Rustrela virus (RusV; species Rubivirus strelense, family Matonaviridae) was discovered in different zoo animal species affected by fatal encephalitis. Simultaneous RusV RNA detection in multiple yellow-necked field mice (Apodemus flavicollis) suggested this rodent as a reservoir of RusV. Here we investigated 1,264 yellow-necked field mice and sympatric other small mammals from different regions in Germany for RusV RNA using an optimized real-time RT-qPCR protocol and high-throughput sequencing. The investigation resulted in the detection of RusV RNA exclusively in 50 of 396 (12.6%) yellow-necked field mice, but absence in other sympatric species. RT-qPCR-determined tissue distribution of RusV RNA revealed the highest viral loads in the central nervous system, with other tissues being only very rarely affected. Histopathological evaluation did not reveal any hints of an encephalitis in the brains of infected animals despite detection of viral RNA in neurons by in situ hybridization. The positive association of body mass of yellow-necked field mice and RusV RNA detection suggests a persistent infection. Phylogenetic analysis of partial E1 and full genome sequences showed a high diversification with at least four RusV lineages (1A-1D) in northeastern Germany. Moreover, phylogenetic and isolation-by-distance analysis indicated evolutionary processes of RusV mostly in local reservoir populations. Comparison of complete genome sequences from all detected RusV lineages demonstrated a high-level of nucleotide and amino acid sequence variability within a part of the p150 peptide of the non-structural polyprotein. The location of this region within the RusV genome and its genetic properties were comparable to the hypervariable region of rubella virus. The broad range of detected RusV spill-over hosts in combination with its geographical distribution in northeastern Germany requires the assessment of its zoonotic potential and further analysis of encephalitis cases in mammals. Additional future studies have to prove a putative co-evolution scenario for RusV in the yellow-necked field mouse reservoir.

中文翻译：

---

德国东北部黄颈田鼠储存种群中持续存在遗传多样性的锈菌病毒谱系

锈菌病毒（RusV；Rubivirus strelense 种，Matonaviridae 科）是在受致命性脑炎影响的不同动物园动物物种中发现的。在多只黄颈田鼠 (Apodemus flavicollis) 中同时检测到 RusV RNA，表明这种啮齿动物是 RusV 的宿主。在这里，我们使用优化的实时 RT-qPCR 方案和高通量测序研究了来自德国不同地区的 1,264 只黄颈田鼠和同域其他小型哺乳动物的 RusV RNA。研究结果仅在 396 只黄颈田鼠中的 50 只（12.6%）中检测到 RusV RNA，但在其他同域物种中未检测到。RT-qPCR 确定的 RusV RNA 组织分布显示，中枢神经系统中的病毒载量最高，其他组织很少受到影响。尽管通过原位杂交在神经元中检测到病毒 RNA，但组织病理学评估并未显示受感染动物大脑中存在任何脑炎迹象。黄颈田鼠的体重与 RusV RNA 检测呈正相关，表明存在持续感染。部分 E1 和完整基因组序列的系统发育分析显示，德国东北部至少有四个 RusV 谱系 (1A-1D)，具有高度多样化。此外，系统发育和距离隔离分析表明RusV的进化过程主要发生在当地的储存种群中。对所有检测到的 RusV 谱系的完整基因组序列进行比较，证明非结构多蛋白的 p150 肽的一部分内存在高水平的核苷酸和氨基酸序列变异性。该区域在 RusV 基因组中的位置及其遗传特性与风疹病毒的高变区相当。检测到的 RusV 溢出宿主范围广泛，再加上其在德国东北部的地理分布，需要评估其人畜共患病的可能性，并进一步分析哺乳动物脑炎病例。未来的更多研究必须证明黄颈田鼠水库中 RusV 的共同进化假设。