E-Learning Course on Bioinformatics of Animal Viruses

Nucleotide sequencing has become a very popular technique for diagnosis and characterization of pathogens and is accessible to most veterinary practices.

A nucleotide sequence provides information on the nature of the pathogen, its source and its main characteristics such as strain, virulence and drug resistance.

Bioinformatics provides tools to gather, store, and analyse these biological sequences, by dissecting and interpreting biological data from different organisms

The Food and Agriculture Organization of the United Nations (FAO) and the International Atomic Energy Agency (IAEA)  in collaboration with the Swiss Institute of Bioinformatics (SIB)  have developed a new e-learning course on bioinformatics of animal viruses to improve prevention and control of animal diseases.


The first module entitled "Phylogenetics of Animal Pathogens: Basic Principles and Applications" was released in 2013. Designed as a self-learning module for animal health laboratory staff, it is organized in four chapters: 1) basic notions on phylogenetic trees;         Book by Isaac Salazar
2) how to build phylogenetic trees; 3) how to interpret phylogenetic trees, and 4) exercises. Many examples are included such as influenza, Foot-and-Mouth Disease and Peste des Petits Ruminants viruses. The entire course can be completed in approximately 4 hours.
The second module, entitled “BLAST and Multiple Sequence Alignment (MSA) Programs” was released in May 2014. This module is subdivided into two parts that outline two of the main bioinformatics tools that help with the analysis of large sequences: Basic Local Alignment Search Tool (BLAST) and Multiple Sequence Alignment (MSA). This new module requires approx. 2 hours to complete the BLAST chapter and 2 more hours are needed to complete the MSA chapter.

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African Swine Fever on the Move – China, the EU and FAO Assessing Preparedness in East and Southeast Asia, the Region with >50% of the World Pig Population

By M Djuric, DVM

African Swine Fever (ASF) continues to spread in traditionally endemic sub-Saharan Africa, but it is also expanding into previously ASF-free countries with a new front opening up along the Caucasus and Eastern Europe.



The risk of ASF entering China is of particular concern since the country keeps almost half of the worldwide pig population. China is also the biggest importer of pork and has very strong links with ASF-infected countries in Africa. China also shares a border with the ASF-endemic Russian Federation.

China and Asia in general have never encountered ASF, and therefore there is a concern that the region may be unprepared for a potential outbreak of ASF, which could have catastrophic consequences on global pork supply.








To build ASF preparedness and to address the policy gaps, the European Union (EU) -funded LinkTADs research consortium brought together 40 experts from the EU and Asia for the “African Swine Fever Policy Event” in Beijing on 24 November 2014.

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Global Milk Production Increasing at Fast Pace

By Miroslav Djuric, Editor (Dairy Science Abstracts)

Global milk production in 2012 is forecast to reach 760 million tonnes, according to a new report published in the Food Outlook by the United Nation’s Food and Agriculture Organisation (FAO). This would represent an annual increase of 3%, largely due to the increased production in Asia, Oceania and South America.

DairybIn Asia, milk production is expected to record strong growth in India, China, Pakistan and Turkey, mainly in response to growing domestic demand for dairy products. In India, the world’s largest milk producing country, milk production in 2012 is forecast to rise by 5 million tonnes to 132 million tonnes compared with the previous year. Herd size expansion, rather than rising productivity, is the principal reason behind the rise in India’s milk production, where more than 55% of the total milk production comes from buffaloes.

In Oceania, an increase in herd size in New Zealand combined with favourable weather conditions and prolonged period of high prices for dairy products is expected to result in a staggering growth rate of 9% compared with the previous year. A growth rate of 4% is expected in Australia.

