Emmenegger E J, Meyers T R, Burton T O, Kurath G
Western Fisheries Research Center, Biological Resources Division, US Geological Survey, Seattle, Washington 98115, USA.
Dis Aquat Organ. 2000 Apr 20;40(3):163-76. doi: 10.3354/dao040163.
Forty-two infectious hematopoietic necrosis virus (IHNV) isolates from Alaska were analyzed using the ribonuclease protection assay (RPA) and nucleotide sequencing. RPA analyses, utilizing 4 probes, N5, N3 (N gene), GF (G gene), and NV (NV gene), determined that the haplotypes of all 3 genes demonstrated a consistent spatial pattern. Virus isolates belonging to the most common haplotype groups were distributed throughout Alaska, whereas isolates in small haplotype groups were obtained from only 1 site (hatchery, lake, etc.). The temporal pattern of the GF haplotypes suggested a 'genetic acclimation' of the G gene, possibly due to positive selection on the glycoprotein. A pairwise comparison of the sequence data determined that the maximum nucleotide diversity of the isolates was 2.75% (10 mismatches) for the NV gene, and 1.99% (6 mismatches) for a 301 base pair region of the G gene, indicating that the genetic diversity of IHNV within Alaska is notably lower than in the more southern portions of the IHNV North American range. Phylogenetic analysis of representative Alaskan sequences and sequences of 12 previously characterized IHNV strains from Washington, Oregon, Idaho, California (USA) and British Columbia (Canada) distinguished the isolates into clusters that correlated with geographic origin and indicated that the Alaskan and British Columbia isolates may have a common viral ancestral lineage. Comparisons of multiple isolates from the same site provided epidemiological insights into viral transmission patterns and indicated that viral evolution, viral introduction, and genetic stasis were the mechanisms involved with IHN virus population dynamics in Alaska. The examples of genetic stasis and the overall low sequence heterogeneity of the Alaskan isolates suggested that they are evolutionarily constrained. This study establishes a baseline of genetic fingerprint patterns and sequence groups representing the genetic diversity of Alaskan IHNV isolates. This information could be used to determine the source of an IHN outbreak and to facilitate decisions in fisheries management of Alaskan salmonid stocks.
使用核糖核酸酶保护分析（RPA）和核苷酸测序对来自阿拉斯加的42株传染性造血坏死病毒（IHNV）分离株进行了分析。利用4种探针N5、N3（N基因）、GF（G基因）和NV（NV基因）进行的RPA分析确定，所有3个基因的单倍型都呈现出一致的空间模式。属于最常见单倍型组的病毒分离株分布于阿拉斯加各地，而小单倍型组的分离株仅从1个地点（孵化场、湖泊等）获得。GF单倍型的时间模式表明G基因存在“遗传适应性变化”，这可能是由于糖蛋白上的正选择作用。对序列数据的成对比较确定，分离株的最大核苷酸多样性对于NV基因是2.75%（10个错配），对于G基因的一个301碱基对区域是1.99%（6个错配），这表明阿拉斯加境内IHNV的遗传多样性明显低于北美范围内IHNV分布更靠南的地区。对阿拉斯加代表性序列以及来自美国华盛顿州、俄勒冈州、爱达荷州、加利福尼亚州和加拿大不列颠哥伦比亚省的12株先前已鉴定的IHNV毒株序列进行的系统发育分析，将分离株分为与地理起源相关的簇，并表明阿拉斯加和不列颠哥伦比亚省的分离株可能有共同的病毒祖先谱系。对来自同一地点的多个分离株的比较为病毒传播模式提供了流行病学见解，并表明病毒进化、病毒引入和遗传停滞是阿拉斯加IHN病毒种群动态所涉及的机制。阿拉斯加分离株的遗传停滞实例和总体较低的序列异质性表明它们在进化上受到限制。本研究建立了代表阿拉斯加IHNV分离株遗传多样性的遗传指纹模式和序列组基线。这些信息可用于确定IHN疫情的源头，并有助于在阿拉斯加鲑鱼种群的渔业管理中做出决策。
