Table 1. Summary of coronavirus positives by taxa and interface.
Co-infection is defined as the detection of two different coronavirus taxonomic units in an individual animal.
| Taxa group | Interface | Sub-interface | Taxa group | % site positive | % individual positive | Viral species | # of co-infected animals |
|---|---|---|---|---|---|---|---|
| Rodents | Rat trade | Rat trader (selling live rats and slaughtering live rats for sale as meat) | Field ratᵅ | 100% (8/8) | 20.7% (39/188) | Murine coronavirus (n = 36), Longquan aa coronavirus (n = 5) | 2 |
| Large market (selling live rats and slaughtering live rats for sale as meat) | Field ratᵅ | 100% (14/14) | 32.0% (116/363) | Murine coronavirus (n = 103), Longquan aa coronavirus (n = 31) | 18 | ||
| Restaurant (slaughtering live rats held on the premises and preparing as food) | Field ratᵅ | 100% (2/2) | 55.6% (84/151) | Murine coronavirus (n = 70), Longquan aa coronavirus (n = 20) | 6 | ||
| Wildlife farm | Hystrix sp. | 47.8% (11/23) | 6.0% (20/331) | Bat coronavirus 512/2005 (n = 19), Infectious bronchitis virus (IBV) (n = 1) | 0 | ||
| Rhizomys sp. | 45.5% (5/11) | 6.3% (6/96) | Bat coronavirus 512/2005 (n = 5), Infectious bronchitis virus (IBV) (n = 1) | 0 | |||
| Rattus sp.b | 100% (1/1) | 100% (1/1) | Bat coronavirus 512/2005 (n = 1) | 0 | |||
| Sciuridae sp. | 0% (0/1) | 0% (0/1) | |||||
| Bats | Human dwelling | Natural bat roost | |||||
| Pteropus sp. | 100% (1/1) | 6.7% (4/60) | PREDICT_CoV-17 (n = 3), PREDICT_CoV-35 (n = 1) | 0 | |||
| Cynopterus horsfieldii | 0% (0/1) | 0% (0/2) | |||||
| Bat guano farm (artificial bat roost) | Microchiropterac | 94.1% (16/17) | 74.8% (234/313) | PREDICT_CoV-17 (n = 1), PREDICT_CoV-35 (n = 38), Bat coronavirus 512/2005 (n = 216) | 21d | ||
| 82.9% (58/70) | 33.5% (504/1506) | 47 |
ᵅ Field rat here refers to a mix of Rattus sp. and Bandicota sp.
ᵇ This environmental sample collected from a porcupine cage on a porcupine farm was barcoded as Rattus sp., suggesting this species was free-ranging at the site (Fig 2). The detection of a bat virus from this sample is suggestive of either environmental mixing or viral sharing.
c Suborder
d Co-infections included PREDICT_CoV-17 with Bat coronavirus 512/2005 (n = 1) and PREDICT_CoV-35 with Bat coronavirus 512/2005 (n = 20).