Explore the vast range of titles available.

Two and a half years into the COVID-19 pandemic, we have gained many insights into the human antibody response to the causative SARS-CoV-2 virus. In this Review, we summarize key observations of humoral immune responses in people with COVID-19, discuss key features of infection- and vaccine-induced neutralizing antibodies, and consider vaccine designs for inducing antibodies that are broadly protective against different variants of the SARS-CoV-2 virus.Qi et al. provide an in-depth analysis of antibody responses generated in response to SARS-CoV-2.

Thirty years ago, China experienced its first indigenous HIV/AIDS cases. Since then, HIV has spread from drug users and blood transfusion recipients to the general urban population, mainly through sexual routes. Particularly worrisome is the recent increase of HIV infection among college students, according to the Chinese Center for Disease Control and Prevention (CDC). The number of newly diagnosed college students has seen an annual growth rate ranging from 30 to 50% over the past several years. A proactive approach is required to spread public awareness of this trend and to promote aggressive prevention and treatment measures.

A new and highly pathogenic coronavirus (severe acute respiratory syndrome coronavirus-2, SARS-CoV-2) caused an outbreak in Wuhan city, Hubei province, China, starting from December 2019 that quickly spread nationwide and to other countries around the world 1 – 3 . Here, to better understand the initial step of infection at an atomic level, we determined the crystal structure of the receptor-binding domain (RBD) of the spike protein of SARS-CoV-2 bound to the cell receptor ACE2. The overall ACE2-binding mode of the SARS-CoV-2 RBD is nearly identical to that of the SARS-CoV RBD, which also uses ACE2 as the cell receptor 4 . Structural analysis identified residues in the SARS-CoV-2 RBD that are essential for ACE2 binding, the majority of which either are highly conserved or share similar side chain properties with those in the SARS-CoV RBD. Such similarity in structure and sequence strongly indicate convergent evolution between the SARS-CoV-2 and SARS-CoV RBDs for improved binding to ACE2, although SARS-CoV-2 does not cluster within SARS and SARS-related coronaviruses 1 – 3 , 5 . The epitopes of two SARS-CoV antibodies that target the RBD are also analysed for binding to the SARS-CoV-2 RBD, providing insights into the future identification of cross-reactive antibodies. High-resolution crystal structures of the receptor-binding domain of the spike protein of SARS-CoV-2 and SARS-CoV in complex with ACE2 provide insights into the binding mode of these coronaviruses and highlight essential ACE2-interacting residues.

Understanding the mechanism for antibody neutralization of SARS-CoV-2 is critical for the development of effective therapeutics and vaccines. We recently isolated a large number of monoclonal antibodies from SARS-CoV-2 infected individuals. Here we select the top three most potent yet variable neutralizing antibodies for in-depth structural and functional analyses. Crystal structural comparisons reveal differences in the angles of approach to the receptor binding domain (RBD), the size of the buried surface areas, and the key binding residues on the RBD of the viral spike glycoprotein. One antibody, P2C-1F11, most closely mimics binding of receptor ACE2, displays the most potent neutralizing activity in vitro and conferred strong protection against SARS-CoV-2 infection in Ad5-hACE2-sensitized mice. It also occupies the largest binding surface and demonstrates the highest binding affinity to RBD. More interestingly, P2C-1F11 triggers rapid and extensive shedding of S1 from the cell-surface expressed spike glycoprotein, with only minimal such effect by the remaining two antibodies. These results offer a structural and functional basis for potent neutralization via disruption of the very first and critical steps for SARS-CoV-2 cell entry. Here, the authors compare the crystal structures and investigate the neutralization mechanisms of three neutralizing antibodies against SARS-CoV-2 and find that one antibody, P2C-1F11, closely mimics binding of receptor ACE2 and displays the most potent neutralizing activity in vitro, as well as conferring protection against SARS-CoV-2 infection in Ad5-hACE2-sensitized mice.

