Background
Methods
Sample collection
RNA extraction
Reverse transcription PCR (RT-PCR) screening of CoVs
Viral culture
Genome sequencing
Sequence analysis
Results
Detection of α-CoVs and β-CoVs in rodents
Scientific name | No. of rodents tested | No. of positives for the following/total no. of animals tested (%): | Detected coronaviruses |
---|---|---|---|
Apodemus chevrieri
| 98 | 21/98 (21.4%) |
Alphacoronavirus and Betacoronavirus
|
Apodemus ilex
| 17 | 1/17 (5.9%) |
Betacoronavirus
|
Eothenomys fidelis
| 62 | 1/62 (1.6%) |
Alphacoronavirus
|
Total
| 177 | 23/177 (13%) |
Genome organization and ORFs of AcCoV-JC34
Viruses | Genome | Pairwise amino acid sequence identity between JC34 and other virus sequences (%) | |||||||
---|---|---|---|---|---|---|---|---|---|
Size (nt) | G + C content(%) | 3CLpro
| RdRp | Hel | S | E | M | N | |
Alphacoronavirus
| |||||||||
RatCoV-JC34 | 27,649 | 40.07 | - | - | - | - | - | - | - |
BatCoV 1A | 28,326 | 38.14 | 57 | 76.6 | 74 | 17.6 | 36.5 | 50.2 | 23.3 |
BatCoV HKU2 | 27,164 | 39.32 | 58.5 | 75.1 | 73.3 | 39.2 | 36 | 53.5 | 27.9 |
BatCoV HKU8 | 28,773 | 41.79 | 61.2 | 76.5 | 73.5 | 18.6 | 33.8 | 51 | 23.5 |
RatCoV LRNV# | 28,763 | 40.29 | 91.9 | 94.3 | 96 | 67.2 | 93.8 | 92.3 | 78 |
BatCoV 512 | 28,203 | 40.12 | 60.9 | 73.3 | 71.8 | 18.3 | 35.5 | 53.1 | 24.6 |
PEDV | 28,033 | 42.02 | 59.7 | 74.3 | 72 | 17 | 34.2 | 52.7 | 23.2 |
HCoV-NL63 | 27,553 | 34.46 | 59.8 | 73.9 | 73 | 17.2 | 35.1 | 50.8 | 24 |
HCoV-229E | 27,317 | 34.46 | 58.9 | 73.3 | 74.3 | 19 | 36.4 | 46.3 | 21.7 |
MiCoV | 28,941 | 37.47 | 59.7 | 77.9 | 73 | 17.5 | 40.7 | 53.2 | 25.9 |
FCoV | 29,277 | 38.34 | 57.8 | 75.3 | 71.4 | 16.8 | 42 | 55.6 | 24.7 |
CCoV | 29,380 | 37.56 | 58.1 | 76.4 | 71.9 | 16.9 | 40.7 | 57.3 | 25.6 |
TGEV | 28,586 | 37.6 | 58.5 | 76.5 | 71.9 | 17.3 | 37 | 56.9 | 26.1 |
Betacoronavirus lineage A | |||||||||
Betacoronavirus 1 | |||||||||
HCoV-OC43 | 30,741 | 36.69 | 44.1 | 55.8 | 59.1 | 21.8 | 17.6 | 37.4 | 21 |
PHEV | 30,480 | 37.25 | 44.1 | 55.9 | 59.1 | 21.4 | 18.8 | 37.4 | 20.9 |
BCoV | 31,032 | 37.02 | 44.4 | 55.7 | 59.5 | 22.1 | 18.8 | 38.7 | 21.4 |
ECoV | 30,992 | 37.23 | 44.4 | 56 | 59.5 | 21.5 | 17.6 | 37.4 | 21.7 |
CrCoV | 31,028 | 37.01 | 44.4 | 55.8 | 59.5 | 21.9 | 18.8 | 38.3 | 21.2 |
Murine coronavirus | |||||||||
MHV | 31,386 | 41.88 | 42.9 | 55.5 | 57.5 | 21.1 | 18.1 | 36.8 | 21.3 |
