Surveillance at the molecular level: Developing an integrated network for detecting variation in avian influenza viruses in Indonesia

Hartaningsih, Nining; Wibawa, Hendra; Pudjiatmoko,; Rasa, Fadjar Sumping Tjatur; Irianingsih, Sri Handayani; Dharmawan, Rama; Azhar, Muhammad; Siregar, E.S.; McGrane, James; Wong, Frank; Selleck, Paul; Allen, John; Broz, Ivano; Torchetti, Mia Kim; Dauphin, Gwenae͏̈lle; Claes, Filip; Sastraningrat, Wiryadi; Durr, Peter A.

doi:10.1016/j.prevetmed.2015.02.015

Cited by 15 publications

(14 citation statements)

References 37 publications

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“…Also, as it has been the case in Indonesia, several new antigenic H5N1 variants have emerged since vaccination was introduced, all of which required change of the detecting HA antigen (Swayne, et al, 2015 ). Selecting the most optimal H5N1 vaccine strain and HA antigen from an array of emerging variants requires significant resources, which are often not available (Fouchier & Smith, 2010;Hartaningsih, et al, 2015). Unlike the HI test, the MP15 ELISA did not significantly detect the antibody response after vaccination with Mex/232/94 which possess three aa substitutions in the HA274-288 epitope and had only 74% sensitivity but 100 % specificity.…”

Section: Discussionmentioning

confidence: 98%

“…There have been 840 confirmed human cases of avian influenza (AI) due to H5N1 between 2003 and 2015, including 447 deaths (WHO, 2015). H5N1 was first reported in Indonesian poultry in 2003 in Java and has spread to neighbouring islands soon after (Hartaningsih et al, 2015). Subsequently, more than 150 million of poultry were culled or died and this resulted in the introduction of vaccination for poultry in 2004 in areas where H5N1 was prevalent (Spackman & Swayne, 2013).…”

Section: Introductionmentioning

confidence: 99%

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Evaluation of a conserved HA_274–288 epitope to detect antibodies to highly pathogenic avian influenza virus H5N1 in Indonesian commercial poultry

et al. 2016

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A peptide enzyme linked immunosorbent assay (ELISA) based on an epitope in the haemagglutinin (HA) of avian influenza virus H5N1, amino acid positions 274-288 (HA274-288) was evaluated for detection of H5N1-specific antibodies. An optimized ELISA based on the tetrameric form of the HA274-288 epitope designated MP15 gave low background with non-immune chicken sera and detected vaccinated and infected birds. The HA274-288 epitope was highly conserved in Indonesian H5N1 strains and antibody responses were detected in the majority of the vaccinated chickens regardless of the H5N1 strain used for vaccination. The HA274-288 epitope was also conserved in the majority of H5N1 strains from the neighbouring Asian region, and other H5 subtypes potentially allowing for a wider use of the MP15 ELISA in H5N1 vaccinated and infected flocks. The MP15 ELISA results correlated significantly with haemagglutination inhibition (HI) test results and test sensitivity and specificity were 87% and 92%, respectively. The MP15 ELISA titres were significantly higher than the HI titres in all immune sera allowing for sera to be tested at a single dilution of 1:400 which is of advantage in routine surveillance. The study indicated that the MP15 ELISA is potentially useful for serological detection of H5N1 vaccinated or infected poultry and to have some advantages over the standard HI test for routine monitoring of flocks' immunity after vaccination.

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Section: Discussionmentioning

confidence: 98%

Section: Introductionmentioning

confidence: 99%

Evaluation of a conserved HA_274–288 epitope to detect antibodies to highly pathogenic avian influenza virus H5N1 in Indonesian commercial poultry

et al. 2016

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“…Even though the newer clade was found to be slight different than the previously found clade in Indonesia (Dharmayanti et al., ), the virus follow similar molecular clock as the previous clade (Figure ). The difference might be caused by antigenic drift that can occur over time (Hartaningsih et al., ). Therefore, we will recommend the further study will investigate more detailed about the introduction of the HPAI H5N1 in Indonesia.…”

