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Viral escape from HIV-1 neutralizing antibodies drives increased plasma neutralization breadth through sequential recognition of multiple epitopes and immunotypes.

Wibmer CK, Bhiman JN, Gray ES, Tumba N, Abdool Karim SS, Williamson C, Morris L, Moore PL - PLoS Pathog. (2013)

Bottom Line: Neutralization by these CD4 binding site antibodies was almost entirely dependent on the glycan at position N276.Early viral escape mutations in the CD4 binding site drove an increase in wave two neutralization breadth, as this second wave of heterologous neutralization matured to recognize multiple immunotypes within this site.The third wave targeted a quaternary epitope that did not overlap any of the four known sites of vulnerability on the HIV-1 envelope and remains undefined.

View Article: PubMed Central - PubMed

Affiliation: Centre for HIV and STIs, National Institute for Communicable Diseases (NICD), of the National Health Laboratory Service (NHLS), Johannesburg, South Africa ; Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.

ABSTRACT
Identifying the targets of broadly neutralizing antibodies to HIV-1 and understanding how these antibodies develop remain important goals in the quest to rationally develop an HIV-1 vaccine. We previously identified a participant in the CAPRISA Acute Infection Cohort (CAP257) whose plasma neutralized 84% of heterologous viruses. In this study we showed that breadth in CAP257 was largely due to the sequential, transient appearance of three distinct broadly neutralizing antibody specificities spanning the first 4.5 years of infection. The first specificity targeted an epitope in the V2 region of gp120 that was also recognized by strain-specific antibodies 7 weeks earlier. Specificity for the autologous virus was determined largely by a rare N167 antigenic variant of V2, with viral escape to the more common D167 immunotype coinciding with the development of the first wave of broadly neutralizing antibodies. Escape from these broadly neutralizing V2 antibodies through deletion of the glycan at N160 was associated with exposure of an epitope in the CD4 binding site that became the target for a second wave of broadly neutralizing antibodies. Neutralization by these CD4 binding site antibodies was almost entirely dependent on the glycan at position N276. Early viral escape mutations in the CD4 binding site drove an increase in wave two neutralization breadth, as this second wave of heterologous neutralization matured to recognize multiple immunotypes within this site. The third wave targeted a quaternary epitope that did not overlap any of the four known sites of vulnerability on the HIV-1 envelope and remains undefined. Altogether this study showed that the human immune system is capable of generating multiple broadly neutralizing antibodies in response to a constantly evolving viral population that exposes new targets as a consequence of escape from earlier neutralizing antibodies.

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Escape from V2 neutralizing antibodies drives the formation/exposure of broadly neutralizing antibody epitopes in the CD4bs.A) Amino acid sequence alignment of the CAP257 B- and C- strands in the V1/V2 sub-domain of gp120, from twelve time points. The number of envelopes per unique V2 sequence is shown on the right. The timing of wave 1 (red), wave 2 (green), and wave 3 (brown) neutralization is summarized to the left with vertical lines. Potential N-linked glycans are shaded grey, and the presence (grey slices) or absence (red slices) of the N160 glycan within the population at each time point is shown with pie charts to the right. B) CAP257 develops a strain-specific V2 response prior to wave 1 broadly neutralizing antibodies. Neutralization of an autologous virus amplified from 174 weeks p.i. (CAP257 3 yr), is shown in grey. The V1/V2 region of this virus was back-mutated to the earliest known sequence (CAP257 3 yr(V1/V2s)) shown in black. Longitudinal neutralization of the N167D, N160D/S, and K169E mutants is shown in orange, purple, and pink respectively. The timing of wave 1 (red), wave 2 (green), and preceding strain-specific V2 (black) neutralization is summarized above with horizontal lines. ID50 titers (y-axis) are shown versus weeks p.i. (x-axis). C) Wave 2 neutralization of Q842 (green) or RHPA (blue) wild-type (wt) viruses, and their N160K mutants (purple). The timing of wave 1 (red), wave 2 (green), and wave 3 (brown) neutralization is summarized above as in Figure 1B. ID50 titers (y-axis) are shown versus weeks p.i. (x-axis).
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ppat-1003738-g003: Escape from V2 neutralizing antibodies drives the formation/exposure of broadly neutralizing antibody epitopes in the CD4bs.A) Amino acid sequence alignment of the CAP257 B- and C- strands in the V1/V2 sub-domain of gp120, from twelve time points. The number of envelopes per unique V2 sequence is shown on the right. The timing of wave 1 (red), wave 2 (green), and wave 3 (brown) neutralization is summarized to the left with vertical lines. Potential N-linked glycans are shaded grey, and the presence (grey slices) or absence (red slices) of the N160 glycan within the population at each time point is shown with pie charts to the right. B) CAP257 develops a strain-specific V2 response prior to wave 1 broadly neutralizing antibodies. Neutralization of an autologous virus amplified from 174 weeks p.i. (CAP257 3 yr), is shown in grey. The V1/V2 region of this virus was back-mutated to the earliest known sequence (CAP257 3 yr(V1/V2s)) shown in black. Longitudinal neutralization of the N167D, N160D/S, and K169E mutants is shown in orange, purple, and pink respectively. The timing of wave 1 (red), wave 2 (green), and preceding strain-specific V2 (black) neutralization is summarized above with horizontal lines. ID50 titers (y-axis) are shown versus weeks p.i. (x-axis). C) Wave 2 neutralization of Q842 (green) or RHPA (blue) wild-type (wt) viruses, and their N160K mutants (purple). The timing of wave 1 (red), wave 2 (green), and wave 3 (brown) neutralization is summarized above as in Figure 1B. ID50 titers (y-axis) are shown versus weeks p.i. (x-axis).

