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Tracing the origin and co-phylogeny of the caliciviruses, by G. J. Etherington, S. M. Ring, M. A. Charleston, J. Dicks, V. J. Rayward-Smith and I. N. Roberts

Journal of General Virology vol. 87, part 5, pp. 1229 - 1235

Calicivirus Supplementary Data

Calicivirus Supplementary Data

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These are the sequences used for the full-genome co-phylogeny mapping
gi|333765|gb|M67473.1|RHVCG Rabbit hemmorhagic disease virus complete genome
gi|1550750|emb|Z69620.1|EBHSVORFS European brown hare syndrome virus RNA
gi|1061311|gb|M87661.1|CVXRNA Norwalk calicivirus nonstructural polyprotein, 58 kd capsid protein and orf3 genes, complete cds
gi|18025351|gb|AY032605.1| Human calicivirus Hu/NLV/GII/MD145-12/1987/US, complete genome
gi|9886086|gb|U07611.2|HCU07611 Hawaii calicivirus nonstructural polyprotein and capsid protein genes, complete cds; and unknown gene
gi|10141004|gb|U15301.2|SMU15301 San Miguel sea lion virus serotype 1, complete genome
gi|323877|gb|M86379.1|CVXCOMGEN Feline calicivirus, complete genome
gi|10141008|gb|U76874.2|VEU76874 Vesicular exanthema of swine virus stain A48, complete genome
gi|6164839|gb|AF182760.1|AF182760 Porcine enteric calicivirus, complete genome
gi|21699776|ref|NC_004064.1|Calicivirus strain NB, complete genome

Dataset One

gi|18149310|dbj|AB074892.1| Swine calicivirus genes for RNA polymerase (outgroup)
gi|15128159|gb|AF397156.1| Human calicivirus NLV/MOH/99 RNA polymerase mRNA
gi|15213698|gb|AF397905.1|AF397905 Human calicivirus NLV/Schwerin 003/00/DE RNA-dependent RNA polymerase gene
gi|15991631|gb|AF414407.1|AF414407 Norwalk-like virus NLV/Florida/269/1993/US RNA polymerase (orf1) gene, partial cds; and capsid protein (orf2) and minor structural protein (orf3) genes, complete cds
gi|15991635|gb|AF414408.1|AF414408 Norwalk-like virus NLV/Baltimore/274/1993/US RNA polymerase (orf1) gene, partial cds; and capsid protein (orf2) and minor structural protein (orf3) genes, complete cds
gi|15991639|gb|AF414409.1|AF414409 Norwalk-like virus NLV/Gwynedd/273/1994/US RNA polymerase (orf1) gene, partial cds; and capsid protein (orf2) and minor structural protein (orf3) genes, complete cds
gi|15991643|gb|AF414410.1|AF414410 Norwalk-like virus NLV/Miami/292/1994/US RNA polymerase (orf1) gene, partial cds; and capsid protein (orf2) and minor structural protein (orf3) genes, complete cds
gi|15991667|gb|AF414416.1|AF414416 Norwalk-like virus NLV/Miami/81/1986/US RNA polymerase (orf1) gene
gi|15991675|gb|AF414418.1|AF414418 Norwalk-like virus NLV/Westover/302/1994/US RNA polymerase (orf1) gene
gi|15991679|gb|AF414419.1|AF414419 Norwalk-like virus NLV/Richmond/283/1994/US RNA polymerase (orf1) gene
gi|15991683|gb|AF414420.1|AF414420 Norwalk-like virus NLV/Honolulu/314/1994/US RNA polymerase (orf1) gene
gi|15991687|gb|AF414421.1|AF414421 Norwalk-like virus NLV/Port Canaveral/301/1994/US RNA polymerase (orf1) gene, partial cds; and capsid protein (orf2) and minor structural protein (orf3) genes, complete cds
gi|15991691|gb|AF414422.1|AF414422 Norwalk-like virus NLV/New Orleans/306/1994/US RNA polymerase (orf1) gene, partial cds; and capsid protein (orf2) and minor structural protein (orf3) genes, complete cds
gi|15991695|gb|AF414423.1|AF414423 Norwalk-like virus NLV/White River/290/1994/US RNA polymerase (orf1) gene, partial cds; and capsid protein (orf2) and minor structural protein (orf3) genes, complete cds
gi|16323004|gb|AY054299.1| Human calicivirus NLV/Idaho Falls/378/1996/US capsid protein gene
gi|16323006|gb|AY054300.1| Human calicivirus NLV/Chesterfield/434/1997/US capsid protein gene
gi|16417805|gb|AF425767.1|AF425767 Human calicivirus NLV/Dillingen 391/01/DE capsid protein gene
gi|16417809|gb|AF425769.1|AF425769 Human calicivirus NLV/Wiesbaden 294/01/DE capsid protein gene
gi|16417843|gb|AF427118.1|AF427118 Human calicivirus NLV/Erfurt/546/00/DE capsid protein gene
gi|16417845|gb|AF427119.1|AF427119 Human calicivirus NLV/Pirna/110/00/DE capsid protein gene
gi|18762692|gb|AY077644.1| Norwalk-like virus Sw/NLV/VA34/1998/NL VP1 capsid protein gene
gi|21586429|gb|AY113106.1| Norwalk-like virus strain Hu/NLV/Fayetteville/1998/US major capsid protein VP1 gene
gi|22858889|gb|AY130761.1| Human calicivirus NLV/M7/1999/US major capsid protein VP1 gene
gi|6180162|gb|AF195848.1|AF195848 Human calicivirus strain Hu/NLV/Amsterdam/98-18/1998/NET capsid protein gene
gi|7328912|dbj|AB028247.2| Norwalk-like virus gene for capsid protein
gi|7649402|emb|AJ277606.1|HCA277606 Human calicivirus HU/NLV/Girlington/93/UK RNA for capsid protein (ORF2)
gi|7649404|emb|AJ277607.1|HCA277607 Human calicivirus HU/NLV/Hillingdon/90/UK RNA for capsid protein (ORF2)
gi|7649406|emb|AJ277608.1|HCA277608 Human calicivirus HU/NLV/Leeds/90/UK RNA for capsid protein (ORF2)
gi|7649455|emb|AJ277620.1|HCA277620 Human calicivirus HU/NLV/Seacroft/90/UK RNA for capsid protein (ORF2)

