Earlier this year, a virology laboratory in Tunisia received the oral samples of cows suspected by veterinarians of having foot and mouth disease (FMD). FMD is a highly contagious disease that affects cloven-hoofed animals, such as cows, pigs and goats, and it can lead to the disruption of regional and international trade of animals and animal products. The disease is characterized by fever and blister-like sores between the hooves, in the mouth and on the tongue and lips.
Within days of submitting the samples to a genetic sequencing service, Soufien Sghaier, a virologist at the Virology Laboratory at the Institute of Veterinary Research of Tunisia (IRVT), received results that helped confirm the circulating strain of FMD. Sghaier was able to notify veterinary authorities to implement control measures to prevent the disease from spreading. The timely confirmation was made possible by the IAEA, in partnership with the Food and Agriculture Organization of the United Nations (FAO), which facilitates the sequencing service and provides the training needed to process the results.
"We received the sequencing results from a FMD suspicion very quickly. Samples were sent to a laboratory in Berlin on Friday, and we received the sequencing results on Monday afternoon," Sghaier explained. "This allowed us to perform an analysis to identify the specific strain of FMD in a record time - less than a week from receipt of samples. By Tuesday, we sent the report on the FMD strain to the veterinary authorities." The strain of FMD needs to be identified to select or develop an effective vaccine.
Genetic sequencing is important to determine if a circulating disease is endemic - or typically found in a certain area - or transferred from another region. "Genetic sequencing can help to understand which cluster a pathogen - an organism that causes disease - belongs to and which vaccine is effective against the pathogen," said Ivancho Naletoski, Animal Health Officer at the Joint FAO/IAEA Centre of Nuclear Techniques in Food and Agriculture. "Sequencing is also important in helping to identify the patterns of mutation of the pathogens." Based on genetic sequencing, a phylogenetic tree can be created, which maps the lineage of a species.
"With our phylogenetic analysis, we determined that we already had a vaccine that could protect our cattle. The veterinary authorities implemented perifocal vaccination to reduce the risk of FMD spreading," Sghaier said. Perifocal vaccination, or buffer vaccination, is implemented within a zone around the affected area to prevent spill over of the virus to other regions.
The IAEA/FAO genetic sequencing service
The Joint FAO/IAEA Centre launched its genetic sequencing service - available at no cost - five years ago to enable countries to perform sequencing for in depth analysis of pathogens. Since then, more than 5 300 samples have been submitted by 30 laboratories from 24 countries across Africa, Asia and the Pacific, Europe and Latin America. African swine fever, astrovirus, avian influenza, capripox, coronavirus, lyssavirus, Newcastle disease, porcine circovirus 2, peste des petits ruminants and West Nile virus are the ten most frequent pathogens sequenced.
"Installing genetic sequencing technologies in local laboratories is quite expensive," Naletoski said. "There is not a massive need to sequence every single isolate, only a few samples from selected outbreaks are needed. In terms of economic feasibility, it is wise to enable a pipeline for counterparts to have access to a sequencing service." The IAEA has developed and disseminated step-by-step technical instructions to process raw data and generate phylogenetic trees for locally circulating pathogens based on results provided.
The Joint FAO/IAEA Centre hosted training courses for laboratories on how to use the service in 2017 and 2018 in Morocco and Argentina, respectively. A virtual introductory course for the generic sequencing service is scheduled under the Zoonotic Disease Integrated Action (ZODIAC) initiative at the end of April 2022, which will be followed by face-to-face trainings.
The benefit of service is twofold. On the national level, the service plays a role in disease monitoring programmes. On the global level, the service supports studies and contributes to genetic sequencing databases accessible to the global scientific community. Thus far, more than 30 articles have been published in peer-reviewed journals based on results obtained through the sequencing service with tens of sequences published on the open-source global databases, GenBank and GISAID.
