Genotype | Strain | Geographic origin and host | Pairwise % identity (nt/aa) | |||||
---|---|---|---|---|---|---|---|---|
S | M | M | L | |||||
Gn | Gc | NSm | ||||||
Genogroup Ia | DHL10M110 | China |
94.7/99.5 | 91.7/95.6 | 92.7/80.7 | 91.3/78.4 | 90.5/75.7 | 97.5/99.4 |
NM/BS/1 | China |
98.1/99.1 | 91.8/96.2 | 92.6/80.7 | 91.5/78.0 | 91.9/79.6 | - | |
GXLCH01 | China |
97.6/99.6 | 96.6/97.9 | 96.8/91.4 | 96.4/91.1 | 96.7/91.7 | 94.5/98.4 | |
GXLCH70N | China |
97.7/99.6 | 96.8/97.9 | 96.4/90.7 | 97.2/93.2 | 95.4/89.0 | 94.6/98.7 | |
HN10174 | China |
- | 91.7/96.3 | 92.0/78.9 | 91.5/78.0 | 91.9/79.6 | 95.1/98.8 | |
KM-1/Br/06 | Japan |
98.4/100 | 97.3/97.9 | 97.4/93.6 | 97.2/93.5 | 97.1/92.3 | 96.2/98.9 | |
AKAV-32/SKR/2010 | Korea |
94.9/98.7 | 97.7/98.4 | 98.1/95.4 | 97.7/94.3 | 97.2/92.8 | - | |
IRIKI | Japan |
95.0/98.7 | 94.7/97.0 | 94.9/81.6 | 94.5/86.0 | 93.4/82.9 | - | |
Genogroup Ib | FO-90-3 | Japan |
95.3/98.3 | 91.7/95.6 | 91.0/71.0 | 91.8/79.6 | 92.3/81.2 | - |
Genogroup II | OBE-1 | Japan |
95.3/98.7 | 87.5/93.8 | 89.3/66.8 | 86.4/66.7 | 89.4/71.8 | 91.8/97.6 |
Genogroup III | B8935 | Australia |
92.7/97.4 | 84.4/91.9 | 85.7/57.6 | 84.1/63.2 | 83.9/58.6 | 96.4/95.8 |
Genogroup IV | MP496 | Kenya |
83.5/90.6 | 70.3/74.4 | 75.2/- | 69.9/38.3 | 65.9/30.4 | - |
Gene | Primer | Sequence (5´–3´) | Position | Product size (bp) |
---|---|---|---|---|
S | AKVS1 | CTCCACTATTAACTACGCAT | 9–26 | 804 |
AKVS2 | GGTGTGCACCACATAGACAT | 793–812 | ||
M | AKVM1 | AGTAGTGAACTACCACAACAAAATG | 1–25 | 4,308 |
AKVM2 | AGTAGTGTTCTACCACAACAAATAATTAT | 4,280–4,308 | ||
L | AKVL1 | AGTAGTGTACCCCTAAATACAACATACA | 1–28 | 4,151 |
AKVL2 | GTCAGCTTGCTTAAATCCC | 4,133–4,151 | ||
AKVL3 | GTGATTGTGCATTCCTTGG | 3,764–3,782 | 3,106 | |
AKVL4 | AGTAGTGTGCCCCTAAATGCAATAATAT | 6,842–6,869 |