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Exosomes are membrane vesicles containing proteins, lipids, DNA, mRNA, and micro RNA (miRNA). Exosomal miRNA from donor cells can regulate the gene expression of recipient cells. Here, Ri chickens were divided into resistant (Mx/A; BF2/B21) and susceptible (Mx/G; BF2/B13) trait by genotyping of Mx and BF2 genes. Then, Ri chickens were infected with H5N1, a highly pathogenic avian influenza virus (HPAIV). Exosomes were purified from blood serum of resistant chickens for small RNA sequencing. Sequencing data were analysed using FastQCv0.11.7, Cutadapt 1.16, miRBase v21, non-coding RNA database, RNAcentral 10.0, and miRDeep2. Differentially expressed miRNAs were determined using statistical methods, including fold-change, exactTest using edgeR, and hierarchical clustering. Target genes were predicted using miRDB. Gene ontology analysis was performed using gProfiler. Twenty miRNAs showed significantly different expression patterns between resistant control and infected chickens. Nine miRNAs were up-regulated and 11 miRNAs were down-regulated in the infected chickens compared with that in the control chickens. In target gene analysis, various immune-related genes, such as cytokines, chemokines, and signalling molecules, were detected. In particular, mitogen-activated protein kinase (MAPK) pathway molecules were highly controlled by differentially expressed miRNAs. The result of qRT-PCR for miRNAs was identical with sequencing data and miRNA expression level was higher in resistant than susceptible chickens. This study will help to better understand the host immune response, particularly exosomal miRNA expression against HPAIV H5N1 and could help to determine biomarkers for disease resistance.

The presence of free-grazing ducks (FGD) has consistently been shown to be associated with highly pathogenic avian influenza virus (HPAIV) H5N1 outbreaks in South-East Asia. However, the lack of knowledge about the transmission pathways limits the effectiveness of control efforts. To address this gap, we developed a probabilistic transmission model of HPAIV H5N1 in the nomadic FGD production system in Viet Nam, assuming different scenarios to address parameter uncertainty. Results suggested that HPAIV H5N1 could spread within the nomadic FGD production system, with an estimated flock-level effective reproduction number (re) ranging from 2.16 (95% confidence interval (CI): 1.39-3.49) to 6.10 (95%CI: 3.93-9.85) depending on the scenario. Indirect transmission via boats and trucks was shown to be the main transmission route in all scenarios. Results suggest that re could be reduced below one with 95% confidence if 86% of FGD flocks were vaccinated in the best-case scenario or 95% in the worst-case scenario. If vaccination was combined with cleaning and disinfection of transport vehicles twice a week, vaccination coverage could be lowered to 60% in the best-case scenario. These findings are of particular relevance for prioritising interventions for effective control of HPAIV in nomadic free-grazing duck production systems.

In Southeast Asia, surveillance at live bird markets (LBMs) has been identified as crucial for detecting avian influenza viruses (AIV) and reducing the risk of human infections. However, the design of effective surveillance systems in LBMs remains complex given the rapid turn-over of poultry. We developed a deterministic transmission model to provide guidance for optimizing AIV surveillance efforts. The model was calibrated to fit one of the largest LBMs in northern Vietnam at high risk of low pathogenic H7N9 virus introduction from China to identify the surveillance strategy that optimizes H7N9 detection. Results show that (i) using a portable diagnostic device would slightly reduce the number of infected birds leaving the LBM before the first detection, as compared to a laboratory-based diagnostic strategy, (ii) H7N9 detection could become more timely by sampling birds staying overnight, just before new susceptible birds are introduced at the beginning of a working day, and (iii) banning birds staying overnight would represent an effective intervention to reduce the risk of H7N9 spread but would decrease the likelihood of virus detection if introduced. These strategies should receive high priority in Vietnam and other Asian countries at risk of H7N9 introduction. ISSN:1742-5689 ISSN:1742-5662

International audience; Interlocked challenges of climate change, biodiversity loss, and land degradation require transformative interventions in the land management and food production sectors to reduce carbon emissions, strengthen adaptive capacity, and increase food security. However, deciding which interventions to pursue and understanding their relative co-benefits with and trade-offs against different social and environmental goals have been difficult without comparisons across a range of possible actions. This study examined 40 different options, implemented through land management, value chains, or risk management, for their relative impacts across 18 Nature's Contributions to People (NCPs) and the 17 Sustainable Development Goals (SDGs). We find that a relatively small number of interventions show positive synergies with both SDGs and NCPs with no significant adverse trade-offs; these include improved cropland management, improved grazing land management, improved livestock management, agroforestry, integrated water management, increased soil organic carbon content, reduced soil erosion, salinization, and compaction, fire management, reduced landslides and hazards, reduced pollution, reduced post-harvest losses, improved energy use in food systems, and disaster risk management. Several interventions show potentially significant negative impacts on both SDGs and NCPs; these include bioenergy and bioenergy with carbon capture and storage, afforestation, and some risk sharing measures, like commercial crop insurance. Our results demonstrate that a better understanding of co-benefits and trade-offs of different policy approaches can help decision-makers choose the more effective, or at the very minimum, more benign interventions for implementation.

