Mutability and hypermutation antagonize immunoglobulin codon optimality (preprint)

The efficacy of polyclonal antibody responses is inherently linked to paratope diversity, as generated through V(D)J recombination and somatic hypermutation (SHM). These processes arose in early jawed vertebrates; however, little is known about how immunoglobulin diversity, mutability, and hypermutation have evolved in tandem with another more ubiquitous feature of protein-coding DNA - codon optimality. Here, we explore these relationships through analysis of germline IG genes, natural V(D)J repertoires, serum VH usage, and monoclonal antibody (mAb) expression, each through the lens of multiple optimality metrics. Strikingly, proteomic serum IgG sequencing showed that germline IGHV codon optimality positively correlated with VH representation after influenza vaccination, and in vitro, codon deoptimization of mAbs with synonymous amino acid sequences caused consistent expression loss. Germline V genes exhibit a range of codon optimality that is maintained by functionality, and inversely related to mutability. SHM caused a load-dependent deoptimization of IGH VDJ repertoires within human tonsils, bone marrow, and lymph nodes (including SARS-CoV-2-specific clones from mRNA vaccinees), influenza-infected mice, and zebrafish. Comparison of natural mutation profiles to true random suggests the presence of selective pressures that constrain deoptimization. These findings shed light on immunoglobulin evolution, providing unanticipated insights into the antagonistic relationship between variable region diversification, codon optimality, and antibody secretion; ultimately, the need for diversity takes precedence over that for the most efficient expression of the antibody repertoire.

No Causal Association Between Cholelithiasis and COVID-19: A Bidirectional Mendelian Randomization Study (preprint)

Background: Gallstone diseases and cholecystectomy are possibly associated with the severity of COVID-19 bidirectionally, yet the casual association remains unclear. Method: Applying genome-wide association study summary statistics of primarily European individuals, we utilized 2-sample Mendelian randomization to estimate the bidirectional causal effects of cholelithiasis, cholecystitis and cholecystectomy on three COVID-19 phenotypes: SARS-CoV-2 infection, COVID-19 hospitalization and severe COVID-19. Results: Inverse variance weighted Mendelian randomization results from the FinnGen consortium showed that none of cholelithiasis, cholecystitis and cholecystectomy was not causally associated with COVID-19 phenotypes, and vice versa. In addition, other methods including MR-Egger, weighted median, weight mode and simple mode exhibited approximate tendency as IVW. These results were all robust to sensitivity analysis. Conclusion:  The forward MR analysis showed no causally significant impact of cholelithiasis, cholecystitis and cholecystectomy on COVID-19 phenotypes. Similarly, reverse MR results also showed no causal association between COVID-19 and cholelithiasis events.

The impact of the COVID-19 pandemic on undergraduate and postgraduate students: A cross-sectional survey.

Background: The COVID-19 pandemic has impacted many facets of life. This study focuses on undergraduate and postgraduate students in China to explore how the pandemic has affected health status, daily life, learning situations, graduation-related situations, and their studies or work planning. Methods: This study sent online questionnaires to 2,395 participants to investigate the extent to which they were affected by the epidemic in the various aspects mentioned above and to understand what help they tend to get in the face of these effects. Results: A total of 2,000 valid questionnaires were collected. The physical health of 82.90% of the respondents was affected to varying degrees, with male students, non-medical students, and graduates being more affected than female students, students with medical majors, and non-graduates, respectively. The proportion of students affected by mental health, the total amount of physical exercise, emotional life, and interpersonal communication was 86.35, 88.65, 80.15, and 90.15%, respectively. Compared with medical students and non-graduates, non-medical students and graduates were more affected. In addition, students' learning and graduation conditions have also been affected to a certain extent: 13.07% of students may not be able to graduate on time, and the proportion of postgraduate students' graduations affected was higher than that of undergraduate students. Conclusion: The COVID-19 pandemic has affected the health status of students, their daily lives, learning situations, and so on to varying degrees. We need to pay attention to the issues, provide practical solutions, and provide a basis for better responses to similar epidemics in the future.

