ORCID Profile
0000-0002-7683-4832
Current Organisation
Utrecht University
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Publisher: Elsevier BV
Date: 2012
DOI: 10.1016/J.PREVETMED.2011.08.013
Abstract: Wild aquatic birds (WABs) are considered as reservoir hosts for Newcastle disease viruses (NDVs) and may act as vectors for transferring these viruses to poultry, causing outbreaks of disease. A 3-year epidemiological study was conducted on WABs of north Queensland from April 2007 to March 2010. Swab and fresh moist faecal s les of WABs were screened to detect Newcastle disease viral (NDV) RNA by one-step real time reverse transcriptase polymerase chain reaction (rRT-PCR) in multiplex primers, targeting the matrix gene. The potential reactor s les in rRT-PCR were processed for sequencing of the different NDV genes using conventional PCR. The overall NDV RNA prevalence was 3.5% for live bird s les (N=1461) and 0.4% for faecal s les (N=1157). Plumed whistling ducks (PWDs) had a higher prevalence (4.2%) than Pacific black ducks (PBDs) (0.9%) (χ(2) test, p=0.001). Univariate and multivariate logistic regression analyses were used to estimate the association between the proportion of reactor and non-reactor NDV RNA s les of PWDs and potential risk factors. The odds of reactor s les were 2.7 (95% Confidence Interval 1.5-4.9) times more likely in younger than older ducks (p=0.001) (data set B, multivariate analysis). Both NDV RNA class-one and class-two types were identified in s les of WABs (12 and 59, respectively) (Supplementary Table 1). Phylogenetic analysis of the matrix gene identified two reactor sequences of class-one type NDV RNA (PWD-48 and 55) which were closely related to the sequences of Australian Ibis and duck isolates (Fig. 2). Another reactor s le sequence was determined as class-two type NDV RNA (PWD-46, avirulent) based on analysis of the matrix and fusion genes which was more similar to the sequences of Australian I-2 progenitor virus and vaccine strain virus (Figs. 3 and 4). Our findings of higher prevalence in PWDs along with confirmation of class-one and class-two type NDV RNAs will significantly contribute to the design of surveillance programs for NDVs in northern Australia.
Publisher: Centers for Disease Control and Prevention (CDC)
Date: 03-2019
Publisher: MDPI AG
Date: 08-10-2022
DOI: 10.3390/V14102216
Abstract: After its first detection in 1996, the highly pathogenic avian influenza A(H5Nx) virus has spread extensively worldwide. HPAIv A(H5N1) was first detected in Indonesia in 2003 and has been endemic in poultry in this country ever since. However, Indonesia has limited information related to the phylodynamics of HPAIv A(H5N1) in poultry. The present study aimed to increase the understanding of the evolution and temporal dynamics of HPAIv H5N1 in Indonesian poultry between 2003 and 2016. To this end, HPAIv A(H5N1) hemagglutinin sequences of viruses collected from 2003 to 2016 were analyzed using Bayesian evolutionary analysis s ling trees. Results indicated that the common ancestor of Indonesian poultry HPAIv H5N1 arose approximately five years after the common ancestor worldwide of HPAI A(H5Nx). In addition, this study indicated that only two introductions of HPAIv A(H5N1) occurred, after which these viruses continued to evolve due to extensive spread among poultry. Furthermore, this study revealed the ergence of H5N1 clade 2.3.2.1c from H5N1 clade 2.3.2.1b. Both clades 2.3.2.1c and 2.3.2.1b share a common ancestor, clade 1, suggesting that clade 2.3.2.1 originated and erged from China and other Asian countries. Since there was limited sequence and surveillance data for the HPAIv A(H5N1) from wild birds in Indonesia, the exact role of wild birds in the spread of HPAIv in Indonesia is currently unknown. The evolutionary dynamics of the Indonesian HPAIv A(H5N1) highlight the importance of continuing and improved genomic surveillance and adequate control measures in the different regions of both the poultry and wild birds. Spatial genomic surveillance is useful to take adequate control measures. Therefore, it will help to prevent the future evolution of HPAI A(H5N1) and pandemic threats.
