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. 2019 Aug 22;10:1945. doi: 10.3389/fmicb.2019.01945

TABLE 1.

Virus taxonomy assignments, virus name abbreviations, GenBank accession numbers, and related Protein Data Bank (PDB) entries of the representative positive-strand RNA virus RdRPs chosen for analyses in this study.

Virus species Genusa Familyb Orderc Abbreviation GenBank Acc. no. PDBd
Equine arteritis virus Alphaarteri- Arteri- Nido- EAV (van Dinten et al., 1999; Ziebuhr et al., 2000) NC_002532
Severe acute respiratory syndrome-related coronaviruse Betacorona- Corona- Nido- SARS-CoV (Snijder et al., 2003; Subissi et al., 2014a) NC_004718
Aplysia abyssovirus 1 Alphaabysso- Abysso- Nido- AAbV GBBW01007738
Charybnivirus 1 Charybni- Euroni- Nido- CharNV KX883628
Turrinivirus 1 Turrini- Medioni- Nido- TurrNV KX883629
Alphamesonivirus 1 Alphamesoni- Mesoni- Nido- NDiV MH520106
Planarian secretory cell nidovirus Alphamononi- Mononi- Nido- PSCNV MH933735
Gill-associated virus Oka- Roni- Nido- GAV NC_010306
White bream virus Bafini- Tobani- Nido- WBV NC_008516
Israel acute paralysis viruse Apara- Dicistro- Picorna- IAPV (de Miranda et al., 2010) NC_009025
Infectious flacherie virus Ifla- Ifla- Picorna- IFV (Isawa et al., 1998) AB000906
Poliovirus 1 Entero- Picorna- Picorna- PV-1 (Harris et al., 1992) NC_002058 1RA6
Cowpea mosaic virus Como- Seco- Picorna- CPMV (Peters et al., 1995) X00206
Solenopsis invicta virus 2 Sopolyci- Polycipi- Picorna- SINV-2 EF428566
Heterosigma akashiwo RNA virus Marna- Marna- Picorna- HaRNAV NC_005281
Turnip yellow mosaic virus Tymo- Tymo- Tymo- TYMV (Morch et al., 1988; Jakubiec et al., 2007; Moriceau et al., 2017) NC_004063
Potato virus X Potex- Alphaflexi- Tymo- PVX NC_011620
Grapevine virus A Viti- Betaflexi- Tymo- GVA AF007415
Sclerotinia sclerotiorum deltaflexivirus 1 Deltaflexi- Deltaflexi- Tymo- SsDFV1 NC_038977
Botrytis virus F Mycoflexi- Gammaflexi- Tymo- BotV-F NC_002604
Nudaurelia capensis beta virus Betatetra- Alphatetra- /f NβV (Gorbalenya et al., 2002) NC_001990
Human astrovirus 8 Mamastro- Astro- / HAstV-8 (Willcocks et al., 1994; Mendez-Toss et al., 2000) AF260508
Mushroom bacilliform virus Barna- Barna- / MBV (Revill et al., 1994) NC_001633
Beet necrotic yellow vein virus Beny- Beny- / BNYVV (Hehn et al., 1997) NC_003514
Ourmia melon virus Ourmia- Botourmia- / OuMV (Rastgou et al., 2009) EU770623
Brome mosaic virus Bromo- Bromo- / BMV (Ahlquist et al., 1984) NC_002027
Norwalk virus Noro- Calici- / NV (Ng et al., 2004; Oliver et al., 2006) AJ583672 1SH0
Providence virus Alphacarmotetra- Carmotetra- / PrV (Walter et al., 2010) NC_014126
Lettuce infectious yellows virus Crini- Clostero- / LIYV (Klaassen et al., 1995) U15440
Yellow fever virus Flavi- Flavi- / YFV (Rice et al., 1985) X03700 4K6M
Hepatitis C virus Hepaci- Flavi- / HCV (Yanagi et al., 1997) AF011751 1C2P
Hepatitis G viruse Pegi- Flavi- / HGV (Xiang et al., 2000; Berg et al., 2015) NC_001710
Bovine viral diarrhea virus 1 Pesti- Flavi- / BVDV (Choi et al., 2004) NC_001461 5YF5
Cutthroat trout virus Piscihepe- Hepe- / CTV (Batts et al., 2011) NC_015521
Blueberry necrotic ring blotch virus Bluner- Kita- / BNRBV (Quito-Avila et al., 2013) JN651149
Escherichia virus Qbeta Allolevi- Levi- / Qβ (Kidmose et al., 2010) AWN02713 3MMP
Barley yellow dwarf virus PAV Luteo- Luteo- / BYDV-PAV (Miller et al., 1988) NC_004750
Saccharomyces 20S RNA narnavirus Narna- Narna- / ScNV-20S (Rodriguez-Cousino et al., 1991, 1998) NC_004051
Nodamura virus Alphanoda- Noda- / NoV (Johnson et al., 2003) AF174533
Thosea asigna virus Alphapermuto tetra- Permutotetra- / TaV (Gorbalenya et al., 2002; Ferrero et al., 2015) AF282930 4XHI
Potato virus Y Poty- Poty- / PVY (Singh and Singh, 1996) U09509
Southern bean mosaic virus Sobemo- Solemo- / SBMV (Ozato Junior et al., 2009) NC_004060
Solenopsis invicta virus 3 Invicta- Solinvi- / SINV-3 (Valles et al., 2016) FJ528584
Sindbis virus Alpha- Toga- / SINV (Strauss et al., 1984) J02363
Tomato bushy stunt virus Tombus- Tombus- / TBSV (Hearne et al., 1990) NC_001554
Gentian ovary ringspot virus Gora- Virga- / GORV (Atsumi et al., 2015) NC_024501
Heterocapsa circularisquama RNA virus 01 Dinorna- Alverna- / HcRNAV01 NC_007518
Rubella virus Rubi- Matona- / RUB RUBCG
Cryphonectria hypovirus 3e Hypo- Hypo- / CHV3 AF188515

ac “-” indicates the omitted suffix “virus,” “viridae,” or “virales,” respectively. dPDB entries chosen in Figure 3 for seven RdRP-structure available virus families. eNon-type species. “/” indicates that virus order has not been assigned. References listed in the abbreviation column are used to define the N- and C-terminal boundaries of the RdRP proteins.