Safety and Efficacy of Oral administrated Cepharathine in Non-hospitalized, asymptomatic or mild COVID-19 patients: A Double-blind, Randomized, Placebo-controlled Trial (preprint)

Cepharanthine (CEP) is a natural remedy that potently inhibits SARS-CoV-2 activity both in vitro and in vivo. We conducted a proof-of-concept, double-blind, randomized, placebo-controlled trial among adults with asymptomatic or mild coronavirus disease 2019 (COVID-19). Patients were stratified randomly to de novo infection or viral rebound, and assigned in a 1:1:1 ratio to receive 60 mg/day or 120 mg/day of CEP or placebo. Primary outcome the time from randomization to negative nasopharyngeal swab, and safety were evaluated. A total of 262 de novo infected and 124 viral rebound patients underwent randomization. In the 188 de novo patients included in modified intention-to-treat (mITT) population, when compared with placebo, 60 mg/day CEP slightly shortened the time to negative (difference=-0.77 days, hazard ratio (HR)=1.40, 95% CI 0.97 to 2.01, p=0.072), and 120 mg/day CEP did not show the trend. Among de novo patients in the per-protocol set (PPS), 60 mg/day CEP significantly shortened the time to negative (difference=-0.87 days, HR=1.56, 95% CI 1.03 to 2.37, p=0.035). Among viral rebound patients in the mITT population, neither 120 mg/day nor 60 mg/day CEP significantly shortened the time to negative compared to placebo. Adverse events were not different among the three groups, and no serious adverse events occurred. Treatment of asymptomatic or mild Covid-19 with 120 mg/day or 60 mg/day CEP did not shorten the time to negative compared with placebo, without evident safety concerns. Among de novo infected patients with good compliance, 60 mg/day CEP significantly shortened the time to negative compared with placebo ( NCT05398705 ).

Differences in User Information Behavior between Official Media and Private Media during the COVID-19 Pandemic.

Weibo is a widely used social media platform showing all kinds of information related to the COVID-19 pandemic promptly in China. Official media and private media are two typical types of media on Weibo. Due to the different characteristics of these two media types, in the context of public health emergencies, it is worth exploring whether there are differences in the users' interactive behavior with information from these two types of media. This is of great significance to the integration and development of these two types of media.This study obtained data on the interaction behaviors of Weibo users with posts published by the two media types at various stages of the pandemic. Statistical analyses have confirmed significant differences in interaction behavior data between users and these two media types. In future research, based on the findings of this study, we will investigate the reasons behind these differences to provide relevant guidelines and suggestions for the release of different media in public health emergencies by conducting a deep dive analysis of user reviews.

Site of vulnerability on SARS-CoV-2 spike induces broadly protective antibody to antigenically distinct omicron SARS-CoV-2 subvariants (preprint)

The rapid evolution of SARS-CoV-2 Omicron variants has emphasized the need to identify antibodies with broad neutralizing capabilities to inform future monoclonal therapies and vaccination strategies. Herein, we identify S728-1157, a broadly neutralizing antibody (bnAb) targeting the receptor-binding site (RBS) and derived from an individual previously infected with SARS-CoV-2 prior to the spread of variants of concern (VOCs). S728-1157 demonstrates broad cross-neutralization of all dominant variants including D614G, Beta, Delta, Kappa, Mu, and Omicron (BA.1/BA.2/BA.2.75/BA.4/BA.5/BL.1). Furthermore, it protected hamsters against in vivo challenges with wildtype, Delta, and BA.1 viruses. Structural analysis reveals that this antibody targets a class 1 epitope via multiple hydrophobic and polar interactions with its CDR-H3, in addition to common class 1 motifs in CDR-H1/CDR-H2. Importantly, this epitope is more readily accessible in the open and prefusion state, or in the hexaproline (6P)-stabilized spike constructs, as compared to diproline (2P) constructs. Overall, S728-1157 demonstrates broad therapeutic potential, and may inform target-driven vaccine design against future SARS-CoV-2 variants.