Publisher: Utrecht University Library
Date: 2023
DOI: 10.33540/1630
Abstract: Highly Pathogenic Avian Influenza (HPAIv) H5N1 virus of the A/Goose/Guandong/1/96 lineage was first reported in Asia in 1996 and has been circulating in Indonesia since 2003. Its spread caused a global impact on poultry health and severe losses to the poultry industry. Furthermore, 200 laboratory-confirmed human cases were reported alone in Indonesia with a case-fatality rate of 84%. Analysis of the contact structure facilitating the transmission of HPAIv(A)H5N1 between different types of poultry farms in West Java showed that visitors of backyard chicken farms had the highest average contact rate, either direct contact with poultry on other farms before the visits or contact during their visits in the farms. These results suggest that backyard chicken farms are most at risk for transmission of HPAIv compared to farms of the other poultry production types and also serve as a vector for transmitting HPAIv H5N1 to commercial poultry. Passive surveillance from outbreak farms in six regions of West Java from November 2015 to November 2016 showed the highest mortality in backyard chickens with dermal apoptosis and lesions and respiratory signs. Neurological signs were most frequently observed in ducks. The rate of visitor contacts onto a farm was positively associated with the odds of HPAI infection. Duck farms had higher odds of being infected than backyard farms. The larger farms had lower odds than small farms. Results indicate that better external biosecurity is needed to reduce transmission of HPAIvA(H5N1) in Indonesia. The phylogenetic analyses of the analysis of 39 full-genome HPAIv(A)H5N1 viruses with additional reference sequences revealed 2 genetic clusters in clade 2.3.2.1c based on the hemagglutinin gene as well as the neuraminidase, nucleoprotein, polymerase, and polymerase basic 1 gene. The polymerase basic 2 gene had a close relation with Eurasian low pathogenic avian influenza virus (LPAIv). Also, several matrix, nonstructural protein and polymerase basic 2 genes were detected in HPAIv with higher identity with clade 2.1.3 than with clade 2.3.2.1c. The phylogenetic analysis of the s les in 2015-2016 thus identified 13 types of reassortment in HPAIv in Indonesia, mostly in native chickens in Indramayu. The BEAST analysis of the Indonesian poultry HPAIvA(H5N1) sequences collected from 2003-2016 were performed with a set of represented global H5Nx that have identities greater than 98%. Temporal dynamic analysis revealed that most likely only two introductions of HPAIvA(H5N1) occurred in Indonesia. The common ancestor (TMRCA) of the first introduction to Indonesian poultry HPAIvA(H5N1) emerged about five to seven years after the global common ancestor of HPAIv A(H5Nx). The ergences and TMRCA of H5N1 clade 2.3.2.1c and clade 2.3.2.1b were identified. The TMRCA of clade 2.3.2.1c and clade 2.3.2.1 indicate that the second introduction of both HPAIvA(H5N1) into Indonesian poultry originated from viruses from the same clade as viruses. detected in China and other Asian countries. Results of studies presented the importance of continued and improved (genomic) surveillance in poultry, live bird markets and wild birds. Adequate control measures such poultry farm biosecurity and poultry reconstruction are required to prevent a new emerging pandemic threat.
Publisher: Elsevier BV
Date: 08-2018
DOI: 10.1016/J.PREVETMED.2018.04.008
Abstract: Highly pathogenic avian influenza virus (HPAIV) H5N1 has been reported in Asia, including Indonesia since 2003. Although several risk factors related to the HPAIV outbreaks in poultry in Indonesia have been identified, little is known of the contact structure of farms of different poultry production types (backyard chickens, broilers, layers, and ducks). This study aims to quantify the contact rates associated with the movement of people, and movements of live birds and products and equipment that affect the risk of HPAIV H5N1 transmission between poultry farms in Indonesia. On 124 poultry farms in 6 districts in West Java, logbooks were distributed to record the movements of farmers/staff and visitors and their poultry contacts. Most movements in backyard chicken, commercial native chicken, broiler and duck farms were visits to and from other poultry farms, whilst in layer farms visits to and from poultry companies, visits to egg collection houses and visit from other poultry farms were most frequent. Over 75% of persons visiting backyard chicken and duck farms had previously visited other poultry farms on the same day. Visitors of backyard chicken farms had the highest average contact rate, either direct contact with poultry on other farms before the visits (1.35 contact/day) or contact during their visits in the farms (10.03 contact/day). These results suggest that backyard chicken farms are most at risk for transmission of HPAIV compared to farms of the other poultry production types. Since visits of farm-to-farm were high, backyard farms could also a potential source for HPAIV transmission to commercial poultry farms.
Publisher: MDPI AG
Date: 06-09-2019
DOI: 10.3390/MICROORGANISMS7090327
Abstract: Knowledge of outbreaks and associated risk factors is helpful to improve control of the Highly Pathogenic Avian Influenza A(H5N1) virus (HPAI) in Indonesia. This study was conducted to detect outbreaks of HPAI H5N1 in endemically infected regions by enhanced passive surveillance, to describe the clinical manifestation of these outbreaks and identify associated risk factors. From November 2015 to November 2016, HPAI outbreak investigations were conducted in seven districts of West Java. In total 64 outbreaks were confirmed out of 75 reported suspicions and outbreak characteristics were recorded. The highest mortality was reported in backyard chickens (average 59%, CI95%: 49–69%). Dermal apoptosis and lesions (64%, CI95%: 52–76%) and respiratory signs (39%, CI95%: 27–51%) were the clinical signs observed overall most frequently, while neurological signs were most frequently observed in ducks (68%, CI95%: 47–90%). In comparison with 60 non-infected control farms, the rate of visitor contacts onto a farm was associated with the odds of HPAI infection. Moreover, duck farms had higher odds of being infected than backyard farms, and larger farms had lower odds than small farms. Results indicate that better external biosecurity is needed to reduce transmission of HPAI A(H5N1) in Indonesia.
No related grants have been discovered for Desniwaty Karo-karo.