Diverse and highly recombinant anelloviruses associated with Weddell seals in Antarctica

Abstract

The viruses circulating among Antarctic wildlife remain largely unknown. In an effort to identify viruses associated with Weddell seals (Leptonychotes weddellii) inhabiting the Ross Sea, vaginal and nasal swabs, and faecal samples were collected between November 2014 and February 2015. In addition, a Weddell seal kidney and South Polar skua (Stercorarius maccormicki) faeces were opportunistically sampled. Using high throughput sequencing, we identified and recovered 152 anellovirus genomes that share 63-70% genome-wide identities with other pinniped anelloviruses. Genome-wide pairwise comparisons coupled with phylogenetic analysis revealed two novel anellovirus species, tentatively named torque teno Leptonychotes weddellii virus (TTLwV) -1 and -2. TTLwV-1 (n = 133, genomes encompassing 40 genotypes) is highly recombinant, whereas TTLwV-2 (n = 19, genomes encompassing three genotypes) is relatively less recombinant. This study documents ubiquitous TTLwVs among Weddell seals in Antarctica with frequent co-infection by multiple genotypes, however, the role these anelloviruses play in seal health remains unknown.

Keywords: Anelloviridae; Antarctica; Ross Sea; South Polar skua; Weddell seal.

Figure 1.

(A) Distribution of genome-wide pairwise identities of TTLwVs from this study. (B) Schematic genome organizations of representatives from TTLwV-1 and TTLwV-2 which highlights three open reading frames and a hypothetical protein.

Figure 2.

Maximum-likelihood phylogenetic tree inferred from aligned ORF1 sequences of all publicly available anellovirus sequences together with those from this study. Branches with <60% bootstrap support have been collapsed.

Figure 3.

Maximum-likelihood phylogenetic tree inferred from aligned ORF1 sequences of TTLwVs and other closely related anelloviruses. Branches with <60% bootstrap support have been collapsed. TTLwV sequences from South Polar skua faeces (SKP) are shown with dotted branches.

Figure 4.

(A) Distribution of the genome-wide pairwise identities of TTLwV-1 and TTLwV-2 supporting 87% genotype demarcation for TTLwV-1 genome sequences. (B) Summary of genotypes found in different sample types. Each bar represents one genome. Total number of genotypes of TTLvW-1 and TTLvW-2 from each sample type are provided at the bottom.

Figure 5.

Summary of recombinant regions identified in (A) TTLwV-1 (light green bars) and (B) TTLwV-2 (dark green bars). Recombination breakpoint distribution plots for (C) TTLwV-1 and (D) TTLwV-2, with breakpoint hot-spots indicated in red and cold-spots in blue. The dark and light grey areas of the plots indicate 95% and 99% confidence intervals, respectively. Detectable breakpoint positions are indicated by vertical lines at the top of the graphs. The thick black line represents the plot of the number of breakpoints detected within the 200-nt window region (window was moved along each of the represented alignments 1 nt at a time).