Novel Graph Topology Learning for Spatio-Temporal Analysis of COVID-19 Spread.

This article presents a new graph-learning technique to accurately infer the graph structure of COVID-19 data, helping to reveal the correlation of pandemic dynamics among different countries and identify influential countries for pandemic response analysis. The new technique estimates the graph Laplacian of the COVID-19 data by first deriving analytically its precise eigenvectors, also known as graph Fourier transform (GFT) basis. Given the eigenvectors, the eigenvalues of the graph Laplacian are readily estimated using convex optimization. With the graph Laplacian, we analyze the confirmed cases of different COVID-19 variants among European countries based on centrality measures and identify a different set of the most influential and representative countries from the current techniques. The accuracy of the new method is validated by repurposing part of COVID-19 data to be the test data and gauging the capability of the method to recover missing test data, showing 33.3% better in root mean squared error (RMSE) and 11.11% better in correlation of determination than existing techniques. The set of identified influential countries by the method is anticipated to be meaningful and contribute to the study of COVID-19 spread.

Low neutralization of SARS-CoV-2 Omicron BA.2.75.2, BQ.1.1, and XBB.1 by parental mRNA vaccine or a BA.5-bivalent booster.

The newly emerged SARS-CoV-2 Omicron sublineages, including the BA.2-derived BA.2.75.2 and the BA.5-derived BQ.1.1 and XBB.1, have accumulated additional spike mutations that may affect vaccine effectiveness. Here we report neutralizing activities of three human serum panels collected from individuals 23-94 days after dose 4 of a parental mRNA vaccine, 14-32 days after a BA.5-bivalent-booster from individuals with 2-4 previous doses of parental mRNA vaccine, or 15-32 days after a BA.5-bivalent-booster from individuals with previous SARS-CoV-2 infection and 2-4 doses of parental mRNA vaccine. The results showed that a BA.5-bivalent-booster elicited a high neutralizing titer against BA.4/5 measured at 14- to 32-day post-boost; however, the BA.5-bivalent-booster did not produce robust neutralization against the newly emerged BA.2.75.2, BQ.1.1, or XBB.1. Previous infection significantly enhanced the magnitude and breadth of BA.5-bivalent-booster-elicited neutralization. Our data support a vaccine update strategy that future boosters should match newly emerged circulating SARS-CoV-2 variants.

Knowledge of SARS-CoV-2 antigen detection and proper use of rapid diagnostic self-test among Shanghai residents in China.

Objectives: To assess and evaluate the knowledge of Shanghai, China, residents on the use of SARS-CoV-2 antigen detection and rapid diagnostic self-test. Methods: A cross-sectional electronic survey using a self-administered questionnaire was sent via the online platform, Sojump, to general individuals. Multiple linear regression analysis was performed to determine the variables associated with knowledge of self-test. Results: A total of 283 participants were recruited between July 1, 2022 and July 20, 2022 through an online survey. The mean score of knowledge on the tests was 14.33 ± 2.85 (out of 21). The questions concerning the depth of swab insertion and minimum number of swab rotations in the nostril, necessity of bilateral sampling, necessity of rotating and squeezing the swab for 10 times in the extraction buffer tube, and waiting time for the results showed the highest rate of incorrect responses. In the multiple regression analysis model, sex, social status, and source of information were associated with the knowledge on the self-test kits. Conclusion: Immediate health education programs should be made available and the kits could be improved appropriately to ensure adequate knowledge. The use of technology should be fully leveraged to achieve accurate self-diagnosis and correct interpretation of the results.

RAMIHM generates fully human monoclonal antibodies by rapid mRNA immunization of humanized mice and BCR-seq.

