Table 1. Standard Leishmania strains used in ITS1-based microsatellite polymorphism and phylogenetic analysis of cutaneous leishmaniasis isolates, Himachal Pradesh, India, 2014–2018*.
| Standard Leishmania strains (place of origin) | WHO code | Genbank accession no. | Zymodeme | Disease form | Strain type† | ITS1 polymorphic microsatellite stretches (nucleotide position, bp) |
|||
|---|---|---|---|---|---|---|---|---|---|
| Poly C (24–39) | Poly A (24–39) | Poly TA (61–76) | Poly A (124–134) | ||||||
| VL- and CL-causing L. infantum and L. donovani parasite strains | |||||||||
| L. infantum (Tunisia) | MHOM/TN/80/IPT1 | AJ000289 | MON-1 | VL | A | 3 | 6 | 4 | 8 |
| L. donovani (India) | MHOM/IN/00/DEVI | AJ634376 | MON-2 | VL | H | 2 | 8 | 5 | 7 |
| L. donovani (Sri Lanka) | MHOM/LK/2002/ L60c | AM901447 | MON-37 | CL | ND | 2 | 8 | 5 | 7 |
| L. donovani (Bangladesh) | ND | KT921417 | ND | VL | ND | 2 | 8 | 5 | 7 |
| L. donovani (Kenya) | MHOM/KE/85/ NLB323 | AJ000297 | MON-37 | VL | G | 2 | 8 | 5 | 7 |
| L. donovani (Sudan) | MHOM/SD/75/ LV139 | AJ000291 | ND | CL | E | 2 | 8 | 6 | 8 |
| MHOM/SD/93/9S | AJ634372 | MON-18 | VL | F | 2 | 9 | 5 | 7 | |
| L. donovani (Ethiopia) | MHOM/ET/67/HU3 | AJ634373 | MON-18 | VL | F | 2 | 9 | 5 | 7 |
| L. donovani (China) | MHOM/CN/00/ Wangjie1 | AJ000294 | MON-35 | VL | C | 3 | 6 | 4 | 7 |
| L. donovani (HP, India) | MHOM/IN/83/ CHANDIGARH | AM901449 | MON-37 | VL | ND | 2 | 8 | 2, TAA, 3 | 7 |
|
L. donovani (Bhutan) |
Trashigang1 | JQ730001 | ND | VL | ND | 2 | 8 | 2, TAA, 3 | 8 |
| Samtse1 |
JQ730002 |
ND |
VL |
ND |
2 |
9 |
2, TAA, 3 |
8 |
|
| CL-causing L. donovani isolates from Himachal Pradesh‡ | |||||||||
| HPCL22 | – | MG982955 | ND | CL | ND | Heterogeneous | 2, TAA, 3 | 8 | |
| HPCL27 | – | MG982958 | ND | CL | ND | Heterogeneous | 2, TAA, 3 | 8 | |
| HPCL28 | – | MG982959 | ND | CL | ND | Heterogeneous | 2, TAA, 3 | 8 | |
| HPCL32 | – | MG982963 | ND | CL | ND | Heterogeneous | 2, TAA, 3 | 8 | |
| HPCL42 | – | MG982972 | ND | CL | ND | Heterogeneous | 2, TAA, 3 | 8 | |
| HPCL45 | – | MG982975 | ND | CL | ND | Heterogeneous | 2, TAA, 3 | 8 | |
| HPCL47 | – | MG982977 | ND | CL | ND | Heterogeneous | 2, TAA, 3 | 8 | |
| HPCL49 | – | MG982978 | ND | CL | ND | Heterogeneous | 2, TAA, 3 | 8 | |
| HPCL52 | – | MG982981 | ND | CL | ND | Heterogeneous | 2, TAA, 3 | 8 | |
| HPCL55 |
– |
MG982983 |
ND |
CL |
ND |
Heterogeneous |
2, TAA, 3 |
8 |
|
| CL-causing standard WHO Leishmania species | |||||||||
| L. major | MHOM/SU/73/ 5ASKH | AJ000310 | MON-4 | CL | ND | 4 | 6 | 6 | 6 |
| L. tropica | MHOM/SU/60/OD | EU326226 | LON-7 | CL | ND | 4 | 9 | 1, TTA, 2 | 3,C,4A |
| L. mexicana | MHOM/MX/85/ SOLIS | AJ000313 | MON-152 | CL | ND | 2 | 8 | 1, | 3,C,7A |
| L. braziliensis | MHOM/BR/00/ LTB300 | FN398338 | MON-166 | CL | ND | 2 | 6 | 1 | 5 |
| L. amazonensis | MHOM/BR/73/ M2269 | HG512964 | MON-132 | CL | ND | 2 | 7 | 1 | 3,C,6A |
*CL, cutaneous leishmaniasis; HP, Himachal Pradesh; ITS1, internal transcribed spacer 1; ND, not determined; VL, visceral leishmaniasis; WHO, World Health Organization. †ITS sequences strain type according to Kuhls et al. (13). ‡These species represent 10/44 samples used in polymorphic microsatellite analysis.