COVID-19, Seasonality, and Historical Epidemiological Risk in Italy: Descriptive Study and Considerations for Public Health (preprint)

(1) Background: This paper investigates the epidemiological risk related to temperature before and during COVID-19 in Italy; (2) Methods: Deaths in 2015-2019 and temperatures were correlated. Excess and COVID-19 deaths were examined to estimate the relationships with temperatures; (3) Results: Annual deaths were higher during the cold months (+45,000, SD = 4,700, S = 21). The scenario worsened during COVID-19. Mortality was higher during minimum temperature periods, although the curve moderately rose in the warmest months (r = -0.75, 95% CI = [-0.87; -0.56], S = 23). COVID-19 deaths showed a decreasing seasonality. Monthly excess deaths during COVID-19 were high (+4,200, IQR = [2,800; 8,000], S = 28) with a doubt of seasonality. COVID-19 mortality was correlated with regional latitude (r = 0.86, 95% CI = [0.68; 0.94], S = 20). Discrepancies between COVID-19 and excess deaths were found. The exposed population was subject to aging; (4) Conclusions: The epidemiological risk in Italy is seasonal and geographically dependent. Low and very high temperatures can lead to mortality peaks. Therefore, COVID-19 and any other epidemiological risk must be evaluated in light of this evidence. Health systems need to be strengthened during cold and extremely hot periods. Future research should investigate these phenomena at the causal level.

Nanobodies against SARS-CoV-2 reduced virus load in the brain of challenged mice and neutralized Wuhan, Delta and Omicron Variants (preprint)

In this work, we developed llama-derived nanobodies (Nbs) directed to the receptor binding domain (RBD) and other domains of the Spike (S) protein of SARS-CoV-2. Nanobodies were selected after the biopanning of two Nb-libraries, one of which was generated after the immunization of a llama (lama glama) with the bovine coronavirus (BCoV) Mebus, and another with the full-length pre-fused locked S protein (S-2P) and the RBD from the SARS-CoV-2 Wuhan strain (WT). Most of the neutralizing Nbs selected with either RBD or S-2P from SARS-CoV-2 were directed to RBD and were able to block S2P/ACE2 interaction. Three Nbs recognized the N-terminal domain (NTD) of the S-2P protein as measured by competition with biliverdin, while some non-neutralizing Nbs recognize epitopes in the S2 domain. One Nb from the BCoV immune library was directed to RBD but was non-neutralizing. Intranasal administration of Nbs induced protection ranging from 40% to 80% against COVID-19 death in k18-hACE2 mice challenged with the WT strain. Interestingly, protection was not only associated with a significant reduction of virus replication in nasal turbinates and lungs, but also with a reduction of virus load in the brain. Employing pseudovirus neutralization assays, we were able to identify Nbs with neutralizing capacity against the Alpha, Beta, Delta and Omicron variants. Furthermore, cocktails of different Nbs performed better than individual Nbs to neutralize two Omicron variants (B.1.529 and BA.2). Altogether, the data suggest these Nbs can potentially be used as a cocktail for intranasal treatment to prevent or treat COVID-19 encephalitis, or modified for prophylactic administration to fight this disease.

Resolving the developmental mechanisms of coagulation abnormalities characteristic of SARS-CoV2 based on single-cell transcriptome analysis (preprint)

The COVID-19 outbreak caused by the SARS-CoV-2 virus has developed into a global health emergency. In addition to causing respiratory symptoms following SARS-CoV-2 infection, COVID-19-associated coagulopathy (CAC) is the main cause of death in patients with severe COVID-19. In this study, we performed single-cell sequencing analysis of the right ventricular free wall tissue from healthy donors, patients who died in the hypercoagulable phase of CAC, and patients in the fibrinolytic phase of CAC. Among these, we collected 61,187 cells, which were enriched in 24 immune cell subsets and 13 cardiac-resident cell subsets. We found that in response to SARS-CoV-2 infection, CD9highCCR2high monocyte-derived mo promoted hyperactivation of the immune system and initiated the extrinsic coagulation pathway by activating CXCR-GNB/G-PI3K-AKT. This sequence of events is the main process contributing the development of coagulation disorders subsequent to SARS-CoV-2 infection. In the characteristic coagulation disorder caused by SARS-CoV-2, excessive immune activation is accompanied by an increase in cellular iron content, which in turn promotes oxidative stress and intensifies intercellular competition. This induces cells to alter their metabolic environment, resulting in an increase in sugar uptake, such as that via the glycosaminoglycan synthesis pathway, in CAC coagulation disorders. In addition, high levels of reactive oxygen species generated in response elevated iron levels promote the activation of unsaturated fatty acid metabolic pathways in endothelial cell subgroups, including vascular endothelial cells. This in turn promotes the excessive production of the toxic peroxidation by-product malondialdehyde, which exacerbates both the damage caused to endothelial cells and coagulation disorders.

