Novel Genotype Classification System for Rotavirus Viral Proteins VP1, VP2 and VP3

1Supplemental Data 6 Phylogenetic dendrogram of VP1 at the nucleotide level (A). Bootstrap

2values (2000 replicates) are shown. Designation of species of origin: Bo: bovine; Hu: human; Rh:

3Rhesus; Po: porcine; Ov: ovine; La: lapine; Si: simian; Av: avian. The dashed line indicates the

4best option to divide the dendrogram into appropriate genotypes. The closing braces on the right

5side of the dendrograms depict the genotypes as they are proposed in this study. Panel B show the

6VP1 identity frequency graph. VP1 nucleotide accession numbers collected from GenBank: RF,

7J04346; RRV, EF583006; MG6, EF554093; PA169, EF554126; UKtc, X55444; B4106,

8AY740741; 30/96, DQ205221; SA11-Both, X16830; SA11-tsC, DQ838601; SA11-H96,

9DQ838640; SA11, AF015955; SA11-5N, DQ838636; SA11-5S, DQ838637; SA11-30/19,

10DQ838638; SA11-30/1A, DQ838639; B10925, EF554115; 111/05-27, EF554137; OVR762,

11EF554148; Hun5, EF554104; TB-Chen, AY787653; B1711, EF554082; DRC88, DQ005114;

12DRC86, DQ005125; N26-02, DQ146682; RV176-00, DQ490551; RV161-00, DQ490545; T152,

13DQ146699; TUCH, EF583010; YM, X76486; Gottfried, M32805; KU, AB022765; Dhaka25-02,

14DQ146649; Dhaka16-03, DQ492669; B4633-03, DQ146638; Matlab13-03, DQ146671;

15Dhaka12-03, DQ146660; PO-13, AB009629.

17Supplemental Data 7 Phylogenetic dendrograms of VP2 at the nucleotide level (A). Bootstrap

19Rhesus; Po: porcine; Ov: ovine; La: lapine; Si: simian; Av: avian. The dashed line indicate the

21side of the dendrograms depict the genotypes as they are proposed in the manuscript. Panel B

22shows the identity frequency graph. Panels C, D and E show details of the boxed region of panel

23B. In panel D, the identities among rotavirus strains belonging to the C2 genotype are shown in

24dark green. In panels E, the above mentioned dark green bars are omitted. VP2 nucleotide

1 1 1accession numbers collected from GenBank: UKtc, X52589; RF, X14057; Hun5, EF554105;

2MG6, EF554094; 30/96, DQ205222; OVR762, EF554149; B4106, AY740740; B10925-97,

3EF554116; 111/05-27, EF554138; PA169, EF554127; B1711, EF554083; TB-Chen, AY787652;

4DRC88, DQ005113; DRC86, DQ005124; RV161-00, DQ490546; N26-02, DQ146683; RV176-

500, DQ490552; T152, DQ146700; TUCH, EF583011; RRV, EF583007; SA11-Cl3, AF474406;

6SA11, X16831; SA11_Ramig, L33364; SA11-tsF, L20084; SA11-H96, DQ838635; SA11-5S,

7DQ838632; SA11-30/19, DQ838633; SA11-5N, DQ838631; SA11-1A, DQ838634; Wa,

8X14942; KU, AB022766; Dhaka12-03, DQ146661; Dhaka16-03, DQ492670; Dhaka25-02,

9DQ146650; Matlab13-03, DQ146672; Beijing, DQ862063; B4633-03, DQ146639; PO-13,

10AB009630.

12Supplemental Data 8 Phylogenetic dendrogram of VP3 at the nucleotide level (A). Bootstrap

14Rhesus; Eq: equine; Po: porcine; Ov: ovine; La: lapine; Si: simian; Av: avian. The dashed line

15indicates the best option to divide the dendrogram into appropriate genotypes. The closing braces

16on the right side of the dendrograms depict the genotypes as they are proposed in this study. B

17shows the identity frequency graphs. VP3 Nucleotide accession numbers collected from

18GenBank: TB-Chen, AY787654; DS-1, AY277914; DRC88, DQ005112; DRC86, DQ005123;

19N26-02, DQ146684; RV161-00, DQ490547; RV176-00, DQ490553; 111/05-27, EF554139;

20Hun5, EF554106; B10925-97, EF554117; OVR762, EF554150; MG6, EF554095; B1711,

21EF554084; PA169, EF554128; 69M, AY277916; UKtc, AY300923; RF, AY116592; RRV,

22EF583008; T152, DQ146701; TUCH, EF583012; B4106, AY740739; 30/96, DQ205223; SA11-

23tsB, DQ838600; SA11-5N, DQ838641; SA11, X16062; SA11-5S, DQ838642; SA11, X16387;

24SA11-H96, DQ838645; SA11-30/1A, DQ838644; SA11-30/10, DQ838643; L338, AY277922;

1 2 1OSU, AY277921; YM1, AY300922; Wa, AY267335; Hochi, AY277915; WI-61, AY277917;

2L26, AY277918; A64, AY277920; KU, AB022767; B4633-03, DQ146640; Dhaka12-03,

3DQ146662; Dhaka25-02, DQ146651; Dhaka16-03, DQ492671; Matlab13-03, DQ146673; ST3,

4AY277919; PO-13, AB009631; CH2, AY277923.

