Computation of Antigenicity Predicts SARS-CoV-2 Vaccine Breakthrough Variants

It has been reported that multiple SARS-CoV-2 variants of concerns (VOCs) including B.1.1.7 (Alpha), B.1.351 (Beta), P.1 (Gamma), and B.1.617.2 (Delta) can reduce neutralisation by antibodies, resulting in vaccine breakthrough infections. Virus-antiserum neutralisation assays are typically performed to monitor potential vaccine breakthrough strains. However, such experimental-based methods are slow and cannot instantly validate whether newly emerging variants can break through current vaccines or therapeutic antibodies. To address this, we sought to establish a computational model to predict the antigenicity of SARS-CoV-2 variants by sequence alone and in real time. In this study, we firstly identified the relationship between the antigenic difference transformed from the amino acid sequence and the antigenic distance from the neutralisation titres. Based on this correlation, we obtained a computational model for the receptor binding domain (RBD) of the spike protein to predict the fold decrease in virus-antiserum neutralisation titres with high accuracy (~0.79). Our predicted results were comparable with experimental neutralisation titres of variants, including B.1.1.7 (Alpha), B.1.351 (Beta), B.1.617.2 (Delta), B.1.429 (Epsilon), P.1 (Gamma), B.1.526 (Iota), B.1.617.1 (Kappa), and C.37 (Lambda), as well as SARS-CoV. Here, we firstly predicted the fold of decrease of B.1.1.529 (Omicron) as 17.4-fold less susceptible to neutralisation. We visualised all 1521 SARS-CoV-2 lineages to indicate variants including B.1.621 (Mu), B.1.630, B.1.633, B.1.649, and C.1.2, which can induce vaccine breakthrough infections in addition to reported VOCs B.1.351 (Beta), P.1 (Gamma), B.1.617.2 (Delta), and B.1.1.529 (Omicron). Our study offers a quick approach to predict the antigenicity of SARS-CoV-2 variants as soon as they emerge. Furthermore, this approach can facilitate future vaccine updates to cover all major variants. An online version can be accessed at http://jdlab.online.

Mapping the Immunodominance Landscape of SARS-CoV-2 Spike Protein for the Design of Vaccines against COVID-19

The ongoing coronavirus disease 2019 (COVID-19) pandemic is a serious threat to global public health, and imposes severe burdens on the entire human society. The severe acute respiratory syndrome (SARS) coronavirus-2 (SARS-CoV-2) can cause severe respiratory illness and death. Currently, there are no specific antiviral drugs that can treat COVID-19. Several vaccines against SARS-CoV-2 are being actively developed by research groups around the world. The surface S (spike) protein and the highly expressed internal N (nucleocapsid) protein of SARS-CoV-2 are widely considered as promising candidates for vaccines. In order to guide the design of an effective vaccine, we need experimental data on these potential epitope candidates. In this study, we mapped the immunodominant (ID) sites of S protein using sera samples collected from recently discharged COVID-19 patients. The SARS-CoV-2 S protein-specific antibody levels in the sera of recovered COVID-19 patients were strongly correlated with the neutralising antibody titres. We used epitope mapping to determine the landscape of ID sites of S protein, which identified nine linearized B cell ID sites. Four out of the nine ID sites were found in the receptor-binding domain (RBD). Further analysis showed that these ID sites are potential high-affinity SARS-CoV-2 antibody binding sites. Peptides containing two out of the nine sites were tested as vaccine candidates against SARS-CoV-2 in a mouse model. We detected epitope-specific antibodies and SARS-CoV-2-neutralising activity in the immunised mice. This study for the first time provides human serological data for the design of vaccines against COVID-19.

Survey on blood pressure and serum lipids in Hei Yi Zhuang Chinese living in Guangxi / 中华心血管病杂志

<p><b>OBJECTIVE</b>To investigate the levels of blood pressure and serum lipids, and examine the relationship between hypertension and hyperlipidemia in Hei Yi Zhuang Chinese living in Guangxi.</p><p><b>METHODS</b>A total of 1056 people of Hei Yi Zhuang ethnicity were studied. Blood pressure, body height, body weight, and serum levels of lipids and apolipoprotein were measured. The data were compared with those in 925 people of Han ethnicity, who live in the same region.</p><p><b>RESULTS</b>Systolic blood pressure and pulse pressure were significantly higher in Hei Yi Zhuang than Han Chinese (P < 0.001). The prevalence of isolated systolic hypertension and hypertension was also significantly higher in Hei Yi Zhuang than Han Chinese (P < 0.001). Serum concentrations of total cholesterol, triglycerides, low-density lipoprotein cholesterol, and apolipoprotein (Apo) B, and the prevalence of hypercholesterolemia and hyperlipidemia were significantly lower in Hei Yi Zhuang than Han Chinese (P < 0.05). Serum concentrations of high-density lipoprotein cholesterol and the Apo A1 to Apo B ratio were significantly higher in Hei Yi Zhuang than Han Chinese (P < 0.001). The prevalence of hypertension in Hei Yi Zhuang Chinese was positively associated with triglycerides (r = 0.425, P < 0.05), whereas the prevalence of hypertension in Han Chinese was positively correlated with total cholesterol (r = 0.623, P < 0.001).</p><p><b>CONCLUSION</b>The present study revealed a significant difference in blood pressure and serum lipids between Hei Yi Zhuang and Han ethnic groups, and an association between hypertension and hyperlipidemia.</p>