Surveillance of anti-SARS-CoV-2 antibodies in plasma pools and in immunoglobulin medicinal products manufactured since 2020 has shown high neutralizing activity against SARS-CoV-2 and current variants

Background: Patients with primary and secondary immunodeficiencies have shown an impaired humoral immune response to COVID-19 vaccination. It is therefore of paramount importance to investigate anti-SARS-CoV-2 antibody levels in plasma pools and in immunoglobulin (IgG) products used to treat these patients. AIM: To assess the evolution of anti-SARS-CoV-2 antibodies (S protein) in plasma pools and IgG products and its neutralizing activity to original-type virus (Wuhan) and the variants of concern (VOC), including Omicron. Method(s): Healthy donors plasma pools collected in the US and Europe, and the subsequent intravenous (Flebogamma DIFand Gamunex-C, Grifols) and subcutaneous (Xembify, Grifols) IgG manufactured batches were followed from March 2020. Anti-SARS-CoV-2 S protein IgG titers were determined in plasma pools and in IgG batches by ELISA. Neutralization assays analyzed the capacity of IgG products to neutralize original-type virus and VOC (Alpha, Beta, Delta, Omicron BA.1 and BA.5), using pseudo viruses expressing S protein. Results were expressed as the dilution producing 50% neutralization (ID50). Result(s): In plasma pools, anti-SARS-CoV-2 S antibodies continuously increased throughout the study period regardless of the geographic origin. In the US, the first positive plasma pools were collected at the end of 2020. Since July 2021, an exponential increase over 30-fold of anti-SARS-CoV-2 S antibodies was reported. This trend continued increasing until the end of study period. Similarly, IgG products showed a similar evolution of anti-SARS-CoV-2 S antibodies. As expected, IgG batches released at the end of 2020 presented low SARS-CoV-2 neutralization activity. However, IgG products manufactured since August 2021 showed high neutralization activity against original-type virus and the rest of VOC. Regarding Omicron BA.5, a 5 to 10-fold increase was observed over time. Conclusion(s): This study reported the onset of elevated anti-SARS-CoV-2 antibody titers in plasma pools and IgG products since mid-2021, reflecting the evolution of the pandemic and vaccine campaigns. Intravenous and subcutaneous IgG products efficiently neutralized the current circulating VOC, Omicron BA.5. Further research is warranted to assess whether a clinical protective titer against SARS-CoV-2 and passive immunization is achieved in patients with immunodeficiencies treated with IgG products.Copyright © 2023 Elsevier Inc.

Design of a cost-effective diagnosis tool for SARSCov-2 variant detection through a next generation sequencing (NGS) based strategy

Background/Objectives: Current pandemic situation, together with the continuous emergence of new SARS-CoV-2 variants reveal the need to develop a more versatile tool than PCR-based methods that allows both high throughput COVID-19 diagnostic and specific variant detection at reduced cost and fast turnaround times. Thus, with the aim of overcoming current test limitations and providing a strategy with these characteristics arises our novel next generation sequencing based approach. Method(s): The developed strategy works with RNA samples obtained from nasopharyngeal swabs. RNA samples are processed with our custom laboratory protocol and can be sequenced with any Illumina platform to generate results within a 24h timeframe. A tailored bioinformatic pipeline analyzes the data and generates a clinical-level report. Result(s): Clinical validation results have shown that the designed solution, sensitively and specifically identifies negative and positive samples that display a broad range in viral loads and readily identifies the following major SARS-CoV-2 variants of concern (VoC): Alpha, Beta, Gamma, Delta, Lambda and Omicron (BA.1 and BA.2). Conclusion(s): The versatility of our solution allows the capability of identifying the presence of other common respiratory viruses as well as identifying patients at risk through the identification of susceptibility human variants in the host. This, together with the possibility of easily adding new VoC as they emerge, will make VoC monitoring in entire populations feasible, providing a new perspective on the application of NGS methods in the field of clinical microbiology.

A tale of two waves: Delineating diverse genomic and transmission landscapes driving the COVID-19 pandemic in Pune, India.

BACKGROUND: Modern response to pandemics, critical for effective public health measures, is shaped by the availability and integration of diverse epidemiological outbreak data. Tracking variants of concern (VOC) is integral to understanding the evolution of SARS-CoV-2 in space and time, both at the local level and global context. This potentially generates actionable information when integrated with epidemiological outbreak data. METHODS: A city-wide network of researchers, clinicians, and pathology diagnostic laboratories was formed for genome surveillance of COVID-19 in Pune, India. The genomic landscapes of 10,496 sequenced samples of SARS-CoV-2 driving peaks of infection in Pune between December-2020 to March-2022, were determined. As a modern response to the pandemic, a "band of five" outbreak data analytics approach was used. This integrated the genomic data (Band 1) of the virus through molecular phylogenetics with key outbreak data including sample collection dates and case numbers (Band 2), demographics like age and gender (Band 3-4), and geospatial mapping (Band 5). RESULTS: The transmission dynamics of VOCs in 10,496 sequenced samples identified B.1.617.2 (Delta) and BA(x) (Omicron formerly known as B.1.1.529) variants as drivers of the second and third peaks of infection in Pune. Spike Protein mutational profiling during pre and post-Omicron VOCs indicated differential rank ordering of high-frequency mutations in specific domains that increased the charge and binding properties of the protein. Time-resolved phylogenetic analysis of Omicron sub-lineages identified a highly divergent BA.1 from Pune in addition to recombinant X lineages, XZ, XQ, and XM. CONCLUSIONS: The band of five outbreak data analytics approach, which integrates five different types of data, highlights the importance of a strong surveillance system with high-quality meta-data for understanding the spatiotemporal evolution of the SARS-CoV-2 genome in Pune. These findings have important implications for pandemic preparedness and could be critical tools for understanding and responding to future outbreaks.