Expedient Synthesis of Ubiquitin‐like Protein ISG15 Tools through Chemo‐Enzymatic Ligation Catalyzed by a Viral Protease Lbpro

Ubiquitin (Ub)‐like protein ISG15 (interferon‐stimulated gene 15) regulates innate immunity and links with the evasion of host response by viruses such as SARS‐CoV‐2. Dissecting ISGylation pathways recently received increasing attention which can inform related disease interventions, but such studies necessitate the preparation and development of various ISG15 protein tools. Here, we find that the leader protease (Lbpro) encoded by foot‐and‐mouth disease virus can promote ligation reactions between recombinant ISG15 and synthetic glycyl compounds, generating protein tools such as ISG15‐propargylamide and ISG15‐rhodamine110, which are needed for cellular proteomic studies of deISGylases, and the screening and evaluation of inhibitors against SARS‐CoV‐2 papain‐like protease (PLpro). Furthermore, this strategy can be also used to load ISG15 onto the lysine of a synthetic peptide through an isopeptide bond, and prepare Ub and NEDD8 (ubiquitin‐like protein Nedd8) protein tools.

The interaction effects of congruence type, assessment perspective and social distance on visit intention

Purpose: The purpose of this study is to explore the three-way interaction effects among congruence type (proximal vs distal) of nonverbal ad messages, assessment perspective (internal vs external) of verbal ad messages and social distance (close vs faraway) on consumers' visit intention. Design/methodology/approach: After developing the four categories of restaurant advertisements and scenarios for each type of social distance, the authors used 780 observations collected from Chinese consumers via the online survey platform Sojump and WeChat. The authors conducted ANOVA to test the hypotheses. Findings: The results reveal that in proximal congruence situations, consumers who feel a close social distance between themselves and their companions report higher visit intentions when exposed to internal versus external perspective-oriented ad messages;in distal congruence situations, external perspective-oriented ad messages elicit higher intention to visit advertised restaurant when consumers feel a far social distance between themselves and their companions. Research limitations/implications: Future research can focus on the different categories of messages, such as functional and experiential messages, to find whether similar interaction effects are explored or not. Practical implications: This paper suggests some practical implications for advertisers to maximize the impact of advertisements on consumers' behavioral outcomes via combining the different characteristics of nonverbal and verbal messages effectively, especially according to their target consumers' characteristics. Originality/value: In the view of the three-way interaction effects, this paper offers a new lens on understanding how advertisements influence consumers' behavioral outcomes, which could contribute to the advancement of advertisement theories.

Evaluation of a Functional Single Nucleotide Polymorphism of the SARS-CoV-2 Receptor ACE2 That Is Potentially Involved in Long COVID

Since the occurrence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in December 2019, SARS-CoV-2 has led to a global coronavirus disease 2019 (COVID-19) pandemic. A better understanding of the SARS-CoV-2 receptor ACE2 at the genetic level would help combat COVID-19, particularly for long COVID. We performed a genetic analysis of ACE2 and searched for its common potential single nucleotide polymorphisms (SNPs) with minor allele frequency >0.05 in both European and Chinese populations that would contribute to ACE2 gene expression variation. We thought that the variation of the ACE2 expression would be an important biological feature that would strongly affect COVID-19 symptoms, such as “brain fog”, which is highlighted by the fact that ACE2 acts as a major cellular receptor for SARS-CoV-2 attachment and is highly expressed in brain tissues. Based on the human GTEx gene expression database, we found rs2106809 exhibited a significant correlation with the ACE2 expression among multiple brain and artery tissues. This expression correlation was replicated in an independent European brain eQTL database, Braineac. rs2106809*G also displays significantly higher frequency in Asian populations than in Europeans and displays a protective effect (p = 0.047) against COVID-19 hospitalization when comparing hospitalized COVID-19 cases with non-hospitalized COVID-19 or SARS-CoV-2 test-negative samples with European ancestry from the UK Biobank. Furthermore, we experimentally demonstrated that rs2106809*G could upregulate the transcriptional activity of ACE2. Therefore, integrative analysis and functional experiment strongly support that ACE2 SNP rs2106809 is a functional brain eQTL and its potential involvement in long COVID, which warrants further investigation.

`Development of a rapid neutralizing antibody test for SARS-CoV-2 and its application for neutralizing antibody screening and vaccinated serum testing

Background : Since the outbreak of coronavirus disease (COVID-19), the high infection rate and mutation frequency of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent, have contributed to the ongoing global pandemic. Vaccination has become the most effective means of controlling COVID-19. Traditional neutralizing tests of sera are complex and labor-intensive, therefore, a rapid test for detecting neutralizing antibodies and antibody status post-immunization is needed. Methods : Based on the fact that antibodies exhibit neutralizing activity by blocking the binding of the S protein receptor-binding domain (S-RBD) to ACE2, we developed a rapid neutralizing antibody test, ACE2-Block-ELISA. To evaluate the sensitivity and specificity, we used 54 positive and 84 negative serum samples. We also tested the neutralizing activities of monoclonal antibodies (mAbs) and 214 sera samples from healthy individuals immunized with the inactivated SARS-CoV-2 vaccine. Results : The sensitivity and specificity of the ACE2-Block ELISA were 96.3% and 100%, respectively. For neutralizing mAb screening, ch-2C5 was selected for its ability to block the ACE2–S-RBD interaction. A plaque assay confirmed that ch-2C5 neutralized SARS-CoV-2, with NT50 values of 4.19, 10.63, and 1.074 μg/mL against the SARS-CoV-2 original strain, and the Beta and Delta variants, respectively. For the immunized sera samples, the neutralizing positive rate dropped from 82.14% to 32.16% within 4 months post-vaccination. Conclusions : This study developed and validated an ACE2-Block-ELISA to test the neutralizing activities of antibodies. As a rapid, inexpensive and easy-to-perform method, this ACE2-Block-ELISA has potential applications in rapid neutralizing mAb screening and SARS-CoV-2 vaccine evaluation.

A high potent synthetic nanobody with broad-spectrum activity neutralizes SARS-Cov-2 virus and Omicron variant through a unique binding mode (preprint)

COVID-19 continues to be a severe public health thread worldwide. The major challenge to control this pandemic is the rapid mutation rate of the SARS-Cov-2 virus, leading to the escape of the protection of vaccines and most of the neutralizing antibodies to date. Thus, it is pivotal to develop neutralizing antibodies with broad-spectrum activity targeting multiple SARS-Cov-2 variants. In this study, we first got a synthetic nanobody (named C5) which could interfere with ACE2 binding to SARS-Cov-2 spike protein and its RBD domain. The affinity matured format of C5 clone, named C5G2, has a single digit nanomolar affinity to RBD domain and inhibit its binding to ACE2 with an IC50 of 3.7 nM. Pseudovirus assay indicated that the monovalent C5G2 could protect the cells from the infection of SARS-Cov-2 wild type virus as well as most of the virus of concern, i.e. Alpha, Beta, Gamma and Omicron variants. Strikingly, C5G2 has the highest potency against omicron among all the variants with the IC50 of 4.9ng/ml (0.3 nM). We further solved the Cryo-EM structure of C5G2 in complex with the Spike trimer. The structure data showed that C5G2 bind to RBD mainly through its CDR3 at a vast region that not overlapping with the ACE2 binding surface. Surprisingly, C5G2 also bind to a distinct epitope residing in the NTD domain of spike protein through the same CDR3 loop, which may further increase its potency against the virus infection. Thus, this bi-paratopic nanobody may be served as an effective drug for the prophylaxis and therapy of the Omicron infection.

Analysis of differences between SARS-CoV-2 and SARS coronavirus (SARS-CoV) from multiple perspectives

Novel coronavirus pneumonia (COVID-19) grows with each passing day worldwide, and the number of infections is increasing. SARS-CoV-2, the virus that causes COVID-19, belongs to coronavirus, which is the same as severe acute respiratory syndrome coronavirus (SARS-CoV) in 2003. In this study, we analyzed and discussed the differences between coronaviruses of COVID-19 and SARS, as well as the intermediate hosts of the two coronaviruses, in order to provide a reference for the prevention and control of viral diseases from the perspective of wild animals, and also for the transmission of coronavirus.

