Butkovic Anamarija, Kraberger Simona, Smeele Zoe, Martin Darren P, Schmidlin Kara, Fontenele Rafaela S, Shero Michelle R, Beltran Roxanne S, Kirkham Amy L, Aleamotu'a Maketalena, Burns Jennifer M, Koonin Eugene V, Varsani Arvind, Krupovic Mart
Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, 25 rue du Dr Roux, Paris 75015, France.
The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, 1001 S. McAllister Ave, Tempe, AZ 85287, USA.
Virus Evol. 2023 May 27;9(1):vead035. doi: 10.1093/ve/vead035. eCollection 2023.
Anelloviruses are highly prevalent in diverse mammals, including humans, but so far have not been linked to any disease and are considered to be part of the 'healthy virome'. These viruses have small circular single-stranded DNA (ssDNA) genomes and encode several proteins with no detectable sequence similarity to proteins of other known viruses. Thus, anelloviruses are the only family of eukaryotic ssDNA viruses currently not included in the realm . To gain insights into the provenance of these enigmatic viruses, we sequenced more than 250 complete genomes of anelloviruses from nasal and vaginal swab samples of Weddell seal () from Antarctica and a fecal sample of grizzly bear () from the USA and performed a comprehensive family-wide analysis of the signature anellovirus protein ORF1. Using state-of-the-art remote sequence similarity detection approaches and structural modeling with AlphaFold2, we show that ORF1 orthologs from all genera adopt a jelly-roll fold typical of viral capsid proteins (CPs), establishing an evolutionary link to other eukaryotic ssDNA viruses, specifically, circoviruses. However, unlike CPs of other ssDNA viruses, ORF1 encoded by anelloviruses from different genera display remarkable variation in size, due to insertions into the jelly-roll domain. In particular, the insertion between β-strands H and I forms a projection domain predicted to face away from the capsid surface and function at the interface of virus-host interactions. Consistent with this prediction and supported by recent experimental evidence, the outermost region of the projection domain is a mutational hotspot, where rapid evolution was likely precipitated by the host immune system. Collectively, our findings further expand the known diversity of anelloviruses and explain how anellovirus ORF1 proteins likely diverged from canonical jelly-roll CPs through gradual augmentation of the projection domain. We suggest assigning to a new phylum, '', and including it into the kingdom (realm ), alongside and .
环曲病毒在包括人类在内的多种哺乳动物中高度流行，但迄今为止尚未发现与任何疾病有关，被认为是“健康病毒组”的一部分。这些病毒具有小的环状单链DNA（ssDNA）基因组，并编码几种蛋白质，这些蛋白质与其他已知病毒的蛋白质没有可检测到的序列相似性。因此，环曲病毒是目前唯一未被纳入该领域的真核ssDNA病毒家族。为了深入了解这些神秘病毒的起源，我们对来自南极洲威德尔海豹（）的鼻拭子和阴道拭子样本以及来自美国的灰熊（）粪便样本中的250多个环曲病毒完整基因组进行了测序，并对标志性的环曲病毒蛋白ORF1进行了全面的全家族分析。使用最先进的远程序列相似性检测方法和AlphaFold2进行结构建模，我们表明所有属的ORF1直系同源物都采用了病毒衣壳蛋白（CPs）典型的果冻卷折叠结构，建立了与其他真核ssDNA病毒，特别是圆环病毒的进化联系。然而，与其他ssDNA病毒的CPs不同，来自不同属的环曲病毒编码的ORF1在大小上表现出显著差异，这是由于插入到果冻卷结构域中。特别是，β链H和I之间的插入形成了一个预测面向衣壳表面之外并在病毒-宿主相互作用界面发挥作用的突出结构域。与这一预测一致并得到最近实验证据的支持，突出结构域的最外层区域是一个突变热点，宿主免疫系统可能在此促使其快速进化。总的来说，我们的发现进一步扩展了已知的环曲病毒多样性，并解释了环曲病毒ORF1蛋白如何可能通过突出结构域的逐渐扩大而与典型的果冻卷CPs产生分歧。我们建议将其归入一个新的门，“”，并将其与和一起纳入界（领域）。