As a clinical vaccine, lipid nanoparticle (LNP) mRNA has demonstrated potent and broad antibody responses, leading to speculation about its potential for antibody discovery. Here, we developed RAMIHM, a highly efficient strategy for developing fully human monoclonal antibodies that employs rapid mRNA immunization of humanized mice followed by single B cell sequencing (scBCR-seq). We immunized humanized transgenic mice with RAMIHM and generated 15 top-ranked clones from peripheral blood, plasma B, and memory B cell populations, demonstrating a high rate of antigen-specificity (93.3%). Two Omicron-specific neutralizing antibodies with high potency and one broad-spectrum neutralizing antibody were discovered. Furthermore, we extended the application of RAMIHM to cancer immunotherapy targets, including a single transmembrane protein CD22 and a multi-transmembrane G protein-coupled receptor target, GPRC5D, which is difficult for traditional protein immunization methods. RAMIHM-scBCR-seq is a broadly applicable platform for the rapid and efficient development of fully human monoclonal antibodies against an assortment of targets.

Neutralization of SARS-CoV-2 Omicron sublineages by 4 doses of the original mRNA vaccine.

Since the initial emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron BA.1, several Omicron sublineages have emerged, leading to BA.5 as the current dominant sublineage. Here, we report the neutralization of different Omicron sublineages by human sera collected from individuals who had distinct mRNA vaccination and/or BA.1 infection. Four-dose-vaccine sera neutralize the original USA-WA1/2020, Omicron BA.1, BA.2, BA.2.12.1, BA.3, and BA.4/5 viruses with geometric mean titers (GMTs) of 1,554, 357, 236, 236, 165, and 95, respectively; two-dose-vaccine-plus-BA.1-infection sera exhibit GMTs of 2,114, 1,705, 730, 961, 813, and 274, respectively; and three-dose-vaccine-plus-BA.1-infection sera show GMTs of 2,962, 2,038, 983, 1,190, 1,019, and 297, respectively. Thus, the four-dose vaccine elicits the lowest neutralization against BA.5; the two-dose vaccine plus BA.1 infection elicits significantly higher GMTs against Omicron sublineages than the four-dose-vaccine; and the three-dose vaccine plus BA.1 infection elicits slightly higher GMTs (statistically insignificant) than the two-dose vaccine plus BA.1 infection. Finally, the BA.2.75 is more susceptible than BA.5 to four-dose-vaccine-elicited neutralization and three-dose-vaccine-plus-BA.1-infection-elicited neutralization.

LRRC15 inhibits SARS-CoV-2 cellular entry in trans.

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection is mediated by the entry receptor angiotensin-converting enzyme 2 (ACE2). Although attachment factors and coreceptors facilitating entry are extensively studied, cellular entry factors inhibiting viral entry are largely unknown. Using a surfaceome CRISPR activation screen, we identified human LRRC15 as an inhibitory attachment factor for SARS-CoV-2 entry. LRRC15 directly binds to the receptor-binding domain (RBD) of spike protein with a moderate affinity and inhibits spike-mediated entry. Analysis of human lung single-cell RNA sequencing dataset reveals that expression of LRRC15 is primarily detected in fibroblasts and particularly enriched in pathological fibroblasts in COVID-19 patients. ACE2 and LRRC15 are not coexpressed in the same cell types in the lung. Strikingly, expression of LRRC15 in ACE2-negative cells blocks spike-mediated viral entry in ACE2+ cell in trans, suggesting a protective role of LRRC15 in a physiological context. Therefore, LRRC15 represents an inhibitory attachment factor for SARS-CoV-2 that regulates viral entry in trans.

Vaccination Decreases the Infectious Viral Load of Delta Variant SARS-CoV-2 in Asymptomatic Patients.

