Multiple Reassortants of H5N8 Clade 2.3.4.4b Highly Pathogenic Avian Influenza Viruses Detected in South Korea during the Winter of 2020-2021

Abstract

During October 2020-January 2021, we isolated a total of 67 highly pathogenic avian influenza (HPAI) H5N8 viruses from wild birds and outbreaks in poultry in South Korea. We sequenced the isolates and performed phylogenetic analysis of complete genome sequences to determine the origin, evolution, and spread patterns of these viruses. Phylogenetic analysis of the hemagglutinin (HA) gene showed that all the isolates belong to H5 clade 2.3.4.4 subgroup B (2.3.4.4b) and form two distinct genetic clusters, G1 and G2. The cluster G1 was closely related to the 2.3.4.4b H5N8 HPAI viruses detected in Europe in early 2020, while the cluster G2 had a close genetic relationship with the 2.3.4.4b H5N8 viruses that circulated in Europe in late 2020. A total of seven distinct genotypes were identified, including five novel reassortants carrying internal genes of low pathogenic avian influenza viruses. Our Bayesian discrete trait phylodynamic analysis between host types suggests that the viruses initially disseminated from migratory waterfowl to domestic duck farms in South Korea. Subsequently, domestic duck farms most likely contributed to the transmission of HPAI viruses to chicken and minor poultry farms, highlighting the need for enhanced, high levels of biosecurity measures at domestic duck farms to effectively prevent the introduction and spread of HPAI.

Keywords: H5N8; domestic duck; highly pathogenic avian influenza virus; reassortant; transmission; wild bird.

Figure 1

H5N8 highly pathogenic avian influenza viruses isolated from wild birds and poultry in South Korea during the winter of 2020–2021. Bars represent the numbers of H5N8 virus isolates in wild bird and poultry in South Korea according to time from October 2020 to January 2021 (green, wild bird; red, poultry). Lines represent the numbers of sampled wild birds and poultry (dotted line, wild bird; solid line, poultry).

Figure 2

Maximum clade credibility (MCC) trees of hemagglutinin gene of H5N8 highly pathogenic avian influenza viruses isolated in South Korea during the winter of 2020–2021 (time shown on the horizontal axis) were inferred using an uncorrelated lognormal distribution relaxed clock in Beast v1.10.4. We reconstructed the phylogenetic tree with a chain length of 50,000,000 steps, sampling every 5000 steps. For trees with an ESS value >200, MCC trees were generated. Branch lengths represent time. Posterior probabilities >0.8 are provided for key nodes. The G1 and G2 clusters isolated in South Korea are highlighted in blue and red, respectively.

Figure 3

Genome constellation of clade 2.3.4.4b H5N8 highly pathogenic avian influenza (HPAI) viruses in South Korea during the winter of 2020–2021. Oval lines represent the avian virus, and horizontal bars indicate the eight gene segments (from top to bottom): polymerase basic protein 2, polymerase basic protein 1, polymerase acidic protein, hemagglutinin, nucleoprotein, neuraminidase, matrix protein, and non-structural protein. Each color represents a different viral origin: black, late 2019–early 2020 Europe H5N8 HPAI virus [17,18]; blue, late 2020 H5N8 Europe HPAI virus [19]; green, red, purple, orange, dark orange, and cyan blue, Eurasian low pathogenic avian influenza viruses.

Figure 4

Host transition and MCC tree for HA gene (clusters G1 and G2) of H5N8 highly pathogenic avian influenza virus for 2020–2021 outbreak in South Korea. Coding region of hemagglutinin was used for the reconstruction of the phylogenetic tree. Branches are colored according to host type. Horizontal bars on the nodes indicate the 95% Bayesian credibility intervals of divergence time estimates. Scale bar indicates the branch lengths in a year.

Figure 5

Markov reward time for each poultry species in South Korea. The violin plot of each poultry species (X-axis) depicts density distribution of the total time spent in years (Y-axis); domestic ducks: 5.53 (95% BCI: 1.62–9.32), chickens: 1.75 (95% BCI: 0.45–3.18), and minor poultry: 0.37 (95% BCI: 0.05–0.79).