improve sequencing success. Samples with excessive bacterial or host DNA can obscure viral genomes.
Phase of Infection: Samples collected during acute infection phases, when viral shedding is highest, are more likely to yield complete genomes.
For Influenza A (e.g. H1avN2) and Rotavirus A (e.g. G5P7) no DeepDive needs to be requested, the genotyping information will be included in the standard PathoSense Diagnostic report. PathoSense Deepdive is currently available for the following viral pathogens (17/03/2025):
Despite its capabilities, PathoSense DeepDive is not always the best option for every diagnostic scenario. In cases where the viral load is too low or the sample is heavily containing bacteria or host, achieving the necessary sequencing depth for accurate analysis may be challenging. Additionally, the tool is not currently suitable for comprehensive bacterial genome typing due to the complexity and size of bacterial genomes. In such situations, veterinarians may need to consider alternative sequencing strategies. Contact us for more information.
DeepDive is an extension of the PathoSense Diagnostic analysis, available as an additional report upon request.
Here is a step-by-step guide on how to request DeepDive:
Submit a PathoSense Sample: Collect and send clinical samples to a PathoSense partner laboratory.
Receive Initial Report: After sequencing, a standard diagnostic report will indicate pathogen presence.
Check for DeepDive Availability: If DeepDive is possible, the original PathoSense report will automatically indicate availability for further phylogenetic analysis as shown in Fig. 2 below.
Request DeepDive via Partner Lab: Follow the provided instructions to initiate additional analysis.
Receive In-Depth Report: Within a few days, you will receive a detailed phylogenetic and subtyping analysis.
Fig. 2: Example of a PathoSense report indicating which pathogens have sufficient data available to request a DeepDive report.
PathoSense DeepDive has already proven its worth in several notable case studies, demonstrating its potential to impact veterinary diagnostics positively.
One such case involved a cattle farm experiencing an unexpected outbreak of bovine respiratory disease complex during the Summer, a time when such infections are rare. By employing PathoSense DeepDive, veterinarians were able to determine that the outbreak was caused by a wild-type virus rather than a vaccine strain, highlighting the need for consistent vaccination practices.
In another instance, a feline parvovirus outbreak in a cat shelter with a high mortality
In a poultry farm dealing with synovitis, DeepDive identified multiple genotypes of reovirus present in the same location. Focussing on the sigma C segment, 3 different genotypes could be positioned in a phylogenetic tree (shown in Fig. 3). These critical provide the vet and farmer insights for biosecurity measures and disease control.
These cases highlight the practical advantages of DeepDive in tracking disease patterns, guiding treatment, and refining prevention strategies.
Fig. 3: Phylogenetic tree illustrating three distinct genotypes of Reovirus.
Despite its capabilities, PathoSense DeepDive is not always the best option for every diagnostic scenario. In cases where the viral load is too low or the sample is heavily containing bacteria or host, achieving the necessary sequencing depth for accurate analysis may be challenging. Additionally, the tool is not currently suitable for comprehensive bacterial genome typing due to the complexity and size of bacterial genomes. In such situations, veterinarians may need to consider alternative sequencing strategies. Contact us for more information.
If you have any questions about DeepDive or PathoSense, feel free to contact us via this form: