Enhanced surface accessibility of SARS-CoV-2 Omicron spike protein due to an altered glycosylation profile (preprint)

SARS-CoV-2 spike (S) proteins undergo extensive glycosylation, aiding proper folding, enhancing stability, and evading host immune surveillance. In this study, we used mass spectrometric analysis to elucidate the N-glycosylation characteristics and disulfide bonding of recombinant spike proteins derived from the SARS-CoV-2 Omicron variant (B.1.1.529) in comparison with the D614G spike variant. Furthermore, we conducted microsecond-long molecular dynamics simulations on spike proteins to resolve how the different N-glycans impact spike conformational sampling in the two variants. Our findings reveal that the Omicron spike protein maintains an overall resemblance to the D614G spike variant in terms of site-specific glycan processing and disulfide bond formation. Nonetheless, alterations in glycans were observed at certain N-glycosylation sites. These changes, in synergy with mutations within the Omicron spike protein, result in increased surface accessibility of the macromolecule, including ectodomain, receptor-binding domain, and N-terminal domain. These insights contribute to our understanding of the interplay between structure and function, thereby advancing effective vaccination and therapeutic strategies. TeaserThrough mass spectrometry and molecular dynamics simulations, SARS-CoV-2 Omicron spike is found to be less covered by glycans when compared to the D614G spike variant.

Bivalent mRNA vaccine improves antibody-mediated neutralization of many SARS-CoV-2 Omicron lineage variants (preprint)

The early Omicron lineage variants evolved and gave rise to diverging lineages that fueled the COVID-19 pandemic in 2022. Bivalent mRNA vaccines, designed to broaden protection against circulating and future variants, were authorized by the U.S. Food and Drug Administration (FDA) in August 2022 and recommended by the U.S. Centers for Disease Control and Prevention (CDC) in September 2022. The impact of bivalent vaccination on eliciting neutralizing antibodies against homologous BA.4/BA.5 viruses as well as emerging heterologous viruses needs to be analyzed. In this study, we analyze the neutralizing activity of sera collected after a third dose of vaccination (2-6 weeks post monovalent booster) or a fourth dose of vaccination (2-7 weeks post bivalent booster) against 10 predominant/recent Omicron lineage viruses including BA.1, BA.2, BA.5, BA.2.75, BA.2.75.2, BN.1, BQ.1, BQ.1.1, XBB, and XBB.1. The bivalent booster vaccination enhanced neutralizing antibody titers against all Omicron lineage viruses tested, including a 10-fold increase in neutralization of BQ.1 and BQ.1.1 viruses that predominated in the U.S. during the last two months of 2022. Overall, the data indicate the bivalent vaccine booster strengthens protection against Omicron lineage variants that evolved from BA.5 and BA.2 progenitors.

Running ahead of evolution - AI based simulation for predicting future high-risk SARS-CoV-2 variants (preprint)

The never-ending emergence of SARS-CoV-2 variations of concern (VOCs) has challenged the whole world for pandemic control. In order to develop effective drugs and vaccines, one needs to efficiently simulate SARS- CoV-2 spike receptor binding domain (RBD) mutations and identify high-risk variants. We pretrain a large pro- tein language model on approximately 408 million pro- tein sequences and construct a high-throughput screen- ing for the prediction of binding affinity and antibody escape. As the first work on SARS-CoV-2 RBD mu- tation simulation, we successfully identify mutations in the RBD regions of 5 VOCs and can screen millions of potential variants in seconds. Our workflow scales to 4096 NPUs with 96.5% scalability and 493.9X speedup in mixed precision computing, while achieving a peak performance of 366.8 PFLOPS (reaching 34.9% theo- retical peak) on Pengcheng Cloudbrain-II. Our method paves the way for simulating coronavirus evolution in or- der to prepare for a future pandemic that will inevitably take place.

Cross-neutralization and viral fitness of SARS-CoV-2 Omicron sublineages (preprint)

The rapid evolution of SARS-CoV-2 Omicron sublineages mandates a better un-derstanding of viral replication and cross-neutralization among these sublineages. Here we used K18-hACE2 mice and primary human airway cultures to examine the viral fit-ness and antigenic relationship among Omicron sublineages. In both K18-hACE2 mice and human airway cultures, Omicron sublineages exhibited a replication order of BA.5 [≥] BA.2 [≥] BA.2.12.1 > BA.1; no difference in body weight loss was observed among differ-ent sublineage-infected mice. The BA.1-, BA.2-, BA.2.12.1-, and BA.5-infected mice de-veloped distinguisable cross-neutralizations against Omicron sublineages, but exhibited little neutralization against the index virus (i.e., USA-WA1/2020) or the Delta variant. Surprisingly, the BA.5-infected mice developed higher neutralization activity against heterologous BA.2 and BA.2.12.1 than that against homologous BA.5; serum neutralizing titers did not always correlate with viral replication levels in infected animals. Our results reveal distinct antigenic cartography of Omicron sublineages and support the bivalent vaccine approach.

Adversarial Learning-based Stance Classifier for COVID-19-related Health Policies (preprint)

The ongoing COVID-19 pandemic has caused immeasurable losses for people worldwide. To contain the spread of the virus and further alleviate the crisis, various health policies (e.g., stay-at-home orders) have been issued which spark heated discussions as users turn to share their attitudes on social media. In this paper, we consider a more realistic scenario on stance detection (i.e., cross-target and zero-shot settings) for the pandemic and propose an adversarial learning-based stance classifier to automatically identify the public's attitudes toward COVID-19-related health policies. Specifically, we adopt adversarial learning that allows the model to train on a large amount of labeled data and capture transferable knowledge from source topics, so as to enable generalize to the emerging health policies with sparse labeled data. To further enhance the model's deeper understanding, we incorporate policy descriptions as external knowledge into the model. Meanwhile, a GeoEncoder is designed which encourages the model to capture unobserved background factors specified by each region and then represent them as non-text information. We evaluate the performance of a broad range of baselines on the stance detection task for COVID-19-related health policies, and experimental results show that our proposed method achieves state-of-the-art performance in both cross-target and zero-shot settings.

EpiGNN: Exploring Spatial Transmission with Graph Neural Network for Regional Epidemic Forecasting (preprint)

Epidemic forecasting is the key to effective control of epidemic transmission and helps the world mitigate the crisis that threatens public health. To better understand the transmission and evolution of epidemics, we propose EpiGNN, a graph neural network-based model for epidemic forecasting. Specifically, we design a transmission risk encoding module to characterize local and global spatial effects of regions in epidemic processes and incorporate them into the model. Meanwhile, we develop a Region-Aware Graph Learner (RAGL) that takes transmission risk, geographical dependencies, and temporal information into account to better explore spatial-temporal dependencies and makes regions aware of related regions' epidemic situations. The RAGL can also combine with external resources, such as human mobility, to further improve prediction performance. Comprehensive experiments on five real-world epidemic-related datasets (including influenza and COVID-19) demonstrate the effectiveness of our proposed method and show that EpiGNN outperforms state-of-the-art baselines by 9.48% in RMSE.

Trajectories of chemosensory and cognitive functions up to 1.5 years after acute COVID-19 (preprint)

There is an increasing recognition of neurological manifestations from SARS-CoV-2 infection. Quantifications of such manifestations and their long-term dynamics in the general infected population are of essence in understanding the health and socioeconomic burden of neurological complications of COVID-19. Through rigorous empirical testing of over 800 volunteers, we present here repeated cross-sectional and longitudinal data that depict the trajectories of chemosensory functions, cognitive performances and depressive symptoms up to 1.5 years after acute COVID-19 in discharged patients with respect to non-infected controls. Overall, deficits in smell, taste and chemesthesis slowly resolved within about a year of discharge. Concerningly, cognitive impairments –– independent of elevated depressive symptoms and evident even in those with nonsevere disease –– showed no sign of improvement over time. In people over 50 years, COVID-19 was associated with a substantially increased risk for mild cognitive impairment. Our findings urge for cognitive and emotional interventions targeting COVID-19 convalescents.

Immunogenicity and Safety Following a Homologous Booster Dose of a SARS-CoV-2 recombinant spike protein vaccine (NVX-CoV2373): A Phase 2 Randomized Placebo-Controlled Trial (preprint)

Background Emerging SARS-CoV-2 variants and evidence of waning vaccine efficacy present significant obstacles toward controlling the COVID-19 pandemic. Booster doses of SARS-CoV-2 vaccines may address these concerns by both amplifying and broadening the immune responses seen with initial vaccination regimens. Methods In a phase 2 study, a single booster dose of a SARS-CoV-2 recombinant spike protein vaccine with Matrix-M adjuvant (NVX-CoV2373) was administered to healthy adult participants 18 to 84 years of age approximately 6 months following their primary two-dose vaccination series. Safety and immunogenicity parameters were assessed, including assays for IgG, MN50, and hACE2 receptor binding inhibition against the ancestral SARS-CoV-2 strain and select variants (B.1.351 [Beta], B.1.1.7 [Alpha], B.1.617.2 [Delta], and B.1.1.529 [Omicron]). This trial is registered with ClinicalTrials.gov, NCT04368988. Findings An incremental increase in the incidence of solicited local and systemic reactogenicity events was observed with subsequent vaccinations. Following the booster, incidence rates of local and systemic reactions were 82.5% (13.4% [≥] Grade 3) and 76.5% (15.3% [≥] Grade 3), respectively, compared to 70.0% (5.2% [≥] Grade 3) and 52.8% (5.6% [≥] Grade 3), respectively, following the primary vaccination series. Events were primarily mild or moderate in severity and transient in nature, with a median duration of 1.0 to 2.5 days. Immune responses seen 14 days following the primary vaccination series were compared with those observed 28 days following the booster (Day 35 and Day 217, respectively). For the ancestral SARS-CoV-2 strain, serum IgG geometric mean titers (GMTs) increased ~4.7-fold from 43,905 ELISA units (EU) at day 35 to 204,367 EU at Day 217. Neutralization (MN50) assay GMTs showed a similar increase of ~4.1-fold from 1,470 at day 35 to 6,023 at Day 217. A functional hACE2 receptor binding inhibition assay analyzing activity against ancestral and variant strains of SARS-CoV-2 at Day 189 vs Day 217 found 54.4-fold (Ancestral), 21.9 fold (Alpha), 24.5-fold (Beta), 24.4-fold (Delta), and 20.1-fold (Omicron) increases in titers. An anti-rS IgG activity assay comparing the same time points across the same SARS-CoV-2 strains found titers improved 61.2-fold, 85.9-fold, 65.0-fold, 92.5 fold, and 73.5 fold, respectively. Interpretation Administration of a booster dose of NVX-CoV2373 approximately 6 months following the primary vaccination series resulted in an incremental increase in reactogenicity along with enhanced immune responses. For both the prototype strain and all variants evaluated, immune responses following the booster were notably higher than those associated with high levels of efficacy in phase 3 studies of the vaccine.

Surveillance and correlation of SARS-CoV-2 viral RNA, antigen, virus isolation, and self-reported symptoms in a longitudinal study with daily sampling (preprint)

The novel coronavirus pandemic incited unprecedented demand for assays that detect viral nucleic acids, viral proteins, and corresponding antibodies. The 320 molecular diagnostics in receipt of FDA emergency use authorization mainly focus on viral detection; however, no currently approved test can be used to infer infectiousness, i.e., the presence of replicable virus. As the number of tests conducted increased, persistent SARS-CoV-2 RNA positivity by RT-PCR in some individuals led to concerns over quarantine guidelines. To this end, we attempted to design an assay that reduces the frequency of positive test results from individuals who do not shed culturable virus. We describe multiplex quantitative RT-PCR (qRT-PCR) assays that detect genomic RNA (gRNA) and subgenomic RNA (sgRNA) species of SARS-CoV-2, including spike (S), nucleocapsid (N), membrane (M), envelope (E), and ORF8. The absolute copy number of each RNA target was determined in longitudinal specimens from a household transmission study. Calculated viral RNA levels over the 14-day follow up period were compared with antigen testing and self-reported symptoms to characterize the clinical and molecular dynamics of infection and infer predictive values of these qRT-PCR assays relative to culture isolation. When detection of sgS RNA was added to the CDC 2019-Novel Coronavirus Real-Time RT-PCR Diagnostic Panel, we found a qRT-PCR positive result was 98% predictive of a positive culture (negative predictive value was 94%). Our findings suggest sgRNA presence correlates with active infection, may help identify individuals shedding culturable virus, and that similar multiplex assays can be adapted to current and future variants.

Differential neutralization and inhibition of SARS-CoV-2 variants by antibodies elicited by COVID-19 mRNA vaccines (preprint)

The divergence of SARS-CoV-2 into variants of concern/interest (VOC/VOI) necessitated analysis of their impact on vaccines. Escape from vaccine-induced antibodies by SARS-CoV-2 VOC/VOIs was analyzed to ascertain and rank their risk. The variants showed differential reductions in neutralization and replication titers by the post-vaccination sera with Beta variant showing the most neutralization escape that was mechanistically driven by mutations in both the N-terminal domain and receptor-binding domain of the spike.

N-glycosylation profiles of the SARS-CoV-2 spike D614G mutant and its ancestral protein characterized by advanced mass spectrometry (preprint)

N-glycosylation plays an important role in the structure and function of membrane and secreted proteins. The spike protein on the surface of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes COVID-19, is heavily glycosylated and the major target for developing vaccines, therapeutic drugs and diagnostic tests. The first major SARS-CoV-2 variant carries a D614G substitution in the spike (S-D614G) that has been associated with altered conformation, enhanced ACE2 binding, and increased infectivity and transmission. In this report, we used mass spectrometry techniques to characterize and compare the N-glycosylation of the wild type (S-614D) or variant (S-614G) SARS-CoV-2 spike glycoproteins prepared under identical conditions. The data showed that half of the N-glycosylation sequons changed their distribution of glycans in the S-614G variant. The S-614G variant showed a decrease in the relative abundance of complex-type glycans (up to 45%) and an increase in oligomannose glycans (up to 33%) on all altered sequons. These changes led to a reduction in the overall complexity of the total N-glycosylation profile. All the glycosylation sites with altered patterns were in the spike head while the glycosylation of three sites in the stalk remained unchanged between S-614G and S-614D proteins.

Lessons learned and lessons missed: Impact of the Covid-19 pandemic on all-cause mortality in 40 industrialised countries prior to mass vaccination (preprint)

Industrialised countries have varied in their early response to the Covid-19 pandemic, and how they have adapted to new situations and knowledge since the pandemic began. These variations in preparedness and policy may lead to different death tolls from Covid-19 as well as from other diseases. We applied an ensemble of 16 Bayesian probabilistic models to vital statistics data to estimate the impacts of the pandemic on weekly all-cause mortality for 40 industrialised countries from mid-February 2020 through mid-February 2021, before a large segment of the population was vaccinated in any of these countries. Taken over the entire year, an estimated 1,401,900 (95% credible interval 1,259,700-1,572,500) more people died in these 40 countries than would have been expected had the pandemic not taken place. This is equivalent to 140 (126-157) additional deaths per 100,000 people and a 15% (13-17) increase in deaths over this period in all of these countries combined. In Iceland, Australia and New Zealand, mortality was lower over this period than what would be expected if the pandemic had not occurred, while South Korea and Norway experienced no detectable change in mortality. In contrast, the populations of the USA, Czechia, Slovakia and Poland experienced at least 20% higher mortality. There was substantial heterogeneity across countries in the dynamics of excess mortality. The first wave of the pandemic, from mid-February to the end of May 2020, accounted for over half of excess deaths in Scotland, Spain, England and Wales, Canada, Sweden, Belgium and Netherlands. At the other extreme, the period between mid-September 2020 and mid-February 2021 accounted for over 90% of excess deaths in Bulgaria, Croatia, Czechia, Hungary, Latvia, Montenegro, Poland, Slovakia and Slovenia. Until the great majority of national and global populations have vaccine-acquired immunity, minimising the death toll of the pandemic from Covid-19 and other diseases will remain dependent on actions to delay and contain infections and continue routine health and social care.

A Cloud-Edge-Terminal Collaborative System for Temperature Measurement in COVID-19 Prevention (preprint)

To prevent the spread of coronavirus disease 2019 (COVID-19), preliminary temperature measurement and mask detection in public areas are conducted. However, the existing temperature measurement methods face the problems of safety and deployment. In this paper, to realize safe and accurate temperature measurement even when a person's face is partially obscured, we propose a cloud-edge-terminal collaborative system with a lightweight infrared temperature measurement model. A binocular camera with an RGB lens and a thermal lens is utilized to simultaneously capture image pairs. Then, a mobile detection model based on a multi-task cascaded convolutional network (MTCNN) is proposed to realize face alignment and mask detection on the RGB images. For accurate temperature measurement, we transform the facial landmarks on the RGB images to the thermal images by an affine transformation and select a more accurate temperature measurement area on the forehead. The collected information is uploaded to the cloud in real time for COVID-19 prevention. Experiments show that the detection model is only 6.1M and the average detection speed is 257ms. At a distance of 1m, the error of indoor temperature measurement is about 3%. That is, the proposed system can realize real-time temperature measurement in public areas.

Severe 2019 novel coronavirus pneumonia may cause lung bullae and bronchiectasis: A case report and concise literature review

Most of the critically ill novel coronavirus 2019 pneumonia (NCP) patients progress promptly, and soon match the ARDS diagnostic criteria. When mechanical ventilation and prone position cannot reverse the fatal hypoxia—extra-corporeal-membrane-oxygenation (ECMO) will be applied as a salvage treatment if available. Here, we report a novel coronavirus 2019 pneumonia (NCP) patient, a male, 67 years old, who was treated with ECMO for 30 days. In the midst, bronchoscopy was utilized to comprehend the airway lesions and clear secretions. And computed tomography (CT) scans were performed before and after the treatment of ECMO. In the recovering phase of his disease, the patient experienced multiple times pneumothorax on both sides. Some newly developed lung bullae in the subpleural area and modest bronchiectasis were found by the CT scan. The newly developed lung bullae was the probable cause of pneumothorax. Notably, in the whole process of his illness, the serum IL-6 only had a slight elevation in the early period, there is no typical cytokine storm as that was seen in non-COVID-19 ARDS. After 3-months meticulous treatment, the patient made a full recovery and now is discharged from our hospital. Though COVID-19 may not cause typical cytokine storm, the inflammation in lung may inflict severe damage to lung. Severe NCP may cause lung bullae and bronchiectasis, making the patients hard to be weaned from mechanical ventilation or ECMO. [ABSTRACT FROM AUTHOR] Copyright of European Journal of Inflammation (Sage Publications, Ltd.) is the property of Sage Publications, Ltd. and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Immunogenicity and In vivo protection of a variant nanoparticle vaccine that confers broad protection against emerging SARS-CoV-2 variants (preprint)

The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) continues to spread globally. As SARS-CoV-2 has transmitted from person to person, variant viruses have emerged with elevated transmission rates and higher risk of infection for vaccinees. We present data showing that a recombinant prefusion-stabilized Spike (rS) protein based on the B.1.351 sequence (rS-B.1.351) was highly immunogenic in mice and produced neutralizing antibodies against SARS-CoV-2/WA1, B.1.1.7, and B.1.351. Mice vaccinated with our prototype vaccine NVX-CoV2373 (rS-WU1) or rS-B.1.351 alone, in combination, or as a heterologous prime boost, were protected when challenged with live SARS-CoV-2/B.1.1.7 or SARS-CoV-2/B.1.351. Virus titer was reduced to undetectable levels in the lungs post-challenge in all vaccinated mice, and Th1-skewed cellular responses were observed. A strong anamnestic response was demonstrated in baboons boosted with rS-B.1.351 approximately one year after immunization with NVX-CoV2373 (rS-WU1). An rS-B.1.351 vaccine alone or in combination with prototype rS-WU1 induced protective antibody- and cell-mediated responses that were protective against challenge with SARS-CoV-2 variant viruses.

Combination Respiratory Vaccine Containing Recombinant SARS-CoV-2 Spike and Quadrivalent Seasonal Influenza Hemagglutinin Nanoparticles with Matrix-M Adjuvant (preprint)

The 2019 outbreak of a severe respiratory disease caused by an emerging coronavirus, SARS-CoV-2, has spread globally with high morbidity and mortality. Co-circulating seasonal influenza has greatly diminished recently, but expected to return with novel strains emerging, thus requiring annual strain adjustments. We have developed a recombinant hemagglutinin (HA) quadrivalent nanoparticle influenza vaccine (qNIV) produced using an established recombinant insect cell expression system to produce nanoparticles. Influenza qNIV adjuvanted with Matrix-M was well-tolerated and induced robust antibody and cellular responses, notably against both homologous and drifted A/H3N2 viruses in Phase 1, 2, and 3 trials. We also developed a full-length SARS-CoV-2 spike protein vaccine which is stable in the prefusion conformation (NVX-CoV2373) using the same platform technology. In phase 3 clinical trials, NVX-CoV2373 is highly immunogenic and protective against the prototype strain and B.1.1.7 variant. Here we describe the immunogenicity and efficacy of a combination quadrivalent seasonal flu and COVID-19 vaccine (qNIV/CoV2373) in ferret and hamster models. The combination qNIV/CoV2373 vaccine produces high titer influenza hemagglutination inhibiting (HAI) and neutralizing antibodies against influenza A and B strains. The combination vaccine also elicited antibodies that block SARS-CoV-2 spike protein binding to the human angiotensin converting enzyme-2 (hACE2) receptor. Significantly, hamsters immunized with qNIV/CoV2373 vaccine and challenged with SARS-CoV-2 were protected against weight loss and were free of replicating SARS-CoV-2 in the upper and lower respiratory tract with no evidence of viral pneumonia. This study supports evaluation of qNIV/CoV2373 combination vaccine as a preventive measure for seasonal influenza and CoVID-19. Highlights Combination qNIV/CoV2373 vaccine induced protective hemagglutination inhibition (HAI) responses to seasonal influenza A and B unchanged when formulated with recombinant spike. Combination qNIV/CoV2373 vaccine maintained clinical and virologic protection against experimental challenge with SARS-CoV-2. Combination qNIV/CoV2373 vaccine showed no clinical or histological sign of enhanced disease following experimental challenge with SARS-CoV-2. Combination qNIV/CoV2373 vaccine induced antibodies against SARS-CoV-2 neutralizing epitopes common between US-WA and B.1.352 variant.

Collaboration between the Fab and Fc Contribute to Maximal Protection Against SARS-CoV-2 Following NVX-CoV2373 Subunit Vaccine with Matrix-M™ Vaccination (preprint)

Recently approved vaccines have shown remarkable protection in limiting SARS-CoV-2 associated disease. However, immunologic mechanism(s) of protection, and how boosting alters immunity to wildtype and newly emerging strains, remains incompletely understood. Here we profiled the humoral immune response in a cohort of non-human primates immunized with a recombinant SARS-CoV-2 spike (S) glycoprotein (NVX-CoV2373) at two dose levels, administered as a one or two-dose regimen with a saponin-based adjuvant Matrix-M™. While antigen dose had minimal effects, boosting significantly altered the humoral response, driving unique vaccine-induced antibody fingerprints. Differences in antibody effector functions and neutralization were associated with protection in the upper and lower respiratory tract, pointing to compartment-specific determinants of protective immunity against infection. Moreover, NVX-CoV2373 elicited antibodies targeting emerging SARS-CoV-2 variants. Collectively, the data presented here suggest that a single dose may prevent disease, but that two doses may be essential to block further transmission of SARS-CoV-2 and emerging variants.Funding: This work was funded by Operation Warp Speed. We thank Colin Mann and Kathryn Hastie for production of Spike antigens. We thank Nancy Zimmerman, Mark and Lisa Schwartz, an anonymous donor (financial support), Terry and Susan Ragon, and the SAMANA Kay MGH Research Scholars award for their support. We acknowledge support from the Ragon Institute of MGH, MIT and Harvard, the Massachusetts Consortium on Pathogen Readiness (Mass CPR), the NIH (3R37AI080289-11S1, R01AI146785, U19AI42790-01, U19AI135995-02, U19AI42790-01, 1U01CA260476 – 01, CIVIC75N93019C00052), National Science Foundation Graduate Research Fellowship Grant No. #1745302, the Gates foundation Global Health Vaccine Accelerator Platform funding (OPP1146996 and INV-001650), and the Musk Foundation.Conflict of Interest: NP, MGX, JHT, BZ, SM, AMG, MJM, ADP, GG, GS, and LE are current or past employees of Novavax, Inc. and have stock options in the company. GA is the founder of Serom Yx Systems, Inc. AZ is a current employee of Moderna, Inc. but conducted this work before employment.Any opinion, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation. YG, RC, MJG, CA, KMP, CL, DY, KB, MEM, JL, DM, CM, SS, FA, FK, EOS, DL, and MBF declare no competing interest.Ethical Approval: The work was conducted in accordance with a protocol approved by Texas Biomed’s Institutional Animal Care and Use Committee. All subjects signed informed consent and safety oversight was monitored by a data monitoring board.

