key: cord-0976286-bb620xw6 authors: Mishra, Nitesh; Kumar, Sanjeev; Singh, Swarandeep; Bansal, Tanu; Jain, Nishkarsh; Saluja, Sumedha; Palanichamy, Jayanth Kumar; Mir, Riyaz A.; Sinha, Subrata; Luthra, Kalpana title: Cross-neutralization of SARS-CoV-2 by HIV-1 specific broadly neutralizing antibodies and polyclonal plasma date: 2020-12-10 journal: bioRxiv DOI: 10.1101/2020.12.09.418806 sha: 6f0c25484a8011a1c7b955a7227d660591fbab05 doc_id: 976286 cord_uid: bb620xw6 Cross-reactive epitopes (CREs) are similar epitopes on viruses that are recognized or neutralized by same antibodies. The S protein of SARS-CoV-2, similar to type I fusion proteins of viruses such as HIV-1 envelope (Env) and influenza hemagglutinin, is heavily glycosylated. Viral Env glycans, though host derived, are distinctly processed and thereby recognized or accommodated during antibody responses. In recent years, highly potent and/or broadly neutralizing human monoclonal antibodies (bnAbs) that are generated in chronic HIV-1 infections have been defined. These bnAbs exhibit atypical features such as extensive somatic hypermutations, long complementary determining region (CDR) lengths, tyrosine sulfation and presence of insertions/deletions, enabling them to effectively neutralize diverse HIV-1 viruses despite extensive variations within the core epitopes they recognize. As some of the HIV-1 bnAbs have evolved to recognize the dense viral glycans and cross-reactive epitopes (CREs), we assessed if these bnAbs cross-react with SARS-CoV-2. Several HIV-1 bnAbs showed cross-reactivity with SARS-CoV-2 while one HIV-1 CD4 binding site bnAb, N6, neutralized SARS-CoV-2. Furthermore, neutralizing plasma antibodies of chronically HIV-1 infected children showed cross neutralizing activity against SARS-CoV-2. Collectively, our observations suggest that human monoclonal antibodies tolerating extensive epitope variability can be leveraged to neutralize pathogens with related antigenic profile. Importance In the current ongoing COVID-19 pandemic, neutralizing antibodies have been shown to be a critical feature of recovered patients. HIV-1 bnAbs recognize extensively diverse cross-reactive epitopes and tolerate diversity within their core epitope. Given the unique nature of HIV-1 bnAbs and their ability to recognize and/or accommodate viral glycans, we reasoned that the glycan shield of SARS-CoV-2 spike protein can be targeted by HIV-1 specific bnAbs. Herein, we showed that HIV-1 specific antibodies cross-react and neutralize SARS-CoV-2. Understanding cross-reactive neutralization epitopes of antibodies generated in divergent viral infections will provide key evidence for engineering so called super-antibodies (antibodies that can potently neutralize diverse pathogens with similar antigenic features). Such cross-reactive antibodies can provide a blueprint upon which synthetic variants can be generated in the face of future pandemics. Broadly neutralizing antibodies (bnAbs) targeting the HIV-1 envelope glycoprotein (Env) can neutralize 38 a broad range of circulating HIV-1 isolates and have been called super-antibodies due to their 39 remarkable potency and neutralization breadth (1). As a result of its extensive genetic diversity, HIV-1 40 is subdivided in multiple clades and circulating recombinant forms (CRFs) Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in late 2019, rapidly spread 49 across different countries, infecting millions of individuals and has caused a global COVID-19 pandemic 50 (5). The SARS-CoV-2 trimeric spike glycoprotein (S) binds to angiotensin-converting enzyme 2 (ACE2) 51 which leads to host cell entry and fusion (6, 7). Type 1 viral fusion machines, including HIV-1 Env, Influenza hemagglutinin (HA), and SARS-CoV-2 S protein, mediate viral entry driven by structural 53 rearrangements and are trimeric in their pre-fusion and post-fusion state (2, 7, 8) . SARS-CoV-2 S 54 protein is covered by host-derived glycans on 66 PNGS on each trimer and site-specific glycan analysis 55 has shown that 28% of glycans on the protein surface are underprocessed oligomannose-type glycans 56 (9). SARS-CoV and HCoV OC43 elicited antibodies have been shown to cross-react with SARS-CoV-57 2. The Neutralizing antibody (nAb), S309, isolated from memory B-cells of a SARS-CoV infected 58 individual targets a glycan epitope conserved within the Sarbecovirus subgenus (10). Several HIV-1 59 bnAbs have been shown to penetrate the glycan shield and contact protein residues in Env via their 60 long complementary determining region (CDR) loops and make stabilizing contacts with the 61 surrounding high mannose and complex glycans (11, 12) . Several HIV-1 bnAbs recognize 62 glycopeptides and/or cluster of N-linked glycans (1-3). The glycans on HIV-1 Env are highly dynamic 63 and can be occupied by different glycoforms due to glycan processing. The glycan shield covering the 64 HIV-1 Env comprises roughly half its mass and shields approximately 70% of the protein surface with 65 glycosylation occurring on potential N-linked glycosylation sites that vary significantly between infected 66 individuals (18 -33 PNGS) (13, 14). Herein, we reasoned that given the unique nature of HIV-1 bnAbs and their ability to recognize and/or 68 accommodate viral glycans, the glycan shield of SARS-CoV-2 spike protein can be targeted by HIV-1 69 specific bnAbs. In the past decade, a large panel of bnAbs and non-nAbs targeting diverse epitopes on the HIV-1 Env 72 glycoprotein have been isolated and extensively characterized (reviewed in refs (1-3)). To evaluate the 73 potential cross-reactivity of these antibodies, we first performed binding ELISA of 30 bnAbs and 7 non-74 3 nAbs with SARS-CoV-2 S2Pecto protein (pre-fusion stabilized ectodomain construct, 1 -1208 amino 75 acid residues) and receptor-binding domain (RBD, residues 319 -541, also called S1 B domain). The HIV-1 bnAbs were categorized into five categories based on their epitopes on the viral Env (figure 1A). CR3022, a nAb isolated from a convalescent SARS-CoV patient (15), which has been shown to cross-78 react with SARS-CoV-2 (7), was used as positive control while two antibodies targeting the envelope Though reactivity against RBD was stronger than S2Pecto protein for majority of the bnAbs tested, a 102 significant positive correlation was seen between binding to S2Pecto protein and RBD ( Figure 1C ). All We are grateful to Dr. Raiees Andrabi for providing the S2Pecto and RBD constructs for SARS-CoV and 284 SARS-CoV-2, and Dr. Paul Bieniasz for providing the full-length envelope constructs of SARS-CoV, 285 SARS-CoV-2 and pNL4-3∆Env-nanoluc. We are thankful to NIH AIDS Reagent program for providing 286 HIV-1 envelope pseudovirus plasmids, bnAbs, non-nAbs and their expression plasmids, and TZM-bl 287 cells, and Neutralizing Antibody Consortium (NAC), IAVI, USA for providing bnAbs. We are thankful to The authors declare no competing interests. All data required to state the conclusions in the paper are present in the paper and/or the supplementary 304 data. Source data are provided with this paper. Additional information related to the paper, if required, 305 can be requested from the authors. 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