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. 2020 Dec 22;13(1):4.
doi: 10.3390/v13010004.

Interface between Bats and Pigs in Heavy Pig Production

Stefania Leopardi  1   2 , Pamela Priori  3 , Barbara Zecchin  1   2 , Gianpiero Zamperin  2   4 , Adelaide Milani  2   4 , Francesco Tonon  5 , Mirco Giorgiutti  6 , Maria Serena Beato  7 , Paola De Benedictis  1   2
Affiliations

Interface between Bats and Pigs in Heavy Pig Production

Stefania Leopardi et al. Viruses. .

Abstract

Bats are often claimed to be a major source for future viral epidemics, as they are associated with several viruses with zoonotic potential. Here we describe the presence and biodiversity of bats associated with intensive pig farms devoted to the production of heavy pigs in northern Italy. Since chiropters or signs of their presence were not found within animal shelters in our study area, we suggest that fecal viruses with high environmental resistance have the highest likelihood for spillover through indirect transmission. In turn, we investigated the circulation of mammalian orthoreoviruses (MRVs), coronaviruses (CoVs) and astroviruses (AstVs) in pigs and bats sharing the same environment. Results of our preliminary study did not show any bat virus in pigs suggesting that spillover from these animals is rare. However, several AstVs, CoVs and MRVs circulated undetected in pigs. Among those, one MRV was a reassortant strain carrying viral genes likely acquired from bats. On the other hand, we found a swine AstV and a MRV strain carrying swine genes in bat guano, indicating that viral exchange at the bat-pig interface might occur more frequently from pigs to bats rather than the other way around. Considering the indoor farming system as the most common system in the European Union (EU), preventive measures should focus on biosecurity rather than displacement of bats, which are protected throughout the EU and provide critical ecosystem services for rural settings.

Keywords: bats; pigs; reassortment; spillover; viruses.

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Conflict of interest statement

The authors declare no conflict of interest. The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript; or in the decision to publish the results.

Figures

Figure 1
Figure 1
Sequences with the highest identity for all original strains found within the study, including the relative host species.
Figure 2
Figure 2
Phylogenetic tree based on the RdRp of alpha and betacoronaviruses. Sequences are coloured based on the host species, with original sequences marked according to the farm of detection.
Figure 3
Figure 3
Phylogenetic tree based on the RdRp of mamastroviruses. Sequences are coloured based on the host species, with original sequences marked according to the farm of detection.
Figure 4
Figure 4
Phylogenetic tree of mammalian orthoreoviruses based on complete S1 (A) and L1 (B) segments. Bootstrap values >80 are not shown. Sequences are coloured based on the host species, with original sequences marked according to the farm of detection.
Figure 5
Figure 5
Graphical reassortment analysis using tanglegrams to explore the phylogenetic congruence between the 10 segments of MRVs. The figure shows the strong phylogenetic correlation across most of the genome between MRV strains found in pigs from farm 1, shown with full and dashed fuchsia lines, with incongruent phylogeny supporting reassortment in S1, S4 and M2 segments. The figure also indicates strains the most likely parental strains for S1 and M2 found in a myotis bat (blue dashed line) and a vole (green dashed line). Finally, the figure highlights how pig strains have different evolutionary origin than the MRV isolated from a myotis bat roosting in the same environment, shown as a full blue line. M1 is not shown as no reads were obtained from the bat’s MRV.
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