APEIR Publication

Authors: Hung Nguyen-Viet, Suwit Chotinun, Esther Schelling, Winda Widyastuti, Nguyen Viet Khong, Manish Kakkar, Arlyne Beeche, Fang Jing, Boualam Khamlome, Sothyra Tum, Wiku Adisasmito

Affiliation: Various Institution

Source: International Journal of Public Health


It is equally important to collaborate across sectors in the Antimicrobial (AMR) and Antimicrobial Use (AMU) because it is not feasible to do it alone. The concern is also to expand partnership from South East Asia to South Asia to strengthen the cross regional opportunity in learning from each other. The researchers proposed for an integrated AMR surveillance system using One Health approach to understand agriculture and health in Asia. The One Health/ Eco-health” interventions to reduce AMR-related human, animal and environmental burdens need to be developed, implemented and monitored. This requires the participation of key stakeholders from the private-, policy- and health-sectors to work collaboratively to reduce these burdens, advance peoples’ health, and grow robust economic”.

Authors: Yuhai Bi, Zhenjie Zhang, Wenjun Liu, Yanbo Yin, Jianmin Hong, Xiangdong Li, Haiming Wang, Gary Wong, Jianjun Chen, Yunfeng Li, Wendong Ru, Ruyi Gao, Di Liu, Yingxia Liu, Boping Zhou, George F. Gao, Weifeng Shi & Fumin Lei

Affiliation: Various Institution

Source: Scientific Reports


Approximately 100 migratory birds, including whooper swans and pochards, were found dead in the Sanmenxia Reservoir Area of China during January 2015. The causative agent behind this outbreak was identified as H5N1 highly pathogenic avian influenza virus (HPAIV). Genetic and phylogenetic analyses revealed that this Sanmenxia H5N1 virus was a novel reassortant, possessing a Clade HA gene and a H9N2-derived PB2 gene. Sanmenxia Clade H5N1 viruses possess the closest genetic identity to A/Alberta/01/2014 (H5N1), which recently caused a fatal respiratory infection in Canada with signs of meningoencephalitis, a highly unusual symptom with influenza infections in humans. Furthermore, this virus was shown to be highly pathogenic to both birds and mammals, and demonstrate tropism for the nervous system. Due to the geographical location of Sanmenxia, these novel H5N1 viruses also have the potential to be imported to other regions through the migration of wild birds, similar to the H5N1 outbreak amongst migratory birds in Qinghai Lake during 2005. Therefore, further investigation and monitoring is required to prevent this novel reassortant virus from becoming a new threat to public health.

Authors: Di Liu*, Weifeng Shi*, Yi Shi, Dayan Wang, Haixia Xiao, Wei Li, Yuhai Bi, Ying Wu, Xianbin Li, Jinghua Yan, Wenjun Liu, Guoping Zhao, Weizhong Yang, Yu Wang, Juncai Ma, Yuelong Shu†, Fumin Lei†, George F Gao†

Institution: Various Collaboration


Background On March 30, 2013, a novel avian influenza A H7N9 virus that infects human beings was identifi ed. This virus had been detected in six provinces and municipal cities in China as of April 18, 2013. We correlated genomic sequences from avian infl uenza viruses with ecological information and did phylogenetic and coalescent analyses to extrapolate the potential origins of the virus and possible routes of reassortment events.


We downloaded H7N9 virus genome sequences from the Global Initiative on Sharing Avian Infl uenza Data (GISAID) database and public sequences used from the Influenza Virus Resource. We constructed phylogenetic trees and did 1000 bootstrap replicates for each tree. Two rounds of phylogenetic analyses were done. We used at least 100 closely related sequences for each gene to infer the overall topology, removed suspicious sequences from the trees, and focused on the closest clades to the novel H7N9 viruses. We compared our tree topologies with those from a bayesian evolutionary analysis by sampling trees (BEAST) analysis. We used the bayesian Markov chain Monte Carlo method to jointly estimate phylogenies, divergence times, and other evolutionary parameters for all eight gene fragments. We used sequence alignment and homology-modelling methods to study specifi c mutations regarding phenotypes, specifi cally addressing the human receptor binding properties.


The novel avian infl uenza A H7N9 virus originated from multiple reassortment events. The HA gene might have originated from avian infl uenza viruses of duck origin, and the NA gene might have transferred from migratory birds infected with avian infl uenza viruses along the east Asian fl yway. The six internal genes of this virus probably originated from two diff erent groups of H9N2 avian infl uenza viruses, which were isolated from chickens. Detailed analyses also showed that ducks and chickens probably acted as the intermediate hosts leading to the emergence of this virulent H7N9 virus. Genotypic and potential phenotypic diff erences imply that the isolates causing this outbreak form two separate subclades.

Interpretation The novel avian infl uenza A H7N9 virus might have evolved from at least four origins. Diversity among isolates implies that the H7N9 virus has evolved into at least two different lineages. Unknown intermediate hosts involved might be implicated, extensive global surveillance is needed, and domestic-poultry-to-person transmission should be closely watched in the future.

Funding China Ministry of Science and Technology Project 973, National Natural Science Foundation of China, China Health and Family Planning Commission, Chinese Academy of Sciences.