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Foot-and-Mouth Disease (FMD) Targeted for Eradication

By Miroslav Djuric, DVM

Following the successful eradication of Rinderpest (Cattle plague, see blog), veterinarians, farmers and donors across the World are turning their focus to combat Foot-and-Mouth Disease (FMD) on a global scale. The FAO and the World Organisation for Animal Health (OIE) have developed a detailed strategy for FMD control under the umbrella of their Global Framework for the Progressive Control of Transboundary Animal Diseases (GF-TADs). However, it is clear that only a massive commitment of national and international resources can make FMD eradication possible, as surveillance and monitoring over a long period is required.


FMD is a highly infectious disease caused by a picornavirus, which affects cloven-hoofed animals, in particular cattle, sheep, goats, pigs and deer. Other animals including camelids and elephants can also be affected. The disease is notifiable, which means that the local veterinary services must be notified immediately if FMD is suspected.Although FMD does not pose a direct threat to human health, and is rarely fatal in animals, it can cause reduced milk yield, weight loss and lower fertility.

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Recent developments in the world of biofuels

Water hyacinth mat on river Opinions on the use of crops for biofuel and bioenergy continue to be polarized – are they a ‘good thing’ or not? When are they a ‘good thing’? Who benefits?

How do you measure the impacts and their interactions at a local, national and international level on food security, land resources, water, greenhouse gas emissions, energy security, poverty, social development, sustainability…and try to remain impartial and objective?

The Bioenergy and Food Security (BEFS) Analytical Framework developed by FAO aims to address these issues by providing an analytical framework and set of tools which can be used to measure these impacts. Using a step-by-step methodology, the goal is to help policymakers make informed decisions on whether development of bioenergy is a viable option for their country and identify suitable policies that will maximize benefits and minimize risks.

Three separate reports describe the implementation of the framework in Peru, Tanzania and Thailand, with suggestions for suitable options for each country.

Another source of information is Recent developments in the world of biofuels, a critical analysis by CABI scientists of the latest research on the potential and realities of growing and processing jatropha, algae and biomass for biofuels or bioenergy – see Biofuels Information Exchange.

Land use and poverty alleviation issues in Mozambique, Tanzania, Kenya, India, China and Brazil are discussed as well as research into using problematic invasive aquatic weeds (water hyacinth – pictured above – is a favourite) for bioenergy. The pros and cons of algal biofuels, and the latest technology for concentrating biomass energy into a more energy-dense form which makes transport to a processing plant more feasible are discussed, and more…

BIE is an impartial site for exchanging information on biofuels research – the exchange on pests of jatropha has generated the longest running discussion over the last 2 years – and the site provides open access to documents on biofuels, including the peer-reviewed Land Use Change: Science and Policy Review (copublished with Hart Energy Consulting) and abstracts of the latest research on biofuels from the CAB Abstracts database.

For a comprehensive resource of published information on research into man’s impact on the environment see CABI’s Environmental Impact which has a special section on biofuels research information – abstracts, books, book chapters, reports, reviews.

…get out of the kitchen

One of the implications of all this energy we waste to swap coffee and wheat
is that we’re giving climate change a helping hand. The contribution made by
today’s food production systems to climate change globally will have tremendous
impacts on the food it produces in the future. So this week, in a document much
less concise that Peter Baker’s BBC article, the FAO released ‘Climate
change – Implications for Food Safety

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Biodiversity – The more the merrier!

May 22nd is the International Day for Biological Diversity
. This year’s
theme is ‘Biodiversity in
‘. According to the Convention on
Biodiversity who are co-promoting the day’s festivities along with such
luminaries of food and nutrition as the FAO, modern food production is
responsible for both increasing and decreasing biodiversity. One of the things
the CBD is interested in is stabilising the balance, so we can benefit from
improved food (and fuel) production, whilst preserving species (the ‘genetic
treasures’) that could become the food ingredients and medicines of the future.

Agriculture is mostly concerned with efficient production of nutritious, safe
foodstuffs. To do this involves the promotion and prevention of growth of an
enormous number of different species, soil, plant and animal-based organisms of
various shapes and sizes – minimising the pests and pathogens while promoting
the useful and edible ones.

Biological diversity in food is a very diverse subject area indeed.

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