Researchers around the world are developing more than vaccines (DNA/mRNA/wholevirus/viral-vector/protein-based/repurposed vaccine) against the SARS-CoV-2 and 21 vaccines are in human trials. However, a limited information is available about which SARS-CoV-2 proteins are recognized by human Band T-cell immune responses. Using a comprehensive computational prediction algorithm and stringent selection criteria, we have predicted and identified potent Band T-cell epitopes in the structural proteins of SARS-CoV and SARS-CoV-2. The amino acid residues spanning the predicted linear B-cell epitope in the RBD of S protein (370-NSASFSTFKCYGVSPTKLNDLCFTNV-395) have recently been identified for interaction with the CR3022, a previously described neutralizing antibody known to neutralize SARS-CoV-2 through binding to the RBD of the S protein. Intriguingly, most of the amino acid residues spanning the predicted B-cell epitope (aa 331-NITNLCPFGEVFNATRFASVYAWNRK-356, 403-RGDEVRQIAPGQTGKIADYNYKLPD-427 and aa 437-NSNNLDSKVGGNYNYLYRLFRKSNL-461) of the S protein have been experimentally verified to interact with the cross-neutralizing mAbs (S309 and CB6) in an ACE2 receptorS protein interaction independent-manner. In addition, we found that computationally predicted epitope of S protein (370-395) is likely to function as both linear B-cell and MHC class II epitope. Similarly, 403-27 and 437-461 peptides of S protein were predicted as linear B cell and MHC class I epitope while, 177-196 and 1253-1273 peptides of S protein were predicted as linear and conformational B cell epitope. We found MHC class I epitope 316-GMSRIGMEV-324 predicted as high affinity epitope (HLA-A*02:03, HLA-A*02:01, HLA-A*02:06) common to N protein of both SARS-CoV-2 and SARS-CoV (N317-325) was previously shown to induce interferon-gamma (IFN-γ) in PBMCs of SARS-recovered patients. Interestingly, two MHC class I epitopes, 1041-GVVFLHVTY-1049

Analysis of the specificity and kinetics of neutralizing antibodies (nAbs) elicited by SARS-CoV-2 infection is crucial for understanding immune protection and identifying targets for vaccine design. In a cohort of 647 SARS-CoV-2-infected subjects we found that both the magnitude of Ab responses to SARS-CoV-2 spike (S) and nucleoprotein and nAb titers correlate with clinical scores. The receptor-binding domain (RBD) is immunodominant and the target of 90% of the neutralizing activity present in SARS-CoV-2 immune sera. Whereas overall RBD-specific serum IgG titers waned with a half-life of 49 days, nAb titers and avidity increased over time for some individuals, consistent with affinity maturation. We structurally defined an RBD antigenic map and serologically quantified serum Abs specific for distinct RBD epitopes leading to the identification of two major receptor-binding motif antigenic sites. Our results explain the immunodominance of the receptor-binding motif and will guide the design of COVID-19 vaccines and therapeutics.

Lymph nodes prevent the systemic dissemination of pathogens such as viruses that infect peripheral tissues after penetrating the body's surface barriers. They are also the staging ground of adaptive immune responses to pathogen-derived antigens. It is unclear how virus particles are cleared from afferent lymph and presented to cognate B cells to induce antibody responses. Here we identify a population of CD11b+CD169+MHCII+ macrophages on the floor of the subcapsular sinus (SCS) and in the medulla of lymph nodes that capture viral particles within minutes after subcutaneous injection. Macrophages in the SCS translocated surface-bound viral particles across the SCS floor and presented them to migrating B cells in the underlying follicles. Selective depletion of these macrophages compromised local viral retention, exacerbated viraemia of the host, and impaired local B-cell activation. These findings indicate that CD169+ macrophages have a dual physiological function. They act as innate 'flypaper' by preventing the systemic spread of lymph-borne pathogens and as critical gatekeepers at the lymph-tissue interface that facilitate the recognition of particulate antigens by B cells and initiate humoral immune responses.

Efficient therapeutic options are needed to control the spread of SARS-CoV-2 that has caused more than 922,000 fatalities as of September 13th, 2020. We report the isolation and characterization of two ultrapotent SARS-CoV-2 human neutralizing antibodies (S2E12 and S2M11) that protect hamsters against SARS-CoV-2 challenge. Cryo-electron microscopy structures show that S2E12 and S2M11 competitively block ACE2 attachment and that S2M11 also locks the spike in a closed conformation by recognition of a quaternary epitope spanning two adjacent receptor-binding domains. Cocktails including S2M11, S2E12 or the previously identified S309 antibody broadly neutralize a panel of circulating SARS-CoV-2 isolates and activate effector functions. Our results pave the way to implement antibody cocktails for prophylaxis or therapy, circumventing or limiting the emergence of viral escape mutants.

