Salazar-Hamm Paris S, Johnson William L, Nofchissey Robert A, Salazar Jacqueline R, Gonzalez Publio, Goodfellow Samuel M, Dunnum Jonathan L, Bradfute Steven B, Armién Blas, Cook Joseph A, Domman Daryl B, Dinwiddie Darrell L
Clinical and Translational Science Center, University of New Mexico, Albuquerque, New Mexico, United States of America.
Center for Global Health, Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, United States of America.
PLoS Negl Trop Dis. 2024 Jan 12;18(1):e0011672. doi: 10.1371/journal.pntd.0011672. eCollection 2024 Jan.
Hantaviruses are negative-stranded RNA viruses that can sometimes cause severe disease in humans; however, they are maintained in mammalian host populations without causing harm. In Panama, sigmodontine rodents serve as hosts to transmissible hantaviruses. Due to natural and anthropogenic forces, these rodent populations are having increased contact with humans.
We extracted RNA and performed Illumina deep metatranscriptomic sequencing on Orthohantavirus seropositive museum tissues from rodents. We acquired sequence reads mapping to Choclo virus (CHOV, Orthohantavirus chocloense) from heart and kidney tissue of a two-decade old frozen museum sample from a Costa Rican pygmy rice rat (Oligoryzomys costaricensis) collected in Panama. Reads mapped to the CHOV reference were assembled and then validated by visualization of the mapped reads against the assembly.
We recovered a 91% complete consensus sequence from a reference-guided assembly to CHOV with an average of 16X coverage. The S and M segments used in our phylogenetic analyses were nearly complete (98% and 99%, respectively). There were 1,199 ambiguous base calls of which 93% were present in the L segment. Our assembled genome varied 1.1% from the CHOV reference sequence resulting in eight nonsynonymous mutations. Further analysis of all publicly available partial S segment sequences support a clear relationship between CHOV clinical cases and O. costaricensis acquired strains.
Viruses occurring at extremely low abundances can be recovered from deep metatranscriptomics of archival tissues housed in research natural history museum biorepositories. Our efforts resulted in the second CHOV genome publicly available. This genomic data is important for future surveillance and diagnostic tools as well as understanding the evolution and pathogenicity of CHOV.
汉坦病毒是负链RNA病毒，有时可导致人类严重疾病；然而，它们在哺乳动物宿主群体中维持存在却不会造成危害。在巴拿马，稻鼠科啮齿动物是可传播汉坦病毒的宿主。由于自然和人为因素，这些啮齿动物群体与人类的接触日益增加。
我们从啮齿动物的正汉坦病毒血清学阳性博物馆组织中提取RNA，并进行了Illumina深度宏转录组测序。我们从一个保存在博物馆的、有二十年历史的冷冻样本中，该样本来自一只在巴拿马采集的哥斯达黎加侏儒稻鼠（Oligoryzomys costaricensis）的心脏和肾脏组织，获得了与乔克洛病毒（CHOV，chocloense正汉坦病毒）匹配的序列读数。将映射到CHOV参考序列的读数进行组装，然后通过将映射读数与组装结果可视化比对来进行验证。
我们通过参考引导组装从CHOV中获得了一个91%完整的共有序列，平均覆盖度为16倍。我们在系统发育分析中使用的S和M片段几乎完整（分别为98%和99%）。有1199个碱基调用不明确，其中93%出现在L片段中。我们组装的基因组与CHOV参考序列有1.1%的差异，产生了8个非同义突变。对所有公开可用的部分S片段序列的进一步分析支持了CHOV临床病例与从哥斯达黎加侏儒稻鼠获得的毒株之间的明确关系。
可以从研究自然历史博物馆生物储存库中保存的档案组织的深度宏转录组学中回收丰度极低的病毒。我们的工作产生了第二个公开可用的CHOV基因组。这些基因组数据对于未来的监测和诊断工具以及了解CHOV的进化和致病性非常重要。