The Delta variant of SARS-CoV-2 has caused many breakthrough infections in fully vaccinated individuals. While vaccine status did not generally impact the number of viral RNA genome copies in nasopharyngeal swabs of breakthrough patients, as measured by Ct values, it has been previously found to decrease the infectious viral load in symptomatic patients. We quantified the viral RNA, infectious virus, and anti-spike IgA in nasopharyngeal swabs collected from individuals asymptomatically infected with the Delta variant of SARS-CoV-2. Vaccination decreased the infectious viral load, but not the amount of viral RNA. Furthermore, vaccinees with asymptomatic infections had significantly higher levels of anti-spike IgA in their nasal secretions compared to unvaccinated individuals with asymptomatic infections. Thus, vaccination may decrease the transmission risk of Delta, and perhaps other variants, despite not affecting the amount of viral RNA measured in nasopharyngeal swabs.

Primary and Secondary Attack Rates by Vaccination Status after a SARS-CoV-2 B.1.617.2 (Delta) Variant Outbreak at a Youth Summer Camp - Texas, June 2021.

Children are capable of initiating COVID-19 transmission into households, but many questions remain about the impact of vaccination on transmission. Data from a COVID-19 Delta variant outbreak at an overnight camp in Texas during June 23-27, 2021 were analyzed. The camp had 451 attendees, including 364 youths aged <18 years and 87 adults. Detailed interviews were conducted with 92 (20.4%) of consenting attendees and 117 household members of interviewed attendees with COVID-19. Among 450 attendees with known case status, the attack rate was 41%, including 42% among youths; attack rates were lower among vaccinated (13%) than among unvaccinated youths (48%). The secondary attack rate was 51% among 115 household contacts of 55 interviewed index patients. Secondary infections occurred in 67% of unvaccinated household members and 33% of fully or partially vaccinated household members. Analyses suggested that household member vaccination and camp attendee masking at home protected against household transmission.

Neutralization Titers in Vaccinated Patients with SARS-CoV-2 Delta Breakthrough Infections.

The continuous emergence of SARS-CoV-2 variants with increased transmission and immune evasion has caused breakthrough infections in the vaccinated population. It is important to determine the threshold of neutralizing antibody titers (NT50) that permit breakthrough infections in humans. Here, we tested the neutralization titers of vaccinated patients who contracted Delta variant. All 64 patients with Delta breakthrough infections exhibited NT50 of less than 70. When the breakthrough sera were tested against USA-WA1/2020 (a strain isolated in late January 2020), 82.8%, 15.6%, and 1.6% of them had the NT50 ranges of <20, 20 to 50, and 50 to 69, respectively. When the same breakthrough sera were tested against Delta-spike SARS-CoV-2, 68.7%, 26.6%, and 4.7% of them had the NT50 ranges of <20, 20 to 50, and 50 to 69, respectively. Overall, the results suggest NT50 of 70 as a potential neutralizing threshold required to prevent Delta breakthrough infections. These clinical laboratory results have implications in vaccine strategy and public health policy. IMPORTANCE Given that neutralizing antibodies play a key role in protection of SARS-CoV-2 infection, it is important to define the neutralization levels in vaccinated individuals when they contracted breakthrough infections. In this study, we analyzed the neutralization levels from 64 vaccinated patients on days 0 to 5 before they tested positive for Delta breakthrough infections. The neutralization titers in these vaccinated individuals were all lower than 70 when they contracted breakthrough infections. The results suggest a neutralization titer of 70 as the potential threshold required to prevent breakthrough infections of Delta variant.

Neutralization of Omicron sublineages and Deltacron SARS-CoV-2 by three doses of BNT162b2 vaccine or BA.1 infection.

