Data from: Ecological connectivity shapes quasispecies structure of RNA viruses in an Antarctic lake

RNA viruses exist as complex mixtures of genotypes, known as quasispecies, where the evolution potential resides in the whole community of related genotypes. Quasispecies structure and dynamics have been studied in detail for virus infecting animals and plants but remain unexplored for those infecting micro-organisms in environmental samples. We report the first metagenomic study of RNA viruses in an Antarctic lake (Lake Limnopolar, Livingston Island). Similar to low-latitude aquatic environments, this lake harbours an RNA virome dominated by positive single-strand RNA viruses from the order Picornavirales probably infecting micro-organisms. Antarctic picorna-like virus 1 (APLV1), one of the most abundant viruses in the lake, does not incorporate any mutation in the consensus sequence from 2006 to 2010 and shows stable quasispecies with low-complexity indexes. By contrast, APLV2-APLV3 are detected in the lake water exclusively in summer samples and are major constituents of surrounding cyanobacterial mats. Their quasispecies exhibit low complexity in cyanobacterial mat, but their run-off-mediated transfer to the lake results in a remarkable increase of complexity that may reflect the convergence of different viral quasispecies from the catchment area or replication in a more diverse host community. This is the first example of viral quasispecies from natural aquatic ecosystems and points to ecological connectivity as a modulating factor of quasispecies complexity.

RNA病毒以基因型的复杂混合物形式存在，这类混合物被称为准种（quasispecies），其进化潜力蕴藏于相关基因型的整个群落之中。针对感染动物与植物的病毒，其准种结构与动态特征已得到详尽研究，但针对环境样本中感染微生物的RNA病毒，此类研究仍属空白。本研究首次针对南极湖泊（利文斯顿岛利姆诺波拉尔湖）中的RNA病毒开展宏基因组学研究。与低纬度水生环境类似，该湖泊的RNA病毒组（RNA virome）以大概率感染微生物的正义单链RNA病毒（positive single-strand RNA virus）为主，这类病毒隶属于小核糖核酸病毒目（Picornavirales）。南极类小核糖核酸病毒1型（Antarctic picorna-like virus 1, APLV1）是该湖泊中丰度最高的病毒之一，在2006年至2010年间，其共识序列未出现任何突变，并呈现出低复杂度指数的稳定准种。与之形成对比的是，APLV2至APLV3仅在夏季样本的湖水中被检出，且为周边蓝藻垫（cyanobacterial mats）的主要组成成分。它们的准种在蓝藻垫中表现出低复杂度，但通过径流介导转移至湖泊后，其复杂度出现显著提升，这一现象可能反映了集水区内不同病毒准种的汇聚，或是宿主群落更为多样情况下的复制过程。本研究是自然水生生态系统中病毒准种的首个研究案例，表明生态连通性可作为调控准种复杂度的关键因素。