Development and application of an RT‒PCR assay for the identification of the delta and omicron variants of SARS-COV-2.

The emergence of mutations in the coronavirus genome provides opportunities for occurrence new strains with higher transmissibility, severity and duration of the disease poses. In 2020, a new variant of the coronavirus SARS-COV-2 - Delta was identified in India. This genetic variant has spread rapidly and became dominant in many countries, including Russia. In November 2021, a new outbreak of COVID-19 occurred in Africa driven by a variant SARS-COV-2 named later Omicron. Both variants had increased transmissibility compared to previously encountered variants and quickly, replacing its around the world. To promptly monitor the epidemiological situation in the country, to assess the spread of dominant genetic variants of the virus and to take appropriate measures, we have developed an RT‒PCR reagent kit for the identification of Delta and Omicron by detecting a corresponding combination of major mutations. The minimum set of mutations was chosen which allows to differentiate Delta and Omicron variants, in order to increase the analysis productivity and reduce costs. Primers and LNA-modified probes were selected to detect mutations in the S gene, typical for the Delta and Omicron. Similar approach can be implemented for the rapid development of assays for differentiating important SARS-COV-2 variants or for other viruses genotyping for epidemiological surveillance or for diagnostic use in order to assist in making clinical decisions. It was demonstrated that the results of VOC Delta and Omicron detection and their typical mutations were concordant with genotyping based on WGS results for all 847 samples of SARS-CoV-2 RNA. The kit has high analytical sensitivity (1х103 copies/mL of SARS-CoV-2 RNA) for each of the detected genetic variants and possesses 100% analytic specificity for microorganism panel testing. The diagnostic sensitivity (95% confidence interval) obtained during pivotal trials was 91.1-100% for Omicron and 91.3-100% for Delta, while the diagnostic specificity with a 95% confidence interval was 92.2-100%. The use of a set of reagents in combination with sequencing of SARS-CoV-2 RNA as part of epidemiological monitoring made it possible to quickly track the dynamics of changes in Delta and Omicron prevalence in the Moscow region in the period from December 2021 to July 2022.

A Methodical Review on Omicron -a New Variant as a Drug Developer

In mid-November 2021, the new OMICRON variety was first discovered in South Africa. As of today, the OMICRON version already appeared on December 15, 2021. Around 77 countries are affected, with the bulk of cases originating in the United States, India, the United Kingdom, and South Africa. OMICRON-positive instances were also reported. The first mortality associated with the novel COVID-19 mutation was reported in the United Kingdom. Recently, a sister variant of OMICRON, 21L or BA.2, has also been discovered. Due to its enormously high number of mutations, viewed enhancement in immune evasion and transmissibility, OMICRON was developed as a new variant of concern (VOC) by the WHO on 26 November 2021. On a global pandemic scale, positive selection of SARSCoV-2 mutations appears to have begun in late 2020. Since then, the virus has been evolving on two fronts: immune evasion and enhanced transmissibility, as expressed by Delta. This review elaborates the effects of drugs in the management of OMICRON.Copyright © 2023 Society of Pharmaceutical Sciences and Research. All rights reserved.

Effects of Homologous and Heterologous Booster Vaccinations of the Inactivated Dual-Adjuvanted Vaccine Vla2001 against Covid-19 Including Variants of Concern: A Phase 3 Randomized Clinical Trial

Intro: VLA2001 is a highly-purified, inactivated whole-virus SARS-CoV-2 vaccine based on a dual-adjuvant system of Alum and CpG1018 for induction of a robust immune response. The vaccine was designed using a well-established technology platform and has received full marketing authorization in Europe. In a pivotal Phase 3 trial, VLA2001 demonstrated superior neutralizing antibody geometric mean titers (GMT) to the comparator, AstraZeneca's AZD1222, as well as non-inferior seroconversion rates two weeks after priming. The extension of the Phase 3 trial evaluated safety and immunogenicity of homologous and heterologous booster vaccinations of VLA2001. Method(s): This is a randomized observer-blind controlled, pivotal trial conducted in the UK in participants aged >=18 years who were randomly assigned 2:1 to receive two doses of VLA2001 or AZD1222, 28 days apart. A booster with VLA2001 was administered to eligible participants at 7 to 8 months after priming. The primary safety outcome was the frequency and severity of any adverse event following the booster vaccination. The primary immunogenicity outcomes were the GMT and fold increase of neutralizing antibodies against SARS-CoV-2 two weeks after the booster vaccination. The study is registered under NCT04864561. Finding(s): A booster dose of VLA2001 is well-tolerated in both AZD1222 and VLA2001 primed participants. High neutralizing antibody titers and fold- increases were generated two weeks following a booster of VLA2001. Cross- neutralizing serological responses against Delta and the Omicron BA.4/BA.5 variants of concern are elicited following a homologous or heterologous booster dose in VLA2001 or AZD1222 primed participants, respectively. Additionally, VLA2001 induced broad T-cell responses with antigen-specific IFN-gamma producing T-cells against the Spike, the Nucleocapsid and the Membrane protein. Conclusion(s): Homologous and heterologous booster doses of VLA2001 demonstrated a favorable tolerability profile irrespective of priming and induced broadly reactive neutralizing antibodies against the ancestral virus and variants of concern, including the currently circulating BA.4/BA.5.Copyright © 2023

Clinical virology and effect of Covid-19 vaccination and monoclonal antibodies against highly infectious SARS- CoV-2 omicron sub variant BF.7 (BA.5.2.1.7): A systematic review.

