Molecular analysis of hemagglutinin-1 fragment of avian influenza H5N1 viruses isolated from chicken farms in Indonesia from 2008 to 2010

Epizootiology, Clinical Signs, and Phylogenetic Analysis of Fowl Adenovirus in Chicken Farms in Indonesia from 2018 to 2019

Fowl adenovirus (FAdV) infection is an emerging problem in the world poultry industry, especially in broilers, as the causal agent of inclusion body hepatitis or hepatitis-hydropericardium syndrome. From December 2017 to January 2019, we recorded 116 cases of suspected hepatitis-hydropericardium syndrome in chicken farms throughout Indonesia. Necropsy was done on each farm site with three to five freshly dead birds per farm. Tissue samples were collected in virus transport medium and frozen at -20 C. The virus was cultivated in 9-day-old fertilized specific-pathogenic-free chicken eggs. FAdV was detected using polymerase chain reaction with a published primer set. The polymerase chain reaction products were sequenced and subjected to a BLAST search. The phylogeny was inferred using the neighbor-joining method and tested using the bootstrap test. FadV-D and -E are present in Indonesia and confirmed in 40 of 116 suspected cases. The affected chicken ages were 27.27 ± 8.94 days. Most affected farms were raising broiler chickens. The only typical clinical sign was unusual daily mortality of >1%, while the three most frequent pathologic lesions were swelling and hemorrhage of kidney and liver, as well as hydropericardium. To reduce economic loss, a vaccine should be developed immediately.

Identification of avian influenza virus subtype H9N2 in chicken farms in Indonesia

Avian influenza virus subtype H9N2 (AIV-H9N2) has become established in domestic poultry in Asia and Africa. AIV-H9N2 has not been reported previously in Indonesia. Here we describe the presence of AIV-H9N2 in chicken farms in Indonesia. Ninety-nine cases were observed in various provinces in Indonesia. Clinical signs, pathologic lesions and egg production were recorded. Confirmation was made using virus isolation, reverse transcriptase PCR (RT-PCR), and sequencing. To construct hemaglutinin (HA) phylogeny, the secondary data of Eurasian lineages were downloaded from GenBank. For neuraminidase, five sequences with the highest similarities with every sequence found in this study were downloaded. Phylogeny was inferred using Neighbor-Joining method in MEGA6 package. Forty-nine AIV-H9N2-positive cases were observed, of which 35 were tested positive for AIV-H9N2 only. The age of the infected chickens was 43.17 ± 16.56 weeks, and their egg production was 35.85 ± 17.80% lower than before outbreak. BLAST search revealed that the nucleotide sequence of the HA-encoding gene identified in this study shared 98% sequence identity with that of A/Muscovy duck/Vietnam/LBM719/2014(H9N2), while its neuraminidase-encoding gene sequences shared 94%, 98%, and 100% identities with three different influenza viruses. The phylogeny shows that the HA of AIV-H9N2 found in this study forms distinct cluster with some Vietnam and China's sequence data. The NA sequence data form three distinct clusters. We conclude that AIV-H9N2 is widespread in many provinces in Indonesia. To lessen economic losses to the poultry industry, flock biosecurity and vaccination against this virus subtype should be implemented rapidly. Thorough and rigid AIV surveillance is paramount to prevent further veterinary and public health consequences of the circulation of this virus in Indonesia.

Vaccine efficacy against Indonesian Highly Pathogenic Avian Influenza H5N1: systematic review and meta-analysis

Indonesia has implemented multiple strategies to control Highly Pathogenic Avian Influenza H5N1 (HPAI/H5N1), including the licensure and use of multiple vaccine formulations. The continuous drift of Indonesian HPAI/H5N1 viruses and emergence of a new clade in 2012 that became dominant in 2016, demands the assessment of commercial vaccine formulations against Indonesian field viruses. Seven databases were explored to identify relevant literature reporting performance of commercial vaccines against Indonesian HPAI/H5N1 viruses. After methodological assessment, data were collated and analyzed to report immunogenicity and vaccine efficacy (VE) to prevent respiratory and cloacal viral shedding 2-day post challenge, and death at the end of the follow-up period. Meta-analyses were performed to assess VE consistency of alternative formulations and to explore sources of heterogeneity in VE. In total, 65 studies and 46 vaccine formulations from 13 articles were grouped per OIE's VE protocols (group 1) and variations of it (groups 2,3,4). We found that concurrence of vaccine-seed and challenge-viruses in a clade designation might be a better proxy of VE than current estimates based on vaccine-homologous HI antibody titers, particularly against current fourth order clade viruses (groups 1&2). Prime-boosting was efficacious across different chicken breeds (group 3), and early vaccination may increase the risk of death (group 4). One Indonesian vaccine was tested against the new dominant clade, conferring consistent protection in chickens but not in ducks. Meta-analyses revealed high inconsistency (I²≥75%) and inefficacy of LPAI formulations against current field viruses, while potential sources of inconsistent VE were formulation of seed-homologous vaccines and the species vaccinated. We conclude that the VE of commercial vaccines in Indonesia changes as Indonesian HPAI/H5N1 evolve into new clades, which should warrant continuous matching between vaccine-seeds and emerging HPAI/H5N1. Furthermore, given the characteristics of the new Indonesian dominant HPAI/H5N1 clade, further studies to confirm VE across species are warranted.