Identification of an immunogenic epitope and protective antibody against the furin cleavage site of SARS-CoV-2.

BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of the global coronavirus disease 2019 (COVID-19) pandemic, contains a unique, four amino acid (aa) "PRRA" insertion in the spike (S) protein that creates a transmembrane protease serine 2 (TMPRSS2)/furin cleavage site and enhances viral infectivity. More research into immunogenic epitopes and protective antibodies against this SARS-CoV-2 furin cleavage site is needed. METHODS: Combining computational and experimental methods, we identified and characterized an immunogenic epitope overlapping the furin cleavage site that detects antibodies in COVID-19 patients and elicits strong antibody responses in immunized mice. We also identified a high-affinity monoclonal antibody from COVID-19 patient peripheral blood mononuclear cells; the antibody directly binds the furin cleavage site and protects against SARS-CoV-2 infection in a mouse model. FINDINGS: The presence of "PRRA" amino acids in the S protein of SARS-CoV-2 not only creates a furin cleavage site but also generates an immunogenic epitope that elicits an antibody response in COVID-19 patients. An antibody against this epitope protected against SARS-CoV-2 infection in mice. INTERPRETATION: The immunogenic epitope and protective antibody we have identified may augment our strategy in handling COVID-19 epidemic. FUNDING: The National Natural Science Foundation of China (82102371, 91542201, 81925025, 82073181, and 81802870), the Chinese Academy of Medical Sciences Initiative for Innovative Medicine (2021-I2M-1-047 and 2022-I2M-2-004), the Non-profit Central Research Institute Fund of the Chinese Academy of Medical Sciences (2020-PT310-006, 2019XK310002, and 2018TX31001), the National Key Research and Development Project of China (2020YFC0841700), US National Institute of Health (NIH) funds grant AI158154, University of California Los Angeles (UCLA) AI and Charity Treks, and UCLA DGSOM BSCRC COVID-19 Award Program. H.Y. is supported by Natural Science Foundation of Jiangsu Province (BK20211554 andBE2022728).

Antibody engineering improves neutralization activity against K417 spike mutant SARS-CoV-2 variants.

BACKGROUND: Neutralizing antibodies are approved drugs to treat coronavirus disease-2019 (COVID-19) patients, yet mutations in severe acute respiratory syndrome coronavirus (SARS-CoV-2) variants may reduce the antibody neutralizing activity. New monoclonal antibodies (mAbs) and antibody remolding strategies are recalled in the battle with COVID-19 epidemic. RESULTS: We identified multiple mAbs from antibody phage display library made from COVID-19 patients and further characterized the R3P1-E4 clone, which effectively suppressed SARS-CoV-2 infection and rescued the lethal phenotype in mice infected with SARS-CoV-2. Crystal structural analysis not only explained why R3P1-E4 had selectively reduced binding and neutralizing activity to SARS-CoV-2 variants carrying K417 mutations, but also allowed us to engineer mutant antibodies with improved neutralizing activity against these variants. Thus, we screened out R3P1-E4 mAb which inhibits SARS-CoV-2 and related mutations in vitro and in vivo. Antibody engineering improved neutralizing activity of R3P1-E4 against K417 mutations. CONCLUSION: Our studies have outlined a strategy to identify and engineer neutralizing antibodies against SARS-CoV-2 variants.

Methods to Identify Immunogenic Peptides in SARS-CoV-2 Spike and Protective Monoclonal Antibodies in COVID-19 Patients.

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and the associated COVID-19 diseases are an emerging threat to global public health. Although considerable scientific research on the immune, especially antibody, responses to SARS-CoV-2 infection have been conducted, additional dominant epitopes and protective antibodies are needed for diagnosis and treatment of COVID-19 patients. Here, two different phage libraries are used to identify immunogenic epitopes across the spike protein and monoclonal antibodies from COVID-19 patients. Three peptides are further characterized in the receptor-binding motif (RBM) and measured their antibody levels in COVID-19 patients, from which one identifies one most immunodominant epitope with the highest antibody response in COVID-19 patients and in immunized mice. More importantly, monoclonal antibodies specifically binding to this peptide isolated from COVID-19 patients have therapeutic potential to neutralize SARS-CoV-2 infection. Thus, the approaches to systemically identify immunogenic peptides and directly identify human monoclonal antibodies from patients will provide useful diagnostic and therapeutic tools for COVID-19 and other emerging infectious diseases.

Measurement report of the change of PM2.5 composition during the COVID-19 lockdown in urban Xi'an: Enhanced secondary formation and oxidation.

Enhanced secondary aerosol formation was observed during the COVID-19 lockdown in Xi'an, especially for polluted episodes. More oxidized­oxygenated organic aerosol (MO-OOA) and sulfate showed the dominant enhancements, especially in large particle-mode. Meanwhile, relative humidity (RH) showed a positive promotion on the formation of sulfate and MO-OOA during the lockdown, but had no obvious correlation with less oxidized­oxygenated organic aerosol (LO-OOA) or nitrate. Organosulfurs (OS) displayed a higher contribution (~58%) than inorganic sulfate to total sulfate enhancement in the polluted episode during the lockdown. Although the total nitrate (TN) decreased during the lockdown ascribing to a larger reduction of inorganic nitrate, organic nitrate (ON) showed an obvious increase from pre-lockdown (0.5 ± 0.6 µg m-3 and 1 ± 2% of TN) to lockdown (5.3 ± 3.1 µg m-3 and 17 ± 9% of TN) in the polluted case (P < 0.05). In addition, RH also displayed a positive promotion on the formation of ON and OS, and the increases of both OS and ON were much efficient in the nighttime than in the daytime. These results suggest that higher RH and stagnant meteorology might facilitate the sulfate and MO-OOA enhancement, especially in the nighttime, which dominated the secondary aerosol enhancement in haze pollution during the lockdown.

Enhanced formation of secondary organic aerosol from photochemical oxidation during the COVID-19 lockdown in a background site in Northwest China.

The COVID-19 pandemic has drastically affected the economic and social activities, leading to large reductions in anthropogenic emissions on a global scale. Despite the reduction of primary emissions during the lockdown period, heavy haze pollution was observed unexpectedly in megacities in North and East China. In this study, we conducted online measurements of organic aerosol in a background site before and during the lockdown in Guanzhong basin, Northwest China. The oxygenated organic aerosol (OOA) increased from 24% of total OA (3.2 ± 1.6 µg m-3) before lockdown to 54% of total OA (4.5 ± 1.3 µg m-3) during lockdown, likely due to substantial decrease of NOx emissions during lockdown which resulted in large increase of O3 and thus atmospheric oxidizing capacity. OOA showed higher mass concentrations and fractional contributions during lockdown than before lockdown, and increased with the increase of Ox in both periods. In comparison, aqueous secondary organic aerosol (aqSOA) showed high mass concentrations and fractional contributions in both polluted periods before and during lockdown with the increase of aerosol liquid water content (ALWC). The increase of aqSOA under high ALWC conditions is very likely the reason of pollution events during lockdown. Combined with trajectory analysis, the absence of Guanzhong cluster in polluted period during lockdown may play a key role in the OA variations between two polluted periods. In addition, when comparing the clusters from the same transmission directions between before lockdown and during lockdown, the OA fractions showed similar variations during lockdown in all clusters, suggesting the OA variations are widespread in northwest China.