Over time, the SARS-CoV-2 virus has acquired several genetic mutations, particularly on the receptor-binding domain (RBD) spike glycoprotein. The Omicron variant is highly infectious, with enhanced immune escape activity, and has given rise to various sub-lineages due to mutations. However, there has been a sudden increase in COVID-19 reports of the Omicron subvariant BF.7 (BA.2.75.2), which has the highest number of reported cases, accounting for 76.2% of all cases worldwide. Hence, the present systematic review aimed to understand the viral mutations and factors associated with the increase in the reports of COVID-19 cases and to assess the effectiveness of vaccines and mAbs against the novel Omicron variant BF.7. The R346T mutation on the spike glycoprotein RBD might be associated with increased infection rates, severity, and resistance to vaccines and mAbs. Booster doses of COVID-19 vaccination with bivalent mRNA booster vaccine shots are effective in curtailing infections and decreasing the severity and mortality by enhancing the neutralizing antibodies (Abs) against the emerging Omicron subvariants of SARS-CoV-2, including BF.7 and future VOCs.

SMALL MOLECULE INHIBITOR FOR BLOCKING SARS-CoV-2 ENTRY

Background: Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is a novel and highly pathogenic coronavirus and is the causative agent of COVID-19, an ongoing pandemic that has posed a serious threat to public health and global economy. Thus, there is a pressing need for therapeutic interventions that target essential viral proteins and regulate virus spread and replication. To invade the host cell, the receptor-binding domain (RBD) of SARS-CoV-2 Spike protein binds to the host cell's ACE2 receptor, followed by cleavage events that allow the Spike protein to fuse with the host cell membrane. Thus, the essential role of Spike protein in ACE2 receptor binding and viral fusion makes it a prime target for therapeutic interventions. Method(s): We performed molecular docking and molecular dynamics (MD) simulation-based virtual screening against SARS-CoV-2 RBD/ACE2 interface using a commercial library of 93,835 drug-like compounds. Compounds with promising docking poses and scores were selected for further MD simulation refinement, from which ten lead compounds were identified. Antiviral potencies of ten lead compounds were evaluated against lentiviral vectors pseudotyped with SARS-CoV-2 Spike to down select to a single lead compound, SAI4. ELISA-based assays were employed to determine the binding affinities of SAI4 to recombinant SARS-CoV-2 RBD. Antiviral potential of SAI4 was validated against genuine SARS-CoV-2 in a BSL3 setting. Result(s): We identified SAI4 as a candidate small molecule, which inhibited SARS-CoV-2 pseudovirus entry with IC50 value of ~18 muM. We determined that SAI4 binds RDB with a Kd of ~20 muM. Using cells engineered to express ACE2 and cells that express physiological levels of ACE2, we found that SAI4 inhibited SARS-CoV-2 pseudovirus entry at both engineered and physiological ACE2 levels. We validated the antiviral potential of SAI4 against genuine SARS-CoV-2 and HCoV-NL63. Lastly, we demonstrated antiviral potential of SAI4 against four SARS-CoV-2 variants of concern (alpha, beta, gamma, and delta). Conclusion(s): Using virtual screening, we identified SAI4 as the promising hit compound which displayed inhibitory activities against SARS-CoV-2 entry and its four variants of concern. Thus, our study will pave the way for further development of small molecules for therapeutic targeting of SARS-CoV-2 entry to combat the COVID-19 pandemic.

SARS-CoV-2 INFECTION AMONG PERSONS WHO INJECT DRUGS AND THEIR PARTNERS IN KENYA

Background: Despite increased social vulnerability and barriers to care, there has been a paucity of data on SARS-CoV-2 incidence among key populations in sub-Saharan Africa. We seek to characterize active infections and define transmission dynamics of SARS-CoV-2 among people who inject drugs (PWID) and their sexual and injecting partners from Nairobi and the coastal region in Kenya. Method(s): This was a nested cross-sectional study of SARS-CoV-2 infection from April to July 2021 within a cohort study of assisted partner services for PWID in Kenya. A total of 1000 PWID and their partners (500 living with and 500 living without HIV) were recruited for SARS-CoV-2 antibody testing, of whom 440 were randomly selected to provide self-collected nasal swabs for real-time PCR testing. Whole genome sequencing (WGS) was completed on a limited subset of samples (N=23) with cycle threshold values 32.0. Phylogenetic tree construction and analysis was performed using the Nextstrain pipeline and compared with publicly available SARS-CoV-2 sequences from GenBank. Result(s): A total of 438 (99.5%) participants provided samples for SARS-CoV-2 PCR testing. Median age was 37 (IQR 32-42);128 (29.2%) were female;and 222 (50.7%) were living with HIV. The overall prevalence of SARS-CoV-2 infection identified by RT-PCR was 86 (19.6%). In univariate analyses, there was no increased relative risk of SARSCoV- 2 infection related to positive HIV status, frequenting an injection den, methadone treatment, unstable housing, report of any high-risk exposure, or having a sexual or injecting partner diagnosed with COVID-19 or who died from COVID-19 or flu-like illness. Eight samples were successfully sequenced via WGS and classified as WHO variants of concern: 3 Delta, 3 Alpha, and 2 Beta. Seven were classified into clades predominantly circulating in Kenya during 2021. Notably, two sequences were identical and matched identically to another Kenyan sequence, which is consistent with, though not indictive of, a transmission linkage. Conclusion(s): Overall, the risk of SARS-CoV-2 infection in this population of PWID and their partners was not significantly associated with risk factors related to injection drug use. At a genomic level, the SARS-CoV-2 strains in this study were consistent with contemporary Kenyan lineages circulating during the time and not unique to PWID. Prevention efforts, therefore, must also focus on marginalized groups for control given the substantial amount of mixing that likely occurs between populations.

