Below is a link to download a pdf of the supplemental figures and table for Latinne et al. 2025 “Diversity and spillover risk of Swine Acute Diarrhea Syndrome and related coronaviruses in China and Southeast Asia”, published in mBio
Supplemental_figures_and_table_for_Latinne_et_al_2025
The full paper can be downloaded here:
Authorship: Alice Latinne1*†, Li-Biao Zhang2†, Cadhla Firth1, Guangjian Zhu1‡, Kevin J. Olival1¶, Cecilia A. Sánchez1, Shirley Chen1, Noam Ross1||, Hongying Li1#, Aleksei A. Chmura1**, Peter Daszak1**††
1EcoHealth Alliance, New York, NY 10018, USA
2 Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, China
*Present address: Wildlife Conservation Society, Southeast Asia-Pacific Program, Suva, Fiji
‡Present address: Shanghai Institute of Wildlife Epidemics, East China Normal University, Shanghai, China.
¶Present address: College of Tropical Agriculture and Human Resilience, University of Hawaiʻi at Mānoa, Honolulu, Hawaii, USA.
||Present address: rOpenSci, New York, USA
#Present address: Columbia Climate School, Columbia University, New York, USA
**Present address: Nature.Health.Global., Inc., Tallman, New York 10982, USA
†Co-first authors
††Corresponding author: [email protected]
Abstract
Bats are the reservoir hosts of emerging coronaviruses (CoVs) affecting human and livestock health. We assessed the diversity, evolution and geographic distribution of two alphacoronaviruses (subgenus Rhinacovirus) with considerable potential for emergence: swine acute diarrhea syndrome coronavirus (SADS-CoV), which has caused large outbreaks in pigs in China, and is able to infect primary human airway epithelial cells in vitro; and the related Rhinolophus bat coronavirus HKU2 (HKU2-CoV). Phylogenetic analyses of 523 rhinacovirus sequences from bats in China and Southeast Asia suggest these viruses should be re-classified into at least two distinct CoV species representing two well-supported monophyletic clades. Stronger phylogenetic clustering by sampling location than by host species suggests infrequent long-distance transmission of rhinacoviruses in southern China. Ancestral state reconstruction analysis indicates that R. sinicus/thomasi and R. affinis have played an important role in rhinacovirus evolution in southern China and that R. affinis is the likely reservoir host of SADS-CoV that spilled over into pigs. We used species distribution modeling of Rhinolophus spp. bat hosts of rhinacoviruses, combined with pig and human density data, to identify potential geographic rhinacovirus spillover risk in Southeast Asia. Areas of high pig density within suitable bat habitat exist primarily in southern China and northern Viet Nam, and hotspots of the highest human density within suitable bat habitat are primarily along the southern coast of China, Java, and central Thailand. Targeted surveillance of pigs and people in these regions may facilitate the timely detection of bat CoV spillover events and mitigate the risk of future outbreaks.
Significance Statement
Bats are the reservoir or ancestral hosts of important emerging coronaviruses affecting people (e.g. SARS, COVID-19) and livestock (e.g. PEDV, SADS). Here we analyzed 523 genetic sequences of SADS-CoV that caused largescale die-offs of pigs in China and is known to be able to infect human cells, and related HKU2-CoVs. We used this information to identify the horseshoe bat Rhinolophus affinis as the likely spillover host for the outbreak in pigs, and identified the bat species within which these viruses evolved. We then modeled the distribution of these host species, and their overlap with dense human and pig populations to identify the regions where surveillance programs can help identify spillover events and prevent future outbreaks.