This document discusses how genome sequencing can be used for animal health monitoring and disease control. It provides examples of how sequencing has been used to monitor virus distribution and evolution, evaluate vaccine matching, and improve molecular epidemiology and diagnostic assays. The document also gives examples of impacts in Indonesia and Egypt, such as informing avian influenza control policies and improving knowledge of circulating H5N1 viruses. It concludes that sequence data is a key component of disease control and that sharing sequences is important, and FAO is working to build sequencing capacity and promote data sharing.

1. Genome sequencing for animal
health – input and impact
Gwenaelle DAUPHIN
AGAH – EMPRES
Lab Unit coordinator

3. Running PCR
Obtaining
genetic
sequence
Analysing
and
sharing

4. Monitoring virus distribution

5. Monitoring virus genetic evolution

6. Monitoring vaccine matching

7. More powerful
molecular epidemiology
Better design of
diagnostic assays
Improved
veterinary vaccination
Molecular DIVA for
CapripoxvirusesCapripoxvirus Genotyping
Whole genome phylogenetic analysis
of Capripoxviruses
Whole genome sequencing

8. Outcomes and impact in Indonesia:
Influenza Virus Monitoring Network
Informed Avian influenza control policies, including vaccination
Improved knowledge of circulating H5N1 viruses
Clear process to support decision making

9. Endemic with influenza H5N1 since 2004:
-3,500 poultry H5N1 outbreaks reported
-1,150 Egyptian influenza H5N1
isolates from poultry which sequences
= deposited to the public domain
Outcomes and impact in Egypt
Phylogenetic analysis of A(H5N1) in Egypt during 2006-2014

10. Conclusions
• Sequence data: key component in the control and
prevention of animal and zoonotic diseases
• Molecular biology used in all countries - use of sequencing
is expanding – high demand for training
• Sharing of sequences of utmost importance
active in building capacities, assisting
countries to apply sequencing and
promoting the use and sharing of
sequences