The Changing Impact of Vaccines in the Covid-19 Pandemic: A Modeling Study

Background: Much of the world's population had already been infected with COVID-19 by the time that the Omicron variant emerged at the end of 2021, but the scale of the Omicron wave was larger than any that had come before or since, and left a global imprinting of immunity which changed the COVID landscape. In this study, we explore the changing value of vaccines in a landscape of dynamic immunity and rapidly evolving variants of concern. Method(s): We use Covasim, an established agent-based model of COVID-19 enhanced with detailed intra-host dynamics. First, we simulate a vaccine trial over March 2020 - April 2022 within a population resembling that of South Africa, and estimate how both vaccine efficacy (reduction in the risk of severe disease for vaccinated vs unvaccinated individuals) and efficiency (number of doses needed to avert a death) change as the population experiences waves of wild-type, Beta, Delta, and Omicron infections. Next, we introduce six hypothetical variants starting from February 2022 and evaluate the impact of (a) the existing set of vaccines, and (b) vaccines specifically targeted to the new variants. Result(s): We estimate that within our simulated population, vaccine efficacy against severe disease decreased from 80% to 20% in the wake of the first wave of wild-type COVID-19, then increased back to ~70% over the latter half of 2020 as population immunity waned. This pattern repeated following each subsequent wave of infections, with vaccine efficacy falling to its lowest (10%) in the immediate wake of the Omicron wave in December 2021. The efficiency of vaccination decreases over time at an increasing rate: at peak efficiency, fewer than 100 doses would have been required to avert a single death, but by the end of January 2022, we estimate that nearly 4,000 doses would be required to avert a single death. We find that variant-chasing vaccines will only add value above pre-existing vaccines if we can shorten the window between variant introduction and vaccine deployment to under three weeks, an impossible time-frame without significant NPI use. Conclusion(s): Although the vaccines have proven to be remarkably effective, our work demonstrates that the population immunity acquired over the first two years of the pandemic significantly reduced the impact per dose of doses delivered after this time. Next-generation vaccines to fight future COVID variants and/or other respiratory diseases must be delivered rapidly at scale for vaccine strategies to be maximally effective.

THE SPIKE OF SARS-CoV-2 VARIANTS ALLOWS FOR MORE EFFICIENT COUNTERACTION OF BST2

Background: BST2/Tetherin is an interferon-stimulated gene with antiviral activity against enveloped viruses. Particularly, BST2 tethers virions at their site of assembly, preventing their release and spread. In addition to this primary role, BST2 is as an important bridge between the innate and adaptive immune system, since (i) BST2 routes tethered particles to lysosomes, which generates viral breakdown products that engage pattern recognition receptors;and (ii) trapped virions facilitate antibody-dependent cell-mediated cytotoxicity (ADCC). In turn, viruses have evolved mechanisms to bypass BST2, either by targeting BST2 for proteasomal/lysosomal degradation or by removing BST2 from sites of virion assembly. However, the role of BST2 in SARS-CoV-2 replication, spread, evolution, and pathogenesis remains largely unknown. Method(s): The antiviral potential of BST2 against SARS-CoV-2 was investigated by infecting different SARS-CoV-2 isolates (Hong Kong, Alpha, Beta, Delta, and Omicron) in BST2+ and BST2- cells. Culture supernatants were collected to assess virion production by ELISA and infectivity by TCID50. Infected cells were analyzed by western blot and flow cytometry to examine viral and cellular protein levels, including BST2. Transfection of individual SARS-CoV-2 ORFs and mutagenesis studies allowed us to identify the genes that the virus uses to downregulate BST2. Immunoprecipitation assays revealed protein-protein interactions and changes in ubiquitination patterns. Experiments with proteasomal and lysosomal inhibitors furthered our mechanistic understanding of how SARS-CoV-2 counteracts BST2. Finally, fluorescence microscopy studies uncovered changes in the subcellular distribution of BST2 in SARS-CoV-2 infected cells. Result(s): While BST2 reduces virion release, SARS-CoV-2 has evolved to counteract this effect. Specifically, SARS-CoV-2 uses the Spike to interact with BST2, sequester the protein at perinuclear locations, and ultimately route it for lysosomal degradation. By surveying different SARS-CoV-2 variants of concern (Alpha-Omicron), we found that each variant is more efficient than the previously circulating strain at downregulating BST2 and facilitating virion production, and that mutations in the Spike account for their enhanced BST2 antagonism. Conclusion(s): As part of its adaptation to humans, SARS-CoV-2 is improving its capacity to counteract BST2, highlighting that BST2 antagonism is important for SARS-CoV-2 infectivity and transmission.

