Sustained RNA virome diversity in Antarctic penguins and their ticks

Abstract

Despite its isolation and extreme climate, Antarctica is home to diverse fauna and associated microorganisms. It has been proposed that the most iconic Antarctic animal, the penguin, experiences low pathogen pressure, accounting for their disease susceptibility in foreign environments. There is, however, a limited understanding of virome diversity in Antarctic species, the extent of in situ virus evolution, or how it relates to that in other geographic regions. To assess whether penguins have limited microbial diversity we determined the RNA viromes of three species of penguins and their ticks sampled on the Antarctic peninsula. Using total RNA sequencing we identified 107 viral species, comprising likely penguin associated viruses (n = 13), penguin diet and microbiome associated viruses (n = 82), and tick viruses (n = 8), two of which may have the potential to infect penguins. Notably, the level of virome diversity revealed in penguins is comparable to that seen in Australian waterbirds, including many of the same viral families. These data run counter to the idea that penguins are subject to lower pathogen pressure. The repeated detection of specific viruses in Antarctic penguins also suggests that rather than being simply spill-over hosts, these animals may act as key virus reservoirs.

Fig. 1. Map of the Antarctic peninsula and locations where Antarctic penguins samples and ticks were collected.

The relief map was sourced from Wikipedia, developed by user Kikos, and is distributed under a CC-by-SA 3.0 attribution.

Fig. 2. Abundance of viruses found in penguins and their ticks.

a Abundance of all viral reads found in penguin libraries. b Abundance and diversity of avian viruses in each of the penguin libraries. c Abundance of the host reference gene RSP13 in penguin libraries. d Abundance of all viral reads found in the tick libraries. e Abundance and diversity of viruses in each of the tick libraries. f Abundance of the host reference gene COX1 in the tick libraries.

Fig. 3. Phylogenetic overview of the viruses found in penguins and ticks.

Viruses found in penguins were divided into two groups—those that infect birds and those that likely to other hosts and are coloured by magenta and orange boxes, respectively. Tick viruses revealed in this study are denoted by blue boxes. Grey boxes refer to reference viruses mined from RefSeq.

Fig. 4. Bipartite network illustrating biologically relevant virus species for which viral genomes were found in each library.

Each library is represented as a central node, with a pictogram of the species, surrounded by each viral species. Line lengths do not correspond to any variable. Where two libraries share a virus species, the networks between the two libraries are linked. Virus colour corresponds to virus taxonomy. Viruses identified in penguin libraries that are unlikely to be bird associated are not shown. A list of viruses from each library is presented in Table S2, and phylogenetic trees for each virus family can be found in Figs. 5–7 and S5–S13.

Fig. 5. Phylogenies of select novel viruses found in penguins.

a Phylogenetic tree of the VP1, containing the RdRp, of rotaviruses. The tree is mid-point rooted for clarity only. b Phylogeny of the concatenated major capsid gene and glycoprotein B gene, the only genes recovered, of the Alphaherpesvirinae. Two betaherpesviruses were used as outgroup to root the tree. The viruses identified in this study are denoted with a filled circle and in bold. Bootstrap values >70% are shown for key nodes. The scale bar represents the number of amino acid substitutions per site.

Fig. 6. Phylogeny of two previously described viruses in penguins.

a Phylogeny of the F gene of Avian avulavirus 17. Detection location for viruses identified in this study and Wille et al. [21] are denoted by either a green filled circle (King George Island) or blue filled triangle (Kopaitik Island). Strain names for reference viruses are as presented with the same nomenclature as originally presented in Wille et al. [21]. Avian avulavirus 18 was used as outgroup to root the tree. The scale bar represents the number of nucleotide substitutions per site. b Phylogenetic tree of the ORF1ab, including the RdRp, of avastroviruses. The tree is mid-point rooted for clarity only. The scale bar represents the number of amino acid substitutions per site. Bootstrap values > 70% are shown for key nodes. Viruses identified in this study are denoted in bold.

Fig. 7. Phylogenies of tick arboviruses.

a The RdRp segment of select members of the Reoviridae, including the genus Coltivirus. b The RdRp of select members of the Bunyavirales including the family Nairoviridae. The novel tick viruses identified in this study are denoted with a filled circle and in bold. The tree has been mid-point rooted for clarity only. Bootstrap values >70% are shown for key nodes. The scale bar represents the number of amino acid substitutions per site.