Viral metagenomics reveals persistent as well as dietary acquired viruses in Antarctic fur seals

Abstract

Viruses linked to animals inhabiting Antarctic latitudes remain poorly studied. Remote environments hosting large pinniped populations may be prone to exposure of immunologically naïve animals to new infectious agents due to increasing human presence or introduction of new animal species. Antarctic fur seals (Arctocephalus gazella) inhabiting the Western Antarctic Peninsula and the South Shetland Islands are challenged because of climate change and increased anthropogenic activity. In the present study, the fecal and serum virome of A. gazella was characterized by applying target enrichment next generation sequencing. The resulting viromes were dominated by CRESS-DNA sequences. Viruses known to infect vertebrate and invertebrate hosts were also observed in fecal samples. Fur seal picornavirus was present in all the fecal pools studied suggesting it is a prevalent virus in these species. Six different viruses presenting similarities with previously described A. gazella viruses or other otariids and mammal viruses were identified as potential new A. gazella viruses. Also, diet-derived viruses such as crustacean viruses were present in fecal content. Penguin viruses, but not fish viruses, were also detected. Obtained results contribute to a better understanding of the viral community present in these species, which is relevant for its conservation.

Comparison of de novo assembly using long-read shotgun metagenomic sequencing of viruses in fecal and serum samples from marine mammals

“…Studies have shown decreasing viral particles between samples with and without DNase treatment ( Bettarel et al, 2000 ; Briese et al, 2015 ). Future studies could incorporate the use of biotinylated oligonucleotide probes (targeted viral enrichment) to capture viruses from complex matrices after sequencing library preparation to avoid upstream enzymatic treatments ( Briese et al, 2015 ; Martínez-Puchol et al, 2020 , 2022 ; Bonny et al, 2021 ). Although several studies use filtration ( Allen et al, 2011 ; Fontenele et al, 2019 ; Garcia-Heredia et al, 2021 ; Patterson et al, 2021 ; Crum et al, 2023 ; LaRocca et al, 2023 ) to reduce background host and bacterial nucleic acids, it too can cause losses of viruses in filtration.…”