Table 3. Virus strains included in the analyses.
| Family/Genus | Species (strain) | Abbreviation | Accession no. |
| Picornaviridae | |||
| Enterovirus | Human enterovirus A | HEV-A | NC_001612 |
| Human enterovirus B | HEV-B | NC_001472 | |
| Human coxsackievirus A1 (Tompkins) | HCV | AF499635 | |
| Human enterovirus D (70) | HEV-D | NC_001430 | |
| Porcine enterovirus B (UKG/410/73) | PEV-B | NC_004441 | |
| Human poliovirus 1 (Mahoney) | HPV | NC_002058 | |
| Human rhinovirus A (89) | HRV-A | NC_001617 | |
| Human rhinovirus B (70) | HRV-B | DQ473489 | |
| Human rhinovirus C (024) | HRV-C | EF582385 | |
| Sapelovirus | Pigeon picornavirus B (03/641)** | PiPV-B | FR727144* |
| Pigeon picornavirus A (03/603-7)** | PiPV-A | FR727145* | |
| Duck picornavirus TW90A | DPV | AY563023 | |
| Simian picornavirus 1 (2383) | SPV-1 | NC_004451 | |
| Porcine enterovirus A (V13) | PEV-A | NC_003987 | |
| Kobuvirus | Aichi virus (A846/88) | AiV | NC_001918 |
| Bovine kobuvirus (U-1) | BKV | NC_004421 | |
| Teschovirus | Porcine teschovirus 1 (F65) | PTV-1 | NC_003985 |
| Erbovirus | Equine rhinitis B virus 1 (P1436/71) | ERBV-1 | NC_003983* |
| Equine rhinitis B virus 2 (P313/75) | ERBV-2 | NC_003077* | |
| Cardiovirus | Encephalomyocarditis virus | EMCV | NC_001479 |
| Theilovirus (GDVII) | TMEV | NC_001366 | |
| Aphtovirus | Foot-and-mouth disease virus C | FMDV-C | NC_002554 |
| Foot-and-mouth disease virus O | FMDV-O | NC_004004 | |
| Hepatovirus | Hepatitis A virus | HAV | NC_001489 |
| Tremovirus | Avian encephalomyelitis virus (Calnek) | AEV | NC_003990 |
| Avihepatovirus | Duck hepatitis virus type 1 (DRL-62) | DHV-1 | DQ219396 |
| Duch hepatitis virus AP (03337) | DHV-AP | DQ256132 | |
| Parechovirus | Human parechovirus 2 (Gregory) | HPeV-2 | NC_001897 |
| Human parechovirus 3 (A308/99) | HPeV-3 | AB084913 | |
| Ljungan virus (174F) | LV-174F | AF327921 | |
| Ljungan virus (M1146) | LV-M1146 | AF538689 | |
| Senecavirus | Seneca valley virus (SVV-001) | SVV | DQ641257 |
| Unassigned | Seal picorna virus type 1 (HO.02.21) | SePV-1 | EU142040 |
| Human cosavirus A1 (0553) | HCoSV-A1 | NC_012800 | |
| Human klassevirus 1 (02394-01) | HKV | GQ184145 | |
| Salivirus NG-J1 | SaV | GQ179640 | |
| Turdivirus 1 (00805) | TV1 | GU182407 | |
| Turdivirus 2 (007167) | TV2 | GU182409* | |
| Turdivirus 3 (10878) | TV3 | GU182411* | |
| Astroviridae | |||
| Mamastrovirus | Human astrovirus 2 (Oxford) | HAstV-2 | L13745* |
| Human astrovirus 3 (Berlin) | HAstV-3 | AF141381* | |
| Human astrovirus 4 (Guangzhou) | HAstV-4 | DQ344027* | |
| Human astrovirus 8 (Yuk-8) | HAstV-8 | AF260508* | |
| Human astrovirus MLB1 (WD0016) | HAstV-MLB1 | FJ402983 | |
| HMO Astrovirus-A (NI-295) | HMOAstV-A | NC_013443* | |
| HMO Astrovirus-B (NI-196) | HMOAstV-B | GQ415661* | |
| HMO Astrovirus-C (NI-295) | HMOAstV-C | GQ415662* | |
| Porcine astrovirus (Tokushima83-74)*** | PAstV | AB037272* | |
| Ovine astrovirus | OAstV | NC_002469* | |
| Mink astrovirus | MAstV | AY179509* | |
| Canine astrovirus (3/05)*** | CaAstV | FM213330* | |
| Feline astrovirus (Bristol)*** | FAstV | AF056197* | |
| Bat astrovirus Tm/Guangxi/LD77/2007 | BatAstV-LD77 | FJ571066* | |
| Bat astrovirus Tm/Guangxi/LD71/2007 | BatAstV-LD71 | FJ571067* | |
| Bat astrovirus Ha/Guangxi/LS11/2007 | BatAstV-LS11 | FJ571068 | |
| Rat Astrovirus/RS118/HKG/2007 | RatAstv-RS118 | HM450381 | |
| Bottlenose dolphin astrovirus 1 (Bd1) | BDAstV-1 | FJ890355 | |
| California sea lion astrovirus 1 (CSL1) | CslAstV-1 | FJ890351* | |
| California sea lion astrovirus 2 (CSL2) | CslAstV-2 | FJ890352* | |
| Avastrovirus | Avian nephritis virus 1 (G-4260) | ANV-1 | AB033998* |
| Avian nephritis virus 2*** | ANV-2 | AB046864* | |
| Turkey astrovirus 1 | TAstV-1 | Y15936* | |
| Turkey astrovirus 2 | TAstV-2 | AF206663 | |
| Duck astrovirus (C-NGB) | DAstV | NC_012437* | |
| Feral pigeon astrovirus (03/594-6) | FPiAstV-03/594-6 | FR727146* | |
| Feral pigeon astrovirus (03/594-9) | FPiAstV-03/594-9 | FR727147* | |
| Feral pigeon astrovirus (03/603-5) | FPiAstV-03/603-5 | FR727148* | |
| Wood pigeon astrovirus (06/15660-1) | WPiAstV-06/15660-1 | FR727149* | |
| Coronaviridae | |||
| Gamma-coronavirus | Avian infectious bronchitis virus (Beaudette CK) | IBV | AJ311317* |
| Turkey coronavirus (TX-1038/98) | TCoV | GQ427176* | |
| Duck coronavirus (03/1094) | DCoV | AJ871024* | |
| Bulbul coronavirus (HKU11-796) | BuCoV | FJ376620* | |
| Goose coronavirus (03/586-50) | GCoV | AJ871017* | |
| Betacoronavirus | Human SARS coronavirus (Tor2) | SARS CoV | AY274119* |
| Bat SARS coronavirus (HKU3-1) | Bat SARS CoV | NC_009694* | |
| Zaria bat coronavirus (ZBCoV) | ZBCoV | HQ166910* | |
| Caliciviridae | |||
| Norovirus | Norovirus dog (Bari/91/07/ITA) | NoV Bari/91 | FJ875027* |
| Norovirus dog (170/07/ITA) | NoV 170 | EU224456* | |
| Norovirus dog (C33/Viseu/2007/PRT) | NoV C33/Viseu | GQ443611* | |
*Viruses harbouring s2m.
**Genus assignment suggested in this paper.
***The ORF1b sequence was not available.