Evaluating targeted COVID-19 vaccination strategies with agent-based modeling (preprint)

We evaluate approaches to vaccine distribution using an agent-based model of human activity and COVID-19 transmission calibrated to detailed trends in cases, hospitalizations, deaths, seroprevalence, and vaccine breakthrough infections in Florida, USA. We compare the incremental effectiveness for four different distribution strategies at four different levels of vaccine availability, reflecting different income settings' historical COVID-19 vaccine distribution. Our analysis indicates that the best strategy to reduce severe outcomes is to actively target high disease-risk individuals. This was true in every scenario, although the advantage was greatest for the middle-income-country availability assumptions, and relatively modest compared to a simple mass vaccination approach for rapid, high levels of vaccine availability. Ring vaccination, while generally the most effective strategy for reducing infections, ultimately proved least effective at preventing deaths. We also consider using age group as a practical, surrogate measure for actual disease-risk targeting; this approach still outperforms both simple mass distribution and ring vaccination. We also find that the magnitude of strategy effectiveness depends on when assessment occurs (e.g., after delta vs. after omicron variants). However, these differences in absolute benefit for the strategies do not change the ranking of their performance at preventing severe outcomes across vaccine availability assumptions.

Generation of a SARS-CoV-2 reverse genetics system and novel human lung cell lines that exhibit high virus-induced cytopathology (preprint)

The global COVID-19 pandemic continues with an increasing number of cases worldwide and the emergence of new SARS-CoV-2 variants. In our study, we have developed novel tools with applications for screening antivirals, identifying virus-host dependencies, and characterizing viral variants. Using reverse genetics, we rescued SARS-CoV-2 Wuhan1 (D614G variant) wild type (WTFL) and reporter virus (NLucFL) using molecular BAC clones. The replication kinetics, plaque morphology and titers were comparable between rescued molecular clones and a clinical isolate (VIDO strain), thus providing confidence that the rescued viruses can be used as effective replication tools. Furthermore, the reporter SARS-CoV-2 NLucFL virus exhibited robust luciferase values over the time course of infection and was used to develop a rapid antiviral assay using remdesivir as proof-of-principle. In addition, as a tool to study lung-relevant virus-host interactions, we established novel human lung cell lines that support SARS-CoV-2 infection with high virus-induced cytopathology. Six lung cell lines (NCI-H23, A549, NCI-H1703, NCI-H520, NCI-H226, and HCC827) and HEK293T cells, were transduced to stably express ACE2 and tested for their ability to support virus infection. A549ACE2 B1 and HEK293TACE2 A2 cell lines exhibited more than 70% virus-induced cell death and a novel lung cell line NCI-H23ACE2 A3 showed about ~99% cell death post-infection. These cell lines are ideal for assays relying on live-dead selection and are currently being used in CRISPR knockout and activation screens in our lab.

What the analysis of causes of death in France in 2020 reveals about the impact of the Covid-19 epidemic (preprint)

