Co‐circulation and characterization of HPAI‐H5N1 and LPAI‐H9N2 recovered from a duck farm, Yogyakarta, Indonesia

Abstract

In July 2016, an avian influenza outbreak in duck farms in Yogyakarta province was reported to Disease Investigation Center (DIC), Wates, Indonesia, with approximately 1,000 ducks died or culled. In this study, two avian influenza (AI) virus subtypes, A/duck/Bantul/04161291‐OR/2016 (H5N1) and A/duck/Bantul/04161291‐OP/2016 (H9N2) isolated from ducks in the same farm during an AI outbreak in Bantul district, Yogyakarta province, were sequenced and characterized. Our results showed that H5N1 virus was closely related to the highly pathogenic AI (HPAI) H5N1 of clade 2.3.2.1c, while the H9N2 virus was clustered with LPAI viruses from China, Vietnam and Indonesia H9N2 (CVI lineage). Genetic analysis revealed virulence characteristics for both in avian and in mammalian species. In summary, co‐circulation of HPAI‐H5N1 of clade 2.3.2.1c and LPAI‐H9N2 was identified in a duck farm during an AI outbreak in Yogyakarta province, Indonesia. Our findings raise a concern of the potential risk of the viruses, which could increase viral transmission and/or threat to human health. Routine surveillance of avian influenza viruses should be continuously conducted to understand the dynamic and diversity of the viruses for influenza prevention and control in Indonesia and SEA region.

Mapping emerging trends and South–South cooperation in regional knowledge networks: A bibliometric analysis of avian influenza research in Southeast Asia

“…Furthermore, only 4 (4.8%) of these intraregional papers can be categorised as purely South–South collaborations, with no involvement of co‐authors from UN agencies or research organisations associated with high‐income countries. This small subset of papers includes two papers focused on disease epidemiology in Indonesia including authors from Thailand and Indonesia (Eyanoer et al, 2011; Lestari et al, 2019), one paper on disease epidemiology in Myanmar involving authors from Myanmar and Thailand (Mon et al, 2012), and one paper on the efficacy of animal vaccination involving Thailand and Vietnam (Huynh et al, 2019).…”

“…This was followed by Japan (10; 14.9%), France (9; 13.4%), the United Kingdom (7; 10.4%) and other countries or categories including charities and multilateral organisations. Only a handful of papers reported funding from countries in the region: five papers acknowledged financial support from the Thai Research Council and/or Thai universities (Huynh et al, 2019; Lestari et al, 2019; Mon et al, 2012; Monteerarat et al, 2010; Win et al, 2014) and one paper benefitted from a scholarship by the Indonesia Endowment Fund for Education (Indrawan et al, 2018).…”

“…Furthermore, only 4 (4.8%) of these intraregional papers can be categorised as purely South-South collaborations, with no involvement of co-authors from UN agencies or research organisations associated with high-income countries. This small subset of papers includes two papers focused on disease epidemiology in Indonesia including authors from Thailand and Indonesia (Eyanoer et al, 2011;Lestari et al, 2019) T A B L E 2 Heat-map of international collaborations on avian influenza research for countries in Southeast Asia, indexed in the Web of Science, 2004-2019. The most frequent collaborators are listed on the vertical axis and ordered by volume of their total collaboration with countries in the region.…”

Avian Influenza Virus Endemicity During the Covid-19 Pandemic in Indonesia

“…The genetic variation of AIV circulation in previous studies showed that the influenza viruses in Indonesia identified in 2003-2020 showed that the subtype H5N1 virus clade 2.1.3, clade 2.3.2, subtype H9N2 and reassortant influenza viruses and other influenza virus subtypes were circulating in the live poultry market and farm in Indonesia. In 2019, co-circulation of HPAI-H5N1 clade 2.3.2.1c and LPAI-H9N2 were identified in duck farms during an AI outbreak in Yogyakarta province, Indonesia [21,22]. Circulation of several viruses in the environment has the opportunity to cause co-infection and subsequently resulted in viral mutations (antigenic drift and antigenic shift), including reassortment events between the H5N1 virus and other influenza viruses including H3 subtype [23,24].…”

Risk factors for H9N2 contamination in live bird markets of the Greater Jakarta, Indonesia

“…Jonas et al (13) conducted research mapping H9N2 infection cases and demonstrated that the virus had spread to Java, Sumatra, Kalimantan, Sulawesi, and Bali. Infections with these viruses led to the death of 1000 ducks in Bantul Regency, Yogyakarta, in 2016 (14). The disease also causes respiratory problems in poultry, resulting in a 50-78% decrease in egg production and up to 2.7% mortality in laying hens in the Sidrap District, South Sulawesi (15).…”