Epidemics of H3N8 and H3N2 influenza A viruses (IAVs) in dogs, along with recognition of spillover infections from IAV strains typically found in humans or other animals, have emphasized the importance of efficient laboratory testing. Given the lack of active IAV surveillance or immunization requirements for dogs, cats, or horses imported into the United States, serotype prediction and whole-genome sequencing of positive specimens detected at veterinary diagnostic laboratories are also needed. The conserved sequences at the ends of the viral genome segments facilitate universal amplification of all segments of viral genomes directly from respiratory specimens. Although several methods for genomic analysis have been reported, no optimization focusing on companion animal strains has been described, to our knowledge. We compared 2 sets of published universal amplification primers using 26 IAV-positive specimens from dogs, horses, and a cat. Libraries prepared from the resulting amplicons were sequenced using Illumina chemistry, and reference-based assemblies were generated from the data produced by both methods. Although both methods produced high-quality data, coverage profiles and base calling differed between the 2 methods. The sequence data were also used to identify the subtype of the IAV strains sequenced and then compared to standard PCR assays for neuraminidase types N2 and N8.

犬中 H3N8 和 H3N2 甲型流感病毒 (IAV) 的流行，以及对通常在人类或其他动物中发现的 IAV 毒株溢出感染的识别，都强调了有效实验室检测的重要性。鉴于对进口到美国的狗、猫或马缺乏主动 IAV 监测或免疫要求，还需要对兽医诊断实验室检测到的阳性标本进行血清型预测和全基因组测序。病毒基因组片段末端的保守序列有助于直接从呼吸道标本中普遍扩增病毒基因组的所有片段。尽管已经报道了几种基因组分析方法，但据我们所知，还没有描述针对伴侣动物品系的优化。我们使用来自狗、马和猫的 26 个 IAV 阳性标本比较了 2 组已发表的通用扩增引物。使用 Illumina 化学对从所得扩增子制备的文库进行测序，并根据两种方法产生的数据生成基于参考的组装。尽管这两种方法都产生了高质量的数据，但两种方法的覆盖范围和碱基检出不同。序列数据还用于鉴定测序的 IAV 毒株的亚型，然后与神经氨酸酶 N2 和 N8 型的标准 PCR 检测进行比较。尽管这两种方法都产生了高质量的数据，但两种方法的覆盖范围和碱基检出不同。序列数据还用于鉴定测序的 IAV 毒株的亚型，然后与神经氨酸酶 N2 和 N8 型的标准 PCR 检测进行比较。尽管这两种方法都产生了高质量的数据，但两种方法的覆盖范围和碱基检出不同。序列数据还用于鉴定测序的 IAV 毒株的亚型，然后与神经氨酸酶 N2 和 N8 型的标准 PCR 检测进行比较。