Impact case study database

The invention of Field Pathogenomics crop disease diagnostic methodology and the establishment of an open-source platform; ‘OpenWheatBlast’ by Kamoun at UEA [ R1 & R2] has transformed plant pathogen diagnosis by providing tools that enable a quick response time to tackle crop disease disasters. This is especially important in low-income countries where growing populations and global warming threaten food security. The International Maize and Wheat Improvement Center (CIMMYT) is responsible for maintaining the health of crops that are responsible for 20% of global calories. The Director of the Global Wheat Program, CIMMYT states that “ The collaboration between CIMMYT and Prof. Kamoun will continue to be vital as global wheat production faces rapidly changing trans-boundary disease threats. The work to date is a blueprint for how we need to respond to crop disease outbreaks in future” [ S1]. Kamoun’s work has achieved impact at multiple levels, including reducing the economic impact on Bangladeshi farmers [ S2]. The Agriculture Minister of Bangladesh states “ The impact of this work has therefore been very considerable in Bangladesh. The open and transparent way in which the data was shared and scientists from Bangladesh were trained was also commendable. Professor Tofazzal Islam [The Director of the Institute of Biotechnology and Genetic Engineering, IBGE] has been an important leader in combatting wheat blast disease and his ongoing collaboration with Professor Kamoun… has had an important and enduring impact on wheat production in this region” [ S3]. In addition, Kamoun’s research has informed international strategies to avoid and combat plant disease disasters [ S6, S7, S8] (described in detail below).

1) Changes to farming practice in Bangladesh, reducing economic loss.

The wheat blast outbreak diagnosed by Kamoun threatened the livelihoods of ~3 million farmers and affected 15,000 hectares of wheat in 2016. It was a direct threat to food security for the 160 million population of Bangladesh, a low-income country, with a highly distributed, resource-poor farming community. The impact of Kamoun’s identification of the precise strain and origin of this pathogen, and open sharing of this information via OpenWheatBlast is recognised by The Minister of Agriculture of Bangladesh who stated that ‘ Knowing this information meant that we were able to draw an effective disease control strategy for Bangladesh to try and limit the spread of the disease” [ S3]. The strategy taken included:

1. Effective pesticides: The Director of IBGE, Bangladesh reported that: ‘Identifying the pathotype of the diseases…allowed effective, specific fungicides that had been used in South America to be provided as management options for farmers… The [Bangladeshi] government suggested farmers change from their usual pesticides and to use specific pesticides, Nativo (Trifloxystrobin and Tebuconazole) for controlling the wheat blast outbreak. This helped to restrict the negative financial and societal impacts of the pathogen by significantly lowering wheat yield loss’ [ S4].

2. Reduction in the amount of wheat grown in Bangladesh to minimise the spread of the disease [ S4, S5]: The Director of IBGE stated that ‘…wheat cultivated area in the blast affected districts was reduced by 52% because the [government] recommended that farmers stop growing wheat and switch to the cultivation of alternate crops such as boro-rice, maize,* [and] lentil’ [ S4].

3. Implementation of crop rotation practices: ‘… the Bangladesh government provided new advice to farmers suggesting that they practice crop rotation… and to cultivate legume or oilseed crops in the wheat blast infected regions for at least three years’ [ S4]. A local farmer affected by the wheat blast outbreak acknowledged that ‘ I didn’t [know what caused the disease] and I burned my entire wheat field. [From the scientists’ research] now I know the disease name and what causes it. [I] got training including farming practice and which fungicide [is best] to use… Now, I mostly cultivate rapeseed and onion [and] I grow a little amount of wheat’ [ S5].

4. Employing resistant wheat strains: The Minister of Agriculture in Bangladesh reported that “ We were also able to draw on knowledge of where this disease had occurred previously in South America and work with the International Maize and Wheat lmprovement Centre (ClMMYT). The research work therefore meant that we could attempt to deploy new, resistant wheat varieties…” [ S3]. CIMMYT translated the knowledge they had gathered from previous Bolivian field trials with ~4500 wheat varieties, to Bangladesh. A new wheat variety (BARI Gom 33) with resistance to the wheat blast strain in Bangladesh was trialled and subsequently released [ S1, S2, S3]. Bangladesh’s national seed board approved this variety for dissemination in 2017, and by 2017-18, the Bangladesh Wheat Research Council had provided BARI Gom 33 seeds for multiplication, and on-farm demonstration in blast prone districts, established by the Department of Agricultural [ S2]. CIMMYT’s Director of the Global Wheat Program stated that: ‘…the impact of Prof. Kamoun’s work in Bangladesh has been considerable. It has enabled a rapid response to an emerging crop disease that immediately threatens food security in a low-income country. The fact that resistant wheat lines are already deployed in the region, is because of this rapid international response, catalysed by Prof. Kamoun’s leadership and commitment to open science.’ [ S1]. This resistant wheat line is estimated to provide a 5.1% increase in yield and ex-ante economic benefits of the dissemination and uptake of the newly approved BARI Gom 33, of between USD230,000 – USD1,600,000 (September 2019) [ S2].