In recognizing the host cellular receptor and mediating fusion of virus and cell membranes, the spike (S) glycoprotein of coronaviruses is the most critical viral protein for cross-species transmission and infection. Here we determined the cryo-EM structures of the spikes from bat (RaTG13) and pangolin (PCoV_GX) coronaviruses, which are closely related to SARS-CoV-2. All three receptor-binding domains (RBDs) of these two spike trimers are in the “down” conformation, indicating they are more prone to adopt the receptor-binding inactive state. However, we found that the PCoV_GX, but not the RaTG13, spike is comparable to the SARS-CoV-2 spike in binding the human ACE2 receptor and supporting pseudovirus cell entry. We further identified critical residues in the RBD underlying different activities of the RaTG13 and PCoV_GX/SARS-CoV-2 spikes. These results collectively indicate that tight RBD–ACE2 binding and efficient RBD conformational sampling are required for the evolution of SARS-CoV-2 to gain highly efficient infection. The spike glycoprotein in coronaviruses is a key viral protein for cross-species transmission and infection. Here, the authors present the cryo-EM structures of the spike ectodomains from bat and pangolin coronaviruses, compare them with the available SARS-CoV-2 spike structures and discuss implications for the evolution and cross-species transmission of SARS-CoV-2.

Neutralizing antibodies (nAbs) to SARS-CoV-2 hold powerful potentials for clinical interventions against COVID-19 disease. However, their common genetic and biologic features remain elusive. Here we interrogate a total of 165 antibodies from eight COVID-19 patients, and find that potent nAbs from different patients have disproportionally high representation of IGHV3-53/3-66 usage, and therefore termed as public antibodies. Crystal structural comparison of these antibodies reveals they share similar angle of approach to RBD, overlap in buried surface and binding residues on RBD, and have substantial spatial clash with receptor angiotensin-converting enzyme-2 (ACE2) in binding to RBD. Site-directed mutagenesis confirms these common binding features although some minor differences are found. One representative antibody, P5A-3C8, demonstrates extraordinarily protective efficacy in a golden Syrian hamster model against SARS-CoV-2 infection. However, virus escape analysis identifies a single natural mutation in RBD, namely K417N found in B.1.351 variant from South Africa, abolished the neutralizing activity of these public antibodies. The discovery of public antibodies and shared escape mutation highlight the intricate relationship between antibody response and SARS-CoV-2, and provide critical reference for the development of antibody and vaccine strategies to overcome the antigenic variation of SARS-CoV-2. Here, the authors combine structural, binding, mutational in vitro and in vivo assays to characterize neutralizing antibodies derived from IGHV3-53/3-66 against SARS-CoV-2, finding one antibody, named P5A-3C8, to exhibit protective efficacy in a golden Syrian hamster model of infection while showing the emergence of mutations at position 417 of the Spike protein that confer resistance.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes the global pandemic of COVID-19. SARS-CoV-2 is classified as a biosafety level-3 (BSL-3) agent, impeding the basic research into its biology and the development of effective antivirals. Here, we developed a biosafety level-2 (BSL-2) cell culture system for production of transcription and replication-competent SARS-CoV-2 virus-like-particles (trVLP). This trVLP expresses a reporter gene (GFP) replacing viral nucleocapsid gene (N), which is required for viral genome packaging and virion assembly (SARS-CoV-2 GFP/ΔN trVLP). The complete viral life cycle can be achieved and exclusively confined in the cells ectopically expressing SARS-CoV or SARS-CoV-2 N proteins, but not MERS-CoV N. Genetic recombination of N supplied in trans into viral genome was not detected, as evidenced by sequence analysis after one-month serial passages in the N-expressing cells. Moreover, intein-mediated protein trans-splicing approach was utilized to split the viral N gene into two independent vectors, and the ligated viral N protein could function in trans to recapitulate entire viral life cycle, further securing the biosafety of this cell culture model. Based on this BSL-2 SARS-CoV-2 cell culture model, we developed a 96-well format high throughput screening for antivirals discovery. We identified salinomycin, tubeimoside I, monensin sodium, lycorine chloride and nigericin sodium as potent antivirals against SARS-CoV-2 infection. Collectively, we developed a convenient and efficient SARS-CoV-2 reverse genetics tool to dissect the virus life cycle under a BSL-2 condition. This powerful tool should accelerate our understanding of SARS-CoV-2 biology and its antiviral development.

