Abstract
The ongoing SARS (severe acute respiratory syndrome)-CoV (coronavirus)-2 pandemic has exposed major gaps in our knowledge on the origin, ecology, evolution, and spread of animal coronaviruses. Porcine epidemic diarrhea virus (PEDV) is a member of the genus Alphacoronavirus in the family Coronaviridae that may have originated from bats and leads to significant hazards and widespread epidemics in the swine population. The role of local and global trade of live swine and swine-related products in disseminating PEDV remains unclear, especially in developing countries with complex swine production systems. Here, we undertake an in-depth phylogeographic analysis of PEDV sequence data (including 247 newly sequenced samples) and employ an extension of this inference framework that enables formally testing the contribution of a range of predictor variables to the geographic spread of PEDV. Within China, the provinces of Guangdong and Henan were identified as primary hubs for the spread of PEDV, for which we estimate live swine trade to play a very important role. On a global scale, the United States and China maintain the highest number of PEDV lineages. We estimate that, after an initial introduction out of China, the United States acted as an important source of PEDV introductions into Japan, Korea, China, and Mexico. Live swine trade also explains the dispersal of PEDV on a global scale. Given the increasingly global trade of live swine, our findings have important implications for designing prevention and containment measures to combat a wide range of livestock coronaviruses.
Highlights
Coronaviruses are single-stranded, positive-sense RNA viruses that cause subclinical as well as respiratory and gastrointestinal diseases in humans, other mammals and birds (Brian and Baric, 2005)
We assembled the largest collection of available Porcine epidemic diarrhea virus (PEDV) sequences, including 247 newly sequenced viruses, and uniquely collated them with previously inaccessible swine trade data
In an increasingly globalized world, animal coronaviruses such as PEDV have ample opportunities to spread between countries and continents
Summary
Coronaviruses are single-stranded, positive-sense RNA viruses that cause subclinical as well as respiratory and gastrointestinal diseases in humans, other mammals and birds (Brian and Baric, 2005). The host range switches of coronaviruses (CoVs) from wildlife to humans have resulted in several novel diseases with high fatality rate, such as severe acute respiratory syndrome (SARS), Middle East respiratory syndrome (MERS), and the recent outbreak of SARS-CoV-2 (Drosten, et al 2003; Zaki, et al 2012; Sun, et al 2020). SARS-CoV-2 is the most widespread and impactful human infectious disease since the start of the twenty-first century (Drosten, et al 2003; Graham and Baric 2020). Despite likely having originated in bats, SARS-CoV and MERS-CoV have infected humans via an intermediate host rather than through direct infection from bats, and this may be the case for SARS-. The number of known intermediate hosts involved in the transmission of bat-origin coronaviruses to humans is limited. Monitoring and understanding the evolution and transmission of porcine coronavirus in swine populations can help the swine breeding industry, and further prevent and control potential public health threats
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