Atypical porcine pestivirus (APPV), an RNA virus member of the Flaviviridae family, has been associated with congenital tremor in newborn piglets. Previously reported quantitative polymerase chain reaction (qPCR)–based assays were unable to detect APPV in novel cases of congenital tremor originated from multiple farms from U.S. Midwest (MW). These assays targeted the viral polyprotein coding genes, which were shown to display substantial variation, with sequence identity ranging from 58.2% to 70.7% among 15 global APPV strains. In contrast, the 5′-untranslated region (5′ UTR) was found to have a much higher degree of sequence conservation. In order to obtain the complete 5′ UTR of the APPV strains originated from MW, the 5′ end of the viral cDNA was obtained by using template switching approach followed by amplification and dideoxy sequencing. Eighty one percent of the 5′ UTR was identical across 14 global and 5 MW strains with complete or relatively complete 5′ UTR. Notably, some of the most highly conserved 5′ UTR segments overlapped with potentially important regions of an internal ribosome entry site (IRES), suggesting their functional role in viral protein translation. A newly designed single qPCR assay, targeting 100% conserved 5′ UTR regions across 19 strains, was able to detect APPV in samples of well documented cases of congenital tremor which originated from five MW farm sites (1–18 samples/site). As these fully conserved 5′ UTR sequences may have functional importance, we expect that assays targeting this region would broadly detect APPV strains that are diverse in space and time.

中文翻译：

---

非典型猪瘟病毒感染的遗传多样性和检测

非典型猪瘟病毒 (APPV) 是黄病毒科的一种 RNA 病毒，与新生仔猪的先天性震颤有关。先前报道的基于定量聚合酶链反应 (qPCR) 的测定无法在源自美国中西部 (MW) 多个农场的先天性震颤新​​病例中检测到 APPV。这些检测针对病毒多蛋白编码基因，这些基因显示出显着变异，在 15 种全球 APPV 毒株中序列同一性范围为 58.2% 至 70.7%。相比之下，发现 5'-非翻译区 (5' UTR) 具有更高程度的序列保守性。为了获得源自 MW 的 APPV 毒株的完整 5' UTR，通过使用模板转换方法获得病毒 cDNA 的 5' 末端，然后进行扩增和双脱氧测序。在具有完整或相对完整的 5' UTR 的 14 个全局和 5 MW 菌株中，81% 的 5' UTR 是相同的。值得注意的是，一些最保守的 5' UTR 片段与内部核糖体进入位点 (IRES) 的潜在重要区域重叠，表明它们在病毒蛋白翻译中的功能作用。一种新设计的单一 qPCR 分析，针对 19 个菌株的 100% 保守的 5' UTR 区域，能够检测来自五个 MW 农场站点（1-18 个样本/站点）的有据可查的先天性震颤病例样本中的 APPV。由于这些完全保守的 5' UTR 序列可能具有重要的功能，我们预计针对该区域的分析将广泛检测空间和时间上不同的 APPV 毒株。