An adjuvanted subunit SARS-CoV-2 spike protein vaccine provides protection against Covid-19 infection and transmission (preprint)

Recombinant protein approaches offer major promise for safe and effective vaccine prevention of SARS-CoV-2 infection. We developed a recombinant spike protein vaccine (called NARUVAX-C19) and characterized its ability when formulated with a nanoemulsion adjuvant to induce anti-spike antibody and T-cell responses and provide protection including against viral transmission in rodent. In mice, NARUVAX-C19 vaccine administered intramuscularly twice at 21-day interval elicited balanced Th1/Th2 humoral and T-cell responses with high titers of neutralizing antibodies against wild-type (D614G) and delta (B.1.617.2) variants. In Syrian hamsters, NARUVAX-C19 provided complete protection against wild-type (D614G) infection and prevented its transmission to naïve animals placed in the same cage as challenged animals. The results contrasted with only weak protection seen with a monomeric spike receptor binding domain (RBD) vaccine even when formulated with the same adjuvant. These encouraging results warrant ongoing development of this Covid-19 vaccine candidate.

Cross neutralization of emerging SARS-CoV-2 variants of concern by antibodies targeting distinct epitopes on spike (preprint)

Several severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants have arisen that exhibit increased viral transmissibility and partial evasion of immunity induced by natural infection and vaccination. To address the specific antibody targets that were affected by recent viral variants, we generated 43 monoclonal antibodies (mAbs) from 10 convalescent donors that bound three distinct domains of the SARS-CoV-2 spike. Viral variants harboring mutations at K417, E484 and N501 could escape most of the highly potent antibodies against the receptor binding domain (RBD). Despite this, we identified 12 neutralizing mAbs against three distinct regions of the spike protein that neutralize SARS-CoV-2 and the variants of concern, including B.1.1.7 (alpha), P.1 (gamma) and B.1.617.2 (delta). Notably, antibodies targeting distinct epitopes could neutralize discrete variants, suggesting different variants may have evolved to disrupt the binding of particular neutralizing antibody classes. These results underscore that humans exposed to wildtype (WT) SARS-CoV-2 do possess neutralizing antibodies against current variants and that it is critical to induce antibodies targeting multiple distinct epitopes of the spike that can neutralize emerging variants of concern.

Shadow Bank and Fintech Mortgage Securitization (preprint)

Agency MBS issuers can choose among three securitization venues: individual securitization where an issuer uses her own loans to create an MBS, collective securitization where different issuers deliver loans into a common MBS, and cash window where issuers receive immediate cash payment by selling loans to Fannie Mae or Freddie Mac, who then conduct securitization. We find that issuers with greater immediate liquidity needs (e.g., smaller issuers and shadow banks) have a larger fraction of their loans securitized through cash window. The uniform pricing feature of collective securitization results in cross-subsidy from traditional banks, who have relatively high-value loans, to shadow banks, especially fintech issuers, who have relatively low-value loans; hence, shadow banks and traditional banks prefer collective and individual securitization, respectively. We further show that securitization venues affect the quality and quantity of loans that issuers securitize, using Fannie Mae's policy shock on collective securitization and the COVID-19 shock on cash window.

Immunisation of ferrets and mice with recombinant SARS-CoV-2 spike protein formulated with Advax-SM adjuvant protects against COVID-19 infection (preprint)

