Our ONETest Influenza EnviroScreen

Enviro blue box The ONETest Influenza EnviroScreen assay allows the sensitive and scalable detection of influenza viruses in environmental samples. The assay is highly optimized for soil and wetland sediment samples from temperate regions, and can simultaneously identify and differentiate all 16 hemagglutinin and 9 neuraminidase subtypes. Thus, the assay can facilitate large-scale environmental screening for influenza viruses.

Why did we develop the ONETest Influenza EnviroScreen?

From December 2014 to January 2015 there was an outbreak of highly-pathogenic Avian Influenza in the Fraser Valley. Approximately 240,000 commercially raised birds died or were culled as a result of the outbreak. A similar outbreak occurred in the Fraser Valley in 2004 and was estimated to have cost about $500M in compensation for birds ordered destroyed, lost production, secondary revenue losses, and downstream losses (feed, litter, hatcheries, etc.).

AvianFluOutBkBC2004

Outbreaks of Avian Flu also occurred in the USA in 2015, with an estimated economic impact of more than $3B, causing shortages of poultry products and doubling the price of eggs.

Wild waterfowl are carriers of Avian Flu and spread the virus to new geographic locations during their annual migrations. Overlap between different migratory routes facilitates long-distance virus transport as well as genetic hybrids. Indeed, the 2014/2015 outbreak in BC was caused by a virus that contained a Eurasian H5 component and a North American N2 component.

Major Global Avian Migration Flyways

Wild Bird Migration Paths

There is concern that global warming and associated changes in migratory patterns might favor increased incursion of Eurasian viruses into North America. This is particularly problematic because Eurasian viruses tend to be more pathogenic for people and poultry, therefore the frequency and severity of North American Avian Flu outbreaks may increase in the future.

Given that wild waterfowl are a source of Avian Flu, they are also the focus of surveillance globally. In Canada, the Canadian Wildlife Health Cooperative coordinates national surveillance in wild waterfowl on behalf of key stakeholders, including the Canadian Food Inspection Agency, the Public Health Agency of Canada, and the provincial Ministry of Agriculture. Increasingly, Canada, the USA and Mexico are attempting to harmonize Avian Flu surveillance programs to increase protection for the continent as a whole.

Thus far, waterfowl surveillance (both in Canada and elsewhere in the world) has been centered on testing individual wild birds – an approach that has significant limitations stemming from the practical and financial impediments to collecting a representative sample of wild waterfowl. Indeed, this surveillance was in place in the USA and Canada in 2014/2015 and failed to predict the outbreaks in either country. This failure highlighted the need for better tools and methods to predict and prevent Avian Flu incursions and outbreaks. One of the methods could be sampling of wetland sediments.

Avian Flu is shed in bird feces so sampling wetland sediments where feces accumulate may be a more efficient and effective way of detecting it in waterfowl populations. Although theoretically appealing, this approach has yet to be widely implemented because of the technological barriers associated with detecting and characterizing Avian Flu viruses in environmental samples.

FUSION GENOMICS’ Quantum Probes technology has successfully overcome these barriers!

A study was conducted by the University of British Columbia and the BC Ministry of Agriculture which used our Quantum Probes technology. Samples from key wetlands in BC within the 2014/2015 outbreak area were collected. These samples underwent “genomic” enrichment using Quantum Probes and were then sequenced on the Illumina Next Generation Sequencing platform. This enrichment allowed them to detect ‘outbreak’ influenza virus in wetlands throughout the outbreak area at a significantly higher rate when compared with testing methods currently used in the national wild-bird surveillance program.

Description Back to Top

FUSION GENOMICS developed our ONETest Influenza EnviroScreen assay to easily and accurately identify all strains of influenza virus from samples taken directly from the environment with one simple test.

The kit contains our influenza-specific Quantum Probes to capture and prepare the target sequences for Next Generation Sequencing on the platform of your choice. Quantum Probes are 1000 times more sensitive than RT-PCR, which is unable to detect influenza virus in environmental samples.

The ONETest Influenza EnviroScreen also gives you access to our FUSIONCloud to upload the raw sequence data and receive the results of your data analysis.

How well does the ONETest Influenza EnviroScreen fill the need?

As part of a multi-million dollar pan-Canadian effort to detect and predict bird flu outbreaks, FUSIONGENOMICS Canadian government organizations and a reference lab in Canada tested our technology for the isolation and sequencing of influenza RNA from wetland sediments in wild bird habitats.

The ONETest Influenza EnviroScreen assay was applied on a set of environmental samples.
Example data shows that the assay can (1) detect a spectrum of influenza subtypes (including H5N2)
and (2) identify co-occurring subtypes.

Enviro figure

Figure: Subtype calls for a set of environmental samples. Data was generated using an Illumina
NextSeq® machine from environmental samples processed using the ONETest Influenza EnviroScreen protocol. Each row is a single sample. Influenza typing was performed on the FUSIONCloud. The data clearly shows that the assay can identify H5N2 and other influenza virus subtypes.

The results showed that only Quantum Probes were able to capture and detect the influenza HA and NA genes for sequencing. Simultaneous testing by PCR based sequencing methods failed to give any results.

Applications Back to Top

The ability of the ONETest Influenza EnviroScreen to capture and sequence environmental/soil samples has major implication for use of such tests in agriculture. Soil based microbiomes, which could be analyzed using our technology, are expected to play a major role in advancing food production

Storage and UsageBack to Top

Store at -20 C. Reactions are conducted on ice.

Testing & DevelopmentBack to Top

The testing is now entering Phase II; to evaluate ONETest Influenza EnviroScreen and FUSIONCloud as a comprehensive testing regimen to be used by Canada and its international partners for Avian Flu surveillance.

FAQs & Tips Back to Top

  1. Q: How much sample material do I need?

    A: As much as it takes to yield a minimum of 200ng of high quality RNA for library construction.

  2. Q: How much does the kit cost?
  3. A: Please contact us for pricing.

  4. Q: Are there extra costs for analysing my data?

    A: No. Web-based data analysis is included in the kit.

Protocols & Manual Back to Top

Please contact us for protocols and manuals.

Is the ONETest Influenza EnviroScreen available?

Please contact us if you would like to obtain this product.

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