Distinct SARS-CoV-2 Omicron sublineages have evolved showing increased fitness and immune evasion than the original Omicron variant BA.1. Here, we report the neutralization activity of sera from BNT162b2 vaccinated individuals or unimmunized Omicron BA.1-infected individuals against Omicron sublineages and "Deltacron" variant (XD). BNT162b2 post-dose 3 immune sera neutralized USA-WA1/2020, Omicron BA.1-, BA.2-, BA.2.12.1-, BA.3-, BA.4/5-, and XD-spike SARS-CoV-2s with geometric mean titres (GMTs) of 1335, 393, 298, 315, 216, 103, and 301, respectively; thus, BA.4/5 SARS-CoV-2 spike variant showed the highest propensity to evade vaccine neutralization compared to the original Omicron variants BA.1. BA.1-convalescent sera neutralized USA-WA1/2020, BA.1-, BA.2-, BA.2.12.1-, BA.3-, BA.4/5-, and Deltacron-spike SARS-CoV-2s with GMTs of 15, 430, 110, 109, 102, 25, and 284, respectively. The unique mutation F486V in the BA.4/5 spike contributes to the increased evasion of antibody neutralization by sublineage BA.4/5. The low neutralization titres of vaccinated sera or convalescent sera from BA.1 infected individuals against the emerging and rapidly spreading Omicron BA.4/5 variants provide important results for consideration in the selection of an updated vaccine in the current Omicron wave.Trial registration: ClinicalTrials.gov; identifier: NCT04368728.

A live-attenuated SARS-CoV-2 vaccine candidate with accessory protein deletions.

We report a live-attenuated SARS-CoV-2 vaccine candidate with (i) re-engineered viral transcription regulator sequences and (ii) deleted open-reading-frames (ORF) 3, 6, 7, and 8 (∆3678). The ∆3678 virus replicates about 7,500-fold lower than wild-type SARS-CoV-2 on primary human airway cultures, but restores its replication on interferon-deficient Vero-E6 cells that are approved for vaccine production. The ∆3678 virus is highly attenuated in both hamster and K18-hACE2 mouse models. A single-dose immunization of the ∆3678 virus protects hamsters from wild-type virus challenge and transmission. Among the deleted ORFs in the ∆3678 virus, ORF3a accounts for the most attenuation through antagonizing STAT1 phosphorylation during type-I interferon signaling. We also developed an mNeonGreen reporter ∆3678 virus for high-throughput neutralization and antiviral testing. Altogether, the results suggest that ∆3678 SARS-CoV-2 may serve as a live-attenuated vaccine candidate and a research tool for potential biosafety level-2 use.

Multisite biologic tissue SARS-CoV-2 PCR testing in kidney transplantation from a COVID-positive donor.

With a high community transmission rate, SARS-CoV-2 has profoundly exacerbated the shortage of organs. Although the risk of donor-recipient transmission of SARS-CoV-2 is anecdotally low, an organ-specific infection analysis of procured organs from SARS-CoV-2 positive donors has yet to be established. Using a combination of clinically available and research-only polymerase chain reaction methods, organ preservation fluid and renal parenchymal tissues were tested for SARS-CoV-2 from the kidney of a SARS-CoV-2-positive donor prior to transplantation. The recipient has remained SARS-CoV-2 negative and clinically well, with excellent graft function 120 days post-transplantation.

Development of an efficient reproducible cell-cell transmission assay for rapid quantification of SARS-CoV-2 spike interaction with hACE2.

Efficient quantitative assays for measurement of viral replication and infectivity are indispensable for future endeavors to develop prophylactic or therapeutic antiviral drugs or vaccines against SARS-CoV-2. We developed a SARS-CoV-2 cell-cell transmission assay that provides a rapid and quantitative readout to assess SARS-CoV-2 spike hACE2 interaction in the absence of pseudotyped particles or live virus. We established two well-behaved stable cell lines, which demonstrated a remarkable correlation with standard cell-free viral pseudotyping for inhibition by convalescent sera, small-molecule drugs, and murine anti-spike monoclonal antibodies. The assay is rapid, reliable, and highly reproducible, without a requirement for any specialized research reagents or laboratory equipment and should be easy to adapt for use in most investigative and clinical settings. It can be effectively used or modified for high-throughput screening for compounds and biologics that interfere with virus-cell binding and entry to complement other neutralization assays currently in use.

Omicron-specific mRNA vaccination alone and as a heterologous booster against SARS-CoV-2.