International audience; The concept of One Health (OH) promotes the decompartmentalisation of human, animal, and ecosystem health for the more efficient and sustainable governance of complex health issues. This means that traditional boundaries between disciplines and sectors must be transgressed and that all relevant stakeholders must be involved in the definition and management of health problems. International efforts have been made to strengthen collaboration across sectors and disciplines and OH surveillance is strongly encouraged at global, national and local-level to efficiently manage hazards involving humans, animals and ecosystems.This concept is intuitively appealing and would suggest the enhanced performance and cost-effectiveness of surveillance systems, as compared to more conventional approaches. Nevertheless, confusion and uncertainty regarding the practical application, outcomes and impacts prevail. We believe that this is due to the lack of a conceptual and methodological framework which would (i) define the characteristics of OH surveillance, and (ii) identify the appropriate mechanisms for inter-sectoral and multi-disciplinary collaboration, to ensure that the surveillance system performs well, with regard to the objective, the context and the health hazard under surveillance.The objective of the study is to define the organisational and functional characteristics of OH surveillance systems, the context in which they are implemented, as well as the influential factors which may obstruct or support their implementation and performance. To achieve this, a systematic literature review of existing OH surveillance systems was conducted using the Prisma guidelines. The selected systems were assessed according to 38 predetermined variables. These allowed the characterisation of their objectives, organisation, functioning, performance and benefits. Data extraction was conducted using a spreadsheet and a database was built using an electronic multiple-choice questionnaire.The literature search identified a total of 1635 records. After the screening phase, 31 references were kept and 22 additional references retrieved from bibliographies were added. From these 53 selected documents, we retrieved 41 different surveillance systems in line with the definition proposed in this study. The analysis of this database enabled the identification of different dimensions and areas of collaboration. Barriers and levers for the implementation of OH surveillance systems were also identified and discussed.Based on our results, we propose a framework to characterise the organisation of collaboration for the governance and operation of an effective OH surveillance system.

International audience; Currently, the pandemic caused by a novel coronavirus, namely severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is one of the most serious issues worldwide. SARS-CoV-2 was first observed in Wuhan, China, on December 31, 2019; this disease has been rapidly spreading worldwide. Iran was the first Middle East country to report a coronavirus death, it has been severely affected. Therefore, it is crucial to forecast the pandemic spread in Iran. This study aims to develop a prediction model for the daily total confirmed cases, total confirmed new cases, total deaths, total new deaths, growth rate in confirmed cases, and growth rate in deaths. The model utilizes SARS-CoV-2 daily data, which are mainly collected from the official website of the European Centre for Disease Prevention and Control from February 20 to May 04, 2020 and other appropriated references. Autoregressive integrated moving average (ARIMA) is employed to forecast the trend of the pandemic spread. The ARIMA model predicts that Iran can easily exhibit an increase in the daily total confirmed cases and the total deaths, while the daily total confirmed new cases, total new deaths, and growth rate in confirmed cases/deaths becomes stable in the near future. This study predicts that Iran can control the SARS-CoV-2 disease in the near future. The ARIMA model can rapidly aid in forecasting patients and rendering a better preparedness plan in Iran.

There is a clear need for transformative change in the land management and food production sectors to address the global land challenges of climate change mitigation, climate change adaptation, combatting land degradation and desertification, and delivering food security (referred to hereafter as “land challenges”). We assess the potential for 40 practices to address these land challenges and find that: Nine options deliver medium to large benefits for all four land challenges. A further two options have no global estimates for adaptation, but have medium to large benefits for all other land challenges. Five options have large mitigation potential (>3 Gt CO2eq/year) without adverse impacts on the other land challenges. Five options have moderate mitigation potential, with no adverse impacts on the other land challenges. Sixteen practices have large adaptation potential (>25 million people benefit), without adverse side effects on other land challenges. Most practices can be applied without competing for available land. However, seven options could result in competition for land. A large number of practices do not require dedicated land, including several land management options, all value chain options, and all risk management options. Four options could greatly increase competition for land if applied at a large scale, though the impact is scale and context specific, highlighting the need for safeguards to ensure that expansion of land for mitigation does not impact natural systems and food security. A number of practices, such as increased food productivity, dietary change and reduced food loss and waste, can reduce demand for land conversion, thereby potentially freeing‐up land and creating opportunities for enhanced implementation of other practices, making them important components of portfolios of practices to address the combined land challenges., There is a clear need for transformative change in the land management and food production sectors to address the global land challenges of climate change mitigation, climate change adaptation, combatting land degradation and desertification, and delivering food security (referred to hereafter as “land challenges”). We assess the potential for 40 practices to address these land challenges and find that most practices deliver across all land challenges. Some practices could result in competition for land, but those that reduce demand for land conversion potentially free‐up land, creating opportunities for enhanced implementation of other practices, making them important for addressing combined land challenge.

