Table 1 List of haplotypes used in phylogenetic analyses
Haplotype | Isolate | References |
|---|---|---|
KFR144 | KFR 144, KFR177, KFR5A, KFR9A, KFR 21, KFR45 | This study |
HM235389_Pts, HM235389_Pts | Liu et al. [18] | |
HM235394 | HM235394_Pts | Liu et al. [18] |
HM235048 | HM235048_Pts | Liu et al. [18] |
HM235391 | HM235391_Pts, HM235388 _Pts | Liu et al. [18] |
HM235029 | HM235029_Ptt | Liu et al. [18] |
HM235028 | HM235028_Ptt | Liu et al. [18] |
HM235328 | HM235364_Pte, HM235328_Ptt, HM235359_Ptt, HM235299_Ptt | Liu et al. [18] |
HM235362 | HM235362_Pte, HM235097_Pte, HM235096_Pte, HM235089_Pte | Liu et al. [18] |
KFR3A | KFR3A | This study |
KFR150 | KFR150, KFR167, | This study |
HM235402_Pts, HM235401_Pts | Liu et al. [18] | |
KFR72 | KFR72 | This study |
HM235341 | KFR149 | This study |
HM235341_Ptt, HM235339_Ptt, HM235108_Pts, HM235340_Ptt, HM235392_Pts, HM235342_Ptt, HM235395_Pts | Liu et al. [18] | |
HM235351 | HM235351_Ptt | Liu et al. [18] |
HM235380 | HM235380_Ggg | Liu et al. [18] |
HM235367 | HM235367_Ggg | Liu et al. [18] |
KC175316 | KC175316 | Sundararaman et al. [49] |
AY282929 | AY282929 | Joy et al. [50] |
HM235382 | HM23538_Ggg, HM235294 Ggg, HM235304 Ggg | Liu et al. [18] |
HM235400 | HM235400_Pts, HM235076_Pts, HM235399_Pts | Liu et al. [18] |
KFR178 | KFR178 | This study |
HM235320 | HM235320 | Liu et al. [18] |
HM235052 | HM235052 | Liu et al. [18] |
GQ355470 | GQ355470_Pts | Krief et al. [17] |
GQ355471 | GQ355471_Pts | Krief et al. [17] |
KFR90 | KFR90 | This study |
KFR36 | KFR36 | This study |
KFR105 | KFR105 | This study |
KFR32A | KFR32A, KFR93, KFR188, KFR7A | This study |
FJ895308 | FJ895308_Ptt | Ollomo et al. [16] |
JX893151 | JX893151_Ptt | Pacheco et al. [21] |
HM235102 | HM235102_Pte | Liu et al. [18] |
HM234997Ptt | HM234997_Ptt, HM235315_Ptt, HM235348_Ptt, HM235309_Ptt, HM235280_Ptt | Liu et al. [18] |
HM235114_Pte, HM235113_Ptt, HM235112_Ptt, HM235088_Pte, HM235086_Pte | ||
HM235083_Pte | ||
HM235100 | HM235100_Pte | Liu et al. [18] |
HM235077 | HM235077_Ptt | Liu et al. [18] |
HM235375 | HM235375_Ggg, HM235284_Ggg | Liu et al. [18] |
HM235313 | HM235313_Ggg | Liu et al. [18] |
JQ240419 | JQ240419 | Miao et al. [51] |
KC175307 | KC175307 | Sundararaman et al. [49] |
AB489194 | AB489194 | Hayakawa et al. [52] |