Characterization and evolution of porcine deltacoronavirus in the United States.
Characterization and evolution of porcine deltacoronavirus in the United States.
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DOI：
10.1016/j.prevetmed.2015.11.001
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发表时间：
2016-01-01
影响因子：
2.6
通讯作者：
Marthaler D
中科院分区：
文献类型：
--
作者：
Homwong N;Jarvis MC;Lam HC;Diaz A;Rovira A;Nelson M;Marthaler D
2014年在美国多个州发现了猪三角洲冠状病毒（PDCoV）。在这项研究中，我们调查了诊断样本中PDCoV的存在，并通过病例识别（ID）进行了进一步分类，以及2014年3月至9月之间发生，年龄，标本和位置之间的关联。大约7%的美国提交的病例ID为PDCoV阳性。样本被分为8组，单变量分析表明，与粪便相比，口腔液体检测PDCoV的几率高1.89倍。虽然43-56天年龄组的PDCoV阳性百分比最高（8.4%），但单变量分析表明年龄组之间没有显着差异。然而，通过样本调整的年龄的多变量分析表明，>147日龄组的PDCoV阳性几率比乳猪低59%。2014年9月，诊断样本中PDCoV的百分比降至<1%。此外，还对19个完整的PDCoV基因组进行了测序，并进行了贝叶斯分析，以估计美国分支的出现。PDCoV基因组的进化速率估计为3.8 × 10−4替换/位点/年（2.3 × 10−4-5.4 × 10−4，95% HPD）。我们的研究结果表明，口腔液仍然是监测猪群健康的有价值的标本，PDCoV在2014年之前已经在美国流行。
Porcine deltacoronavirus (PDCoV) was identified in multiple states across the United States (US) in 2014. In this study, we investigate the presence of PDCoV in diagnostic samples, which were further categorized by case identification (ID), and the association between occurrence, age, specimen and location between March and September 2014. Approximately, 7% of the case IDs submitted from the US were positive for PDCoV. Specimens were categorized into eight groups, and the univariate analysis indicated that oral fluids had 1.89 times higher odds of detecting PDCoV compared to feces. While the 43–56 day age group had the highest percentage of PDCoV positives (8.4%), the univariate analysis indicated no significant differences between age groups. However, multivariable analysis for age adjusted by specimen indicated the >147 day age group had 59% lower odds than suckling pigs of being positive for PDCoV. The percentage of PDCoV in diagnostic samples decreased to <1% in September 2014. In addition, 19 complete PDCoV genomes were sequenced, and Bayesian analysis was conducted to estimate the emergence of the US clade. The evolutionary rate of the PDCoV genome is estimated to be 3.8 × 10−4 substitutions/site/year (2.3 × 10−4–5.4 × 10−4, 95% HPD). Our results indicate that oral fluids continue to be a valuable specimen to monitor swineherd health, and PDCoV has been circulating in the US prior to 2014.
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影响因子：
3.7
作者：
Marthaler, Douglas;Rossow, Kurt;Matthijnssens, Jelle
通讯作者：
Matthijnssens, Jelle
影响因子：
2.7
作者：
FIRTH, D
通讯作者：
FIRTH, D
影响因子：
9.8
作者：
Drummond AJ;Ho SY;Phillips MJ;Rambaut A
通讯作者：
Rambaut A
影响因子：
3.1
作者：
Marthaler, Douglas;Homwong, Nitipong;Ciarlet, Max
通讯作者：
Ciarlet, Max
影响因子：
1.5
作者：
Olsen, Chris;Wang, Chong;Zimmerman, Jeffrey
通讯作者：
Zimmerman, Jeffrey