TABLE 1.
V3-loop amino acid sequence alignmenta
| Clade | Isolateb | Sequencec |
|---|---|---|
| 1 11 21 31 38 | ||
| Consensus | CTRPNNNTRK SIHIGPGQAF YA---TGDII GDIRQAHC | |
| C | 94IN11246 | ---------- --r-----t- --···--e-v -n------ |
| C | 93IN905 | ---------- --r-----t- --···----m -------- |
| C | 93IN999 | -vr------e --r-----t- --···--e-- -------- |
| C | Consensus | ---------- --r-----t- --···----- -------- |
| C | ind8 | ---------- -tr-----t- --···----- -------- |
| 97cn54-v3 | ----g----- --r-----t- --···----- -------- | |
| cn-con-v3 | ----g----- --r-----t- --···----- -------- | |
| C | bro025 | ---------- --r------- --···--e-- -------- |
| C | ind1024 | ---------- --r-----t- --···----- ----r-y- |
| C | nof | ---------- r-rv----tv --···-na-- -------- |
| C | zam20 | -a--g----- --r-----t- f-···--a-- -------- |
| C | sm145 | ---ya----- -vr-----t- -····-n--- -------- |
| A | Consensus | ---------- -vr------- --···----- -------- |
| B | Consensus | ---------- -------r-- -t···--e-- -------- |
| D | Consensus | ----y----q rt-------l -····-tr-- -------- |
| E | Consensus | ----s----t --t-----v- -r···----- ----k-y- |
| F | Consensus | ---------- ---l------ --···----- ----k--- |
| G | Consensus | ---------- --t------- --···----- -------- |
| H | Consensus | ---------- --s------- --···----- ----k-y- |
| O | Consensus | -e--gidiqe ·-r---·m-w -smglg-tng nss-a-y- |
a
The V3 amino acid alignment of consensus sequences from different HIV-1 clades (A to O) and selected subtype C isolates from different countries is given. The overall V3 consensus sequence was constructed by aligning consensus sequences from different clades (A to O).
b
cn-con-V3 represents the consensus sequence of HIV-1 subtype C strains prevalent in China. 97cn54 has been selected as the standard representative isolate of the most prevalent clade C HIV-1 strains circulating throughout China.
c
−, no exchange to the V3 consensus sequence; lowercase letters, an amino acid substitution; ·, gaps. All consensus and isolate sequences for multiple alignments were obtained from the Los Alamos database.