Characteristics of Envelope Genes in a Chinese Chronically HIV-1 Infected Patient With Broadly Neutralizing Activity

Abstract

Exploring the characteristics of the HIV-1 envelope glycoprotein ( env ) gene in a natural HIV-1 infected individual, with broadly neutralizing activity, may provide insight into the generation of such broadly neutralizing antibodies and initiate the design of an appropriate immunogen. Recently, a chronically HIV-1 infected patient with broadly neutralization activity was identified and a VRC01-class neutralizing antibody DRVIA7 (A7) was isolated from the patient. In the present study, 155 full length HIV-1 env gene fragments (including 68 functionally Env clones) were amplified longitudinally from the plasma of six time points spanning over 5 years in this donor. Viral features were analyzed by comparing Env clones of different time points, as well as 165 Chinese HIV-1 subtype B env sequences from HIV Sequence Database (Chinese B_database). Shorter V1 length, less potential glycan and a lower ratio of NXT: NXS in gp160 were observed in the first five time points compared to that from the last time points, as well that from the Chinese B_database. A sequence analysis and a neutralization assay of Env-pseudoviruses showed that the increasing diversity of env sequences in the patient was consistent with the appearance and maturation of A7 lineage antibodies. The potent neutralization activity and viruses that escaped from the neutralization of the concurrent autologous plasma, are consistent with higher residue variations at the antibody recognition sites. Almost all viruses from the plasmas were neutralization-resistant to VRC01 and A7 lineage antibodies. For a chronically HIV-1 infected individual over 10 years, we found that greater viral diversity, short V1 sequences and less potential N-linked glycosylation (PNGS) in V1, might be associated with the development of broadly neutralizing antibody responses.

Virus Evolution and Neutralization Sensitivity in an HIV-1 Subtype B′ Infected Plasma Donor with Broadly Neutralizing Activity

“…In addition, nearly all pseudoviruses were sensitive to autologous plasma at the three time points except 06-20 and 08-23; these two viruses were resistant to 2005 plasma ( Table 3 ). This result was not in accordance with previous reports that proved that autologous plasma could neutralize HIV-1 viruses from earlier time points but could not neutralize concurrent viruses and later-time-point viruses [ 35 , 36 , 37 , 38 ]. This may be why we did not find direct phenotypic evidence that viruses of Cluster I disappeared in 2006, while viruses of Cluster II persisted in this four-year period.…”

Neutralization Sensitivity and Evolution of Virus in a Chronic HIV-1 Clade B Infected Patient with Neutralizing Activity against Membrane-Proximal External Region

“…These processes were performed as previously described [ 20 , 21 , 22 ]. Briefly, viral RNA was extracted from the plasma using a QIAamp viral RNA mini kit (Qiagen, Valencia, CA, USA) according to the manufacturer’s protocol, and transcribed into cDNA immediately using SuperScript III reverse transcriptase (Invitrogen, Grand Island, NY, USA).…”

Neutralization Sensitivity of HIV-1 CRF07_BC From an Untreated Patient With a Focus on Evolution Over Time

“…The Env single-genome amplification (SGA) PCR products were cloned into the vector pcDNA™ 3.1 Directional TOPO ® Expression Kit (Invitrogen, USA), which allows the Env gene to be inserted in the correct orientation with a cytomegalovirus promoter for protein expression ( Hu et al., 2021 ). Pseudoviruses were prepared and titrated, as described previously ( Zhang et al., 2019 ). Briefly, 293T/17 cells were co-transfected with the Env/Rev expression plasmid and an Env-deficient HIV-1 backbone vector (pSG3ΔEnv), using Lipofectamine™ 3000 Transfection Reagent (Invitrogen, USA), and the cultures were incubated for 48 h at 37°C.…”