ISOLATION OF PAN-SARBECOVIRUS mABs THAT NEUTRALIZE SARS-CoV-1 AND SARS-CoV-2 VARIANTS

Background: The continued emergence of severe acute respiratory syndrome coronaviruses (SARS-CoVs) and recent explosion of the SARS-CoV-2 pandemic highlights the need for broad and potent antibody recognition and understanding the contexts in which they may develop. Antibodies with cross reactivity across SARS lineages may be of particular value in preparing for future outbreaks of new sarbecoviruses. Method(s): We isolated monoclonal antibodies (mAbs) from an individual 60-days post-vaccination, 30-days post Delta-infection. Reconstructed antibodies were screened for binding to a panel of prefusion-stabilized Spike trimers from SARS-CoV-2 and other beta-coronaviruses using enzyme-linked immunosorbent assay (ELISA). Neutralization potency and breadth was assessed using a spike-pseudotyped lentivirus neutralization assay. Additionally, epitope and escape mutant profiling was conducted by deep mutational scanning (DMS) to identify mutations that affect antibody binding. Lastly, binding breadth was further evaluated using a yeast display library of RBDs from SARS-CoV-2 variants and related sarbecoviruses. Result(s): We identified several SARS-CoV-2-specific mAbs that neutralized SARS-CoV-2 variants of concern (VOCs) and SARS-CoV-1. Notably, two of these mAbs (C68.61 and C68.185) neutralized SARS-CoV-1 with an IC50 = 307 and 139 ng/mL (respectively) that is similar to or better than the potency of S309 (IC50 = 206 ng/mL) and CR3022 (IC50 = 981 ng/mL), which are mAbs isolated from individuals with SARS-CoV-1 infections. C68.61 also neutralized all Omicron VOCs tested and retained neutralization activity against currently circulating variants BQ1.1 (IC50=790 ng/ml) and XBB (IC50=590 ng/ml). Key C68.61 mAbescape mutations identified by DMS in the Omicron BA.2 background yeast display library included sites K462, E465, R466, and I468, which are conserved sites across all VOCs and SARS-CoV-1. The isolated mAbs displayed crossreactive binding to RBDs from diverse SARS-CoV-1-related CoVs and African and European sarbecovirus isolates as well as SARS-CoV-2 VOCs. Conclusion(s): Here we describe mAbs from a SARS-CoV-2-infected individual that bound and neutralized both SARS-CoV-2 and SARS-CoV-1, including one that showed breadth across recent VOCs. Given their breadth, these SARS-CoV-2 cross-reactive mAbs may be robust to viral escape and thus could contribute to therapeutic efforts. In addition, these mAbs displayed broad cross-reactive activity across sarbecoviruses and may be beneficial against future spillover events.

REMDESIVIR RETAINS POTENT ACTIVITY AGAINST SARS-CoV-2 VARIANTS OF CONCERN

Background: Recent SARS-CoV-2 variants of concern (VOCs) have shown a progressive loss of sensitivity to monoclonal antibody therapeutics. Remdesivir (RDV) is a nucleotide analog prodrug that targets the viral RNA-dependent RNA polymerase (RdRp) Nsp12 and is approved to treat COVID-19 in hospitalized and non-hospitalized patients. Nsp12 is highly conserved across VOCs to date and RDV antiviral activity against previous VOCs (Alpha to Omicron BA.1) has been maintained. Here, we conduct a structural analysis of Nsp12 substitutions observed in recent Omicron subvariants (BA.2, BA.2.12.1, BA.4, BA.5 and BA.2.75) and assess RDV antiviral activity against clinical isolates and sitedirected mutants (SDMs) in a replicon system. Method(s): The prevalence of Nsp12 substitutions in Omicron subvariants was evaluated by analysis of sequences from the Global Initiative on Sharing Avian Influenza Data (GISAID) EpiCoV database. Structural analysis of identified substitutions was conducted on a prior cryo-electron microscopy-based model of the replication-transcription complex. Antiviral activity against subvariant clinical isolates was assessed by nucleoprotein ELISA in A549-hACE2-TMPRSS2 cells and by SDMs in the replicon system. Result(s): Genomic analysis of >1.4 million Omicron subvariant sequences revealed unique substitutions in Nsp12 compared to the ancestral WA1 strain. Besides P323L, present in all subvariants, G671S was observed in 95.9% of BA.2.75 sequences, F694Y was observed in <=1.9% of BA.4, BA.5 and BA.2.75 sequences, and Y521C was observed in 1.7% of BA.5 sequences. As anticipated, structural analysis of these substitutions showed no direct interaction with the incoming RDV nucleotide triphosphate or the viral RNA. Phenotyping of clinical isolates of Omicron subvariants BA.2, BA.2.12.1, BA.4, BA.5, and BA.2.75 consistently resulted in mean RDV EC50 values of 24.5 nM (BA.2) to 106.0 nM (BA.5). This represented 0.15-to 0.66-fold changes compared to WA1, indicating no loss of in vitro RDV antiviral activity against these VOCs. P323L, G671S, and F694Y were shown previously to have no impact on RDV antiviral activity. Similarly, the individual substitution Y521C showed no change in RDV susceptibility in the SARS-CoV-2 replicon system. Conclusion(s): RDV retained potent in vitro antiviral activity against all tested Omicron VOCs with potencies comparable to the WA1 isolate. These data support the continued use of RDV in patients infected with Omicron subvariants.

