21-ICRAD: Assessing swine as potential hosts for emerging Coronaviruses

Lead Research Organisation: University of Sussex
Department Name: Sch of Life Sciences

Abstract


Technical Summary

Recently, the number of CoVs emerging from wildlife is increasing, also as a consequence of blurred interface between humans, domestic animals and wildlife driven by industrialization of farming, that translates into increased likelihood of viral spillover. Emerging CoVs are also a major threat for swine production worldwide. Also, the dramatic consequences of the current COVID-19 pandemic highlights that further efforts should be directed towards understanding the mechanisms behind their emergence from the natural reservoir. Among wildlife, CoVs are frequent and highly diversified in bats, suggested as a source for most epidemic CoVs such as the Porcine Epidemic Diarrhoea virus (PEDV) and the Swine Acute Diarrhoea Syndrome Coronavirus (SADS-CoV), and human viruses such as Middle East Respiratory Syndrome (MERS-CoV), Severe Acute Respiratory Syndrome (SARS-CoV) and SARS-COV-2, the agent of COVID-19.

We recently confirmed that Italian swine are in contact with several bat species, providing chances for pathogen spillover. Similarly, swine are highly exposed to SARS-CoV-2, which is extensively circulating in humans, increasing odds for infection even if pigs are scarcely susceptible. Spillover of SARS-CoV-2 in swine might result in serious consequences for human and animal health. Critically, most CoVs cause similar symptoms in pigs so that initial spillover of novel viruses might be easily missed or delayed due to misdiagnosis with one of the seven endemic CoVs. Indeed, these viruses are mostly unreported and little is known about their epidemiology. In addition, the presence of endemic CoVs in swine herds may provide a backbone for recombination events, generating variants with unknown zoonotic and epizootic potential.

ConVErgence aims to address knowledge gaps regarding the emergence of novel CoVs in swine trough spillover from humans and bats, and to provide a genetic and biological characterization of emerging CoVs, including the zoonotic potential.
 
Title Pig transmission model 
Description The model simulate the trsansmission dyanmics of a pathogen within a pig farm. The model account for both farm size and structure, as well as age structure among pig. The model is flexble and can accomodate a variety of pathogen charaterisitics, incl. transmission intensity, and life history. The model is approrpiate for a diversity of farm-production pathogens, from low severity pathogen (e.g. coronaviruses) to high severity ones (e.g. African Swine Fever). The mode is setup to also determine the probability of detecting an outbreak as a function of either background mortality, or relying on symptomatic surveillance. 
Type Of Material Computer model/algorithm 
Year Produced 2023 
Provided To Others? Yes  
Impact Having developped the model, it is now being used toward 2 publications: 1) describing the general features that make disease detection more likely 2) model calibration/fitting to data related to the transmisssion of endemic coronaviruses in pig farm in Italy 
URL https://github.com/KimYounjung/ConVERgence
 
Title bats transmission model 
Description The database include information on bat demography: colony sizes, their age structure, and virological status (seroprevalence). We developped a compartmental model describing the bats demographic and transmission dynamics. The model is fitted to data using bayesian statistics (MCMC). 
Type Of Material Computer model/algorithm 
Year Produced 2022 
Provided To Others? Yes  
Impact No direct impact yet, but we expect this model can form the basis for other researchers to expand on. A publication in preperation has been accepted for publication in Proceedings of the Royal Society B. We are currently waiting for the proof. 
 
Description Erasmus Medical Centre - Department of Viroscience 
Organisation Erasmus MC
Department Department of Viroscience
Country Netherlands 
Sector Academic/University 
PI Contribution We are inputting information about which diagnostic tests are needed, and in particular involved in discuss related to required sensitivity and specificity of serological assays.
Collaborator Contribution In turn, the Department of Viroscience (Erasmus Medical Centre) is providing diagnostic tool to be used in the field. They are also involved in assessing viral affinity of various coronaviruses (sampled as part of the project as well as relaying on viral banks) to various mammals species (using organoids). This include affinity to pig, bats and domestic species. Their work is exploring viral tropism within host. The work will help our modelling effort to quantify (or at least qualitatively characterise) the risk of spillover and cross-species transmission of cornoviruses.
Impact Development of new serological assay for pig and bat coronaviruses.
Start Year 2022
 
Description Istituto Zooprofilattico Sperimentale delle Venezie 
Organisation Experimental Zooprophylactic Institute of the Venezie
Country Italy 
Sector Public 
PI Contribution As part of the project, we are collaborating with the Istituto Zooprofilattico Sperimentale delle Venezie in Italy. We are advising their sampling collection on both pigs and bats, both in term of information collected at the sites (environmental conditions), methods of sampling (direct sampling vs. environmental sampling) and sample sizes
Collaborator Contribution The partner is in turn sharing all the data collected to inform our modelling effort. This include general information on pig farms: - number of pigs, - age structure of pig populations - biosecurity practices - workforce Coronavirus sampling of pigs: - direct sample (nasal, blood, anal) - indirect sampling (feces) General information on bats - presence/absence - level of activity - colony sizes - Coronavirus sampling on bats - direct and indirect
Impact We are collating and adding to a database of cornoviruses linked to pig farms.
Start Year 2021
 
Description farms workshops 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Study participants or study members
Results and Impact In partnership with Experimental Zooprophylactic Institute of the Venezie, we organised focus discussion with the farmer involved in our sampling effort. Their inputs proved valuable to refine our sampling scheme on both bats and pigs. in particular more environmental sample resulted from this activities, and imporved collection of data related to farming practice. Finally, engagement with farmer has allowed us to involved them in informing us on bat presence which is expected to help us target field work activities.
Year(s) Of Engagement Activity 2021