Table 2.
Genotypic and phenotypic analyses of full-length envelope.
| Pseudovirusesa | V1b | V2b | V3b | V4b | V5b | V3 loopd | FPR(%) | V3 net charge | Coreceptorf |
|---|---|---|---|---|---|---|---|---|---|
| 1.29c | 0.39c | 0.14c | 0.54c | 0.71c | CTRPGNNTRKSIRIGPGQTFYATGDIIGDIRQAHCe | ||||
| In1808-3 | 23 | 47 | 35 | 25 | 12 | ————n—t————–—–———havf——er––——–—k——— | 0.8 | 7 | X4 |
| In1808-4 | 23 | 41 | 35 | 25 | 11 | ————n——————–—–———h——f————t––——–—k——— | 88.5 | 5 | R5 |
| In1809-4 | 19 | 41 | 35 | 36 | 12 | ——————————g–g—–————————rea––——–————— | 1.7 | 4 | R5 |
| In1809-8 | 19 | 39 | 35 | 36 | 12 | ——————————g–g—–————————rea––——–————— | 1.7 | 4 | R5 |
| In1810-1 | 23 | 44 | 35 | 36 | 12 | ————n——————–—–———————————––—n—–————— | 86.5 | 5 | R5 |
| In1810-3 | 22 | 44 | 35 | 30 | 12 | a———n——————–—–———————————––—n—–————— | 53.8 | 5 | R5 |
| In1813-1 | 25 | 39 | 35 | 33 | 12 | ————n——————–—–———————————––—–—–————— | 83 | 4 | R5 |
| In1813-8 | 19 | 39 | 35 | 33 | 12 | ————n——————–—–———————————––—–—–————— | 83 | 4 | R5 |
| In1821-1 | 17 | 41 | 35 | 26 | 12 | ———————————–—–——————————ev–—–—–————— | 45.4 | 4 | R5 |
| In1821-8 | 19 | 41 | 35 | 31 | 12 | ———————————–—–——————————q–—–—–————— | 53.5 | 5 | R5 |
| In1821-9 | 19 | 41 | 35 | 31 | 12 | ———————————–—–——————————q–—–—–————— | 53.5 | 5 | R5 |
| In1822-8 | 20 | 40 | 34 | 26 | 12 | —i——–———————–—–———————————––——–————y— | 42.3 | 3 | R5 |
| In1825-4 | 22 | 44 | 35 | 30 | 12 | ———–———————–—–———————————––——–—————— | 69.8 | 4 | R5 |
| In1837-2 | 18 | 45 | 35 | 28 | 12 | —i——n——r—————–—–———a————————––——–———y— | 13.8 | 4 | R5 |
| In1837-3 | 19 | 49 | 35 | 28 | 12 | —i——n——r—————–—–———a————————––——–———y— | 13.8 | 4 | R5 |
| In1838-1 | 9 | 44 | 35 | 28 | 12 | —–——–——–—————–—–———a————————––——–———–— | 34.3 | 4 | R5 |
| In1838-3 | 9 | 44 | 35 | 28 | 12 | —–——–——–—————–—–———a————————––——–———–— | 34.3 | 4 | R5 |
| In1839-4 | 22 | 44 | 35 | 30 | 12 | ———–———————–—–———————————––——–—————— | 69.8 | 4 | R5 |
| In1841-9 | 22 | 44 | 35 | 30 | 12 | ———n———————–—–————m————e—––——–—————— | 69.8 | 4 | R5 |
| In1846-7 | 19 | 37 | 35 | 33 | 12 | ———–———————–—–———————————––——–—————— | 56.9 | 4 | R5 |
| In1852-8 | 23 | 38 | 35 | 32 | 12 | —i——n——r—————–—–———a—————m——––——–———y— | 63.1 | 2 | R5 |
aPseudoviruses were named on the principle of “individual serial number-clone serial number”. For example, In1808-3 means number #3 clone of individual 1808.
bNumber of amino acids in variable regions V1–V5.
cOverall mean distance of the V1–V5 amino acid sequences, calculated by MEGA 11.0.10.
dAmino acid sequences compared to consensus sequences; dashes denote sequence identity, and dots denote absence of amino acids.
eThe consensus sequences of all pseudoviruses’ V3 region with crown motif in bold.
fThe coreceptor usage is the result from phenotypic testing.