The Omicron variant of SARS-CoV-2 recently swept the globe and showed high level of immune evasion. Here, we generate an Omicron-specific lipid nanoparticle (LNP) mRNA vaccine candidate, and test its activity in animals, both alone and as a heterologous booster to WT mRNA vaccine. Our Omicron-specific LNP-mRNA vaccine elicits strong antibody response in vaccination-naïve mice. Mice that received two-dose WT LNP-mRNA show a > 40-fold reduction in neutralization potency against Omicron than WT two weeks post boost, which further reduce to background level after 3 months. The WT or Omicron LNP-mRNA booster increases the waning antibody response of WT LNP-mRNA vaccinated mice against Omicron by 40 fold at two weeks post injection. Interestingly, the heterologous Omicron booster elicits neutralizing titers 10-20 fold higher than the homologous WT booster against Omicron variant, with comparable titers against Delta variant. All three types of vaccination, including Omicron alone, WT booster and Omicron booster, elicit broad binding antibody responses against SARS-CoV-2 WA-1, Beta, Delta variants and SARS-CoV. These data provide direct assessments of an Omicron-specific mRNA vaccination in vivo, both alone and as a heterologous booster to WT mRNA vaccine.

Highly sensitive and selective surface plasmon resonance biosensor for the detection of SARS-CoV-2 spike S1 protein.

The reality that the coronavirus disease 2019 (COVID-19) is still raging around the world and making a comeback with a strong presence has highlighted the need for rapid and sensitive quantitative detection methods of viral RNA, antibody and antigen for widespread tracking and screening applications. Surface plasmon resonance (SPR) detection technology has achieved rapid development and become a standard measurement method in the fields of biosensing, biomedicine, biochemistry and biopharmaceuticals due to its advantages of high sensitivity, fast response and no need for labelling. Here, we report a sandwiched structure-based SPR biosensor for detecting a specific viral antigen, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike S1 protein. The sensor combines a Ti3C2-MXene nanosheet modified sensing platform and polydopamine (PDA)-Ag nanoparticle (AgNP)/anti-SARS-CoV-2 spike S1 protein nanoconjugate signal enhancers, exhibiting a wide linear range of 0.0001 to 1000 ng mL-1 with a low detection limit of 12 fg mL-1 (S/N = 3). In the analysis of artificial saliva and human serum samples, the proposed SPR biosensor exhibits good reproducibility and high specificity, which indicates its potential for application in complex bodily fluids. The exploitation of the MXene-based SPR biochip for recognizing the SARS-CoV-2 antigen provides an accessible and rapid way for COVID-19 diagnosis, and promotes the application of 2D nanomaterial-based sensing chips in clinical diagnosis and disease screening. Significantly, the proposed method possesses general applicability that can be reprogrammed to detect any protein antigen if a corresponding specific nanobody is available.

Cross-neutralization of Omicron BA.1 against BA.2 and BA.3 SARS-CoV-2.

The Omicron SARS-CoV-2 has several distinct sublineages, among which sublineage BA.1 is responsible for the initial Omicron surge and is now being replaced by BA.2 worldwide, whereas BA.3 is currently at a low frequency. The ongoing BA.1-to-BA.2 replacement underscores the importance to understand the cross-neutralization among the three Omicron sublineages. Here we test the neutralization of BA.1-infected human sera against BA.2, BA.3, and USA/WA1-2020 (a strain isolated in late January 2020). The BA.1-infected sera neutralize BA.1, BA.2, BA.3, and USA/WA1-2020 SARS-CoV-2s with geometric mean titers (GMTs) of 445, 107, 102, and 16, respectively. Thus, the neutralizing GMTs against heterologous BA.2, BA.3, and USA/WA1-2020 are 4.2-, 4.4-, and 28.4-fold lower than the GMT against homologous BA.1, respectively. These findings have implications in COVID-19 vaccine strategy.