Context: In 2020, the French population lived under the threat of the Covid-19 epidemic, which would allegedly cause an exceptional excess mortality rate. Mortality data by cause of death for the year 2020 are now available. These data allow us to quantify and qualify the impact of the epidemic. This analysis presents the evolution of the main mortality indicators by cause and by age group. It is intended to demonstrate how 2020 was an exceptional year. Materials and methods: In France, causes of death are labeled according to the International Classification of Diseases (ICD-10) based on medical death certificates. The study focuses on aggregated data for the year 2020 as well as complete data from 1979 to 2017 available online. To estimate excess mortality by cause of death, mortality data were standardized to 2020 to take into account changes in the age structure of the population. Results: The year 2020 is marked, on the one hand, by the introduction of "Covid-19" as a cause of death, which accounts for 10.4% of deaths; and, on the other hand, by a strong downward trend in most other causes of death. Discussion: In 2020, we show that the overall number of additional deaths due to the Covid-19 epidemic is paradoxically lower than the number of deaths caused by this disease. According to official sources, the number of Covid-19-labeled deaths is nearly 50% higher than the number of additional deaths. Besides excess mortality in 2020 being modest compared to other years that saw health events and it affecting only individuals over 65 years of age, what could explain that this disease has caused more deaths than additional deaths? This analysis shows that the emergency implementation of the "Covid-19" classification led to many biases. A significant number of deaths, usually labeled for other major causes (e.g., neoplasm, circulatory system diseases) were, in a way, transferred to this new label. This analysis of mortality by cause of death provides quantitative answers to the overestimation of the impact of the Covid-19 epidemic in France.

A standardised protocol for assessment of relative SARS-CoV-2 variant severity, with application to severity risk for COVID-19 cases infected with Omicron BA.1 compared to Delta variants in six European countries (preprint)

Several SARS-CoV-2 variants that evolved during the COVID-19 pandemic have appeared to differ in severity, based on analyses of single-country datasets. With decreased SARS-CoV-2 testing and sequencing, international collaborative studies will become increasingly important for timely assessment of the severity of newly emerged variants. The Joint WHO Regional Office for Europe and ECDC Infection Severity Working Group was formed to produce and pilot a standardised study protocol to estimate relative variant case-severity in settings with individual-level SARS-CoV-2 testing and COVID-19 outcome data during periods when two variants were co-circulating. To assess feasibility, the study protocol and its associated statistical analysis code was applied by local investigators in Denmark, England, Luxembourg, Norway, Portugal and Scotland to assess the case-severity of Omicron BA.1 relative to Delta cases. After pooling estimates using meta-analysis methods (random effects estimates), the risk of hospital admission (adjusted hazard ratio [aHR]=0.41, 95% CI 0.31-0.54), ICU admission (aHR=0.12, 95% CI 0.05-0.27), and death (aHR=0.31, 95% CI 0.28-0.35) was lower for Omicron BA.1 compared to Delta cases. The aHRs varied by age group and vaccination status. In conclusion, this study has demonstrated the feasibility of conducting variant severity analyses in a multinational collaborative framework. The results add further evidence for the reduced severity of the Omicron BA.1 variant.

Surviving COVID-19 according to race: evidence by a Brazilian retrospective cohort (preprint)

The COVID-19 pandemic did not impact and still now does not impact people homogeneously. In Brazil, race shows itself as an important difference in health events, including COVID-19 outcomes. We observed, during the pandemic, a higher lethality pattern among black and brown populations. Considering the most important factor for the disease severity in Brazil are, in order of relevance, age, socioeconomic factors and, only then, comorbidities, and that black and brown Brazilians have much poorer socioeconomic conditions compared to white people, we can understand these populations as part of a group under greater risk of aggravation by COVID-19. Besides, it is known that black and brown people face more difficulties to access healthcare services, a way that sometimes they are not even aware of the comorbidities possessed, which can potentially aggravate COVID-19, or present fewer possibilities to control these diseases. Nonetheless, intrinsic, institutional, and structural racism, a health social determinant shown by many indicators such as mortality rates of black and brown populations, presents itself in all healthcare levels in Brazil. Thus, this study aims to analyze the racial differential for COVID-19 survival amongst hospitalized patients in Rio de Janeiro during the COVID-19 pandemic. We performed a survival analysis from selected notifications of COVID-19-induced induced Severe Acute Respiratory Syndrome in Rio de Janeiro from the date of the first death registered in Brazil to the end of the Public Healthcare Emergency of National Interest, in order to evaluate the times between the first symptoms and hospitalization; hospitalization and outcome (death); and first symptoms and outcomes (death), relating those to the variable of interest race and the covariables age; sex; presence or absence of major signs/symptoms; presence or absence of multimorbidities; resident of Rio de Janeiro or not; resident of urban/rural areas; ICU hospitalization or not. With that, we aim to characterize hospitalized COVID-19 cases in Rio de Janeiro regarding sociodemographic and clinical variables, describe the course between initial symptomatology and outcomes of the in-patients who utterly passed, analyze the survival probability of in-patients according to their race/skin color; relate social health determinants aspects to the survival rates of the hospitalized patients.

