Divergent sapovirus strains and infection prevalence in wild carnivores in the Serengeti ecosystem: A long-term study

The genus Sapovirus, in the family Caliciviridae, includes enteric viruses of humans and domestic animals. Information on sapovirus infection of wildlife is limited and is currently lacking for any free-ranging wildlife species in Africa. By screening a large number of predominantly fecal samples (n = 631) obtained from five carnivore species in the Serengeti ecosystem, East Africa, sapovirus RNA was detected in the spotted hyena (Crocuta crocuta, family Hyaenidae), African lion (Panthera leo, family Felidae), and bat-eared fox (Otocyon megalotis, family Canidae), but not in golden or silver-backed jackals (Canis aureus and C. mesomelas, respectively, family Canidae). A phylogenetic analysis based on partial RNA-dependent RNA polymerase (RdRp) gene sequences placed the sapovirus strains from African carnivores in a monophyletic group. Within this monophyletic group, sapovirus strains from spotted hyenas formed one independent sub-group, and those from bat-eared fox and African lion a second sub-group. The percentage nucleotide similarity between sapoviruses from African carnivores and those from other species was low (< 70.4%). Long-term monitoring of sapovirus in a population of individually known spotted hyenas from 2001 to 2012 revealed: i) a relatively high overall infection prevalence (34.8%); ii) the circulation of several genetically diverse variants; iii) large fluctuations in infection prevalence across years, indicative of outbreaks; iv) no significant difference in the likelihood of infection between animals in different age categories. The likelihood of sapovirus infection decreased with increasing hyena group size, suggesting an encounter reduction effect, but was independent of socially mediated ano-genital contact, or the extent of the area over which an individual roamed

The likelihood of infection of spotted hyenas with sapovirus as a function of clan size.

<p>Note that the probabilities were adjusted for the potential effects of the other covariates, contact rate and lifetime range, by setting them to the median of their values (for details see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0163548#sec002" target="_blank">Material and Methods</a>). Circles represent predicted values within the range of actual clan sizes observed.</p

Prevalence of sapovirus infection in spotted hyenas in the Serengeti National Park.

<p>Numbers at the top of the plot indicate sample sizes for each year from 2001 to 2012.</p

Sapovirus infection prevalence in spotted hyenas during outbreak years and non-outbreak years.

<p>Sapovirus infection prevalence in spotted hyenas during outbreak years and non-outbreak years.</p

RT-PCR fecal screening results for known spotted hyenas sampled at least three dates.

<p>RT-PCR fecal screening results for known spotted hyenas sampled at least three dates.</p

The effect of social contact rate, individual lifetime range and clan size on the likelihood of sapovirus infection in spotted hyenas.

<p>The effect of social contact rate, individual lifetime range and clan size on the likelihood of sapovirus infection in spotted hyenas.</p

Phylogenetic relationship of sapovirus strains from wild carnivores in the Serengeti National Park.

<p>Maximum likelihood (ML) phylogeny under the GTR+I+G model for a fragment of 210 nucleotides of the RdRp gene depicting the relationships between sapovirus (SaV) strains from spotted hyena, bat-eared fox and African lions (in bold) with other strains of the family <i>Caliciviridae</i>. The details for strains from the Serengeti National Park include the host species, year of collection and for spotted hyena strains, clan membership of the host (I, M, P) and Z when clan membership was unknown. Numbers at the nodes indicate bootstraps from 1000 replicates/ Bayesian posterior probabilities.</p