Section: Discussionmentioning

confidence: 99%

Phylogeography of H5N1 avian influenza virus in Indonesia

Njoto

Scotch

Bui

et al. 2018

Transbound Emerg Dis

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Highly pathogenic avian influenza (HPAI) viruses of the H5N1 subtype are a major concern to human and animal health in Indonesia. This study aimed to characterize transmission dynamics of H5N1 over time using novel Bayesian phylogeography methods to identify factors which have influenced the spread of H5N1 in Indonesia. We used publicly available hemagglutinin sequence data sampled between 2003 and 2016 to model ancestral state reconstruction of HPAI H5N1 evolution. We found strong support for H5N1 transmission routes between provinces in Java Island and inter-island transmissions, such as between Nusa Tenggara and Kalimantan Islands, not previously described. The spread is consistent with wild bird flyways and poultry trading routes. H5N1 migration was associated with the regions of high chicken densities and low human development indices. These results can be used to inform more targeted planning of H5N1 control and prevention activities in Indonesia.

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“…The zoonotic strain prediction model is proposed as an influenza virologic surveillance tool to detect changes in protein sequences in avian strains that may indicate a zoonotic jump event. As influenza sequence data are already regularly sampled and collected [18,19], this tool could complement existing methods to rapidly screen for possible zoonotic strains. Future work to integrate geographical and ecological data [72] would bring more significant advancements in predicting future influenza outbreaks beyond current sequence prediction capabilities.…”

Section: Discussionmentioning

confidence: 99%

“…Antigenic and genetic characterization of the new strains by phylogenetic analyses with existing strains are performed to understand how the outbreak started as well as to formulate effective response and treatment [16,17]. There have been increasing efforts in surveillance recently, with disease surveillance in wild birds and poultry farms where influenza sequence data are collected and deposited online [18,19]. Yet, the computational methods to identify possible zoonotic strains remain rudimentary, with the reliance on host-associated genetic markers [20].…”

Section: Introductionmentioning

confidence: 99%

Predicting Zoonotic Risk of Influenza A Viruses from Host Tropism Protein Signature Using Random Forest

Eng

Tong

Tan³

2017

IJMS

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Influenza A viruses remain a significant health problem, especially when a novel subtype emerges from the avian population to cause severe outbreaks in humans. Zoonotic viruses arise from the animal population as a result of mutations and reassortments, giving rise to novel strains with the capability to evade the host species barrier and cause human infections. Despite progress in understanding interspecies transmission of influenza viruses, we are no closer to predicting zoonotic strains that can lead to an outbreak. We have previously discovered distinct host tropism protein signatures of avian, human and zoonotic influenza strains obtained from host tropism predictions on individual protein sequences. Here, we apply machine learning approaches on the signatures to build a computational model capable of predicting zoonotic strains. The zoonotic strain prediction model can classify avian, human or zoonotic strains with high accuracy, as well as providing an estimated zoonotic risk. This would therefore allow us to quickly determine if an influenza virus strain has the potential to be zoonotic using only protein sequences. The swift identification of potential zoonotic strains in the animal population using the zoonotic strain prediction model could provide us with an early indication of an imminent influenza outbreak.

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Surveillance at the molecular level: Developing an integrated network for detecting variation in avian influenza viruses in Indonesia

Cited by 15 publications

References 37 publications

Evaluation of a conserved HA_274–288 epitope to detect antibodies to highly pathogenic avian influenza virus H5N1 in Indonesian commercial poultry

Evaluation of a conserved HA_274–288 epitope to detect antibodies to highly pathogenic avian influenza virus H5N1 in Indonesian commercial poultry

Phylogeography of H5N1 avian influenza virus in Indonesia

Predicting Zoonotic Risk of Influenza A Viruses from Host Tropism Protein Signature Using Random Forest

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Surveillance at the molecular level: Developing an integrated network for detecting variation in avian influenza viruses in Indonesia

Cited by 15 publications

References 37 publications

Evaluation of a conserved HA274–288 epitope to detect antibodies to highly pathogenic avian influenza virus H5N1 in Indonesian commercial poultry

Evaluation of a conserved HA274–288 epitope to detect antibodies to highly pathogenic avian influenza virus H5N1 in Indonesian commercial poultry

Phylogeography of H5N1 avian influenza virus in Indonesia

Predicting Zoonotic Risk of Influenza A Viruses from Host Tropism Protein Signature Using Random Forest

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Evaluation of a conserved HA_274–288 epitope to detect antibodies to highly pathogenic avian influenza virus H5N1 in Indonesian commercial poultry

Evaluation of a conserved HA_274–288 epitope to detect antibodies to highly pathogenic avian influenza virus H5N1 in Indonesian commercial poultry