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European PORTFASTFLU project to develop rapid screening systems that will revolutionize control of influenza epidemics (CIRAD press release, 06/05/2009)

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Emerging and Exotic Animal Disease Control Research Unit

It will soon be possible to detect every flu virus in record time

11/05/2009 - Article

The European PORTFASTFLU project set out to find a way of identifying all the flu viruses currently known within two hours. CIRAD has developed a test to screen all the existing sub-types and strains. Interview with Saliha Hammoumi, a CIRAD virologist and scientific leader of the project.

In what way is the new diagnostic system developed under the PORTFASTFLU project better than the existing protocol?

Saliha Hammoumi, virologist at CIRAD © CIRAD, Marie Adell

Saliha Hammoumi: It is a new device that uses a diagnostic test suitable for every influenza type and sub-type. It is fully integrated, whereas diagnoses are generally established in several stages: genetic information has to be extracted from the sample taken and then placed in a reaction medium for detection. This generally takes up to half a day. Sequencing is subsequently used to identify the virus precisely within a few days. With the new device, developed by ten European partners, any flu virus can be identified within two hours.

Why is it so quick?

S.H.: The system discriminates between different strains using probes that are specific DNA sequences. There are several probes per virus sub-type, making it possible to detect a broad panel of strains. These probes are integrated into a biochip that enables identification of the virus in the sample in a single stage. Eight sub-types can currently be detected in this way, including those that are pathogenic to humans: H1N1, H3N2, H5N1, H7N7 and H9N2. Within a few months, measurements should become much more precise, making it possible to discriminate between strains within a given sub-type. Viruses of sub-type H1N1, for instance, can be of different strains, which the device will be able to measure. In particular, this applies to the new H1N1 strain current affecting Mexico and the rest of the world, which out test has detected in a Spanish patient.

What role has CIRAD played in developing this new technology?

S.H.: CIRAD has played a key role in the PORTFASTFLU consortium, working upstream to develop the influenza virus detection system and downstream to validate this all-in-one technology on biology samples of animal origin. This scientific challenge and its impact on public and veterinary health are what I have liked most about this three-year project, of which I am in charge at CIRAD. We know that the influenza virus mutates quickly, which with conventional techniques means constantly looking for sequences that have just appeared as a result of those mutations. To date, the available techniques were based on analysing a few hundred sequences. To identify the best molecular markers with a view to covering the whole range of known and future viruses, I have analysed all the sequences available in the public domain, in other words almost 26 000. The markers I have developed have been validated in the laboratory and are to be integrated into a biochip in the next few days.

How and when will the device be used?

S.H.: Doctors, veterinary surgeons and anyone capable of taking samples will be able to use the new system. It will be extremely useful in airports, ports and hospitals. Knowing the type and sub-type of a virus as early as possible will enable us to control flu epidemics more effectively by taking preventive steps earlier. The systems is to be tested in hospitals in 2009 and validated on samples from birds at CIRAD. It should be operational by the end of 2010 at the latest.

Interview by Marie Adell and Elsa Bru