Relationship between SARS-CoV-2 nucleocapsid protein and N gene and its application in antigen testing kits evaluation.

More than forty antigen testing kits have been approved to response the prevalence of SARS-CoV-2 and its variant strains. However, the approved antigen testing kits are not capable of quantitative detection. Here, we successfully developed a lateral flow immunoassay based on colloidal gold nanoparticles (CGNP-based LFIA) for nucleocapsid (N) protein of SARS-CoV-2 quantitative detection. Delta strain (NMDC60042793) of SARS-CoV-2 have been cultured and analyzed by our developed digital PCR and LFIA methods to explore the relationship between N protein amount and N gene level. It indicated that the linear relationship (y = 47 ×) between N protein molecule number and N gene copy number exhibited very well (R2 = 0.995), the virus titers and N protein amount can be roughly estimated according to nucleic acid testing. Additionally, detection limits (LODs) of nine approved antigen testing kits also have been evaluated according to the Guidelines for the registration review of 2019-nCoV antigen testing reagents. Only three antigen testing kits had LODs as stated in the instructions, the LODs of Kits have been converted into the N gene and N protein levels, according to the established relationships among virus titer vers. N gene and antigen. Results demonstrated that the sensitivity of nucleic acid testing is at least 1835 times higher than that of antigen testing. We expect that the relationship investigation and testing kits evaluation have the important directive significance to precise epidemic prevention.

Characteristics of replication and pathogenicity of SARS-CoV-2 Alpha and Delta isolates.

The continuously arising of SARS-CoV-2 variants has been posting a great threat to public health safety globally, from B.1.17 (Alpha), B.1.351 (Beta), P.1 (Gamma), B.1.617.2 (Delta) to B.1.1.529 (Omicron). The emerging or re-emerging of the SARS-CoV-2 variants of concern is calling for the constant monitoring of their epidemics, pathogenicity and immune escape. In this study, we aimed to characterize replication and pathogenicity of the Alpha and Delta variant strains isolated from patients infected in Laos. The amino acid mutations within the spike fragment of the isolates were determined via sequencing. The more efficient replication of the Alpha and Delta isolates was documented than the prototyped SARS-CoV-2 in Calu-3 and Caco-2 â€‹cells, while such features were not observed in Huh-7, Vero E6 and HPA-3 â€‹cells. We utilized both animal models of human ACE2 (hACE2) transgenic mice and hamsters to evaluate the pathogenesis of the isolates. The Alpha and Delta can replicate well in multiple organs and cause moderate to severe lung pathology in these animals. In conclusion, the spike protein of the isolated Alpha and Delta variant strains was characterized, and the replication and pathogenicity of the strains in the cells and animal models were also evaluated.

A Smartphone-based Zero-Effort Method for Mitigating Epidemic Propagation (preprint)

A large number of epidemics, including COVID-19 and SARS, spread through droplets, quickly swept the world and claimed the precious lives of large numbers of people. Building a low-cost and real-time epidemic early warning system to identify individuals who have been in contact with infected individuals and determine whether they need to be quarantined is an effective means to mitigate the spread of the epidemic. In this paper, we propose a smartphone-based zero-effort epidemic warning method for mitigating epidemic propagation. Firstly, we recognize epidemic-related voice activity relevant to epidemics spread by hierarchical attention mechanism and temporal convolutional network. The hierarchical attention mechanism is used to find local important information through global scanning, then enhances useful information and suppresses useless information. Subsequently, we estimate the social distance between users through sensors built-in smartphone. Furthermore, we combine Wi-Fi network logs and social distance to comprehensively judge whether there is spatiotemporal contact between users and determine the duration of contact. Finally, we estimate infection risk based on epidemic-related vocal activity, social distance, and contact time. We conduct a large number of well-designed experiments in typical scenarios to fully verify the proposed method. The proposed method does not rely on any additional infrastructure and historical training data, which is conducive to integration with epidemic prevention and control systems and large-scale applications.

A variant-proof SARS-CoV-2 vaccine targeting HR1 domain in S2 subunit of spike protein.