State-Level Excess Mortality in US Adults During the Delta and Omicron Waves of COVID-19 (preprint)

Introduction The US has continued to see excess mortality through the Delta and Omicron periods. We sought to quantify excess mortality on a state level and calculate potential deaths averted if all states matched the excess mortality rates of those with the 10 lowest excess mortality rates. Methods Observational cohort, US and state-level data. Expected monthly deaths were modeled using pre-pandemic US and state-level data (2015-2020). Mortality data was accessed from CDC public reporting. Results We find that during the Delta and Omicron waves, the US recorded over 596,000 excess deaths. 60% of the nation's total excess mortality during these periods could have been averted if all states had excess mortality rates equal to those with the 10 lowest excess mortality rates. Conclusion With large differences in excess mortality across US states in our 15-month study period, we note that a significant portion of deaths could have been averted with higher vaccination rates, policies and other behaviors.

Forecasting the trajectory of the COVID-19 pandemic into 2023 under plausible variant and intervention scenarios: a global modelling study (preprint)

Background The recent Omicron-related waves of the COVID-19 pandemic have resulted in unprecedented levels of population transmission due to the variant's high level of infectiousness across most of the world. China, the last large country to end its "zero-COVID" policies, is currently facing its own massive Omicron-related wave, and the final impact of that wave remains uncertain. We have seen repeatedly that the epidemiological characteristics of new variants can have profound impacts on global health outcomes. While the characteristics of these new variants are difficult to predict ahead of their emergence, considering the impact of potential future scenarios is of central importance for prudent planning and policy making. This paper samples across a range of potential variant-level characteristics to provide global forecasts of infections, hospitalisations, and deaths in the face of ongoing Omicron-related transmission and waning levels of past immunity and evaluates a range of interventions that may diminish the impact of future waves. Methods We created a susceptible-exposed-infectious dynamic model that accounts for vaccine uptake and effectiveness, antiviral administration, the emergence of new variants, and waning protection from both infection- and vaccine-derived immunity. Using this model, we first estimated past infections, hospitalisations, and deaths by variant, location, and day. We used these findings to more fully understand the global progression of the COVID-19 pandemic through December 12, 2022. Second, we forecasted these same outcome measures under five potential variant emergence scenarios. Third, we evaluated three different interventions in isolation and in concert within each potential variant scenario, to assess the impact of available intervention strategies through June 30, 2023. Findings We estimated that from November 15, 2021, through December 12, 2022, there were 8.60 billion (95% uncertainty interval [UI] 6.37-11.7) SARS-CoV-2 infections, 13.1 million (10.6-16.5) hospitalisations, and 3.04 million (2.65-3.55) deaths, the majority of which were attributable to Omicron variants (98.5% [97.4-99.1] of infections, 82.6% [76.7-86.3] of hospitalisations, and 72.4% [66.4-76.0] of deaths). Compared to the pre-Omicron pandemic period from January 1, 2020, to November 15, 2021, we estimated that there were more than twice as many infections (214% [163-286]) globally from November 15, 2021, to December 12, 2022, but only 20.6% (19.8-21.4) of the estimated deaths. The massive Omicron waves and high vaccination rates in many high-income countries have together contributed to high levels of immunity against SARS-CoV-2 infection, leaving only 97.3% (96.3-98.2) of the global population with no protection as of December 1, 2022. Concurrently, however, China, where only 17.6% [5.28-34.8] of the population have ever experienced infection due to its zero-COVID policy, requires special attention over the next few months, as all our future scenarios predict substantial increases in transmission, hospitalisation, and death in China in now that zero-COVID policies have been relaxed. Under the future scenario we consider most plausible (a scenario with another new Omicron-like variant emerging and reference levels of the drivers of transmission), we estimated there will be an additional 5.19 billion (3.11-7.78) infections, 13.6 million (8.50-21.8) hospitalisations, and 2.74 million (1.40-5.68) deaths between December 12, 2022, and June 30, 2023, with the Western Pacific region projected to sustain the highest rates of additional deaths, driven primarily by the uncontained outbreak in China. By comparison, a baseline scenario in which no new variant emerges results in 3.54 billion (2.24-5.43) infections, 6.26 million (4.11-9.65) hospitalisations, and 1.58 million (0.829-3.95) deaths in the same forecast period. The ability for a new variant to break through past infection- and vaccine-derived immunity greatly influences future outcomes: we estimate a new variant with the high severity of Delta, but correspondingly moderate immunity breakthrough rates will have difficulty overtaking current variants and will result in similar outcomes to the Omicron-like variant scenario with 3.64 billion (2.26-5.83) new infections, 7.87 million (4.81-13.0) new hospitalisations, and 2.87 million (1.03-5.56) new deaths. Finally, if we consider a variant that combines the high infectiousness and breakthrough rates of Omicron with the high severity of Delta, we again estimate 5.19 billion (3.11-7.78) new infections, but due to the presumed increase in severe outcomes, we estimate 30.2 million (13.4-51.2) new hospitalisations and 15.9 million (4.31-35.9) deaths over the forecasted period. The impacts of interventions vary by variant characteristics and region of the world, with increased mask usage and reimplementation of some mandates having massive impact in some regions while having less impact in others. Finally, assuming variant spread was as rapid as observed for Omicron, we find almost no impact of a rapidly developed and deployed variant-targeted booster. Interpretation As infection-derived and vaccine-conferred protection wanes, we expect infections to rise, but as most of the world's population has some level of immunity to SARS-CoV-2 as of December 12, 2022, all but the most pessimistic forecasts in this analysis do not predict a massive global surge by June 30, 2023. Paradoxically, China, due to its lower levels of population immunity and effective vaccination will likely experience substantial numbers of infections and deaths that, due to its large population size, will adversely affect the global toll. This could be substantially mitigated by existing intervention options including masking, vaccination, health-care preparedness, and effective antiviral compounds for those at most at risk of poor outcomes. While still resulting in morbidity and mortality, this endemic transmission provides protection from less transmissible variants and particularly protects against sub-lineages of the more severe pre-Omicron variants. In the scenarios where a new variant does emerge and spread globally, however, the speed of this spread may be too fast to rely on even the most quickly developed mRNA vaccines to provide protection soon enough. Existing vaccines and boosters have played an important role in increasing immunity worldwide, but the continued contribution of mask usage (both past and future) in the prevention of infection and death cannot be understated. The characteristics of future COVID-19 variants are inherently difficult to predict, and our forecasts do show considerable differences in outcomes as a function of these variant properties. Given the uncertainty surrounding what type of variant will next emerge, the world would be wise to remain vigilant in 2023 as we move to the next phase of the COVID-19 pandemic.

Excess Mortality in the Vaccination Era in the United States, By State and 6-Month Period (preprint)

Introduction The US continued to record all-cause excess mortality after the rollout of vaccines. We sought to quantify excess mortality by state and compare these rates to primary series vaccination completion levels. Methods Observational cohort, US and state-level data. Expected monthly deaths were modeled using pre-pandemic US and state-level data (2015-2020). Mortality data was accessed from CDC public reporting. Results We find that in a two-year period since the rollout of vaccines, the US recorded >874,000 excess deaths. Vaccination rates and excess mortality were most strongly correlated in first two periods before the Omicron variant. Conclusion The association between vaccination and lower excess mortality rates was strongest in 2021 and early 2022, prior to high population rates of infection-acquired immunity. The findings underscore the benefits of the rapid vaccination rollout campaign and the continued need to boost at-risk populations.