SHANGHAI, CHINA—If the infl uenza virus known as H7N9 had a bumper sticker, it would read, “HUGE MYSTERY.” Nearly a month after the fi rst reported cases of people infected with the bird fl u virus, many puzzles remain about how it made the jump to humans and adapted to us, how to prevent transmission, and how frequently an infection causes disease.

Authors: Pornpit Silkavute1 *, Dinh Xuan Tung2 and Pongpisut Jongudomsuk1

Institutions: 1 Health Systems Research Institute, Ministry of Public Health, Nonthaburi, Thailand; 2 National Institute of Animal Sciences, Ministry of Agriculture and Rural Development Hanoi, Vietnam

The Asia Partnership on Emerging Infectious Diseases Research (APEIR) was initiated in 2006 to promote regional collaboration in avian influenza research. In 2009, the partnership expanded its scope to include all emerging infectious diseases. APEIR partners include public health and animal researchers, officials and practitioners from Cambodia, China, Lao PDR, Indonesia, Thailand and Vietnam. APEIR has accomplished several major achievements in three key areas of activity: (i) knowledge generation (i.e., through research); (ii) research capacity building (e.g., by developing high-quality research proposals, by planning and conducting joint research projects, by adopting a broader Ecohealth/OneHealth approach); and (iii) policy advocacy (e.g., by disseminating research results to policy makers). This paper describes these achievements, with a focus on the partnership’s five major areas of emerging infectious disease research: wild migratory birds, backyard poultry systems, socio-economic impact, policy analysis, and control measures. We highlight two case studies illustrating how the partnership’s research results are being used to inform policy. We also highlight lessons learned after five years of working hard to build our partnership and the value added by a multi-country, multi-sectoral, multi-disciplinary research partnership like APEIR. Keywords: APEIR; pandemic preparedness; multi-country; multi-sectoral; multi-disciplinary; trust-based research network; emerging infectious disease; policy.

Authors: APEIR Coordinating Office

Institution: APEIR

In 2009 a new pandemic, H1N1 swine flu, threatened to kill millions around the world. Members of APAIR saw the opportunity to apply lessons learned from avian influenza to this and other infectious diseases. Thus, APAIR expanded its scope to include all emerging infectious diseases and was renamed the Asia Partnership on Emerging Infectious Diseases Research (APEIR). APEIR is a regional initiative composed of researchers, practitioners and senior government officials from Cambodia, China, Indonesia, Lao PDR, Thailand and Vietnam. APEIR brings together representatives from more than 30 partner institutions (research institutions, universities, ministry departments) to form an alliance to conduct research, mobilize knowledge, and advocate for policy and practice change in agricultural and public health. A steering committee sets the strategic directions of the work of APEIR and appoints and guides the activities of the partnership.

Authors: Petcharat Pongcharoensuk,1 Wiku Adisasmito,2 Le Minh Sat,3 Pornpit Silkavute,4 Lilis Muchlisoh,2 Pham Cong Hoat3 and Richard Coker5 *

Institutions: Faculty of Pharmacy, Mahidol University, Bangkok, Thailand 2 Department of Health Policy & Administration, Faculty of Public Health, University of Indonesia, Depok, Indonesia 3 Department of Science and Technology in Economical and Technical Sector, Ministry of Science and Technology, Hanoi, Vietnam Health Systems Research Institute, Ministry of Public Health, Nonthaburi, Thailand and 5 Communicable Diseases Policy Research Group (CDPRG), London School of Hygiene and Tropical Medicine, at Mahidol University, Bangkok, Thailand

The aim of this study was to analyse the contemporary policies regarding avian and human pandemic influenza control in three South-East Asia countries: Thailand, Indonesia and Vietnam. An analysis of poultry vaccination policy was used to explore the broader policy of influenza A H5N1 control in the region. The policy of antiviral stockpiling with oseltamivir, a scarce regional resource, was used to explore human pandemic influenza preparedness policy. Several policy analysis theories were applied to analyse the debate on the use of vaccination for poultry and stockpiling of antiviral drugs in each country case study. We conducted a comparative analysis across emergent themes. The study found that whilst Indonesia and Vietnam introduced poultry vaccination programmes, Thailand rejected this policy approach. By contrast, all three countries adopted similar strategic policies for antiviral stockpiling in preparation. In relation to highly pathogenic avian influenza, economic imperatives are of critical importance. Whilst Thailand’s poultry industry is large and principally an export economy, Vietnam’s and Indonesia’s are for domestic consumption. The introduction of a poultry vaccination policy in Thailand would have threatened its potential to trade and had a major impact on its economy. Powerful domestic stakeholders in Vietnam and Indonesia, by contrast, were concerned less about international trade and more about maintaining a healthy domestic poultry population. Evidence on vaccination was drawn upon differently depending upon strategic economic positioning either to support or oppose the policy. With influenza A H5N1 endemic in some countries of the region, these policy differences raise questions around regional coherence of policies and the pursuit of an agreed overarching goal, be that eradication or mitigation. Moreover, whilst economic imperatives have been critically important in guiding policy formulation in the agriculture sector, questions arise regarding whether agriculture sectoral policy is coherent with public health sectoral policy across the region.

Keywords Influenza, pandemic, avian influenza, policy, South-East Asia, Indonesia, Thailand, Vietnam