Estimation of the Basic Reproduction Numbers of the Subtypes H5N1, H5N8, and H5N6 During the Highly Pathogenic Avian Influenza Epidemic Spread Between Farms

Abstract

It is important to understand pathogen transmissibility in a population to establish an effective disease prevention policy. The basic reproduction number (R0) is an epidemiologic parameter for understanding the characterization of disease and its dynamics in a population. We aimed to estimate the R0 of the highly pathogenic avian influenza (HPAI) subtypes H5N1, H5N8, and H5N6, which were associated with nine outbreaks in Korea between 2003 and 2018, to understand the epidemic transmission of each subtype. According to HPAI outbreak reports of the Animal and Plant Quarantine Agency, we estimated the generation time by calculating the time of infection between confirmed HPAI-positive farms. We constructed exponential growth and maximum likelihood (ML) models to estimate the basic reproduction number, which assumes the number of secondary cases infected by the index case. The Kruskal-Wallis test was used to analyze the epidemic statistics between subtypes. The estimated generation time of H5N1, H5N8, and H5N6 were 4.80 days [95% confidence interval (CI) 4.23–5.38] days, 7.58 (95% CI 6.63–8.46), and 5.09 days (95% CI 4.44–5.74), respectively. A pairwise comparison showed that the generation time of H5N8 was significantly longer than that of the subtype H5N1 (P = 0.04). Based on the ML model, R0 was estimated as 1.69 (95% CI 1.48–2.39) for subtype H5N1, 1.60 (95%CI 0.97–2.23) for subtype H5N8, and 1.49 (95%CI 0.94–2.04) for subtype H5N6. We concluded that R0 estimates may be associated with the poultry product system, climate, species specificity based on the HPAI virus subtype, and prevention policy. This study provides an insight on the transmission and dynamics patterns of various subtypes of HPAI occurring worldwide. Furthermore, the results are useful as scientific evidence for establishing a disease control policy.

Spatial epidemiology of highly pathogenic avian influenza subtype H5N6 in Gyeonggi Province, South Korea, 2016–2017

“…An experimental study of HPAI H5N6 has provided evidence of different likelihoods of transmission from wild birds to ducks or chickens, with the results suggesting a more efficient transmission from wild birds to ducks than to chickens (Seekings et al., 2021). Furthermore, the previous HPAI epidemiological study in South Korea suggested that the species specificity of HPAIV contributes to transmission dynamics (W. H. Kim & Cho, 2021). Our findings suggest that it has different epidemiological characteristics depending on the species raised on the farm, implying that different biosecurity measures are required.…”

“…The clinical samples are transferred to the provincial centre for pathological examination and confirmatory diagnostic testing by RT‐PCR for the presence of the H5 and H7 subtypes of avian influenza. For RT‐PCR as definitive diagnostic testing including identification of the N subtype, the sample is transferred to the Animal and Plant Quarantine Agency (W. H. Kim & Cho, 2021). The other reporting source for HPAI‐positive farms was from contact tracing by the provincial veterinary service centre.…”

“…Spatial epidemiological HPAI‐related studies have supported the design of risk‐based surveillance systems (Artois et al., 2016; Gilbert & Pfeiffer, 2012; Gilbert et al., 2014; Mellor et al., 2018; Nguyen et al., 2020). While several spatial epidemiological studies have been conducted on HPAI H5N1 epidemics in Southeast Asia (Gilbert & Pfeiffer, 2012; Guinat et al., 2019), relatively few spatial epidemiological studies have been conducted on HPAI H5N6 (Mellor et al., 2018) despite the evidence suggesting that epidemiology of HPAI might be different on the subtypes (W. H. Kim & Cho, 2021; Son et al., 2018).…”

Emergence and interstate spread of highly pathogenic avian influenza A(H5N1) in dairy cattle

“…We estimated when HPAI H5N1 clade 2.3.4.4b were introduced into dairy cattle under a Bayesian framework in BEAST v.1.10.4 ( 71 ) with the BEAGLE library ( 72, 73 ). We merged the subsampled public data with newly generated whole genome data and aligned the hemagglutinin dataset (n=606 HA genes).…”

“…To reconstruct the spatial diffusion of the H5N1 virus across states within the US and different hosts (poultry, wild bird, cattle, mammal, domestic mammal, and humans), we applied an asymmetric discrete-trait phylogeographic analyses with Bayesian stochastic search variable selection, a strict molecular clock, and an exponential growth model in BEAST v.1.10.4 ( 71 ). We conducted this analysis on the subsampled and aligned hemagglutinin dataset and an extracted the monophyletic clade of cattle HA clade 2.3.4.4b genes with any host category (host) or cattle only (location).…”