6Supplemental Data 9 Phylogenetic dendrogram of NSP1 at the nucleotide level (A). Bootstrap

7values (2000 replicates) above 50 are shown. Designation of species of origin: Bo: bovine; Hu:

8human; Rh: Rhesus; Eq: equine; Po: porcine; Ov: ovine; La: lapine; Si: simian; Fe: feline; Ca:

9canine; Mu: murine; Av: avian. The dashed line indicates the best option to divide the

10dendrogram into appropriate genotypes. The closing braces on the right side of the dendrograms

11depict the 14 A-genotypes as they are proposed in this study. Panel B shows the identity

12frequency graph. NSP1 nucleotide accession numbers collected from GenBank: B223, Z12105;

13Hochii, Z12106; OSU(a), Z12107; UKtc, Z12108; UK, L11575; St3(a), Z32534; RRV(d),

14Z32535; 69M(a), Z32552; ST3(b), U11492; C-11, AF084550; Alabama, AF084549; BAP-2,

15AF084551; RRV(a), AY117048; RRV(b), U08433; RRV(c), AY117053; K9, AF111946;

16FRV64, D78362; L338, D38158; FI14, D38155; FI23, D38156; H2, D38157; SA11-4F,

17AF290883; SA11-4S, L29185; SA11-FEM, AF290881; SA11-both, X14914; SA11-Patton,

18L18944; EHP, U08423; EW, U08428; T152, AB097459; 116E, U85999; K8, D38152; Wa,

19L18943; RF, M22308; B641, AF458087; I321, U08418; A44, U23726; IGV-80-3, X59297; IGV-

20re, AF190169; OSU(b), U08432; KU, AB022769; Cat2, U23727; MP409, AF141916; A5-13,

21D38148; M37, U11491; AU-1, D45244; YM, BAA20545; Gottfried, U08431; DS-1(a), L18945;

22L26(a), D38150; 69M(b), D38151; H1, U23728; PO-13, AB009633; B4106, AY740735; NR1,

23AF506017; RMC321, AF506292; 4S, L29185; 4F, L29183; TB-Chen, AY787647; DRC88,

24DQ005108; B4633-03, DQ146644; RMC/G7, AY601547; RMC100, AY601546; Dhaka25-05,

1 3 1DQ146655; Dhaka12-03, DQ146666; Dhaka16-03, DQ492675; Matlab13-03, DQ146677; N26-

202, DQ146688; 30/96, DQ205225; DRC86, DQ005119; RV176-00, DQ490557; RV161-00,

3DQ490540; 111/05-27, EF554143; B10925-97, EF554121; Hun5, EF554110; MG6, EF554099;

4PA169, EF554132; R14a, DQ199658; R1a, DQ199657; KJ44, DQ494396; KJ75, DQ494395;

5B1711, EF554088; TUCH, DQ838651; SA11-H96, DQ838599; O, DQ838595; OVR762,

6EF554154.

10human; Po: porcine; Ov: ovine; La: lapine; Si: simian; Av: avian. The dashed line indicates the

12side of the dendrograms depict the 5 N-genotypes as they are proposed in this study. Panel B

13shows the identity frequency graph. NSP2 nucleotide accession numbers collected from

14GenBank: NCDV, L04530; UK, J02420; SA11-both, J02353; RF, Z21640; I321, Z47975; OSU,

15X06722; KU, AB022770; IS2, CAA64262; Hu, X57944; SA11-Ramig, L04532; SA11-Patton,

16L04531; SA11-tsE, L20901; PO-13, AB009625; Ty-1, Q03244, of, AAA47300; B4106,

17AF506293; RMC321, AAQ07959; NR1, AF506018; TB-Chen, AY787648; DRC88, DQ005107;

18DRC86, DQ005118; RMC100, AF506014; 30/96, DQ205227; Dhaka25-02, DQ146656;

19Dhaka12-03, DQ146667; Matlab13-03, DQ146678; N26-02, DQ146689; RV161-00, DQ490541;

20Dhaka16-03, DQ492676; RV176-00, DQ490558; B4633-03, DQ146645; L26(a), DQ146696;

21T152, DQ146703; Wa, L04534; DS-1(a), L04529; Au-1, DQ490534; 111/05-27, EF554144;

22B10925-97, EF554122; Hun5, EF554111; MG6, EF554100; PA169, EF554133; B1711,

23EF554089; KJ75, DQ494402; KJ44, DQ494401; SA11-H96, DQ838615; SA11-30/1A,

1 4 1DQ838614; SA11-30/19, DQ838613; SA11-5S, DQ838612; SA11-5N, DQ838611; O,

2DQ838597; OVR762, EF554155.

6human; Po: porcine; Ov: ovine; La: lapine; Si: simian; Rh: Rhesus; Av: avian. The dashed line

8on the right side of the dendrograms depict the 7 T-genotypes as they are proposed in this study.