Mentions: To define escape from wave 1 neutralizing antibodies, we examined sequences from the V2 region of CAP257 over time. Using single genome amplification (SGA) we obtained 125 full envelope sequences from twelve time points between 7 and 213 weeks p.i., and focused on the N160 glycan and the cationic C-strand in V2 that are the targets of wave 1 antibodies (Figure 3A). Interestingly, the earliest virus (7 weeks p.i.) had an asparagine at position 167. This N167 residue is rare, occurring in only 5.6% (196 of 3,478) of sequences in the Los Alamos National Laboratory (LANL) HIV sequence database. By the time of the earliest detectable heterologous neutralization (30 weeks p.i., maximum titer of 1∶49) mutations in sites forming part of the wave 1 V2 epitope were already apparent in 6/14 autologous sequences at positions R166, K169, and Q170 (Figure 3A). Of the remaining eight sequences, six exhibited other mutations either in the N160 glycosylation sequon or the V1/V2 C-strand. This rapid selection pressure in the C-strand of V1/V2 was sometimes an N167D mutation (4/14 autologous sequences) that was unlikely to be selected for by wave 1 broadly neutralizing antibodies, as all the heterologous viruses neutralized by wave 1 had a D167 residue. Since the V1/V2 region is a common target of strain-specific neutralizing responses [38]–[41], these data suggested the possibility of an earlier neutralizing response targeting N167 in V2 that preceded the development of broadly neutralizing antibodies. Wave 1 mapping data (Figure 2A) further supported this possibility because the reverse D167N mutation enhanced the neutralization of ConC by wave 1 antibodies only, and resulted in earlier neutralization kinetics (Figure 2A – orange curve).


Viral escape from HIV-1 neutralizing antibodies drives increased plasma neutralization breadth through sequential recognition of multiple epitopes and immunotypes.

Wibmer CK, Bhiman JN, Gray ES, Tumba N, Abdool Karim SS, Williamson C, Morris L, Moore PL - PLoS Pathog. (2013)

Escape from V2 neutralizing antibodies drives the formation/exposure of broadly neutralizing antibody epitopes in the CD4bs.A) Amino acid sequence alignment of the CAP257 B- and C- strands in the V1/V2 sub-domain of gp120, from twelve time points. The number of envelopes per unique V2 sequence is shown on the right. The timing of wave 1 (red), wave 2 (green), and wave 3 (brown) neutralization is summarized to the left with vertical lines. Potential N-linked glycans are shaded grey, and the presence (grey slices) or absence (red slices) of the N160 glycan within the population at each time point is shown with pie charts to the right. B) CAP257 develops a strain-specific V2 response prior to wave 1 broadly neutralizing antibodies. Neutralization of an autologous virus amplified from 174 weeks p.i. (CAP257 3 yr), is shown in grey. The V1/V2 region of this virus was back-mutated to the earliest known sequence (CAP257 3 yr(V1/V2s)) shown in black. Longitudinal neutralization of the N167D, N160D/S, and K169E mutants is shown in orange, purple, and pink respectively. The timing of wave 1 (red), wave 2 (green), and preceding strain-specific V2 (black) neutralization is summarized above with horizontal lines. ID50 titers (y-axis) are shown versus weeks p.i. (x-axis). C) Wave 2 neutralization of Q842 (green) or RHPA (blue) wild-type (wt) viruses, and their N160K mutants (purple). The timing of wave 1 (red), wave 2 (green), and wave 3 (brown) neutralization is summarized above as in Figure 1B. ID50 titers (y-axis) are shown versus weeks p.i. (x-axis).
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC3814426&req=5