International Vaccine Allocation: An Optimization Framework (preprint)

The global SARS-CoV-2 (COVID-19) pandemic highlighted the challenge of equitable vaccine distribution between high- and low-income countries. High-income countries, such as the United States, were among the first to acquire the rapidly developed vaccines against COVID-19. However, many such high-income countries were reluctant or slow to distribute extra doses of the vaccine to lower-income countries via the COVID-19 Vaccines Global Access (COVAX) collaboration [Clinton and Yoo 2022]. In addition to moral objections to such vaccine nationalism, vaccine inequity during a pandemic could contribute to the evolution of new variants of the virus and possibly increase total deaths, including in the high-income countries. This paper uses the COVID-19 pandemic as a case study to identify scenarios under which it might be in a high-income nation's own interest to donate vaccine doses to another country before its own population has been fully vaccinated. Using an epidemiological model embedded in an optimization framework, we identify realistic scenarios under which a donor country prefers to donate vaccines before distributing them locally in order to minimize local deaths. We demonstrate that a nondonor-first vaccination policy can, under some circumstances, dramatically delay the emergence of more-contagious variants. Moreover, we find that vaccine distribution is not a zero-sum game between donor and nondonor countries: weighting the objective function even slightly in favor of minimizing total deaths can achieve dramatic reduction in total deaths with only a small increase in donor-country deaths. The insights yielded by this framework can be used to guide equitable vaccine distribution in future pandemics.

SARS-CoV-2 viral replication persists in the human lung for several weeks after onset of symptomatic severe COVID-19 and is associated with attenuated pulmonary immunity and variant-specific clinical sequalae (preprint)

The immunopathogenesis of severe COVID-19 is incompletely understood. In contradistinction to the upper respiratory tract where replicating (culturable) SARS-CoV-2 is recoverable approximately ~ 4 to 8 days after symptom onset, there is paucity of data about the frequency or duration of replicating virus in the lower respiratory tract (the human lung). We undertook lung tissue sampling (needle biopsy), within ~2 hours of death, in 42 mechanically ventilated decedents during the Beta and Delta waves. Lung biopsy cores underwent viral culture, histopathological analysis, electron microscopy, transcriptomic profiling, immunohistochemistry and cell-based flow cytometry of deconstructed tissue. 38% (16/42) of patients had culturable virus in the lung (persisting for up to 4 weeks after symptom onset). This, hitherto, undescribed bio-phenotype of lung-specific persisting viral replication was associated with an enhanced pulmonary pro-inflammatory response and variant-specific increased rates of bacterial bronchopneumonia and accelerated death. These findings question existing paradigms and suggest that in a subset of patients, concurrent, rather than sequential active viral replication continues to drive a heightened pro-inflammatory response. Our findings have potential implications for the design of therapeutic interventional strategies and clinical management of severe COVID-19 disease.

COVID-19 Infection and Dementia: A Prospective Analysis of Time-Varying Risk, Subtypes, and Subpopulations from the UK Biobank (preprint)

Background: Although COVID-19 patients were suggested to experience worse cognitive outcomes, there is a paucity of evidence on time-varying risk of dementia, especially the subtypes, as well as among critical subpopulations. Methods: Out of over 50000 individuals from general population in the UK Biobank, SARS-COV-2 infected patients between March 1, 2020, and July 31, 2021 and maximally 5:1 propensity score matched contemporary non-infected individuals were selected, with baseline dementia excluded. Matching was done on demographic characteristics, lifestyle, and comorbidities. Dementia was captured according to primary care, inpatient records, and death registry, with the follow-up ending at the earliest of outcome occurrence, death, or August 31, 2021. Associations were evaluated using time-varying hazard ratios (HRs) and odds ratios (ORs). Results: With a mean age of 64.5 years for 18032 COVID-19 patients and 83,008 controls, participants were followed for a median of 247 (IQR: 204–305) days and 255 dementia cases occurred, including 90 Alzheimer’s disease (AD) cases and 42 vascular dementia (VaD) cases. Compared with matched controls, dementia risk declined drastically after COVID-19 infection and sustained for all-cause dementia, VaD, and other dementia. During the acute phase (first 30 days), COVID-19 infection was associated with increased risks of dementia, with HRs (95% CIs) being 12.77 (6.77, 24.08) for all-cause dementia, 9.21 (2.77, 30.59) for AD, 5.53 (1.69, 18.11) for VaD, and 25.35 (8.74, 73.56) for other dementia. Among those not hospitalized within 30 days of enrollment, elevated dementia risk remained for all-cause dementia, VaD, and other dementia, with ORs being 1.82, 4.55, and 1.64, respectively. Among most of the subpopulations classified by demographic characteristics, APOE genotype, and comorbidities (except for those with chronic obstructive pulmonary diseases at enrollment), COVID-19 infection was associated with an elevated all-cause dementia risk and no modification effect was detected. Conclusion: Declined yet sustained elevated dementia risk since COVID-19 infection was found and vascular risk factors may need extra attention during the long-term follow-up. Increased dementia risk from COVID-19 infection also applied for the non-hospitalized during the acute phase and most subpopulations. The potential dementia risk associated with Omicron and newer variants warrants further evaluation.

