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A rare mutation in an infant-derived HIV-1 envelope glycoprotein alters interprotomer stability and susceptibility to broadly neutralizing antibodies targeting the trimer apex

A rare mutation in an infant-derived HIV-1 envelope glycoprotein alters interprotomer stability and susceptibility to broadly neutralizing antibodies targeting the trimer apex
A rare mutation in an infant-derived HIV-1 envelope glycoprotein alters interprotomer stability and susceptibility to broadly neutralizing antibodies targeting the trimer apex

The envelope glycoprotein (Env) of human immunodeficiency virus type 1 (HIV-1) is the sole target of broadly neutralizing antibodies (bnAbs). Several mechanisms, such as the acquisition of mutations, variability of the loop length, and alterations in the glycan pattern, are employed by the virus to shield neutralizing epitopes on Env to sustain survival and infectivity within the host. The identification of mutations that lead to viral evasion of the host immune response is essential for the optimization and engineering of Env-based trimeric immunogens. Here, we report a rare leucine-to-phenylalanine escape mutation (L184F) at the base of hypervariable loop 2 (population frequency of 0.0045%) in a 9-month-old perinatally HIV-1-infected infant broad neutralizer. The L184F mutation altered the trimer conformation by modulating intramolecular interactions stabilizing the trimer apex and led to viral escape from autologous plasma bnAbs and known N160 glycan-targeted bnAbs. The L184F amino acid change led to the acquisition of a relatively open trimeric conformation, often associated with tier 1 HIV-1 isolates and increased susceptibility to neutralization by polyclonal plasma antibodies of weak neutralizers. While there was no impact of the L184F mutation on free virus transmission, a reduction in cell-to-cell transmission was observed. In conclusion, we report a naturally selected viral mutation, L184F, that influenced a change in the conformation of the Env trimer apex as a mechanism of escape from contemporaneous plasma V2 apex-targeted nAbs. Further studies should be undertaken to define viral mutations acquired during natural infection, to escape selection pressure exerted by bnAbs, to inform vaccine design and bnAb-based therapeutic strategies. IMPORTANCE The design of HIV-1 envelope-based immunogens capable of eliciting broadly neutralizing antibodies (bnAbs) is currently under active research. Some of the most potent bnAbs target the quaternary epitope at the V2 apex of the HIV-1 Env trimer. By studying naturally circulating viruses from a perinatally HIV-1-infected infant with plasma neutralizing antibodies targeted to the V2 apex, we identified a rare leucine-to-phenylalanine substitution, in two out of six functional viral clones, that destabilized the trimer apex. This single-amino-acid alteration impaired the interprotomeric interactions that stabilize the trimer apex, resulting in an open trimer conformation and escape from broadly neutralizing autologous plasma antibodies and known V2 apex-directed bnAbs, thereby favoring viral evasion of the early bnAb response of the infected host. Defining the mechanisms by which naturally occurring viral mutations influence the sensitivity of HIV-1 to bnAbs will provide information for the development of vaccines and bnAbs as anti-HIV-1 reagents.

HIV-1, Infants, Interprotomer interactions, Rare mutation, V2 apex bnAbs
0022-538X
Mishra, Nitesh
296376dd-f36f-4b32-a250-ff56067067b7
Sharma, Shaifali
cc9baac5-68d3-42c2-8feb-88098d84420f
Dobhal, Ayushman
ac13aa18-8b42-4706-b6ab-254e211e224e
Kumar, Sanjeev
72adbe62-7c8b-4430-aab6-6e54e94b2a91
Chawla, Himanshi
07b9e983-4c35-4314-999d-fe3222a6c03b
Singh, Ravinder
4f8eac9d-8675-4603-ba25-796eec5f003f
Das, Bimal Kumar
dc79149c-9b26-44f1-8b6f-4b6faa1540e6
Kabra, Sushil Kumar
ba01266c-dc15-497d-8555-64e776d115ca
Lodha, Rakesh
cdfb40fa-c83b-4ec0-bfe2-33a589209a62
Luthra, Kalpana
40fc2436-ee10-4d8b-a414-70e7214a2bf2
Simon, Viviana
ddac3faa-ef4f-4e63-b983-ebfa72006e6b
Mishra, Nitesh
296376dd-f36f-4b32-a250-ff56067067b7
Sharma, Shaifali
cc9baac5-68d3-42c2-8feb-88098d84420f
Dobhal, Ayushman
ac13aa18-8b42-4706-b6ab-254e211e224e
Kumar, Sanjeev
72adbe62-7c8b-4430-aab6-6e54e94b2a91
Chawla, Himanshi
07b9e983-4c35-4314-999d-fe3222a6c03b
Singh, Ravinder
4f8eac9d-8675-4603-ba25-796eec5f003f
Das, Bimal Kumar
dc79149c-9b26-44f1-8b6f-4b6faa1540e6
Kabra, Sushil Kumar
ba01266c-dc15-497d-8555-64e776d115ca
Lodha, Rakesh
cdfb40fa-c83b-4ec0-bfe2-33a589209a62
Luthra, Kalpana
40fc2436-ee10-4d8b-a414-70e7214a2bf2
Simon, Viviana
ddac3faa-ef4f-4e63-b983-ebfa72006e6b