The development of a safe and effective vaccine is a key requirement to overcoming the COVID-19 pandemic. Recombinant proteins represent the most reliable and safe vaccine approach but generally require a suitable adjuvant for robust and durable immunity. We used the SARS-CoV-2 genomic sequence and in silico structural modelling to design a recombinant spike protein vaccine (Covax-19). A synthetic gene encoding the spike extracellular domain (ECD) was inserted into a baculovirus backbone to express the protein in insect cell cultures. The spike ECD was formulated with Advax-SM adjuvant and first tested for immunogenicity in C57BL/6 and BALB/c mice. The Advax-SM adjuvanted vaccine induced high titers of binding antibody against spike protein that were able to neutralise the original wildtype virus on which the vaccine was based as well as the variant B.1.1.7 lineage virus. The Covax-19 vaccine also induced potent spike-specific CD4+ and CD8+ memory T-cells with a dominant Th1 phenotype, and this was shown to be associated with cytotoxic T lymphocyte killing of spike labelled target cells in vivo. Ferrets immunised with Covax-19 vaccine intramuscularly twice 2 weeks apart made spike receptor binding domain (RBD) IgG and were protected against an intranasal challenge with SARS-CoV-2 virus 2 weeks after the second immunisation. Notably, ferrets that received two 25 or 50ug doses of Covax-19 vaccine had no detectable virus in their lungs or in nasal washes at day 3 post-challenge, suggesting the possibility that Covax-19 vaccine may in addition to protection against lung infection also have the potential to block virus transmission. This data supports advancement of Covax-19 vaccine into human clinical trials.

Genomic Elucidation of a COVID-19 Resurgence and Local Transmission of SARS-CoV-2 in Guangzhou, China.

While China experienced a peak and decline in coronavirus disease 2019 (COVID-19) cases at the start of 2020, regional outbreaks continuously emerged in subsequent months. Resurgences of COVID-19 have also been observed in many other countries. In Guangzhou, China, a small outbreak, involving less than 100 residents, emerged in March and April 2020, and comprehensive and near-real-time genomic surveillance of SARS-CoV-2 was conducted. When the numbers of confirmed cases among overseas travelers increased, public health measures were enhanced by shifting from self-quarantine to central quarantine and SARS-CoV-2 testing for all overseas travelers. In an analysis of 109 imported cases, we found diverse viral variants distributed in the global viral phylogeny, which were frequently shared within households but not among passengers on the same flight. In contrast to the viral diversity of imported cases, local transmission was predominately attributed to two specific variants imported from Africa, including local cases that reported no direct or indirect contact with imported cases. The introduction events of the virus were identified or deduced before the enhanced measures were taken. These results show the interventions were effective in containing the spread of SARS-CoV-2, and they rule out the possibility of cryptic transmission of viral variants from the first wave in January and February 2020. Our study provides evidence and emphasizes the importance of controls for overseas travelers in the context of the pandemic and exemplifies how viral genomic data can facilitate COVID-19 surveillance and inform public health mitigation strategies.

Knowledge of medical professionals, their practices, and their attitudes toward traditional Chinese medicine for the prevention and treatment of coronavirus disease 2019: A survey in Sichuan, China.

This study aimed to investigate the knowledge, practices, and attitudes of medical professionals toward Traditional Chinese Medicine (TCM) for the prevention and treatment of coronavirus disease 2019 (COVID-19). All 401 medical professionals were surveyed using an anonymous with an investigator using the Questionnaire star APP. The participants answered 14 questions; of the 401 participants, 55.2% agreed with the statement "TCM can be used for the prevention and treatment of COVID-19," 40.4% remained neutral, and 4.4% disagreed. Moreover, 75.3% agreed with the statement "There is no specific drug for COVID-19," 67% agreed with the statement "TCM can develop immunity to COVID-19" and 62.1% agreed with "TCM can alleviate the symptoms of patients with COVID-19." Meanwhile, 69.1% were aware that TCM has been recommended for COVID-19 by the National Health Commission of the People's Republic of China. Regarding the selection of sources of knowledge on whether "TCM can be used for the prevention and treatment of COVID-19," There were 277, 123, 82, 369, and 17 participants selected sources from "Hospital training," "Academic journals," "Academic Conferences," "Social media platforms (such as WeChat)" and "Others," respectively. Further, 358 participants will take TCM for the prevention of COVID-19. Multiple logistic regression analysis showed that age, major and received TCM treatment within the last five years were independent factors affecting the participants' attitudes. In the absence of specific drugs for COVID-19, more than half of the participants agreed that TCM could be used for the prevention and treatment of COVID-19 and most participants are willing to take TCM to prevent COVID-19, although unsure about its effectiveness. The main information sources on TCM for the treatment and prevention of COVID-19 were social platforms and hospital training.