Epidemiology and phylodynamics of multiple clades of H5N1 circulating in domestic duck farms in different production systems in Bangladesh.
Epidemiology and phylodynamics of multiple clades of H5N1 circulating in domestic duck farms in different production systems in Bangladesh.
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孟加拉国不同生产系统的国内养鸭场中传播的 H5N1 多个分支的流行病学和系统动力学。
DOI：
10.3389/fpubh.2023.1168613
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发表时间：
2023
影响因子：
5.2
通讯作者：
Shirin, Tahmina
中科院分区：
文献类型：
--
作者：
Islam, Ariful;Hossain, Mohammad Enayet;Amin, Emama;Islam, Shariful;Islam, Monjurul;Sayeed, Md Abu;Hasan, Md Mehedi;Miah, Mojnu;Hassan, Mohammad Mahmudul;Rahman, Mohammed Ziaur;Shirin, Tahmina
水禽被认为是禽流感病毒（AIV）的天然宿主。然而，孟加拉国养鸭场内禽流感病毒及其亚型的传播动态和进化模式的记录仍然很少。因此，2019年至2021年间在孟加拉国九个地区进行了一项横断面研究，以确定AIV及其H5和H9亚型的流行情况，并确定危险因素和国内养鸭场传播的H5N1病毒分支的系统动力学。使用 rRT-PCR 检测口咽和泄殖腔拭子样本的 AIV 基质基因（M 基因），然后检测 H5、H7 和 H9 亚型。通过探索性分析估算不同生产系统中 AIV 及其亚型的流行情况，并使用多变量 Logistic 回归模型确定影响鸭子 AIV 感染的危险因素。进行贝叶斯系统发育分析以生成最大进化枝可信度 (MCC) 树和最大似然法来确定从鸭中分离的 H5N1 病毒的系统发育关系。 40%（95% CI：33.0–48.1）的养鸭场检测到 AIV。游牧鸭中 AIV 患病率最高（39.8%；95% CI：32.9–47.1），其次是商品鸭（24.6%；95% CI：14.5–37.3）和散养鸭（14.4%；95% CI：10.5–19.2）。游牧鸭中的 H5 患病率也最高（19.4%；95% CI：14.0–25.7）。多变量逻辑回归模型显示，游牧农场的鸭子（AOR：2.4；95% CI：1.45-3.93）、幼鸭（AOR：2.2；95% CI：1.37-3.61）和病鸭（AOR：11.59；95% CI：4.82-32.44）感染AIV的风险较高。同样，病鸭中检测到 H5 的可能性也较高（AOR：40.8；95% CI：16.3–115.3）。贝叶斯系统发育分析显示，鸭体内的 H5N1 病毒属于两个不同的进化枝：2.3.2.1a 和 2.3.4.4b。自 2015 年以来，进化枝 2.3.2.1a（重新分类）一直在悄然进化，并基于 >90% 的后验概率形成至少 9 个子群。值得注意的是，2.3.4.4b 分支于 2020 年底被引入孟加拉国的鸭子中，该病毒在基因上与在日本、中国和非洲的野生鸟类中检测到的病毒相似，表明新出现的全动物疾病分支与迁徙相关的传播。我们建议继续在鸭生产系统中进行禽流感病毒监测，并防止家鸭与湿地迁徙水禽混合。
Waterfowl are considered to be natural reservoirs of the avian influenza virus (AIV). However, the dynamics of transmission and evolutionary patterns of AIV and its subtypes within duck farms in Bangladesh remain poorly documented. Hence, a cross-sectional study was conducted in nine districts of Bangladesh between 2019 and 2021, to determine the prevalence of AIV and its subtypes H5 and H9, as well as to identify risk factors and the phylodynamics of H5N1 clades circulating in domestic duck farms. The oropharyngeal and cloacal swab samples were tested for the AIV Matrix gene (M-gene) followed by H5, H7, and H9 subtypes using rRT-PCR. The exploratory analysis was performed to estimate AIV and its subtype prevalence in different production systems, and multivariable logistic regression model was used to identify the risk factors that influence AIV infection in ducks. Bayesian phylogenetic analysis was conducted to generate a maximum clade credibility (MCC) tree and the maximum likelihood method to determine the phylogenetic relationships of the H5N1 viruses isolated from ducks. AIV was detected in 40% (95% CI: 33.0–48.1) of the duck farms. The prevalence of AIV was highest in nomadic ducks (39.8%; 95% CI: 32.9–47.1), followed by commercial ducks (24.6%; 95% CI: 14.5–37.3) and backyard ducks (14.4%; 95% CI: 10.5–19.2). The H5 prevalence was also highest in nomadic ducks (19.4%; 95% CI: 14.0–25.7). The multivariable logistic regression model revealed that ducks from nomadic farms (AOR: 2.4; 95% CI: 1.45–3.93), juvenile (AOR: 2.2; 95% CI: 1.37–3.61), and sick ducks (AOR: 11.59; 95% CI: 4.82–32.44) had a higher risk of AIV. Similarly, the likelihood of H5 detection was higher in sick ducks (AOR: 40.8; 95% CI: 16.3–115.3). Bayesian phylogenetic analysis revealed that H5N1 viruses in ducks belong to two distinct clades, 2.3.2.1a, and 2.3.4.4b. The clade 2.3.2.1a (reassorted) has been evolving silently since 2015 and forming at least nine subgroups based on >90% posterior probability. Notably, clade 2.3.4.4b was introduced in ducks in Bangladesh by the end of the year 2020, which was genetically similar to viruses detected in wild birds in Japan, China, and Africa, indicating migration-associated transmission of an emerging panzootic clade. We recommend continuing AIV surveillance in the duck production system and preventing the intermingling of domestic ducks with migratory waterfowl in wetlands.
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DOI：
10.1016/j.cimid.2008.01.001
发表时间：
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影响因子：
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