Live bird markets (LBMs) are major targets for avian influenza virus (AIV) surveillance programmes. While sampling the LBM environment has become a widely used alternative to the labour-intensive sampling of live poultry, the design of surveillance programmes and the interpretation of their results are compromised by the lack of knowledge about the effectiveness of these sampling strategies. We used latent class models and a unique empirical dataset collated in Vietnamese LBMs to estimate the sensitivity and specificity of five different sample types for detecting AIVs subtypes H5N1 and H5N6: oropharyngeal duck samples, solid and liquid wastes, poultry drinking water and faeces. Results suggest that the sensitivity of environmental samples for detecting H5N1 viruses is equivalent to that of oropharyngeal duck samples; however, taking oropharyngeal duck samples was estimated to be more effective in detecting H5N6 viruses than taking any of the four environmental samples. This study also stressed that the specificity of the current surveillance strategy in LBMs was not optimal leading to some false positive LBMs. Using simulations, we identified 42 sampling strategies more parsimonious than the current strategy and expected to be highly sensitive for both viruses at the LBM level. All of these strategies involved the collection of both environmental and oropharyngeal duck samples.

International audience; Highly pathogenic avian influenza (HPAI) viruses continue to threaten smallholder poultry producers in several Southeast Asian countries, including Vietnam. In particular , the free-grazing duck system has been repeatedly highlighted as a major risk factor for HPAI outbreaks. Free-grazing ducks, which scavenge on rice paddies after the harvest, account for a large proportion of the duck population in Vietnam and the wider Southeast Asian region. However, the structure and dynamics of the free-grazing duck production from farm to consumption has not been described for Vietnam. In this study, we used a value chain approach to provide a complete picture of the actors involved in the production and marketing of free-grazing duck eggs and spent layer ducks, as well as to investigate the governance structure of this food system. Group interviews and key informant interviews were conducted in two provinces located in the Mekong River Delta (MRD) and the Red River Delta (RRD). The results presented here highlight similarities and differences in farming and trade practices between the two provinces. The trade of spent layer ducks involved large volumes of live ducks being sent to China and Cambodia for consumption , generating a substantial risk of transboundary spread of pathogens, including HPAI viruses. We describe the major role of "duck yards", which act as hubs in the northbound trade of spent layer ducks. These yards should be considered as essential links in the value chain of spent layer ducks when considering HPAI surveillance and control. The veterinary authorities are only marginally involved in the value chain activities, and their influence could be strengthened by increasing surveillance activities for instance in duck yards. Last, we discuss the dynamics of the duck value chain and further implications for future HPAI management policies.

Foot-and-mouth disease (FMD) is a highly contagious disease of livestock affecting animal production and trade throughout Asia and Africa. Understanding FMD virus (FMDV) global movements and evolution can help to reconstruct the disease spread between endemic regions and predict the risks of incursion into FMD-free countries. Global expansion of a single FMDV lineage is rare but can result in severe economic consequences. Using extensive sequence data we have reconstructed the global space-time transmission history of the O/ME-SA/Ind-2001 lineage (which normally circulates in the Indian sub-continent) providing evidence of at least 15 independent escapes during 2013–2017 that have led to outbreaks in North Africa, the Middle East, Southeast Asia, the Far East and the FMD-free islands of Mauritius. We demonstrated that sequence heterogeneity of this emerging FMDV lineage is accommodated within two co-evolving divergent sublineages and that recombination by exchange of capsid-coding sequences can impact upon the reconstructed evolutionary histories. Thus, we recommend that only sequences encoding the outer capsid proteins should be used for broad-scale phylogeographical reconstruction. These data emphasise the importance of the Indian subcontinent as a source of FMDV that can spread across large distances and illustrates the impact of FMDV genome recombination on FMDV molecular epidemiology.