9Panel B shows the identity frequency graph. NSP3 nucleotide accession numbers collected from

10GenBank: Hg17, X81427; RF, Z21639; MP409, AF141917; KU, AB022771; ST3, X81436;

11I321, X81433; IGV-S, AF190171; Gottfried, X81430; M, AF338246; IGV-P, AF190170; OSU,

12X81431; Wa, X81434; PRICE, X81432; WI61, X81437; RRV, AY065842; RRV-bis, X81426;

13S2, X81428; 69M, X81425; SA11-4F, M87502; SA11-C14, AY065843; SA11-both, X00355;

14IS2, X76645; PO-13, AB009626; RMC321, AF541920; NR1, AF506019; UK, K02170; IGV-F,

15AF190172; NCDV, X81429; TB-Chen, AY787649; DRC88, DQ005106; DRC86, DQ005117;

16B4633-03, DQ146646; L26, DQ146697; T152, DQ146704; RMC100, AF506015; Dhaka25-02,

17DQ146657; Dhaka12-03, DQ146668; Dhaka16-03, DQ492677; Matlab13-03, DQ146679; N26-

1802, DQ146690; B4106, AY740733; 30/96, DQ205228; RV161-00, DQ490542; RV176-00,

19DQ490559; DS-1, EF136660; Au-1, DQ490535; 111/05-27, EF554145; B10925-97, EF554123;

20Hun5, EF554112; MG6, EF554101; PA169, EF554134; B1711, EF554090; KJ75, DQ494404;

21KJ44, DQ494403; SA11-H96, DQ838610; SA11-30/1A, DQ838609; SA11-30/19, DQ838608;

22SA11-5S, DQ838607; SA11-5N, DQ838606; OVR762, EF554156; GO, X81430.

1 5 1Supplemental Data 13 Phylogenetic dendrogram of NSP5 at the nucleotide level (A). Bootstrap

3human; Rh: Rhesus; Po: porcine; Ov: ovine; La: lapine; Si: simian; Av: avian. The dashed line

5on the right side of the dendrograms depict the 6 H-genotypes as they are proposed in this study.

6Panel B shows the identity frequency graph. Panels C, D and E show details of the boxed region

7of panel B. In panel D, the identities among rotavirus strains belonging to the H2, E1 and E3

8genotypes are shown in green, blue and red bars, respectively. In panels E, the above mentioned

9bars are omitted. NSP5 nucleotide accession numbers collected from GenBank: ALA, J04361;

10RF, AF188126; RRV(ATCC), AF306492; Wa(ATCC), AF306494; Wa(b), V01191; K8,

11AB008655; Au-1, AB008656; O264, AB008657; M318, AB008658; 512A, AB008659; 512B,

12AB008660; KUa, AB008661; KUb, AB022773; 512C, AB008662; 470, AB008663; 582,

13AB008664; Wa(a), AB091726; KUN, AB091727; 87H134, AB091353; 88H185, AB091354;

1492H085, AB091355; 88H116, AB091356; 92H069, AB091357; 88H242, AB091358; 92H102,

15AB091359; 96H001, AB045217; 96H026, AB045218; 96H063, AB045219; 96H070, AB045220;

16SA11, M28347; UK, K03385; VMRI, M33606; 69M, M33607; DS-1(a), M33608; RMC321,

17AY033396; Mc323, U54772; Mc345, U54773; YM, X69486; Z10262, U96698; OSU, X15519;

18M/clM0, AF338244; M/clM2, AF338245; B37, M28377; RV-5, M28378; v115, X76777; v158,

19X76778; v183, X76779; v252, X76780; v47, X76781; v51, X76782; v61, X76783; PO-13,

20AB009628; B4106, AY740731; Lamb, AY622998; NR1, AF508732; RMC100, AF373605;

21CC86, X80537; CN86, X80538; C60, D00474; TB-Chen, AY787651; DRC88, DQ005104;

22B4633-03, DQ146648; L26(a), DQ146698; RMC83, AY601548; 30/96, DQ205231; Dhaka25-

2302, DQ146659; Dhaka12-03, DQ146670; Dhaka16-03, DQ492679; Matlab13-03, DQ146681;

24N26-02, DQ146692; T152, DQ146706; DRC86, AH014893; RMC61, AY841126; RMC437,

1 6 1AY803730; RMC/G60, AY770974; RMC/G7, AY769695; RMC/G66, AY769694; RV161-00,

2DQ490544; RV176-00, DQ490561; RU172, DQ204739; 111/05-27, EF554147; B10925-97,

3EF554125; Hun5, EF554114; MG6, EF554103; PA169, EF554136; B1711, EF554092; KJ75,

4DQ494400; KJ44, DQ494399; SA11-H96, DQ838630; SA11-30/1A, DQ838629; SA11-30/19,

5DQ838628; SA11-5S, DQ838627; SA11-5N, DQ838626; HP140, DQ003299; HP113,

6DQ003298; IS2, EF185863; OVR762, EF554158; CMP034, DQ916134.