Table 2. Summary of the analysis.
| Genotype | Lineages | Description† | Representative virus‡ | ‘Within-group’ mean genetic distance |
‘Between group’ smallest mean genetic distance |
Reference | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Name | No. | Primary | No.* | Secondary | No. | Tertiary | No. | Time period | Geographic source | WHO name | GB-ID | |||
| 1G (g)§ | 77 (17) | L0 | 36 | 1991–2008 | 10 countries (Europe, North Africa, South America) | RVi/Ontario.CAN/27.05-REF_Netherlands | EF588970 | 0.0149 | 0.0219 | |||||
| L1* | 17 (5) | L1a (b)*,§ | 7 (3) | 2008–2012 | Ivory Coast | RVs/Gagnoa.CIV/6.08 | JX679265 | 0.0125 | 0.0289 | |||||
| L1b* | 10 (2) | 2004–2012 | Ghana, Ivory Coast, Nigeria, Cape Verde | RVs/GHA/39.04 | JX679275 | 0.0205|| | 0.0250 | |||||||
| L2 (g)§ | 24 (12) | L2a (b)§ | 2 (1) | 2005–2010 | Kenya | RV/KEN/0.05 | KM267090 | 0.0054 | 0.0198 | |||||
| L2b | 17 (11) | L2b1 (b)§ | 2 | 2001–2003 | Uganda | RVi/UGA/20.01-REF | EF588978 | 0.0068 | 0.0178 | [11] | ||||
| L2b2* | 11 (9) | 2003–2012 | Uganda, Tanzania, DRC | RVi/Kiboga.UGA/13.03 | KC884222 | 0.0093 | 0.0178 | |||||||
| L2b3 (b)*,§ | 4 (2) | 2007–2011 | Uganda | Rvi/Boston.MA.USA/13.07_Uganda | JN635289 | 0.0136 | 0.0215 | |||||||
| L2c (b)§ | 4 | 2004 | Ethiopia | RVs/Jigiga.ETH/09.04 | EF210043 | 0.0099 | 0.0198 | |||||||
| L2d | 1 | 2005 | Sudan | RVi/Deweim.SDN/50.05CRS | FJ774999 | n/c | 0.0198 | |||||||
| 1E (g)§ | 460 (198) | L0 | 96 | 1995–2008 | 17 countries (Europe, Americas, Africa, Asia) | RVs/Caen.FRA/23.95 | FN546967 | 0.0112 | 0.0189 | |||||
| L1* | 306 (161) | 2001–2014 | China, Taiwan, Japan, Russia, Hong Kong, Vietnam | RVI/DEZHOU.CHN/02-REF | KF201674 | 0.0127 | 0.0189 | [14] | ||||||
| L2 (b)*,§ | 47 (29) | 2001–2014 | Taiwan, Japan, Malaysia, Kazakhstan, Indonesia, China, Hong Kong | RVi/MYS/01-REF | AY968221 | 0.0152 | 0.0252 | |||||||
| L3 (b)*,§ | 7 (5) | 2008–2011 | Tunisia | RVi/Ariana.TUN/08.08 | KF018682 | 0.0114 | 0.0288 | |||||||
| L4 (b)*,§ | 4 (3) | 2005–2013 | Yemen, Sudan, Uganda | RVi/Deweim.SDN/24.05CRS | FJ775000 | 0.01738|| | 0.0240 | |||||||
| 2B (g)§ | 542 (414) | L0* | 72 (3) | 1992–2010 | 14 countries (Europe, Americas, Africa, Asia) | RVi/Milan.ITA/42.94 | AY161370 | 0.0127 | 0.01446¶ | [12] | ||||
| L1* | 354 (347) | 2008–2014 | 14 countries (Asia, Europe) | RVs/HongKong.CHN/49.08 | FJ656218 | 0.0073 | 0.01446¶ | |||||||
| L2 (g)*,§ | 94 (61) | L2a* | 25 (3) | 2000–2013 | South Africa, India, Pakistan, Kazakhstan, Taiwan | RVi/Seattle.WA.USA/16.00-REF_India | JN635293 | 0.0113 | 0.0265 | |||||
| L2b (b)*,§ | 11 (5) | 2005–2011 | India, Thailand, Japan, Taiwan, USA | RVi/Tamilnadu.IND/20.05CRS | KC618672 | 0.0082 | 0.0279 | |||||||
| L2c (b)*,§ | 58 (53) | 2005–2014 | 15 countries (Europe, Africa, Asia) | RVs/Kerala.IND/42.05CRS | KC618675 | 0.0119 | 0.0305 | |||||||
| L3 (b)*,§ | 14 (3) | 2006–2010 | Taiwan, Vietnam, China | RVi/Chendu.Sichuan.CHN/18.06/1 | FJ875057 | 0.0092 | 0.0409 | |||||||
| L4 (b)§ | 8 | 1995–2008 | South Korea, China | RVi/Anqing.Anhui.CHN/00-ref | AY968218 | 0.0197|| | 0.0344 | |||||||
No. represents number of analysed sequences (only viruses with true geographic source were included in the analysis); DRC, Democratic Republic of the Congo.
*Lineages containing sequences reported since 2010. Number of sequences from the 2010–2014 time period are indicated in parentheses.
†‘Time period’ and ‘geographic source’ are based on the phylogenetic trees.
‡The representative virus is either a WHO reference virus or the ‘oldest’ virus collected.
§Criteria for grouping: (b): bootstrap>70 %; (g): Mantel test, P=1×104.
||‘Within-group’ mean genetic distance >1.5 %. There are not enough data to break the groups at the time of the analysis.
¶Smallest ‘between-group’ distance <1.5 %. Although the genetic distance is small between these two groups, these groups are kept to differentiate between currently circulating viruses and those collected at an earlier time.