International audience; The naturally acquired microbiota of Anopheles can influence vector's susceptibility to Plasmodium and its capacity to transmit them. Microbiota modification is a new challenge to limit disease transmission but it still needs advanced knowledges on bacterial community in Anopheles, especially in wild and infected specimens from diverse origin and species. Bacterial culture and 16S rRNA gene-PCR associated to Temporal Temperature Gradient Electrophoresis (TTGE) were applied to explore the bacterial diversity in the abdomen of 100 wild specimens (eight Anopheles species) collected in the Binh Phuoc Province, Vietnam. Culture and PCR-TTGE were complementary. The bacterial richness of the mosquito collection encompassed 105 genera belonging to seven phyla, mostly Proteobacteria, Firmicutes, and Actinobacteria. Staphylococcus, Clostridium, and Bacillus in Firmicutes were the most prevalent genera. However, Proteobacteria represented by 57 genera was the most diversified phylum in Anopheles microbiota. The high overall of Anopheles-associated bacteria is confirmed with, to our knowledge, 51 genera described for the first time in Anopheles microbiota. However, the diversity per specimen was low with average diversity index and the average Shannon-Wiener score (H) of 4.843 and 5.569, respectively. The most represented bacterial genera were present in

International audience; In Vietnam, serological post H5N1 vaccination surveillance using the HI test is applied to assess the efficiency of the vaccination in addition to virological monitoring. In this paper we report on the evaluations of the performances of the haemagglutination inhibition (HI) test and of a H5-ELISA, using chicken and duck field samples. The evaluations were conducted by comparison with a pseudotyped-based virus neutralization test (H5pp VNT) performed in a reference laboratory and considered as a "gold standard" and also by using methods developed for imperfect reference test. Their global accuracy and best cut-offs were also estimated. Results from the HI test for several haemagglutinin subtypes and from a commercial type A influenza competition ELISA were also compared. The results showed that performance of the HI test was very good in comparison with the H5pp VNT. Data also clearly supported the cut-off of ≥4log(2) used for the HI test for chickens but, a 3log(2) positivity cut-off would be more appropriate for ducks. When compared with the VNT, the H5-ELISA showed poor specificity when using the positivity cut-off specified by the manufacturer but could be used as a screening test if confirmed by the HI test or the H5ppVNT which presents some interests for large scale testing (no need for biosafety level 3 conditions and high performance). A general and highly sensitive pre-screening can also be achieved using the detection of NP-specific antibodies with a competition ELISA. This appears of little interest in a context of high subtypes diversity where only a subtype is targeted for surveillance and control.

International audience; Epidemiological surveys of avian influenza infections rarely focus on backyard poultry systems in remote locations because areas with low levels of poultry production are considered to have little influence on the emergence, re-emergence, persistence or spread of avian influenza viruses. In addition, routine disease investigations in remote areas often are neglected due to the lower availability and relatively high cost of veterinary services there. A bank of avian sera collected in 2005 from ethnic minority households in Ha Giang province (Northern Vietnam), located on the Chinese border, was analysed to estimate the seroprevalence of avian influenza virus (AIV) during a H5N1 epidemic and to identify potential risk factors for infection. The results suggest that the chicken population had been exposed to AIV with a seroprevalence rate of 7.2% [1.45; 10.5]. The H5 and H9 subtypes were identified with a seroprevalence of 3.25% [2.39; 4.11] and 1.12% [0.61; 1.63], respectively. The number of inhabitants in a village and the distance to the main national road were the most influential risk factors of AIV infection, and high-risk clusters were located along the road leading to China. These two results suggest a virus spread through commercial poultry exchanges and a possible introduction of AIV from southern China. Remote areas and small-scale farms may play an under-estimated role in the spread and persistence of AIV.

ACL (avec facteur d'impact); International audience; The effectiveness of animal health surveillance systems depends on their capacity to gather sanitary information from the animal production sector. In order to assess this capacity we analyzed the flow of sanitary information regarding Highly Pathogenic Avian Influenza (HPAI) suspicions in poultry in Vietnam. Participatory methods were applied to assess the type of actors and likelihood of information sharing between actors in case of HPAI suspicion in poultry. While the reporting of HPAI suspicions is mandatory, private actors had more access to information than public actors. Actors of the upstream sector (medicine and feed sellers) played a key role in the diffusion of information. The central role of these actors and the influence of the information flow on the adoption by poultry production stakeholders of behaviors limiting (e.g. prevention measures) or promoting disease transmission (e.g. increased animal movements) should be accounted for in the design of surveillance and control programs.