2. Informing international Biosecurity measures to prevent global spread of emerging crop diseases, thereby alleviating yield losses.

The appearance of wheat blast disease in Bangladesh in 2016 was of global concern. As Director of the Global Wheat Program at CIMMYT states: ‘It also presents the potential for spread to the largest wheat producing regions in the Indian sub-continent…[and] is therefore of enormous concern to global food security’ [ S1]. Kamoun’s research enabled a number of measures to ameliorate this global threat, including the adoption of new biosecurity measures on a global stage. The Director of IBGE who worked with Kamoun states that ‘ Bangladesh and many countries also stopped the import of wheat from South American Wheat Blast affected countries. Our transcriptomics data, available in OpenWheatBlast Framework Website also enabled us to develop specific primers for detection of this Wheat Blast fungus. More recently, we used this genomics information to develop a rapid diagnostics system based on the CRISPR-Cas12a enzymes. Subsequently, a molecular diagnosis protocol based on our research findings has been used in quarantine and surveillance practices to identify and control this pathogen in wheat that is imported in Bangladesh and grown in the field’ [ S4].

1. Wheat Blast response in India: The Head of Wheat Pathology at CIMMYT describes how following Kamoun’s identification of the wheat blast pathogen, ‘[t] o avert further spread of wheat blast beyond Bangladesh, the Indian Council for Agricultural Research (ICAR) has implemented in 2017 a temporary ‘wheat holiday’ […], documentation of the occurrence of the wheat blast strain in Bangladesh, particularly in the Indian border area, prompted these actions which served as preventive measures to preempt disastrous outbreaks. With colleagues, we demonstrated how alternative crops to wheat can alleviate the economic burden of the wheat blast holiday in West Bengal’ [ S6a]. CIMMYT scientists calculated the gross return from wheat cultivation in 287,000 hectares across nine districts of West Bengal was USD31,600,000 [ S6b, p.9]. CIMMYT scientists recommended to the Indian Government that farmers in all border districts should cultivate economically viable legumes such as gram (chickpea), urad (an Indian pulse), rapeseed, mustard, and potatoes, instead of wheat [ S4, S6]. This decision was estimated to provide the same gross economic return to the region while disease-control strategies were developed [ S4, S6].

2. Wheat Blast response in Australia: Wheat is critical component to Australia’s economy. It produces 25-30 million tonnes of high-quality grain per annum, and its listed in the top 10 Australian exports (by value). Australia places great emphasis on biosecurity and disease management. The emergence of wheat blast, first in South America, and then Bangladesh prompted questions about the impact wheat blast could have if it arrived in Australia. A national response involved pre-emptive wheat breeding and evaluation of wheat blast resistance in locally adapted wheat germplasm. A Professor in the Research School of Biology at the Australian National University states that “Field Pathogenomics has provided us with very valuable information on pathogen evolution and movement over growing seasons. …Professor Kamoun’s contributions have been significant in enabling Australia to carry out pro-active planning for a potential wheat blast incursion with pre-emptive attempts to breed disease resistance and thereby safeguard wheat production. In addition, the methods developed in his laboratory have been used widely against a wide range of diseases of economic significance in Australia” [ S7].

3. Wheat Blast Response in Zambia: Recently, wheat blast emerged in Zambia – the first report of the disease in Africa. CIMMYT immediately contacted Kamoun and UEA colleagues (November 2020), to characterise the wheat blast pathogen and determine its origin and genetic relatedness [ S1, S6]. This work demonstrates the impact of Field Pathogenomics and OpenWheatBlast initiatives on the wider wheat breeding community, who are turning to Kamoun, for leadership in controlling the spread of this wheat disease.