Dataset Two

gi|9626440|ref|NC_001434.1| Hepatitis E virus, capsid sequence (outgroup)
gi|23194381|gb|AF538679.1| Human calicivirus NLV/Boxer/2001/US capsid and minor structural protein mRNAs
gi|7649414|emb|AJ277612.1|HCA277612 Human calicivirus HU/NLV/Birmingham/93/UK RNA for capsid protein (ORF2)
gi|5002239|gb|AF145709.1|AF145709 Human calicivirus NLV/Stav/95/Nor capsid protein gene
gi|16974754|gb|AF439267.1|AF439267 Human calicivirus NLV/Potsdam 196/2000/DE capsid protein gene
gi|15192707|gb|AY038598.1| Human calicivirus NLV/VA98115/1998 RNA polymerase mRNA
gi|15991615|gb|AF414403.1|AF414403 Norwalk-like virus NLV/Honolulu/219/1992/US RNA polymerase (orf1) gene
gi|15991623|gb|AF414405.1|AF414405 Norwalk-like virus NLV/Little Rock/316/1994/US RNA polymerase (orf1) gene
gi|457314|gb|L23828.1|NOR89JB Norwalk virus (SRSV-KY-89/89/J) RNA polymerase mRNA, 3'end and capsid protein mRNA, complete cds
gi|7328912|dbj|AB028247.2| Norwalk-like virus gene for capsid protein
gi|23194378|gb|AF538678.1| Human calicivirus NLV/VA497/1999/US capsid and minor structural protein mRNAs
gi|7649420|emb|AJ277615.1|HCA277615 Human calicivirus HU/NLV/Sindlesham/95/UK RNA for capsid protein (ORF2)
gi|15991627|gb|AF414406.1|AF414406 Norwalk-like virus NLV/Appalachicola Bay/318/1995/US RNA polymerase (orf1) gene, partial cds; and capsid protein (orf2) and minor structural protein (orf3) genes, complete cds
gi|7649418|emb|AJ277614.1|HCA277614 Human calicivirus HU/NLV/Musgrove/89/UK RNA for capsid protein (ORF2)
gi|16923711|gb|AF435807.1| Human calicivirus NLV/C59/99 capsid protein and minor structural protein genes
gi|7649410|emb|AJ277610.1|HCA277610 Human calicivirus HU/NLV/Whiterose/96/UK RNA for capsid protein (ORF2)
gi|15991611|gb|AF414402.1|AF414402 Norwalk-like virus NLV/New Orleans/266/1993/US RNA polymerase (orf1) gene, partial cds; and capsid protein (orf2) and minor structural protein (orf3) genes, complete cds
gi|15991619|gb|AF414404.1|AF414404 Norwalk-like virus NLV/Baltimore/277/1993/US RNA polymerase (orf1) gene, partial cds; and capsid protein (orf2) and minor structural protein (orf3) genes, complete cds
gi|14669792|gb|AF394960.1|AF394960 Human calicivirus HU/NLV/Koblenz/433/2000/DE capsid protein gene
gi|7649422|emb|AJ277616.1|HCA277616 Human calicivirus HU/NLV/Valetta/95/Malta RNA for capsid protein (ORF2)
gi|14330428|emb|AJ313030.1|HCA313030 Human calicivirus Hu/NLV/Queen's Arms/Leeds/92/UK ORF1 (partial)
gi|7649457|emb|AJ277621.1|HCA277621 Human calicivirus HU/NLV/Thistlehall/90/UK RNA for capsid protein (ORF2)
gi|1495370|emb|X98002.1|EBHSVVP European brown hare syndrome virus gene encoding capsid protein VP60
gi|30144878|gb|AY269825.1| Rabbit hemorrhagic disease virus isolate NJ/China/1985 capsid protein VP60 (VP60) gene, complete cds
gi|4218157|emb|AJ009721.1|FCA9721 Feline calicivirus isolate V66/97 capsid protein gene
gi|334882|gb|M87481.1|SMS1POLCAP San Miguel sea lion virus RNA-dependent RNA polymerase gene, 3' end and capsid protein gene, complete cds
gi|10141008|gb|U76874.2|VEU76874 Vesicular exanthema of swine virus stain A48, complete genome
gi|6164839|gb|AF182760.1|AF182760 Porcine enteric calicivirus, complete genome

Phylogenetic trees used in TipDate analysis

DNAML tree for Dataset 1 (Norviruses only).

DNAML tree for Dataset 2 (Caliciviruses as a family)

This Article Abstract Full Text Services Email this article to a friend Alert me to new issues of the journal Citing Articles Citing Articles via CrossRef