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Broadening of neutralization activity to directly block a dominant antibody-driven SARS-coronavirus evolution pathway.

Sui J, Aird DR, Tamin A, Murakami A, Yan M, Yammanuru A, Jing H, Kan B, Liu X, Zhu Q, Yuan QA, Adams GP, Bellini WJ, Xu J, Anderson LJ, Marasco WA - PLoS Pathog. (2008)

Bottom Line: Phylogenetic analyses have provided strong evidence that amino acid changes in spike (S) protein of animal and human SARS coronaviruses (SARS-CoVs) during and between two zoonotic transfers (2002/03 and 2003/04) are the result of positive selection.Structure-based amino acid changes in an activation-induced cytidine deaminase (AID) "hot spot" in a light chain CDR (complementarity determining region) alone, introduced through shuffling of naturally occurring non-immune human VL chain repertoire or by targeted mutagenesis, were successful in generating these BnAbs.These results demonstrate that nAb-mediated immune pressure is likely a driving force for positive selection during intra-species transmission of SARS-CoV.

View Article: PubMed Central - PubMed

Affiliation: Department of Cancer Immunology & AIDS, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA. Jianhua_sui@dfci.harvard.edu

ABSTRACT
Phylogenetic analyses have provided strong evidence that amino acid changes in spike (S) protein of animal and human SARS coronaviruses (SARS-CoVs) during and between two zoonotic transfers (2002/03 and 2003/04) are the result of positive selection. While several studies support that some amino acid changes between animal and human viruses are the result of inter-species adaptation, the role of neutralizing antibodies (nAbs) in driving SARS-CoV evolution, particularly during intra-species transmission, is unknown. A detailed examination of SARS-CoV infected animal and human convalescent sera could provide evidence of nAb pressure which, if found, may lead to strategies to effectively block virus evolution pathways by broadening the activity of nAbs. Here we show, by focusing on a dominant neutralization epitope, that contemporaneous- and cross-strain nAb responses against SARS-CoV spike protein exist during natural infection. In vitro immune pressure on this epitope using 2002/03 strain-specific nAb 80R recapitulated a dominant escape mutation that was present in all 2003/04 animal and human viruses. Strategies to block this nAb escape/naturally occurring evolution pathway by generating broad nAbs (BnAbs) with activity against 80R escape mutants and both 2002/03 and 2003/04 strains were explored. Structure-based amino acid changes in an activation-induced cytidine deaminase (AID) "hot spot" in a light chain CDR (complementarity determining region) alone, introduced through shuffling of naturally occurring non-immune human VL chain repertoire or by targeted mutagenesis, were successful in generating these BnAbs. These results demonstrate that nAb-mediated immune pressure is likely a driving force for positive selection during intra-species transmission of SARS-CoV. Somatic hypermutation (SHM) of a single VL CDR can markedly broaden the activity of a strain-specific nAb. The strategies investigated in this study, in particular the use of structural information in combination of chain-shuffling as well as hot-spot CDR mutagenesis, can be exploited to broaden neutralization activity, to improve anti-viral nAb therapies, and directly manipulate virus evolution.

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Broadly neutralizing activity of cs- and fm-Abs.A, sequence comparison of eight Abs identified from 80R-cs or -fm library selection. *Amino acid sequence in CDRL1 (161–164). ** 80R was identified from Tor2-S1 targeted library selection [17]; five fm-Abs were from both D480A or D480G and GD03 targeted library selection. B, Neutralization activity of the eight Abs (full-length IgG1) was tested with the same pseudotyped viruses as used in Fig. 3A at indicated Ab concentration. Cs5, cs84, fm6 and fm39 appeared to be the four BnAbs.
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ppat-1000197-g005: Broadly neutralizing activity of cs- and fm-Abs.A, sequence comparison of eight Abs identified from 80R-cs or -fm library selection. *Amino acid sequence in CDRL1 (161–164). ** 80R was identified from Tor2-S1 targeted library selection [17]; five fm-Abs were from both D480A or D480G and GD03 targeted library selection. B, Neutralization activity of the eight Abs (full-length IgG1) was tested with the same pseudotyped viruses as used in Fig. 3A at indicated Ab concentration. Cs5, cs84, fm6 and fm39 appeared to be the four BnAbs.

Mentions: The 80R-fm libraries were panned against three RBD targets, D480A, D480G and GD03 and five clones that were positive by ELISA for all four targets (including Tor2) were chosen for further characterization. The amino acid sequences in CDRL1 (161–164) of these 5 clones were shown in Fig. 5A. Four of these fm Abs were identified from D480A and GD03 and one (fm39) from D480G and GD03 panning. Consistent with the results from the 80R-Vκ-cs studies, four of these fm Abs had the S→N change at position 163 and all five maintained the 164N mutation found in parental 80R. Thus, this “hot spot” is indeed of central importance in controlling the breadth of binding activity.


