The genus Gyrovirus was assigned to the family Anelloviridae in 2017 [20] to better align with the genomic properties of the viruses in this family. Like other members of the family Anelloviridae, gyroviruses have negative-sense single-stranded DNA genomes that contain at least three large open reading frames. As Chicken anemia virus [8] has been the sole species in the genus Gyrovirus, there have been no established guidelines for the classification of a new species within this genus. However, over the last decade, the nucleotide sequences of 49 genomes of viruses related to chicken anemia virus (CAV) have been determined from various species (Elaphe carinata, Felis catus, Fulmarus glacialis, Gallus gallus, Homo sapiens, Hydrobates homochroa, Mustela putorius furo, and Myrmoderus ferrugineus) (Table 1) but have remained unclassified [3,4,5,6, 9,10,11, 15,16,17, 19, 23, 29,30,31,32].

Table 1 Summary of the classification of new members of the genus Gyrovirus
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Here, we provide a framework for the classification of viruses in the genus Gyrovirus. We extracted the large open reading frame (ORF) VP1 [22] sequences of gyroviruses (n = 229) from full-genome sequences available in the GenBank database (including those of CAV, GenBank accessed on 6 July 2020) to determine the distribution of pairwise identity values using SDT v1.2 [14]. The plot of the distribution of the pairwise identity values (Fig. 1A) reveals a clear trough in the distribution between 67% and 92% pairwise identity. In a revision of the species demarcation criteria for members of the genus Anellovirus based on pairwise alignments (rather than global-alignment-derived pairwise identity scores) [28], we propose a species demarcation criterion of 69% based on the ORF1 coding open reading frame (ORF) of mammalian-infecting anelloviruses. To align species demarcation across the family Anelloviridae, we define a 69% VP1 nucleotide sequence pairwise identity threshold for species demarcation also for gyroviruses. Based on this, we establish nine new species to accommodate the 49 unclassified gyroviruses (Table 1). We provide further support for these species assignments using a colour-coded pairwise identity matrix and a midpoint-rooted maximum-likelihood phylogenetic tree of the VP1 nucleotide sequences (Fig. 1B and C).

Fig. 1
figure 1

A Distribution of pairwise identity values for VP1 nucleotide sequences of gyroviruses available in the GenBank database (n = 229). B Pairwise identity matrix of representative sequences from each species inferred using SDT v1.2 [14]. C Maximum-likelihood phylogenetic tree of the aligned VP1 sequences of representative gyroviruses inferred using PHYML [7] with the GTR+G model (determined using jModelTest) [18] and aLRT branch support. The tree is rooted at the midpoint. New species are shown in blue.

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For naming of the nine new species, we adopted the binomial “Genus + freeform epithet” species nomenclature outlined by Siddell et al. [21]. A summary of the 47 newly classified gyroviruses is provided in Table 1.

We recommend the following guidelines for establishing new species within the genus Gyrovirus to align with what has been recommended previously for classification of viruses in the families Circoviridae [20], Geminiviridae [2, 13, 24, 25], Genomoviridae [26], and Smacoviridae [27] as well as single-stranded DNA satellite molecules in the family Alphasatellitidae [1]:

  1. 1.

    If the complete VP1 ORF of a new gyrovirus has >69% nucleotide pairwise identity to that of any member assigned to a currently classified gyrovirus species, the virus belongs to that particular species.

    1. a.

      In the event that the complete VP1 ORF of a new gyrovirus has >69% nucleotide pairwise identity to those of members of more than one gyrovirus species, the virus should be considered a member of the species with whose members it shares the highest percentage VP1 pairwise identity.

    2. b.

      In the event that the complete VP1 ORF of a new gyrovirus has >69% nucleotide pairwise identity to those of one or more members assigned to a particular gyrovirus species, even if it shares <69% identity with those of the majority of the members assigned to that particular gyrovirus species, the virus should nevertheless be considered a member of that particular species.

  2. 2.

    If the complete VP1 ORF of a new gyrovirus has <69% nucleotide pairwise identity to those of all members of currently classified gyrovirus species, the virus should be considered a member of a new species.

We would like to highlight that different tools can yield different pairwise identity values, depending on how they are calculated. We recommend that true pairwise identity determination tools be used rather than those that infer pairwise identity values from multiple alignments. The latter generally tend to deflate the score due to gaps in the global multiple alignment and thus do not reflect the true pairwise identity between two sequences.