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NGS Application in Animal Health Today and Future Perspectives

The NGS Hub  executed a survey in order to depict the current situation of NGS application in animal health. Furthermore, different opinions from industry, research and diagnostic labs are requested in order to depict the potential future outlook of NGS applications in animal health.


NGS Application Areas and it´s Regional Distribution

NGS is most often applied in North America and Europe followed by Asia and Australia. This is also reflected by the information and feedback we obtained in the field of animal health. According to the feedback NGS is most often applied in animal health in Europe and in North America, including in the leading animal research and diagnostics institutes such as the CVI, DTU, FLI, IVI, and The Pirbright Institute (Figure 1).

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Most participants work in research institutes or diagnostic service laboratories, whereas less than 1/3 of the participants work in the industry. The clear focus on NGS application is currently in animal health related to farming animals followed by zoonotic diseases. According to our data NGS is less often applied in the field of companion animals (Figure 2 and 3).

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AHSurveyIIIAbout half of all NGS projects are perform in house, almost 1/3 of the NGS projects are outsourced to research or industry partner. Whereas less than 1/3 of NGS services is outsourced to diagnostic labs or commercial NGS service provider (Figure 4).

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The average number of animal health related NGS samples is very low as shown in figure 5. Some laboratories process only sporadic samples. None of the participating laboratories reported high throughput NGS application. These results underline the assumption that NGS application in animal health covers only a very small proportion of the global NGS market.

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Current NGS Applications and Challenges in Animal Health

NGS is currently most often used in animal health for research projects followed by genotyping (epidemiology) and detection of unknown pathogens and difficult diagnostics. In less cases it is also applied in routine diagnostics, confirmatory diagnostics, decision making such as treatment or surveillance or in drug and vaccine development (Figure 6).

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The most often applied method is whole genome sequencing followed by targeted sequencing. Metagenome studies are relatively often performed and in some labs 16S rRNA sequencing is used for bacterial identification (Figure 7).

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Most labs plan to use NGS more often in the future in research projects, followed by epidemiology, confirmatory diagnostics and routine diagnostics. Some labs also plan to use NGS more often for drug and vaccine development (Figure 8).

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The biggest problems during NGS application in animal health are currently the long time to results, the complex workflow, and the lack of automatization. Other challenges are the sample preparation (nucleic acid extraction), missing sensitivity, contamination risk, and the bioinformatic analysis (Figure 9).

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Future Perspective on NGS Applications in Animal Health

Most participants believe that NGS will be more often applied in the future for the characterization of pathogens (including virulence and resistance testing), in phylogeny and epidemiology studies, and for the detection of new pathogens (Figure 10).

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The expected pathogens for which NGS will be applied most often in the future in animal health are Influenza followed by PRRSV, and Pestiviruses (mainly BVDV). It is also expected that NGS will be applied more often in general antibiotic resistance testing of bacteria (Figure 11). For other pathogens including IBV, Coronaviruses, FMDV and Salmonella NGS is expected to be applied as well more often in the future (data not provided).

AHSurveyXFacts that might impact NGS application in animal health in the future most are: high sequencing costs, long time to results, and missing knowledge about NGS applications and its limitations (Figure 12). It has to be stated that the response missing knowledge about NGS is clearly underrepresented as a number of less experienced clients did not answered the survey at all.

AHSurveyXIIIn two more questions we tried to figure out what prices are acceptable for different NGS applications in animal health and what time to results would be acceptable. These question are in place in order to find out if NGS could be an option for future animal health diagnostics and if so for which application and methods this would be reasonable.
The accepted price for diagnostic samples vary between 20 and 100 Euro depending on the region and business sector. The average is about 50 Euro/ sample. If genotyping and classification is added as a service, accepted prices are still in the same range. For unsolved diagnostic samples clients accepting slightly higher costs starting from 70 to 200 Euro. For more detailed pathogen characterization including genotyping and resistance or virulence determination (if possible) most clients accept costs between 70-100 Euro with still some participants accepting to pay up to 200 Euro per sample. For small research projects with 1 million short reads clients accepting costs between 70 to 200 Euros, with some participants still accepting to pay more than 200 Euro per sample.

AHSurveyXIIIThe accepted time to result for diagnostic samples is between 24 hours and 5 working days with an average time of about 48 hours. For more detailed classification the average accepted time is slightly higher between 72 hours and 5 working days depending on the extent of information obtained. For research projects most people accept two weeks for their sequencing project including basic data analysis.

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