Genetic Characterization of Clade 2.3.2.1 Avian Influenza A(H5N1) Viruses, Indonesia, 2012

Dharmayanti, Ni Luh Putu Indi; Hartawan, Risza; Pudjiatmoko, Hendra; Wibawa,; Hardiman, Amanda; Balish, Ruben; Donis, C. Todd; Davis, W. Rhett; Samaan, Gina

doi:10.3201/eid2004.130517

Cited by 45 publications

(44 citation statements)

References 10 publications

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“…In addition, Figure S4 has shown that a new clade was found in 2012 among ducks. Even though the newer clade was found to be slight different than the previously found clade in Indonesia (Dharmayanti et al, 2014), the virus follow similar molecular clock as the previous clade (Figure 3). The difference might be caused by antigenic drift that can occur over time (Hartaningsih et al, 2015).…”

Section: Discussionsupporting

confidence: 58%

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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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Section: Discussionsupporting

confidence: 58%

“…However, the genetic diversity increased again after 2012. In 2012, several studies mentioned the introduction of a new HPAI H5N1 clade that has never been found previously in Indonesia (Dharmayanti et al, 2014). In fact, this new clade has raised the possibility of multiple introductions into Indonesia (Dharmayanti et al, 2014).…”

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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“…Nine flocks (75%) had recently been HPAI H5N1‐vaccinated a median of 3 days [IQR 2–5] prior to onset of clinical signs (Table ). The reported mortality (16.0%) was lower compared with that observed in 2.3.2.1 clade outbreaks in India, Bangladesh and Indonesia (>60%) (Nagarajan et al., ; Dharmayanti et al., ; Haider et al., ). In our study farms, the variable mortality was statistically correlated with the length of time between onset of signs and farm visit (Pearson's correlation = 0.61, P = 0.01) (data not shown).…”

Section: Resultsmentioning

confidence: 80%

Highly Pathogenic Avian Influenza Virus A/H5N1 Infection in Vaccinated Meat Duck Flocks in the Mekong Delta of Vietnam

Cương

Truc

Nhung

et al. 2016

Transbound Emerg Dis

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SummaryWe investigated episodes of suspected highly pathogenic avian influenza (HPAI)‐like illness among 12 meat duck flocks in two districts in Tien Giang province (Mekong Delta, Vietnam) in November 2013. In total, duck samples from 8 of 12 farms tested positive for HPAI virus subtype A/haemagglutinin 5 and neuraminidase 1 (H5N1) by real‐time RT‐PCR. Sequencing results confirmed clade of 2.3.2.1.c as the cause of the outbreaks. Most (7/8) laboratory‐confirmed positive flocks had been vaccinated with inactivated HPAI H5N1 clade 2.3.4 vaccines <6 days prior to onset of clinical signs. A review of vaccination data in relation to estimated production in the area suggested that vaccination efforts were biased towards larger flocks and that vaccination coverage was low [21.2% ducks vaccinated with two shots (range by district 7.4–34.9%)]. The low‐coverage data, the experimental evidence of lack of cross‐protection conferred by the currently used vaccines based on clade 2.3.4 together with the short lifespan of meat duck flocks (60–70 days), suggest that vaccination is not likely to be effective as a tool for control of H5N1 infection in meat duck flocks in the area.

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“…Until December 2008, Sukabumi and Cianjur were the districts with the highest cases of H5N1 in West Java, and West Java was the province with the highest number of H5N1 outbreaks in Indonesia (Yupiana et al 2010 (Dharmayanti et al 2014). However, this new clade H5N1 caused disease and mortalities mostly in ducks, whereas poultry including, native chicken, apparently were not affected (Empres 2014).…”

Section: Discussionmentioning

confidence: 99%

Circulating H5N1 virus among native chicken living around commercial layer farms

Tarigan¹,

Indriani²,

Ignjatovic³

2015

JITV

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ABSTRAK Tarigan Sejak diterapkannya program vaksinasi kasus penyakit avian influenza (AI) H5N1 pada ayam pembibitan dan ayam ras petelur jarang terdengar. Penelitian in bertujuan menganalisis apakah redanya kasus tersebut berhubungan dengan hilangnya sumber infeksi di sekitar peternakan. Sampel serum dikumpulkan dari 421 ayam buras yang tinggal di sekitar peternakan ayam petelur di Kabupaten Cianjur dan Sukabumi, Jawa Barat pada Maret-April 2014. Antibodi virus AI H5N1 dianalisis dengan uji haemagglutination ihibition (HI), ELISA dan immunoblotting untuk mendeteksi antibodi terhadap haemagglutin virus H5N1, domain eksternal protein M2 (M2E) dan nukleoprotein (NP) virus AI. Sebanyak 8,6% dari ayam buras yang diperiksa seropositif terhadap virus AI berdasarkan satu atau lebih dari uji serologis. Hasil penelitian mengungkapkan bahwa virus H5N1 masih beredar pada ayam buras yang berkeliaran disekitar kandang ayam ras petelur. Sera yang positif dengan uji HI, M2E dan NP ELISA berturut turut 2,4%, 3,3% dan 3,8%. Tidak terlihat kesesuaian antara hasil satu uji dengan uji lainya. Penyebab ketidaksesuaian hasil tersebut diduga karena HI test, MM2e ELISA dan NP ELISA mengukur antibody yang berbeda yang kemunculan dan durasi masing masing antibodi tersebut berbeda. Kenyataan bahwa virus H5N1 masih beredar di sekitar peternakan ayam petelur menunjukkan bahwa ancaman virus AI masih membayangi peternakan ayam komersial dan karena itu vaksinasi dan biosekuriti yang ketat masih dibutuhkan. Soon after the application of vaccination programme against high pathogenic avian influenza H5N1 outbreak of the disease in breeder and commercial layer farms has diminished remarkably in West Java. This study aimed to investigate whether the H5N1 decline is related to the disappearance of source of infection around the farms. Serum samples were collected from 421 native chicken living around commercial layer farms in the Districs of Cianajur and Sukabumi, West Java in March-April 2014. Antibodies to avian influenza virus (AIV) H5N1 were measured using haemaglutination inhibition (HI), ELISAs and immunoblotting that measured presence of antibodies to the haemagglutin of H5N1 strain, as well as the M2e and nucleoprotein (NP) of all avian influenza viruses. Based on the combined results, 8.6% of the native chickens were seropositive to AI virus based on one or more of serological tests. This study provided serological evidence that H5N1 virus was still circulating among native chicken living around commercial layer farms. Many positive sera were however positive for antibodies in one test only: 2.4%, 3.3% and 3.8% by HI test, M2e and NP ELISA, respectively. It could be speculated that the incongruity of the results is due to the fact that HI, MM2e ELISA and NP ELISA all measure different type of antibodies and the duration of these antibodies in serum following infection with H5N1 differ. The fact that H5N1 virus is still circulating around commercial layer farms infers that the commercial farms are still under threat and therefore vaccination ...

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Genetic Characterization of Clade 2.3.2.1 Avian Influenza A(H5N1) Viruses, Indonesia, 2012

Cited by 45 publications

References 10 publications

Phylogeography of H5N1 avian influenza virus in Indonesia

Phylogeography of H5N1 avian influenza virus in Indonesia

Highly Pathogenic Avian Influenza Virus A/H5N1 Infection in Vaccinated Meat Duck Flocks in the Mekong Delta of Vietnam

Circulating H5N1 virus among native chicken living around commercial layer farms

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