4. A New Technology for Wheat Rust surveillance in Ethiopia & Europe: Field Pathogenomics has become an integral part of a plant disease surveillance programme called MARPLE diagnostics. A former Postdoctoral Researcher from Kamoun’s Laboratory (currently a Project Leader at the John Innes Centre (JIC)) collaborates in a large international partnership including 7 industrial partners to further developing the Field Pathogenomics methodology [ S8]. They study the global spread of wheat yellow rust pathogen strains, generating unprecedented data resolution about the global diversity of this pathogen. They have used many innovative ideas from Field Pathogenomics methodologies to create a modified version called Mobile And Real-time PLant disEase (MARPLE) diagnostics, swapping reliance on large, immobile Illumina sequencing technology for a portable nanopore MinION sequencer, ensuring capacity building as MARPLE can be used directly in resource-poor regions such as Ethiopia - the largest wheat producer in sub-Sahara Africa - but a high priority country for yellow rust surveillance. Total loss estimates for yellow rust in Ethiopia is approximately USD250,000,000 [ S8]. The precise pathogen/s causing these problems was unknown resulting in further losses caused by ineffective use of pesticides. The Principal Investigator states ‘ training and support for integration of the methodology within the wheat rust early warning system in Ethiopia is underway, however, this is […] on hold due to covid-19’ [ S8].

The implementation of the Field Pathogenomics system in the UK cereal pathogen virulence survey (UKCPVS) has led to changes in the naming system for wheat rust races in the UK that is now much more reflective of the genetic diversity of strains [ S8]. Training events for researchers leading rust surveillance programs across Europe have occurred and work is underway to integrate the MARPLE diagnostics system into UK cereal pathogen virulence survey.

In summary, Kamoun’s research has had a global impact on food security, by changing farming practice and improvements in biosecurity measures to reduce losses of staple crops.

The review commissioned by the WHO ( R3) has informed WHO global guidance. Public policy change through the translation of UEA research has been delivered in 47 countries saving lives.

Driving changes to WHO guidance on sodium intake for adults and children

The updated, expanded systematic review commissioned by WHO formed the scientific basis of WHO sodium guidance for adults and children released in 2012. At page 11 it states “This guideline is based on a review of the epidemiologic literature, including three new systematic reviews conducted by WHO (49-51). One review included a reanalysis of data of a fourth systematic review (36, [ R1] )”. The WHO references 49-51 cited in this quotation were published as R3 in 2013. Not only did this WHO guidance set out recommended daily salt intakes for adults, based on the results of R3, but it contained the first ever WHO recommended intake for children and was a springboard to influencing international sodium intake goals (discussed below). The WHO guidelines were completed in the previous REF period but influenced changes in policy and practice for many nations occurring throughout the current REF period. On the back of this work, as well as being an editor of the Cochrane Heart Group and leading WHO systematic reviews on health effects of dietary fats, Hooper became and has continued to be a core member of the WHO NUGAG subgroup on diet and health.

Influencing International sodium intake goals: General

As global sodium intakes in 2010 were double the safe limits suggested by R3, a target for reduction in mean population sodium intake was included in the WHO Global Action Plan for the Prevention and Control of Noncommunicable Diseases 2013−2020. Citing 2012 WHO guidance driven by UEA research, this reduction was declared essential to enabling a 25% reduction in premature mortality from non-communicable diseases by 2025. The recommendation was endorsed by the World Health Assembly in May 2013 and agreed for collective action by all member states.

Since August 2013, this recommendation, alongside WHO guidance, has gone on to underpin professional and governmental sodium guidance in 47 countries and regions ( S1). For example, European Society of Cardiology and European Society of Hypertension 2018 hypertension guidelines state “Salt restriction to <5g/d is recommended” (Evidence class 1 Level A) as their first lifestyle recommendation for those with hypertension or high-normal blood pressure ( S2, referencing R2 & R3 plus 2 other SRs). The Pan-African Society of Cardiology Taskforce on Hypertension recommends as one of its ten recommendations to “Invest in population-level interventions for preventing hypertension, such as reducing salt intake and obesity levels….” citing “High-quality evidence in nonacutely ill adults shows that reduced sodium intake reduces BP [blood pressure] …” ( S3, referencing R3).