Cause Analysis of PM2.5 pollution during the COVID-19 lockdown in Nanning, China (preprint)

To analyze the cause of atmospheric PM2.5 pollution occurred during the COVID-19 lockdown in Nanning of Guangxi, China, Single Particulate Aerosol Mass Spectrometer, Aethalometer, Particulate Lidar, coupled with the monitoring of near-surface gaseous pollutants, meteorological conditions, remote fire spots sensing by satellite and Backward Trajectory Models were conducted during 18–24, Feb 2020. Three haze stages of pre-pollution period (PPP), pollution accumulation period (PAP) and pollution dissipation period (PDP) were identified. The dominant source of PM2.5 in PPP was biomass burning (BB) (40.4%), followed by secondary inorganics (28.1%) and motor vehicle exhaust (11.7%). The PAP was characterized by a large abundance of secondary inorganics, which contributed for 56.1% of the total PM2.5 concentration, followed by BB (17.4%). The absorption Ångström exponent (2.2) in PPP was higher than those of the other two periods. The analysis of fire spots monitored by remote satellite sensing indicated that open BB in regions around Nanning city could be one of the main facotrs matters. The planetary boundary layer-relative humidity-secondary particles matter-particulate matter positive feedback mechanism was employed to elucidate the atompheric process in this study. This study highlights the importance of understanding the role of BB and meteorology in air pollution formation to call for policy for emission control strategies.

Collaboration between the Fab and Fc contribute to maximal protection against SARS-CoV-2 in nonhuman primates following NVX-CoV2373 subunit vaccine with Matrix-M™ vaccination (preprint)

Recently approved vaccines have already shown remarkable protection in limiting SARS-CoV-2 associated disease. However, immunologic mechanism(s) of protection, as well as how boosting alters immunity to wildtype and newly emerging strains, remain incompletely understood. Here we deeply profiled the humoral immune response in a cohort of non-human primates immunized with a stable recombinant full-length SARS-CoV-2 spike (S) glycoprotein (NVX-CoV2373) at two dose levels, administered as a single or two-dose regimen with a saponin-based adjuvant Matrix-M. While antigen dose had some effect on Fc-effector profiles, both antigen dose and boosting significantly altered overall titers, neutralization and Fc-effector profiles, driving unique vaccine-induced antibody fingerprints. Combined differences in antibody effector functions and neutralization were strongly associated with distinct levels of protection in the upper and lower respiratory tract, pointing to the presence of combined, but distinct, compartment-specific neutralization and Fc-mechanisms as key determinants of protective immunity against infection. Moreover, NVX-CoV2373 elicited antibodies functionally target emerging SARS-CoV-2 variants, collectively pointing to the critical collaborative role for Fab and Fc in driving maximal protection against SARS-CoV-2. Collectively, the data presented here suggest that a single dose may prevent disease, but that two doses may be essential to block further transmission of SARS-CoV-2 and emerging variants.

Collaboration between the Fab and Fc contribute to maximal protection against SARS-CoV-2 following NVX-CoV2373 subunit vaccine with Matrix-M™ vaccination (preprint)

Recently approved vaccines have already shown remarkable protection in limiting SARS-CoV-2 associated disease. However, immunologic mechanism(s) of protection, as well as how boosting alters immunity to wildtype and newly emerging strains, remain incompletely understood. Here we deeply profiled the humoral immune response in a cohort of non-human primates immunized with a stable recombinant full-length SARS-CoV-2 spike (S) glycoprotein (NVX-CoV2373) at two dose levels, administered as a single or two-dose regimen with a saponin-based adjuvant Matrix-M™. While antigen dose had some effect on Fc-effector profiles, both antigen dose and boosting significantly altered overall titers, neutralization and Fc-effector profiles, driving unique vaccine-induced antibody fingerprints. Combined differences in antibody effector functions and neutralization were strongly associated with distinct levels of protection in the upper and lower respiratory tract, pointing to the presence of combined, but distinct, compartment-specific neutralization and Fc-mechanisms as key determinants of protective immunity against infection. Moreover, NVX-CoV2373 elicited antibodies functionally target emerging SARS-CoV-2 variants, collectively pointing to the critical collaborative role for Fab and Fc in driving maximal protection against SARS-CoV-2. Collectively, the data presented here suggest that a single dose may prevent disease, but that two doses may be essential to block further transmission of SARS-CoV-2 and emerging variants.