Remdesivir Reduces Mortality in Immunocompromised Patients Hospitalized for Covid-19

Background: There is limited information on effectiveness of COVID-19 therapies in immunocompromised patients, who are at higher risk of hospitalizations, complications, and mortality due to COVID-19. We examined hospital all-cause mortality for early RDV use vs. no RDV use among immunocompromised COVID-19 patients across several distinct dominant variants of concern (VOC) periods: pre-Delta (Dec'20-Apr'21), Delta (May-Nov'21) and Omicron (Dec'21-Apr'22). Method(s): Using the Premier Healthcare Database, we identified adults with an immunocompromised condition (cancer, solid organ and hematopoietic stem cell transplant, hematologic malignancies, primary immunodeficiencies, asplenia, bone marrow failure/aplastic anemia, severe combined immunodeficiencies or HIV), hospitalized with a primary diagnosis of COVID-19. Patients treated with RDV in first 2 days of admission vs. those not treated with RDV during the hospitalization were matched using 1:1 preferential withinhospital propensity matching with replacement. Patients were excluded if discharged within 3 days of RDV initiation. Cox Proportional Hazards Model was used to examine time to 14-and 28-day mortality. Result(s): Overall (Dec'20-Apr'22), 14,169 RDV-treated patients were matched to 5,341 unique non-RDV patients. Post-matching balance was achieved with 59% being 65+ years, 40.5% with no supplementary oxygen charges, 39% received low-flow oxygen, 19% on high-flow oxygen/non-invasive ventilation and 1.5% on invasive mechanical ventilation/ECMO at baseline. During the study period, unadjusted mortality rate was significantly lower for RDV patients at 14 days (11% [95% CI: 11%-12%] vs 15% [15%-16%];p< .0001) and 28 days (18% [17%-18%];p< .0001 vs 22% [22%-23%];p< .0001) as compared to patients that did not receive RDV. After adjusting for baseline and clinical covariates, 14-day results showed that RDV had significantly lower mortality risk compared to non-RDV across all VOC periods [overall (30% lower risk), pre-delta (41%), Delta (23%), Omicron (25%)]. Similarly, 28-day results showed that RDV had significantly lower mortality risk compared to non-RDV across all VOC periods [overall (25%), pre-delta (35%), Delta (21%), Omicron (16%)] (Fig). Conclusion(s): Timely initiation of RDV in first two days of hospital admission demonstrated significant mortality reduction in immunocompromised patients hospitalized with primary diagnosis of COVID-19. RDV demonstrated consistent benefit in an immunocompromised cohort across all variant periods of the pandemic.

Remdesivir Reduces Mortality in Hospitalized Covid-19 Patients across Variant Eras

Background: Clinical management of COVID-19 based on oxygenation requirements continues to change over time as variants of concern (VOC) evolve. We examine hospital all-cause mortality for early hospital RDV use vs. no RDV use across dominant VOC periods: pre-Delta (Dec'20-Apr'21), Delta (May-Nov'21) and Omicron (Dec'21-Apr'22). Method(s): We examined adults with a primary discharge diagnosis of COVID-19 (ICD-10: U07.1) using the Premier Healthcare Database. Patients treated with RDV in the first 2 days of admission vs. those not treated with RDV during the hospitalization were matched using a 1:1 preferential within-hospital propensity matching with replacement. Patients were excluded if discharged within 3 days of RDV initiation. Time to mortality at 14-and 28-days was examined for patients with no supplemental oxygen charges (NSOc), low-flow oxygen (LFO), high-flow oxygen/non-invasive ventilation (HFO/NIV) and invasive mechanical ventilation/ECMO (IMV/ECMO) at baseline. Baseline was defined as first 2 days of hospitalization. Result(s): 164,791 RDV-treated patients were matched to 48,473 unique non-RDV patients. Post-matching balance was achieved across groups with different baseline oxygenation levels and VOC periods. In the matched weighted cohort, 35% required NSOc, 41% LFO, 21% HFO/NIV and 3% IMV/ECMO. During the overall study period (Dec'20-Apr'22), unadjusted mortality rate was significantly lower for RDV patients across all oxygenation levels at 14 days (NSOc: 5.4% vs. 7.3%, LFO: 6.4% vs. 8.8%, HFO/NIV: 16.8% vs. 19.4%, IMV/ECMO: 27.8% vs. 35.3%) and 28 days (NSOc: 8.0% vs. 9.8%, LFO: 9.8% vs. 12.3%, HFO/ NIV: 25.8% vs. 28.3%, IMV/ECMO: 41.4% vs. 50.6%). After adjusting for baseline and clinical covariates, 14-day mortality results showed that RDV significantly lower risk compared to non-RDV across all oxygenation levels at baseline [NSO (26%), LFO (28%), HFO/NIV (17%), IMV/ ECMO (27%)]. Similarly, 28-day mortality results showed that RDV significantly lower risk compared to non-RDV across all oxygenation levels at baseline [NSO (19%), LFO (21%), HFO/NIV (12%), IMV/ECMO (26%)]. This lower mortality risk associated with RDV was consistently observed across all variant periods (Figure). Conclusion(s): Timely initiation of RDV within first two days of hospital admission demonstrated significant mortality reduction in patients hospitalized for a primary diagnosis of COVID-19 across all oxygenation levels. Remdesivir demonstrated consistent benefit across all variant periods of the pandemic to-date.

