Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2020 Jul;21(4):e56.
doi: 10.4142/jvs.2020.21.e56.

Genetic diversity of the H5N1 viruses in live bird markets, Indonesia

Ni Luh Putu Indi Dharmayanti  1 , Dyah Ayu Hewajuli  1 , Atik Ratnawati  1 , Risza Hartawan  2
Affiliations

Genetic diversity of the H5N1 viruses in live bird markets, Indonesia

Ni Luh Putu Indi Dharmayanti et al. J Vet Sci. 2020 Jul.

Abstract

Background: The live bird market (LBM) plays an important role in the dynamic evolution of the avian influenza H5N1 virus.

Objectives: The main objective of this study was to monitor the genetic diversity of the H5N1 viruses in LBMs in Indonesia.

Methods: Therefore, the disease surveillance was conducted in the area of Banten, West Java, Central Java, East Java, and Jakarta Province, Indonesia from 2014 to 2019. Subsequently, the genetic characterization of the H5N1 viruses was performed by sequencing all 8 segments of the viral genome.

Results: As a result, the H5N1 viruses were detected in most of LBMs in both bird' cloacal and environmental samples, in which about 35% of all samples were positive for influenza A and, subsequently, about 52% of these samples were positive for H5 subtyping. Based on the genetic analyses of 14 viruses isolated from LBMs, genetic diversities of the H5N1 viruses were identified including clades 2.1.3 and 2.3.2 as typical predominant groups as well as reassortant viruses between these 2 clades.

Conclusions: As a consequence, zoonotic transmission to humans in the market could be occurred from the exposure of infected birds and/or contaminated environments. Moreover, new virus variants could emerge from the LBM environment. Therefore, improving pandemic preparedness raised great concerns related to the zoonotic aspect of new influenza variants because of its high adaptivity and efficiency for human infection.

Keywords: H5N1 virus; Indonesia; genetic diversity; live bird market; reassortant viruses.

PubMed Disclaimer

Conflict of interest statement

The authors declare no conflicts of interest.

Figures

Fig. 1
Fig. 1. The general profiles of live bird markets in Indonesia. (A) The slaughter facility for poultry on site in the markets. (B) The modified motor cycle for poultry transportation. (C) The cages to keep poultry for temporary time. (D) The merchants who display chicken carcass or meat in the traditional market.
Fig. 2
Fig. 2. The phylogenetic trees of the H5N1 viruses were generated in MEGA 5.2 (maximum likelihood analysis and 1,000 bootstrap replicates) for HA (A) and NA gene (B). The characterized viruses in the study were indicated with triangle marking.
Fig. 3
Fig. 3. The phylogenetic trees of the H5N1 viruses were generated in MEGA 5.2 (maximum likelihood analysis and 1,000 bootstrap replicates) for PB2 (A), PB1 (B), and PA gene (C). The characterized viruses in the study were indicated with triangle marking.
Fig. 4
Fig. 4. The phylogenetic trees of the H5N1 viruses were generated in MEGA 5.2 (maximum likelihood analysis and 1,000 bootstrap replicates) for NP (A), MP (B), and NS gene (C). The characterized viruses in the study were indicated with triangle marking.
Fig. 5
Fig. 5. The gene constellation of the Indonesian reassortant H5N1 viruses from live bird markets from 2014–2019 between clade 2.1.3 and 2.3.2. (1) PB2 gene, (2) PB1 gene, (3) PA gene, (4) HA gene, (5) NP gene, (6) NA gene, (7) MP gene, and (8) NS gene.
See this image and copyright information in PMC

References

    1. Fournié G, Guitian FJ, Mangtani P, Ghani AC. Impact of the implementation of rest days in live bird markets on the dynamics of H5N1 highly pathogenic avian influenza. J R Soc Interface. 2011;8(61):1079–1089. - PMC - PubMed
    1. Gilbert M, Golding N, Zhou H, Wint GR, Robinson TP, Tatem AJ, et al. Predicting the risk of avian influenza A H7N9 infection in live-poultry markets across Asia. Nat Commun. 2014;5(1):4116. - PMC - PubMed
    1. He F, Chen EF, Li FD, Wang XY, Wang XX, Lin JF. Human infection and environmental contamination with avian influenza A (H7N9) virus in Zhejiang Province, China: risk trend across the three waves of infection. BMC Public Health. 2015;15(1):931. - PMC - PubMed
    1. Naysmith S. Observations from a live bird market in Indonesia following a contained outbreak of avian influenza A (H5N1) EcoHealth. 2014;11(1):50–52. - PubMed
    1. Mellor KC, Meyer A, Elkholly DA, Fournié G, Long PT, Inui K, et al. Comparative epidemiology of highly pathogenic avian influenza virus H5N1 and H5N6 in Vietnamese live bird markets: spatiotemporal patterns of distribution and risk factors. Front Vet Sci. 2018;5:51. - PMC - PubMed