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Depending on the tissue microenvironment, T cells can differentiate into highly diverse subsets expressing unique trafficking receptors and cytokines. Studies of human lymphocytes have primarily focused on a limited number of parameters in blood, representing an incomplete view of the human immune system. Here, we have utilized mass cytometry to simultaneously analyze T cell trafficking and functional markers across eight different human tissues, including blood, lymphoid, and non-lymphoid tissues. These data have revealed that combinatorial expression of trafficking receptors and cytokines better defines tissue specificity. Notably, we identified numerous T helper cell subsets with overlapping cytokine expression, but only specific cytokine combinations are secreted regardless of tissue type. This indicates that T cell lineages defined in mouse models cannot be clearly distinguished in humans. Overall, our data uncover a plethora of tissue immune signatures and provide a systemic map of how T cell phenotypes are altered throughout the human body.

Anti-helminth immunity involves CD4+ T cells, yet the precise effector mechanisms responsible for parasite killing or expulsion remain elusive. We now report an essential role for antibodies in mediating immunity against the enteric helminth Heligmosomoides polygyrus (Hp), a natural murine parasite that establishes chronic infection. Polyclonal IgG antibodies, present in naive mice and produced following Hp infection, functioned to limit egg production by adult parasites. Comparatively, affinity-matured parasite-specific IgG and IgA antibodies that developed only after multiple infections were required to prevent adult worm development. These data reveal complementary roles for polyclonal and affinity-matured parasite-specific antibodies in preventing enteric helminth infection by limiting parasite fecundity and providing immune protection against reinfection, respectively. We propose that parasite-induced polyclonal antibodies play a dual role, whereby the parasite is allowed to establish chronicity, while parasite load and spread are limited, likely reflecting the long coevolution of helminth parasites with their hosts.

20 21 22SARS-CoV-2 is a newly emerged coronavirus responsible for the current COVID-2319 pandemic that has resulted in more than one million infections and 73,000 24 deaths 1,2 . Vaccine and therapeutic discovery efforts are paramount to curb the 25 pandemic spread of this zoonotic virus. The SARS-CoV-2 spike (S) glycoprotein 26 promotes entry into host cells and is the main target of neutralizing antibodies. 27Here we describe multiple monoclonal antibodies targeting SARS-CoV-2 S 28 identified from memory B cells of a SARS survivor infected in 2003. One 29 antibody, named S309, potently neutralizes SARS-CoV-2 and SARS-CoV 30 pseudoviruses as well as authentic SARS-CoV-2 by engaging the S receptor-31 binding domain. Using cryo-electron microscopy and binding assays, we show 32 that S309 recognizes a glycan-containing epitope that is conserved within the 33 sarbecovirus subgenus, without competing with receptor attachment. Antibody 34 cocktails including S309 along with other antibodies identified here further 35 enhanced SARS-CoV-2 neutralization and may limit the emergence of 36 neutralization-escape mutants. These results pave the way for using S309 and 37 S309-containing antibody cocktails for prophylaxis in individuals at high risk of 38 exposure or as a post-exposure therapy to limit or treat severe disease. 39 40 : bioRxiv preprint 2 Coronavirus entry into host cells is mediated by the transmembrane spike (S) 41 glycoprotein that forms homotrimers protruding from the viral surface 3 . The S 42 glycoprotein comprises two functional subunits: S1 (divided into A, B, C and D domains) 43 that is responsible for binding to host cell receptors and S2 that promotes fusion of the 44 viral and cellular membranes 4,5 . Both SARS-CoV-2 and SARS-CoV belong to the 45 sarbecovirus subgenus and their S glycoproteins share 80% amino acid sequence 46 identity 6 . SARS-CoV-2 S is closely related to the bat SARS-related CoV (SARSr-CoV) 47RaTG13 with which it shares 97.2% amino acid sequence identity 1 . We and others 48 recently demonstrated that human angiotensin converting enzyme 2 (hACE2) is a 49 functional receptor for SARS-CoV-2, as is the case for SARS-CoV 1,6-8 . The S domain 50 B (S B ) is the receptor binding domain (RBD) and binds to hACE2 with high-affinity, 51possibly contributing to the current rapid SARS-CoV-2 transmission in humans 6,9 , as 52 previously proposed for SARS-CoV 10 . 53As the coronavirus S glycoprotein mediates entry into host cells, it is the main 54 target of neutralizing antibodies and the focus of therapeutic and vaccine design 55 efforts 3 . The S trimers are extensively decorated with N-linked glycans that are 56 important for protein folding 11 and modulate accessibility to host proteases and 57 neutralizing antibodies 12-15 . Cryo-electron microscopy (cryoEM) structures of SARS-58CoV-2 S in two distinct functional states 6,9 along with cryoEM and crystal structures of 59 SARS-CoV-2 S B in complex with hACE2 16-18 revealed dynamic states of S B domains, 60 providing a blueprint for the desig...