Remdesivir Is Associated with Reduced Readmission after Covid-19 Hospitalization

Background: There is limited data on the association between COVID-19 therapy and hospital readmissions, including during evolution of the pandemic over time. We examine all cause 30-day readmissions after a COVID-19 hospitalization among remdesivir (RDV)-treated vs non-RDV treated patients across different dominant variants of concern (VOC) periods: pre-Delta (May'20-Apr'21), Delta (May-Nov'21) and Omicron (Dec'21-Apr'22). Method(s): Using the Premier Healthcare Database, we examined adults hospitalized with a primary diagnosis of COVID-19 (ICD-10:U07.1) who were discharged alive from the COVID-19 hospitalization. All-cause readmission to the same hospital was examined using multivariate logistic regression. The model adjusted for: age, corticosteroids use, VOC period, Charlson comorbidity index, maximum oxygenation requirements and ICU admission during COVID-19 hospitalization. Result(s): In the study period (May'20-Apr'22), 440,601 patients with a primary diagnosis of COVID-19 were discharged alive, of which 53% received RDV. As compared to non-RDV, RDV patients were younger (median[IQR]: 62[51-73] vs 64[52-76]), with a lower proportion with no supplementary oxygen charges (30% vs 52%), a higher proportion with low-flow oxygen (46% vs 36%), highflow oxygen/non-invasive ventilation (20% vs 10%), and invasive mechanical ventilation/ECMO (4% vs 2%). Among RDV-treated, the all-cause 30-day readmission was 6.3% compared to 9.1% (p< .0001) in non-RDV treated. Lower readmission for RDV vs non-RDV was seen in Pre-delta (6.3% vs 9.3%;p< .0001), Delta (5.1% vs 7.8%;p< .0001), and Omicron (8.7% vs 9.9%;p< .0001) (Fig). After adjusting for age and characteristics at index hospitalization including corticosteroid, RDV patients had significantly lower likelihood of all-cause 30-day readmission (OR[95% CI]:0.73[0.72-0.75]) as compared to non-RDV. Significantly Lower odds of 30-day readmission for RDV vs non-RDV patients were observed in Pre-delta (0.69[0.67-0.71]), Delta (0.72[0.68-0.76]) and Omicron-(0.87[0.83-0.92]) (Fig). Similarly, RDV-related reduction in readmissions was also seen for COVID-19 related readmissions. Conclusion(s): RDV use during the COVID-19 hospitalization was associated with significantly lower likelihood of all-cause 30-day readmission across the VOC periods of the pandemic May 2020 till April 2022. The lower rate of hospital re-admission for RDV-treated patients was observed despite the RDV group having higher supplemental oxygen requirement during their index COVID-19 hospitalization.

A novel computational approach for rapid screening of antibody therapeutics for efficacy against SARS-CoV-2 variants of concern including Omicron variant

Multiple severe acute respiratory syndrome coronavirus 2 (SARSCoV- 2) variants continue to evolve carrying flexible amino acid substitutions in the spike protein's receptor binding domain (RBD). These substitutions modify the binding of the SARS-CoV-2 to human angiotensin-converting enzyme 2 (hACE2) receptor and have been implicated in altered host fitness, transmissibility and efficacy against antibody therapeutics and vaccines. Reliably predicting the binding strength of SARS-CoV-2 variants RBD to hACE2 receptor and neutralizing antibodies (NAbs) can help assessing their fitness, and rapid deployment of effective antibody therapeutics, respectively. Here, we introduced a two-step computational framework with threefold validation that first identified dissociation constant as a reliable predictor of binding affinity in hetero-dimeric and -trimeric protein complexes. The second step implements dissociation constant as descriptor of the binding strengths of SARS-CoV-2 variants RBD to hACE2 and NAbs. Then, we examined several variants of concern (VOCs) such as Alpha, Beta, Gamma, Delta, and Omicron and demonstrated that these VOCs RBD bind to the hACE2 with enhanced affinity. Furthermore, the binding affinity of Omicron variant's RBD was reduced with majority of the RBD-directed NAbs, which is highly consistent with the experimental neutralization data. By studying the atomic contacts between RBD and NAbs, we revealed the molecular footprints of four NAbs (GH-12, P2B-1A1, Asarnow-3D11, and C118)-that may likely neutralize the recently emerged omicron variant-facilitating enhanced binding affinity. Finally, our findings suggest a computational pathway that could aid researchers identify a range of current NAbs that may be effective against emerging SARS-CoV-2 variants.

What Impact Will Worsening Air Pollution Have on the Burden of Covid-19?

Background: Evidence suggests association between long-term exposure to air pollutants and increased risk of becoming infected with SARS-CoV- 2, the causative agent of COVID-19, and increased severity of COVID-19. However, it remains unclear whether breathing more polluted air over many years affects susceptibility to infection or only affects disease severity, with uncertainty around the intensity of these associations. It has been estimated that anthropogenic emissions have contributed to over 10% of the over 660 million cases of SARS-CoV-2 and the over 7.5 million COVID-19 deaths reported worldwide over the course of the pandemic. Furthermore, as the world continues to warm and if air pollution levels increase, then so might the burden of respiratory infectious disease, including COVID-19. Method(s): Here we explore the potential impact of long-term exposure to increasing levels of particulate matter 2.5 microns or less in diameter (PM2.5) (+1 to +5 mug/m3) assuming an association on either (1) SARS-CoV-2 susceptibility or (2) COVID-19 disease severity by projecting SARS-CoV-2 infections and COVID-19-related hospital admissions over a two-year period. Simulations were conducted using a SARS-CoV-2 transmission model in a global setting capturing age and comorbidity risk, considering seasonality, emerging variants, and vaccination and treatment options. We model linear, log, and log10 relationships between these associations. Result(s): We show that if long-term exposure to higher levels of air pollution only affects COVID-19 severity, then as expected, the projected number of COVID-19-related hospitalisations would proportionally increase. However, if exposure directly affects the susceptibility of becoming infected, then while infections would be higher, hospitalizations would also be even higher due to the potential for onward transmission. This aligns with associations between air pollution and other respiratory infections and their associated health outcomes. Conclusion(s): The anticipated additional impact air pollution is having on the public health burden of respiratory infectious disease, like COVID-19, should be considered in strategic action plans to mitigate and adapt to changing levels of air pollution. It is important to better understand at which point air pollution affects SARS-CoV-2 infection acquisition through to disease progression, to enable improved protection and to better support those most vulnerable. Modelled impact of air pollution on COVID-19. The projected cumulative impact of long-term exposure to incrementally higher PM2.5 levels (+1 to +5 mug/m3) affecting either SARS-CoV-2 susceptibility or COVID-19 disease severity on cumulative SARS-CoV-2 infections and COVID-19-related hospital admissions over a two-year period in a global setting of 100,000 people. Age and comorbidity risk are captured, seasonality considered, and it is assumed SARS-CoV-2 variants of concern (with 10% more infectious and 20% more immune-evading than the previous variant, and Omicron-level severity) emerge every six months, and COVID-19 vaccination and treatment (monoclonalantibody PrEP and antivirals) are implemented for all those eligible. While the associations between PM2.5 exposure and either SARS-CoV-2 susceptibility or COVID-19 disease severity remains unclear and there is much uncertainty around estimated assumptions, here we show a modelled log10 relationship between these two potential associations. COVID-19: coronavirus disease 2019. PM2.5: particulate matter 2.5 microns or less in diameter. PrEP: pre-exposure prophylaxis. SARS-CoV-2: severe acute respiratory syndrome coronavirus 2.