The emerging SARS-CoV-2 variants, commonly with many mutations in S1 subunit of spike (S) protein are weakening the efficacy of the current vaccines and antibody therapeutics. This calls for the variant-proof SARS-CoV-2 vaccines targeting the more conserved regions in S protein. Here, we designed a recombinant subunit vaccine, HR121, targeting the conserved HR1 domain in S2 subunit of S protein. HR121 consisting of HR1-linker1-HR2-linker2-HR1, is conformationally and functionally analogous to the HR1 domain present in the fusion intermediate conformation of S2 subunit. Immunization with HR121 in rabbits and rhesus macaques elicited highly potent cross-neutralizing antibodies against SARS-CoV-2 and its variants, particularly Omicron sublineages. Vaccination with HR121 achieved near-full protections against prototype SARS-CoV-2 infection in hACE2 transgenic mice, Syrian golden hamsters and rhesus macaques, and effective protection against Omicron BA.2 infection in Syrian golden hamsters. This study demonstrates that HR121 is a promising candidate of variant-proof SARS-CoV-2 vaccine with a novel conserved target in the S2 subunit for application against current and future SARS-CoV-2 variants.

SARS-CoV-2 Mpro inhibitors with antiviral activity in a transgenic mouse model.

The COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continually poses serious threats to global public health. The main protease (Mpro) of SARS-CoV-2 plays a central role in viral replication. We designed and synthesized 32 new bicycloproline-containing Mpro inhibitors derived from either boceprevir or telaprevir, both of which are approved antivirals. All compounds inhibited SARS-CoV-2 Mpro activity in vitro, with 50% inhibitory concentration values ranging from 7.6 to 748.5 nM. The cocrystal structure of Mpro in complex with MI-23, one of the most potent compounds, revealed its interaction mode. Two compounds (MI-09 and MI-30) showed excellent antiviral activity in cell-based assays. In a transgenic mouse model of SARS-CoV-2 infection, oral or intraperitoneal treatment with MI-09 or MI-30 significantly reduced lung viral loads and lung lesions. Both also displayed good pharmacokinetic properties and safety in rats.

Chemical composition and pharmacological mechanism of Ephedra-Glycyrrhiza drug pair against coronavirus disease 2019 (COVID-19) (preprint)

Background: Coronavirus disease 2019 (COVID-19) is currently spreading all over the world, and the prospect of a very rapid increase in COVID-19 cases prompted us to seek effective antiviral therapeutics, from the identification of possible drugs to their potential mechanisms. Purpose: The aim of this study was to explore the efficacy of the Ephedra-Glycyrrhiza (EG) drug pair on coronavirus disease 2019 (COVID-19) by network pharmacology and molecular docking. Methods: The main active compounds, target information, meridians and properties of EG were obtained through the TCMSP and ETCM databases. The targeted information of COVID-19 was acquired from the GeneCards database. EG drug pair applied diseases were analysed by DAVID and the drug-bank database, and visualized by Rstudio and Cytoscape 3.7.2. Then, we carried out targeted intersection of the EG drug pair and COVID-19 to map the compound-target-disease interactions and visualize them with Cytoscape 3.7.2 and Venny 2.1. In addition, the enrichment analysis of the GO and KEGG pathways were visualized with Rstudio and PathVisio software through the DAVID database. Finally, we carried out the molecular docking of the EG active compounds with M hydrolase (Mpro), spike protein (S protein) and angiotensin-converting enzyme 2 (ACE2), and the binding modes between GE and the protein were verified via molecular dynamics (MD) simulation. Results: We identified 112 active EG compounds by network pharmacological analysis. Drug pair enrichment analysis demonstrated that these compounds may participate in the cAMP, PI3K-Akt, JAK-STAT and chemokine signalling pathways, which had a high correlation with respiratory system, nervous system, blood circulation system and digestive system related diseases. Pathway analysis between EG and COVID-19 showed that the key targets were TNF, IL2, FOS, ALB and PTGS2. They may regulate the PI3K-Akt signalling pathway and natural killer cell-mediated cytotoxicity to play roles in immune regulation, organ protection, antiviral, immune regulation, and organ protection as well as having antiviral effects. Molecular docking results showed that the active EG compounds bind well to Mpro, S protein and ACE2. The binding modes between the active compounds of the EG and protein were verified via MD simulation. Conclusion: The EG drug pair can treat COVID-19 through multiple targets and pathways, which can provide a theoretical basis for further study of the mechanism of action of the EG drug pair on COVID-19.