Broadening of neutralization activity to directly block a dominant antibody-driven SARS-coronavirus evolution pathway.

Sui J, Aird DR, Tamin A, Murakami A, Yan M, Yammanuru A, Jing H, Kan B, Liu X, Zhu Q, Yuan QA, Adams GP, Bellini WJ, Xu J, Anderson LJ, Marasco WA - PLoS Pathog. (2008)

Broadly neutralizing activity of cs- and fm-Abs.A, sequence comparison of eight Abs identified from 80R-cs or -fm library selection. *Amino acid sequence in CDRL1 (161–164). ** 80R was identified from Tor2-S1 targeted library selection [17]; five fm-Abs were from both D480A or D480G and GD03 targeted library selection. B, Neutralization activity of the eight Abs (full-length IgG1) was tested with the same pseudotyped viruses as used in Fig. 3A at indicated Ab concentration. Cs5, cs84, fm6 and fm39 appeared to be the four BnAbs.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2572002&req=5

ppat-1000197-g005: Broadly neutralizing activity of cs- and fm-Abs.A, sequence comparison of eight Abs identified from 80R-cs or -fm library selection. *Amino acid sequence in CDRL1 (161–164). ** 80R was identified from Tor2-S1 targeted library selection [17]; five fm-Abs were from both D480A or D480G and GD03 targeted library selection. B, Neutralization activity of the eight Abs (full-length IgG1) was tested with the same pseudotyped viruses as used in Fig. 3A at indicated Ab concentration. Cs5, cs84, fm6 and fm39 appeared to be the four BnAbs.
Mentions: The 80R-fm libraries were panned against three RBD targets, D480A, D480G and GD03 and five clones that were positive by ELISA for all four targets (including Tor2) were chosen for further characterization. The amino acid sequences in CDRL1 (161–164) of these 5 clones were shown in Fig. 5A. Four of these fm Abs were identified from D480A and GD03 and one (fm39) from D480G and GD03 panning. Consistent with the results from the 80R-Vκ-cs studies, four of these fm Abs had the S→N change at position 163 and all five maintained the 164N mutation found in parental 80R. Thus, this “hot spot” is indeed of central importance in controlling the breadth of binding activity.

Bottom Line: Phylogenetic analyses have provided strong evidence that amino acid changes in spike (S) protein of animal and human SARS coronaviruses (SARS-CoVs) during and between two zoonotic transfers (2002/03 and 2003/04) are the result of positive selection.Structure-based amino acid changes in an activation-induced cytidine deaminase (AID) "hot spot" in a light chain CDR (complementarity determining region) alone, introduced through shuffling of naturally occurring non-immune human VL chain repertoire or by targeted mutagenesis, were successful in generating these BnAbs.These results demonstrate that nAb-mediated immune pressure is likely a driving force for positive selection during intra-species transmission of SARS-CoV.

View Article: PubMed Central - PubMed

Affiliation: Department of Cancer Immunology & AIDS, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA. Jianhua_sui@dfci.harvard.edu

ABSTRACT
Phylogenetic analyses have provided strong evidence that amino acid changes in spike (S) protein of animal and human SARS coronaviruses (SARS-CoVs) during and between two zoonotic transfers (2002/03 and 2003/04) are the result of positive selection. While several studies support that some amino acid changes between animal and human viruses are the result of inter-species adaptation, the role of neutralizing antibodies (nAbs) in driving SARS-CoV evolution, particularly during intra-species transmission, is unknown. A detailed examination of SARS-CoV infected animal and human convalescent sera could provide evidence of nAb pressure which, if found, may lead to strategies to effectively block virus evolution pathways by broadening the activity of nAbs. Here we show, by focusing on a dominant neutralization epitope, that contemporaneous- and cross-strain nAb responses against SARS-CoV spike protein exist during natural infection. In vitro immune pressure on this epitope using 2002/03 strain-specific nAb 80R recapitulated a dominant escape mutation that was present in all 2003/04 animal and human viruses. Strategies to block this nAb escape/naturally occurring evolution pathway by generating broad nAbs (BnAbs) with activity against 80R escape mutants and both 2002/03 and 2003/04 strains were explored. Structure-based amino acid changes in an activation-induced cytidine deaminase (AID) "hot spot" in a light chain CDR (complementarity determining region) alone, introduced through shuffling of naturally occurring non-immune human VL chain repertoire or by targeted mutagenesis, were successful in generating these BnAbs. These results demonstrate that nAb-mediated immune pressure is likely a driving force for positive selection during intra-species transmission of SARS-CoV. Somatic hypermutation (SHM) of a single VL CDR can markedly broaden the activity of a strain-specific nAb. The strategies investigated in this study, in particular the use of structural information in combination of chain-shuffling as well as hot-spot CDR mutagenesis, can be exploited to broaden neutralization activity, to improve anti-viral nAb therapies, and directly manipulate virus evolution.

Show MeSH
Related in: MedlinePlus