Attenuation of highly pathogenic avian influenza A(H5N1) viruses in Indonesia following the reassortment and acquisition of genes from low pathogenicity avian influenza A virus progenitors

Abstract

The highly pathogenic avian influenza (HPAI) A(H5N1) virus is endemic in Indonesian poultry and has caused sporadic human infection in Indonesia since 2005. Surveillance of H5N1 viruses in live bird markets (LBMs) during 2012 and 2013 was carried out to provide epidemiologic and virologic information regarding viral circulation and the risk of human exposure. Real-time RT-PCR of avian cloacal swabs and environmental samples revealed influenza A-positive specimens, which were then subjected to virus isolation and genomic sequencing. Genetic analysis of specimens collected at multiple LBMs in Indonesia identified both low pathogenicity avian influenza (LPAI) A(H3N8) and HPAI A(H5N1) viruses belonging to clade 2.1.3.2a. Comparison of internal gene segments among the LPAI and HPAI viruses revealed that the latter had acquired the PB2, PB1, and NS genes from LPAI progenitors and other viruses containing a wild type (wt) genomic constellation. Comparison of murine infectivity of the LPAI A(H3N8), wt HPAI A(H5N1) and reassortant HPAI A(H5N1) viruses showed that the acquisition of LPAI internal genes attenuated the reassortant HPAI virus, producing a mouse infectivity/virulence phenotype comparable to that of the LPAI virus. Comparison of molecular markers in each viral gene segment suggested that mutations in PB2 and NS1 may facilitate attenuation. The discovery of an attenuated HPAI A(H5N1) virus in mice that resulted from reassortment may have implications for the capability of these viruses to transmit and cause disease. In addition, surveillance suggests that LBMs in Indonesia may play a role in the generation of reassortant A(H5) viruses and should be monitored.

Reassortments among Avian Influenza A(H5N1) Viruses Circulating in Indonesia, 2015–2016

“…A parallel study on contacts of different poultry sectors revealed that backyard chicken farms have the highest contact rate ( 30 ), which may have facilitated reassortment in West Java. Of interest, a recent study described reassortant HPAI H5N1 viruses in samples collected from live-bird markets associated with suspected human HPAI H5N1 cases in Indonesia ( 13 ). More intense surveillance programs are required to confirm the prevalence and distribution of the clade 2.1.3.2a and 2.3.2.1c subgroups and its reassortments and to be able to unveil the transmission of HPAI from different sectors, vaccination practices, and regions.…”

“…Clarifying the epidemiology of HPAI H5N1 requires more intense monitoring of outbreaks of HPAI in Indonesia and performing genetic and phylogenetic analysis on viruses detected during these outbreaks. However, recent information on the genetic divergence of HA, and in particular on other gene segments, is very limited ( 8 , 11 – 13 ), and samples are often collected in a nonsystematic way. Therefore, the aim of this study was to perform genetic and phylogenetic analysis on recent HPAI H5N1 viruses that were obtained from poultry during active searches for outbreaks in West Java, a province of Indonesia.…”

The Thrift of Avian Influenza in Indonesia

“…Three reassortant viruses (A/Muscovy Duck/East Java/ SB29/2012, A/Muscovy Duck/East Java/LM47/ 2012 and A/Ck/East Java/BP21/2012) possessed PB2, PB1 and NS genes of LPAI virus, while the surface glycoproteins (HA and NA) and other internal genes (PA, NP and M) were contribution of HPAI A(H5N1) virus lineage. The experimental data of the reassortant HPAI A(H5N1) viruses showed slight attenuation possibly due to acquisition of LPAI internal genes to HPAI virus [8]. In 2017, the government of Indonesia has officially announced the introduction of enzootic H9N2 subtype; however, it is still poorly documented.…”

“…The number of human deaths in Indonesia were outgrowing to 150 by 2011 ( Figure 1) [2,[5][6][7] with 46% reported to have direct contact with infected poultry [7]. Although, to date the virus demonstrated inefficient person-to-person transmission, ongoing outbreaks in poultry pose warning to possibly establish human reassortant Avian Influenza virus [8]. New outbreaks of H5N1 in 2014 in Cambodia, China, India, Korea, Lybia, Russia and Vietnam have shown high adaptability in a heterogeneous ecosystem, requiring urgent need for reliable surveillance tool to improved strategies to control and eradicate this enzootic disease.…”

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

“…Initially, the HPAI-H5N1 clade 2.3.2.1 affected duck farms in Central Java, Yogyakarta and East Java. Then, the virus became the predominant clade circulating in Indonesia (Dharmayanti et al, 2014(Dharmayanti et al, , 2018Wibawa et al, 2018).…”