Is this the reason Covid-19 has broken out at pork plants?
Abstract
The ongoing SARS-CoV-2 pandemic is the third zoonotic coronavirus identified in the last
twenty years. Previously, four other known coronaviruses moved from animal reservoirs into
humans and now cause primarily mild-to-moderate respiratory disease. The emergence of
these viruses likely involved a period of intense transmission before becoming endemic,
highlighting the recurrent threat to human health posed by animal coronaviruses. Enzootic and
epizootic coronaviruses of diverse lineages pose a significant threat to livestock, as most
recently observed for virulent strains of porcine epidemic diarrhea virus (PEDV) and swine acute
diarrhea-associated coronavirus (SADS-CoV). Unique to RNA viruses, coronaviruses encode a
proofreading exonuclease (ExoN) that lowers point mutation rates to increase the viability of
large RNA virus genomes, which comes with the cost of limiting virus adaptation via point
mutation. This limitation can be overcome by high rates of recombination that facilitate rapid
increases in genetic diversification. To compare dynamics of recombination between related
sequences, we developed an open-source computational workflow (IDPlot) to measure
nucleotide identity, locate recombination breakpoints, and infer phylogenetic relationships. We
analyzed recombination dynamics among three groups of coronaviruses with impacts on
livestock or human health: SARSr-CoV, Betacoronavirus-1, and SADSr-CoV. We found that all
three groups undergo recombination with highly diverged viruses, disrupting phylogenetic
relationships and revealing contributions of unknown coronavirus lineages to the genetic
diversity of established groups. Dynamic patterns of recombination impact inferences of
relatedness between diverse coronaviruses and expand the genetic pool that may contribute to
future zoonotic events. These results illustrate the limitations of current sampling approaches for
anticipating zoonotic threats to human and animal health
