US Geological Survey, Alaska Science Center, 4210 University Drive, Anchorage, AK 99508, USA.
Infect Genet Evol. 2011 Dec;11(8):2004-10. doi: 10.1016/j.meegid.2011.09.011. Epub 2011 Sep 23.
The reassortment and geographic distribution of low pathogenic avian influenza (LPAI) virus genes are well documented, but little is known about the persistence of intact LPAI genomes among species and locations. To examine persistence of entire LPAI genome constellations in Alaska, we calculated the genetic identities among 161 full-genome LPAI viruses isolated across 4 years from five species of duck: northern pintail (Anas acuta), mallard (Anas platyrhynchos), American green-winged teal (Anas crecca), northern shoveler (Anas clypeata) and American wigeon (Anas americana). Based on pairwise genetic distance, highly similar LPAI genomes (>99% identity) were observed within and between species and across a range of geographic distances (up to and >1000 km), but most often between isolates collected 0-10 km apart. Highly similar viruses were detected between years, suggesting inter-annual persistence, but these were rare in our data set with the majority occurring within 0-9 days of sampling. These results identify LPAI transmission pathways in the context of species, space and time, an initial perspective into the extent of regional virus distribution and persistence, and insight into why no completely Eurasian genomes have ever been detected in Alaska. Such information will be useful in forecasting the movement of foreign-origin avian influenza strains should they be introduced to North America.
低致病性禽流感（LPAI）病毒基因的重配和地理分布已有充分记录，但对于物种和地理位置之间完整的 LPAI 基因组的持续存在知之甚少。为了研究阿拉斯加完整的 LPAI 基因组结构的持续存在情况，我们计算了从 5 种鸭（北方针尾鸭（Anas acuta）、绿头鸭（Anas platyrhynchos）、美洲绿翅鸭（Anas crecca）、北方鹊鸭（Anas clypeata）和美洲赤颈鸭（Anas americana））中分离的 161 株全基因组 LPAI 病毒在 4 年间的遗传同一性。基于成对遗传距离，在物种内和物种间以及在一系列地理距离（最多和>1000 公里）内观察到高度相似的 LPAI 基因组（>99%同一性），但最常见于相距 0-10 公里的分离株之间。在不同年份检测到高度相似的病毒，表明存在年度间的持续存在，但在我们的数据集中，这些病毒很少见，大多数发生在采样 0-9 天内。这些结果确定了物种、空间和时间背景下的 LPAI 传播途径，初步了解了区域病毒分布和持续存在的程度，并深入了解了为什么在阿拉斯加从未检测到完全欧亚基因组的原因。此类信息将有助于预测如果外来来源的禽流感菌株被引入北美，它们的传播情况。