RCoV | 31,250 | 41.26 | 42.9 | 56 | 58.9 | 21 | 20.5 | 38 | 21.3 |
RatCoV HKU24# | 31,249 | 40.07 | 43.3 | 56 | 60.5 | 21.6 | 20.5 | 39.6 | 21 |
RatCoV-708#@ | 30,821 | 39.06 | 44.1 | 56 | 58.5 | 20.6 | 20.5 | 36.8 | 20.8 |
HCoV-HKU1 | 29,926 | 32.06 | 44.8 | 55.8 | 58.3 | 21.2 | 30 | 37.9 | 21.8 |
RabbitCoV HKU14 | 31,100 | 37.64 | 44.8 | 56 | 59.7 | 21.8 | 17.6 | 38.7 | 21.5 |
Betacoronavirus lineage B | |||||||||
SARS-CoV | 29,727 | 40.80 | 43 | 58.9 | 60.8 | 22.1 | 19 | 27 | 19.4 |
Betacoronavirus lineage C | |||||||||
MERS-CoV | 30,112 | 41.18 | 40.9 | 58.7 | 63.6 | 21.2 | 19.3 | 34.8 | 18.6 |
Betacoronavirus lineage D | |||||||||
BatCoV HKU9 | 29,114 | 41.05 | 39.8 | 57.2 | 62.3 | 22.2 | 17.7 | 29.6 | 16 |
ORF | Location (nt) | Length (nt/aa) | TRS location | TRS sequence(s) (distance to AUG) |
---|---|---|---|---|
1ab | 437–20376 (shift at 12361) | 19940/6645 | 181 | CAACTCAACUAAACG(247)ATG
|
S | 20376–23756 | 3381/1126 | 20306 | TGGTAAACUUATTGTTAG(64)ATG
|
3 | 23753–24397 | 645/214 | 23711 | TGTTGUACUAAACCT(36)ATG
|
E | 24397–24633 | 237/78 | 24392 | CCACTTAACUA
A
TG
|
M | 24643–25389 | 747/248 | 24636 | TTGATCAACUAAAATG
|
6 | 25401–25901 | 501/166 | 25389 | GGTCTAAACUAAACCATTATG
|
N | 25903–27072 | 1170/389 | 25896 | AATTTCAACUAAAATG
|
8 | 26530–27702 | 543/180 | 26484 | TAGATCGCACUAA(40)ATG
|
9 | 27074/27391 | 318/105 | 27060 | TGATGAAACUAACGCCTAAAATG
|
nsp | First-last amino acid residues | Protein size (aa) | Cleavage site | Putative functional domain(s) |
---|---|---|---|---|
nsp1 | M1-G218
| 218 | SCPCG|KSAFT | Unknown |
nsp2 | K219-G820
| 602 | WVCKCG|AEVQLS | Unknown |
nsp3 | A821-A2277
| 1457 | TRVGTA|DLAVFN | ADRP, PL1pro, PL2pro
|
nsp4 | D2278-Q2779
| 502 | LNAQ|SCAK | Hydrophobic domain |
nsp5 | S2780-Q3042
| 263 | AKVQ|IEGA | 3CLpro
|
nsp6 | I3043-Q3319
| 277 | SGMQ|CSWA | Hydrophobic domain |
nsp7 | C3320-Q3437
| 118 | STIQ|SKLT | Unknown |
nsp8 | S3438-Q3715
| 278 | VKLQ|NNEI | Unknown |
nsp9 | N3716-Q3820
| 105 | VRLQ|AGKP | Unknown |
nsp10 | A3821-Q3955
| 135 | STVQ|SNII | Unknown |
nsp11 | S3956-N3974
| 19 | - | Short peptide at the end of ORF1a |
nsp12 | L3956-Q4881
| 926 | SVLQ|SAGL | RdRp |
nsp13 | S4882-Q5478
| 597 | TDLQ|SVLS | Hel |
nsp14 | S5479-Q5998
| 520 | PILQ|GLEN | ExoN |
nsp15 | G5999-Q6334
| 346 | PQLQ|NSEW | NendoU |
nsp16 | N6345-K6646
| 302 | - | O-MT |