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Volume 17, Number 1—January 2011

Genotyping Rotavirus RNA from Archived Rotavirus-Positive Rapid Test Strips

Lester M. ShulmanComments to Author , Ilana Silberstein, Jacqueline Alfandari, and Ella Mendelson
Author affiliations: Author affiliations: Central Virology Laboratory, Tel Hashomer, Israel (L.M. Shulman, I. Silberstein, J. Alfandari, E. Mendelson); Tel Aviv University, Ramat Aviv, Israel (L.M. Shulman, E. Mendelson)

Main Article


Table. Rotavirus genotypes and reference isolates, Israel

Genotype and lineage Sublineage Isolate name* GenBank accession no. Reference
G1 genotype 515 nt (equivalent to nt 479–nt 993 of isolate VN-281 (DQ508167)
1 a Dhak8 AY631049 (15)
1 b VN-281 DQ508167 (15)
1 c Mvd9816 AF480293 (15)
1 d 6916/JP EF079067 (15)
1 e CH631 AF183837 (15)
2 a DC03 AF183859 (15)
2 b PA5/03 DQ377596 (15)
2 c JP-7026 EF079065 (15)
2 d PA164 DQ377588 (15)
2 e Russia-407 S83903 (15)
3 b Israel-56 U26376 (15)
4 None K54 U26377 (15)
5 None PA5/90 QD377573 (15)
6 None AU19 AB018697 (15)
7 None Ban-56 U26366 (15)
8 None Egypt-7 U26373 (15)
9 A P19 DQ377593 (15)
10 None SW2021 AF426162 (15)
11 b C60 L24164 (15)
2 c RoV_09_ISR05[G1.2c]D FN582119 New
2 c RoV_09_ISR05[G1.2c]S FN298858 New
1 a RoV_10_ISR05[G1.1a]D FN582120 New
1 a RoV_10_ISR05[G1.1a]S FN582121 New
2 c RoV_14_ISR05[G1.2c]S FN582122 New
1 a RoV_41_ISR05[G1.1a]D FN582123 New
1 a RoV_41_ISR05[G1.1a]S FN298860 New
G2 genotype 547 nt (equivalent to nt 455–nt 1,001 of isolate TN1529 (AY261357)
1 None sa514 gr ay261338 (16)
2 a KY3303 AY261350 (16)
2 b SA3958GR AY261344 (16)
2 c TN1529 AY261357 (16)
2 d BF3767 AY261355 (16)
2 e† RoV_39_ISR05[G2.2e]D FN582124 New
2 e† RoV_39_ISR05[G2.2e]S FN298861 New
2 B RoV_51_ISR05[G2.2b]S FN298862 New
2 e† RoV_63_ISR06[G2.2e]D FN298864 New
2 e† RoV_63_ISR06[G2.2e]S FN298863 New
G3 genotype 274 nt (equivalent to nt 701–nt 982 of isolate AU-1 (D86271)
1 None CMH222 AY707792 (17)
2 None CHW17 D86276 (17)
2 None CH-55 D86274 (17)
3 1 AU-1 D86271 (17)
3 2 TK28 D86283 (17)
3 3 CMH120/04 DQ923797 (17)
3 4 E887 EU708579 (17)
3 4 CMH272 AY707790 GenBank
3 4 Rus32 EF495127 GenBank
3 4 47–2536Madrid DQ440624 GenBank
3 4 VN-933 EF495123 GenBank
4 None CMP096 (porcine) DQ256502 (17)
3 4 RoV_28_ISR05[G3.3.4]D FN298865 New
3 4 RoV_28_ISR05[G3.3.4]S FN298866 New
3 4 RoV_64_ISR02[G3.3.4]D‡ FN298867 New
3, NA¶ 4, NA RoV_65_ISR02[G3.3.4]D,‡ RoV_65_ISR02[P[8]]D§ FN298868, HQ174462 New
3, NA 4, NA RoV_68_ISR02[G3.3.4]D,‡ RoV_68_ISR02[P[8]]D§ FN298869,
HQ174463 New
G9 genotype 207 nt (equivalent to nt 77–nt 983 of isolate AU32 (AB045372)
1 None. AU32 AB045372 (18)
2 None 116E L14072 (18)
3 None INL1 AJ250277 (18)
4 None 97'SZ37 AF260959 (18)
5 None OM67 AJ491179 (18)
6 None SP1542 AB091753 (18)
7† None RoV_24_ISR05[G9.7]S FN298870 New
8† None RoV_56_ISR06[G9.8]D FN298873 New
8† None RoV_56_ISR06[G9.8]S FN298872 New
8† None RoV_57_ISR06[G9.8]S FN298874 New
8† None RoV_60_ISR06[G9.8]S FN298875 New

*Isolate names were taken from European Molecular Biology Laboratory/GenBank/DNA Data Bank of Japan. Israeli samples have been named RoV_the isolate number_ISR for Israel and a 2-digit code indicating the year the sample was sent to the laboratory for initial testing.

†New lineages or sublineages inferred by phylogenetic comparison to equivalent segments from reference lineages and sublineages, as described in the text.

‡G genotypes determined from RNA isolated from dipsticks stored at room temperature for 5 y. RNA from all other dipsticks was extracted 1–6 wk after the rapid test strips (dipsticks) were used.

§P genotypes determined from RNA isolated from dipsticks stored at room temperature for 5 y. The 457-nt sequence is equivalent to nt 222– 678 of a G3P[8] isolate, 95–87 (AB008290).

¶NA, not applicable.

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Page created: July 08, 2011
Page updated: July 08, 2011
Page reviewed: July 08, 2011
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