Remarkable progress has been achieved for prophylactic and therapeutic interventions against human immunodeficiency virus type I (HIV-1) through antiretroviral therapy. However, vaccine development has remained challenging. Recent discoveries in broadly neutralizing monoclonal antibodies (bNAbs) has led to the development of multiple novel vaccine approaches for inducing bNAbs-like antibody response. Structural and dynamic studies revealed several vulnerable sites and states of the HIV-1 envelop glycoprotein (Env) during infection. Our review aims to highlight these discoveries and rejuvenate our endeavor in HIV-1 vaccine design and development.

[...]efficacies of all vaccine modalities are severely compromised, particularly toward Omicron, followed by Beta, Delta, Gamma, and Alpha [9–13,18–20]. The first three combinations have been approved by the U.S. Food and Drug Administration, the fourth one by the Chinese National Medical Products Administration, and the last one by South Korea regulatory agencies. A recent comprehensive study has categorized 186 RBD-directed antibodies with potential therapeutic use into seven core “communities” (RBD-1 to RBD-7) based on their distinct footprints and broad competition profiles (Figure 2 ) [52]. The RRM face of RBD is depicted on the up-left corner, together with some of the representative antibodies with unknown crystal structure information.

BackgroundTumor-infiltrating CD8 cells and expression of programmed cell death ligand 1 (PD-L1) are immune checkpoint markers in patients with hepatocellular carcinoma (HCC). We aimed to determine the ability of preoperative gadoxetic acid-enhanced magnetic resonance imaging (MRI) findings to predict CD8 cell density and PD-L1 expression in HCC.MethodsA total of 120 patients with HCC who underwent 3.0-T gadoxetic acid-enhanced MRI before curative resection from January 2016 to June 2020 were enrolled and divided into a training set (n = 84) and a testing set (n = 36). Thirty-four patients with advanced stage HCC who received anti-PD-1 inhibitor between January 2017 and April 2020 and underwent pretreated gadoxetic acid-enhanced MRI scans were enrolled in an independent validation set. PD-L1 expression and CD8 cell infiltration were assessed with immunohistochemical staining, respectively. Two radiologists blinded to pathology results evaluated the pretreated MR features in consensus. Logistic regression and the receiver operating characteristic curve (ROC) analyses were used to determine the value of image features to predict high CD8 cell density, PD-L1 positivity and the combination of high CD8 cell density and PD-L1 positivity in HCC in the training set and validated the findings in the testing set. The associations of MRI predictors with the objective response to immunotherapy were assessed in the independent validation.ResultsIn the training set, the independent MRI predictors were irregular tumor margin (ITM, P = 0.008) and peritumoral low signal intensity (PLSI) on hepatobiliary phase (HBP) images (P < 0.001) for PD-L1 positivity, absence of an enhancing capsule (AEC, P = 0.001) and PLSI on HBP images (P = 0.025) for high CD8 cell density, and PLSI on HBP images (P = 0.001) and ITM (P = 0.023) for the both. The area under the curves (AUCs) of the predictive models for evaluating PD-L1 positivity, high CD8 cell density and the combination of high CD8 cell density and PD-L1 positivity were 0.810 and 0.809, 0.740 and 0.728, and 0.809 and 0.874 in the training and testing set, respectively. The objective response was demonstrated to be associated with the combination of PLSI on HBP images and ITM (PHI, P = 0.004), and the combination of PLSI on HBP images and AEC (PHA, P = 0.012) in the independent validation set.ConclusionsPretreated MRI features have the potential to identify patients with HCC in an immune-activated state and predict outcomes of immunotherapy.Trial registrationThe study was retrospectively registered on March 5, 2020 with registration no. [2020] 02–012-01.