The fecal viral flora of California sea lions

Abstract

California sea lions are one of the major marine mammal species along the Pacific coast of North America. Sea lions are susceptible to a wide variety of viruses, some of which can be transmitted to or from terrestrial mammals. Using an unbiased viral metagenomic approach, we surveyed the fecal virome in California sea lions of different ages and health statuses. Averages of 1.6 and 2.5 distinct mammalian viral species were shed by pups and juvenile sea lions, respectively. Previously undescribed mammalian viruses from four RNA virus families (Astroviridae, Picornaviridae, Caliciviridae, and Reoviridae) and one DNA virus family (Parvoviridae) were characterized. The first complete or partial genomes of sapeloviruses, sapoviruses, noroviruses, and bocavirus in marine mammals are reported. Astroviruses and bocaviruses showed the highest prevalence and abundance in California sea lion feces. The diversity of bacteriophages was higher in unweaned sea lion pups than in juveniles and animals in rehabilitation, where the phage community consisted largely of phages related to the family Microviridae. This study increases our understanding of the viral diversity in marine mammals, highlights the high rate of enteric viral infections in these highly social carnivores, and may be used as a baseline viral survey for comparison with samples from California sea lions during unexplained disease outbreaks.

Fig. 1.

Virome comparisons for three California sea lion groups based on BLASTx comparison to the GenBank nonredundant database (E value of <0.001). (A) Percentage of virus-like sequence reads with similarity to bacteriophages and eukaryotic viruses. (B) Percentage of phage-related sequences in different viral families. (C) Percentage of eukaryotic virus-related sequences in different viral groups.

Fig. 2.

(A) Genome organization of California sea lion astroviruses (Csl AstVs). (B) Phylogenetic analysis of California sea lion astroviruses. Trees are based on complete capsid (ORF2) proteins. The novel Csl AstV4 and Cs2 AstV11 are marked by black circles, and the previously reported Csl AstV1 and Csl AstV2 are marked by gray diamonds. nt, nucleotides.

Fig. 3.

(A) Genome organization of California sea lion sapeloviruses (Csl SaVs). (B) Phylogenetic analysis of the partial P1 region of sapeloviruses, including representative enteroviruses.

Fig. 4.

(A) Genome organization of California sea lion sapovirus 1 (Csl SaV1). (B) Phylogenetic analysis of the VP1 regions of Csl SaV1 and sapoviruses from different genogroups. GenBank accession numbers are shown at the end of the branches. GV, genogroup V; RHDV, rabbit hemorrhagic disease virus.

Fig. 5.

Phylogenetic analysis of California sea lion norovirus (Csl NV1170) and representatives from different genogroups based on the amino acid sequence of the partial VP1 region.

Fig. 6.

Phylogenetic analysis of California sea lion rotavirus 1 (Csl RV1) and representative rotaviruses from other species based on the amino acid sequence of the partial VP4 region.

Fig. 7.

(A) Genome organization of California sea lion bocaviruses (Csl BoVs). (B) Phylogenetic analysis of Csl BoVs and representative bocaviruses based on the complete VP1 protein.