Mishra, Nitesh, Sharma, Shaifali, Dobhal, Ayushman, Kumar, Sanjeev, Chawla, Himanshi, Singh, Ravinder, Das, Bimal Kumar, Kabra, Sushil Kumar, Lodha, Rakesh and Luthra, Kalpana , Simon, Viviana (ed.) (2020) A rare mutation in an infant-derived HIV-1 envelope glycoprotein alters interprotomer stability and susceptibility to broadly neutralizing antibodies targeting the trimer apex. Journal of Virology, 94 (19), [e00814-20]. (doi:10.1128/JVI.00814-20).

Record type: Article

Abstract

The envelope glycoprotein (Env) of human immunodeficiency virus type 1 (HIV-1) is the sole target of broadly neutralizing antibodies (bnAbs). Several mechanisms, such as the acquisition of mutations, variability of the loop length, and alterations in the glycan pattern, are employed by the virus to shield neutralizing epitopes on Env to sustain survival and infectivity within the host. The identification of mutations that lead to viral evasion of the host immune response is essential for the optimization and engineering of Env-based trimeric immunogens. Here, we report a rare leucine-to-phenylalanine escape mutation (L184F) at the base of hypervariable loop 2 (population frequency of 0.0045%) in a 9-month-old perinatally HIV-1-infected infant broad neutralizer. The L184F mutation altered the trimer conformation by modulating intramolecular interactions stabilizing the trimer apex and led to viral escape from autologous plasma bnAbs and known N160 glycan-targeted bnAbs. The L184F amino acid change led to the acquisition of a relatively open trimeric conformation, often associated with tier 1 HIV-1 isolates and increased susceptibility to neutralization by polyclonal plasma antibodies of weak neutralizers. While there was no impact of the L184F mutation on free virus transmission, a reduction in cell-to-cell transmission was observed. In conclusion, we report a naturally selected viral mutation, L184F, that influenced a change in the conformation of the Env trimer apex as a mechanism of escape from contemporaneous plasma V2 apex-targeted nAbs. Further studies should be undertaken to define viral mutations acquired during natural infection, to escape selection pressure exerted by bnAbs, to inform vaccine design and bnAb-based therapeutic strategies. IMPORTANCE The design of HIV-1 envelope-based immunogens capable of eliciting broadly neutralizing antibodies (bnAbs) is currently under active research. Some of the most potent bnAbs target the quaternary epitope at the V2 apex of the HIV-1 Env trimer. By studying naturally circulating viruses from a perinatally HIV-1-infected infant with plasma neutralizing antibodies targeted to the V2 apex, we identified a rare leucine-to-phenylalanine substitution, in two out of six functional viral clones, that destabilized the trimer apex. This single-amino-acid alteration impaired the interprotomeric interactions that stabilize the trimer apex, resulting in an open trimer conformation and escape from broadly neutralizing autologous plasma antibodies and known V2 apex-directed bnAbs, thereby favoring viral evasion of the early bnAb response of the infected host. Defining the mechanisms by which naturally occurring viral mutations influence the sensitivity of HIV-1 to bnAbs will provide information for the development of vaccines and bnAbs as anti-HIV-1 reagents.

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More information

Accepted/In Press date: 7 July 2020
e-pub ahead of print date: 15 September 2020
Published date: October 2020
Additional Information: Copyright © 2020 American Society for Microbiology.
Keywords: HIV-1, Infants, Interprotomer interactions, Rare mutation, V2 apex bnAbs

Identifiers

Local EPrints ID: 452156
URI: http://eprints.soton.ac.uk/id/eprint/452156
ISSN: 0022-538X
PURE UUID: 9074e6d7-b2d8-4d42-8d4b-27cbebf9743c
ORCID for Himanshi Chawla: ORCID iD orcid.org/0000-0001-9828-6593

Catalogue record

Date deposited: 26 Nov 2021 00:01
Last modified: 17 Mar 2024 03:57

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Contributors

Author: Nitesh Mishra
Author: Shaifali Sharma
Author: Ayushman Dobhal
Author: Sanjeev Kumar
Author: Himanshi Chawla ORCID iD
Author: Ravinder Singh
Author: Bimal Kumar Das
Author: Sushil Kumar Kabra
Author: Rakesh Lodha
Author: Kalpana Luthra
Editor: Viviana Simon

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