Visualization and functional annotation of coronavirus spike protein glycoshields

Spike proteins of coronaviruses are highly glycosylated and responsible for host recognition and viral entry. The glycans provide a camouflaging shield to help coronaviruses evade host immunity and, in some cases, modulate functional domain structures and dynamics pertinent to host recognition. However, the glycans are chemically and conformationally heterogeneous, making it challenging to determine the chemical compositions and conformations quantitatively. Combining cryo-electron microscopy, mass spectrometry, and molecular modeling, we systematically characterize a panel of spike protein variants of human and animal coronaviruses, including those of the variants of concern of SARS-CoV-2. We have established a robust workflow to quantify the heterogeneity of individual N-glycans by mass spectrometry. We also demonstrated the ability to visualize long glycan structures directly in regions where the dynamics are restricted. In places where the N-glycans are too dynamic, their structural information is generally lost after extended cryo-EM data processing that aims to achieve high resolution. To address this issue, we developed a computational tool called GlycoSHIELD to generate ensembles of glycan conformers to recapitulate the fuzzy structures that are in quantitative agreement with the experimental cryo-EM data. The ability to generate fully glycosylated spike protein models enables the prediction of hitherto unknown receptor and antibody binding sites. This work was supported by Academia Sinica intramural fund, an Academia Sinica Career Development Award, Academia Sinica to STDH (AS-CDA-109- L08), an Infectious Disease Research Supporting Grant to STDH (AS-IDR- 110-08), and the Ministry of Science and Technology (MOST), Taiwan (MOST 109-3114-Y-001-001, MOST 110-2113-M-001- 050-MY3 and MOST 110-2311-B-001-013-MY3) to STDH.Copyright © 2023 The American Society for Biochemistry and Molecular Biology, Inc.

Quantification of functional antibody titers in a mouse model of SARS-CoV-2 infection

Towards the end of 2019 a novel severe acute respiratory syndrome (SARS)-like coronavirus (SARS-CoV-2) caused the ongoing global pandemic. The virus surface consists of spike proteins that mediate SARS-CoV-2 entry into cells through its receptor-binding domain (RBD) that attaches to the human receptor Angiotensin- Converting Enzyme 2 (ACE2). Upon infection with foreign material, like viruses and bacteria, the human immune system responds by producing a humoral response specific to the viral antigen. Cells from the innate immune system and antibodies generated in the humoral response work to destroy and block infectious antigens from causing damage to the human cells. The S protein of SARSCoV- 2 is the key protein that stimulates the immune system to generate neutralizing antibodies. To safely test and investigate SARS-CoV-2 in BSL-2 lab setting, we propagated a surrogate pseudo typed virus to evaluate the ability of antibodies to reduce viral cell entry and replication in SARS-CoV-2 infected mice model. Quantifying the functional ability of neutralizing antibodies would help us understand how they influence reinfection in recovered individuals. We hypothesize that antibodies generated in SARS-CoV-2 infected mice models will induce a protective immune response against the SARSCoV- 2 infection. To detect and quantify the protective immune response generated in mice, we performed two different serological assays and identified antibodies endpoint titers. Mice were infected with Delta and Beta at time points Day 3 and Day 4. We performed a SARS-CoV-2 Spike pseudo virus neutralization assay and measured luminescence to determine the percentage neutralization of functional antibodies induced in mice serum samples upon infection. Utilizing indirect ELISAs,' we measured absorbance for IgA antibodies in Bronchoalveolar lavage fluid (BALF) serum and total IgG antibodies in cardiac bleeds. Our results showed we did not obtain neutralizing activity of antibodies in mice serum samples taken at early time points, 24 hrs and 4 days, after infection with the Delta variant of SARS CoV2 virus using both the pseudo viruses Omicron andWA spike.We obtained 100% neutralizing activity in mice serum samples taken at day 21 and infected with Beta variant of SARS CoV2 virus using both the pseudo viruses Omicron and WA spike demonstrating that there is cross-neutralization against various variants of concern. Antibodies (IgA, IgM, IgG) generated in mice 3 weeks post infection with SARS CoV2 (Beta) virus are capable of neutralizing and inhibiting the entry of WA spike and Omicron pseudo viruses in human HEK293 T Ace2 cells. Moving forward utilizing samples with timepoints surpassing 3 weeks could possibly yield higher concentrations of IgA and IgM antibodies that can neutralize the SARS-CoV-2 pseudo virus. Thank you to Dr. Rhea Coler, the entire Coler lab, National Institutes of Health (NIH), and Seattle Children's Research Institute.Copyright © 2023 The American Society for Biochemistry and Molecular Biology, Inc.