UEA analysed data on sodium intake both before and after 2013 across 190 countries, using data from nationally representative surveys wherever possible. This confirms that concerted efforts including WHO guidance and support (leading to national and professional guidance, policy, education and campaign packages) have reduced sodium intake from a mean of 3.63 g/d (SD 0.8) worldwide in 2004-2012 to 3.55 g/d (SD 0.8) per person since 2013 ( S4).

Greater reductions in salt intake in countries incorporating reviews and/or WHO guidance compared to those who have not

Forty seven of 190 countries had national or professional body sodium guidance citing Hooper’s systematic reviews ( R1, R2, R3) and/or 2012 WHO guidance based on R3 (S4). Falls in national adult sodium intake were on average 146mg/d greater in the 47 citing countries (-191mg/d, 95% CI -355 to -28), than in non-citing countries (-45mg/d, 95% CI -80 to -11), p=0.0045 ( S4), providing highly significant evidence of a link.

Influencing International sodium intake goals: Case Studies and Modelling

i) Changes to US guidelines, sodium intake and health

UEA research and/or resulting new WHO guidance are cited in ten major US guidelines on dietary intakes of sodium published since 2013, including guidance by the American Heart Association, Academy of Nutrition and Dietetics, National Academies of Sciences (US Dietary Reference Intake for Sodium) and American Academy of Paediatrics (all referenced in S1). For example, the American College of Cardiology/American Heart Association Task Force states “ Best proven non-pharmacological interventions: Reduced intake of dietary sodium, optimal goal is <1500mg/d but aim for at least a 1000mg/d reduction in most adults” ( S5, referencing R3 plus one other SR).

US National Health and Nutrition Examination Survey (NHANES) data suggest US sodium intakes fell by 0.06g/d or 2% from 2011-2 to 2015-6 ( S6 & S7). Although this seems a small reduction, modelling estimates that these reductions are associated with reductions of 12,600 US deaths each year and 207,000 DALYs annually (UEA calculations, see below and S8). Sodium reductions in children were even greater (0.12g/d over the same period). If sustained into adulthood these falls would lead to more significant health benefits.

ii) Changes to Japanese guidelines, sodium intakes and health

Dietary Reference Intakes for Japanese (2015) set daily recommended intakes for sodium based on a compromise between the WHO guideline recommendations and current Japanese sodium intakes, to ensure health benefits and a realistic sodium goal. “The 2013 WHO guideline for the general population strongly recommends achieving a dietary salt intake goal of 5 g/day …. the DG [dietary goal] for sodium was set at the median of 5 g/day and the current intake (the median intake from the 2010 and 2011 NHNS)” ( **S9)**]. The 5g/d goal comes directly from R3.

Sodium intake, tracked by the Japanese National Health and Nutrition Survey, fell by 0.26g/d or 8.7%, between 2010 and 2016 ( S10). Modelling suggests that these changes reduced annual deaths by 6300 in Japan, and annual DALYs by 77,000 (UEA calculations, see below and S8).

iii) Changes to European guidelines, sodium intakes and health

The additional sodium reductions associated with European guidance (above and S4) have reduced annual deaths by an estimated 21,200 annually in European Union countries citing the systematic reviews and/or WHO guidance, and DALYs by 279,000 annually (estimated by UEA modelling based on national sodium intake data, S8).

iv) Modelling deaths and DALY reduction due to changes in sodium intake

Modelling is presented in S8. Summarising to assess effects of sodium reductions across the world on mortality and disability adjusted life years (DALYs) assumed that sodium intake of 2g/d would eliminate health risk from superfluous sodium (as calculated by R3 and cited in WHO guidance). As mean global adult sodium intake was 3631mg/d in 2007 ( S4), reduction of 1631mg/d was needed to eliminate excess deaths related to sodium intake. The additional fall of 146mg/d in those countries citing UEA research is the equivalent of 9% of this excess sodium. With respect to deaths The Global Burden of Disease Study 2017 suggests that globally the age-standardised proportion of deaths associated with diet is 22%, of which sodium contributes approximately 23%, so excess sodium underlies 5% of deaths globally (2.5 million deaths). Nine percent of this 5% of deaths is 0.45% of deaths (225,000 deaths annually, S8). A similar calculation for DALYs estimates that if we could reduce sodium intake by 146mg/d across the world we would avoid an extra 4.8million DALYs annually ( S8). Calculations for Europe, Japan and Europe are presented above.