ppat-1003738-g003: Escape from V2 neutralizing antibodies drives the formation/exposure of broadly neutralizing antibody epitopes in the CD4bs.A) Amino acid sequence alignment of the CAP257 B- and C- strands in the V1/V2 sub-domain of gp120, from twelve time points. The number of envelopes per unique V2 sequence is shown on the right. The timing of wave 1 (red), wave 2 (green), and wave 3 (brown) neutralization is summarized to the left with vertical lines. Potential N-linked glycans are shaded grey, and the presence (grey slices) or absence (red slices) of the N160 glycan within the population at each time point is shown with pie charts to the right. B) CAP257 develops a strain-specific V2 response prior to wave 1 broadly neutralizing antibodies. Neutralization of an autologous virus amplified from 174 weeks p.i. (CAP257 3 yr), is shown in grey. The V1/V2 region of this virus was back-mutated to the earliest known sequence (CAP257 3 yr(V1/V2s)) shown in black. Longitudinal neutralization of the N167D, N160D/S, and K169E mutants is shown in orange, purple, and pink respectively. The timing of wave 1 (red), wave 2 (green), and preceding strain-specific V2 (black) neutralization is summarized above with horizontal lines. ID50 titers (y-axis) are shown versus weeks p.i. (x-axis). C) Wave 2 neutralization of Q842 (green) or RHPA (blue) wild-type (wt) viruses, and their N160K mutants (purple). The timing of wave 1 (red), wave 2 (green), and wave 3 (brown) neutralization is summarized above as in Figure 1B. ID50 titers (y-axis) are shown versus weeks p.i. (x-axis).
Mentions: To define escape from wave 1 neutralizing antibodies, we examined sequences from the V2 region of CAP257 over time. Using single genome amplification (SGA) we obtained 125 full envelope sequences from twelve time points between 7 and 213 weeks p.i., and focused on the N160 glycan and the cationic C-strand in V2 that are the targets of wave 1 antibodies (Figure 3A). Interestingly, the earliest virus (7 weeks p.i.) had an asparagine at position 167. This N167 residue is rare, occurring in only 5.6% (196 of 3,478) of sequences in the Los Alamos National Laboratory (LANL) HIV sequence database. By the time of the earliest detectable heterologous neutralization (30 weeks p.i., maximum titer of 1∶49) mutations in sites forming part of the wave 1 V2 epitope were already apparent in 6/14 autologous sequences at positions R166, K169, and Q170 (Figure 3A). Of the remaining eight sequences, six exhibited other mutations either in the N160 glycosylation sequon or the V1/V2 C-strand. This rapid selection pressure in the C-strand of V1/V2 was sometimes an N167D mutation (4/14 autologous sequences) that was unlikely to be selected for by wave 1 broadly neutralizing antibodies, as all the heterologous viruses neutralized by wave 1 had a D167 residue. Since the V1/V2 region is a common target of strain-specific neutralizing responses [38]–[41], these data suggested the possibility of an earlier neutralizing response targeting N167 in V2 that preceded the development of broadly neutralizing antibodies. Wave 1 mapping data (Figure 2A) further supported this possibility because the reverse D167N mutation enhanced the neutralization of ConC by wave 1 antibodies only, and resulted in earlier neutralization kinetics (Figure 2A – orange curve).

Bottom Line: Neutralization by these CD4 binding site antibodies was almost entirely dependent on the glycan at position N276.Early viral escape mutations in the CD4 binding site drove an increase in wave two neutralization breadth, as this second wave of heterologous neutralization matured to recognize multiple immunotypes within this site.The third wave targeted a quaternary epitope that did not overlap any of the four known sites of vulnerability on the HIV-1 envelope and remains undefined.

View Article: PubMed Central - PubMed

Affiliation: Centre for HIV and STIs, National Institute for Communicable Diseases (NICD), of the National Health Laboratory Service (NHLS), Johannesburg, South Africa ; Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.

ABSTRACT
Identifying the targets of broadly neutralizing antibodies to HIV-1 and understanding how these antibodies develop remain important goals in the quest to rationally develop an HIV-1 vaccine. We previously identified a participant in the CAPRISA Acute Infection Cohort (CAP257) whose plasma neutralized 84% of heterologous viruses. In this study we showed that breadth in CAP257 was largely due to the sequential, transient appearance of three distinct broadly neutralizing antibody specificities spanning the first 4.5 years of infection. The first specificity targeted an epitope in the V2 region of gp120 that was also recognized by strain-specific antibodies 7 weeks earlier. Specificity for the autologous virus was determined largely by a rare N167 antigenic variant of V2, with viral escape to the more common D167 immunotype coinciding with the development of the first wave of broadly neutralizing antibodies. Escape from these broadly neutralizing V2 antibodies through deletion of the glycan at N160 was associated with exposure of an epitope in the CD4 binding site that became the target for a second wave of broadly neutralizing antibodies. Neutralization by these CD4 binding site antibodies was almost entirely dependent on the glycan at position N276. Early viral escape mutations in the CD4 binding site drove an increase in wave two neutralization breadth, as this second wave of heterologous neutralization matured to recognize multiple immunotypes within this site. The third wave targeted a quaternary epitope that did not overlap any of the four known sites of vulnerability on the HIV-1 envelope and remains undefined. Altogether this study showed that the human immune system is capable of generating multiple broadly neutralizing antibodies in response to a constantly evolving viral population that exposes new targets as a consequence of escape from earlier neutralizing antibodies.

Show MeSH
Related in: MedlinePlus