Bivalent booster effectiveness against severe COVID-19 outcomes in Finland, September 2022 - January 2023 (preprint)

Bivalent COVID-19 vaccines were introduced in 2022 but knowledge of how their effectiveness against severe COVID-19 outcomes is sustained over time is currently limited. In Finnish register-based cohort analyses, we compared the risk of severe COVID-19 outcomes among those who received bivalent vaccination (exposed) between 1 September 2022 and 31 January 2023 to those who did not (unexposed). Among elderly aged 65-120 years, bivalent vaccination reduced the risk of hospitalisation and death due to COVID-19. Among the elderly the hazard ratios comparing exposed and unexposed ranged from 0.36 to 0.43 during the first 14-30 days since bivalent vaccination but signs of waning were observed as soon as two months after vaccination. Among the chronically ill aged 18-64 years bivalent vaccination did not reduce the risk of severe COVID-19 outcomes. These results are crucial for further developing COVID-19 vaccination programme worldwide.

The infectivity of SARS-CoV-2 progeny virions requires the activity of host cell N-myristoyltransferases and it is severely compromised by their inhibition (preprint)

Acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the COVID-19 pandemic. Despite vaccinations, the development and use of neutralising antibodies against the viral surface spike proteins, and small molecule inhibitors targeting the viral replication machinery, COVID-19 remains a global public health crisis. Emerging mutations in the viral genome have the potential to reduce prophylactic and therapeutic efficacy of virus-directed treatments. Targeting host cell factors required for infection could, therefore, be a potential strategy to overcome this problem since mutations in the viral genome are unlikely to bypass the requirement for the targeted host factor or function. The enzymatic activity of N-myristoyltransferases (NMTs) are essential to mediate stable membrane binding and function of a diverse class of cellular proteins, many of which regulate intracellular membrane trafficking. Here we report that nanomolar concentrations of the NMT inhibitor IMP-1088 inhibited SARS-CoV-2 spreading in human cells by compromising the infectivity of released viral particles, which was reduced by up to 90%. IMP-1088 also inhibited human Respiratory syncytial virus, the main cause of viral death in infants world-wide, but not the mosquito-delivered alphavirus Semliki Forest virus and the vesiculovirus Vesicular stomatitis virus. The antiviral effect of IMP-1088 against SARS-CoV-2 displayed remarkably slow reversibility, was well tolerated by cells, and is, therefore, a promising candidate for COVID-19 prophylaxis and therapy.

Association of SARS-CoV-2 Nucleocapsid Protein Mutations with Patient Demographic and Clinical Characteristics during the Delta and Omicron Waves (preprint)

SARS-CoV-2 genomic mutations outside the spike protein that may increase transmissibility and disease severity have not been well characterized. This study identified mutations in the nucleocapsid protein and their possible association with patient characteristics. We analyzed 695 samples from patients with confirmed COVID-19 in Saudi Arabia between April 1, 2021, and April 30, 2022. Nucleocapsid protein mutations were identified through whole genome sequencing. {chi}2 tests and T tests assessed associations between mutations and patient characteristics. Logistic regression estimated risk of intensive care unit (ICU) admission or death. Of 60 mutations identified, R203K was most common followed by G204R, P13L, and E31del, R32del, and S33del. These mutations were associated with reduced risk of ICU admission. P13L, E31del, R32del, and S33del were also associated with reduced risk of death. By contrast, D63G, R203M, and D377Y were associated with increased risk of ICU admission. Most mutations were detected in the SR-rich region, which was associated with low risk of death. C-tail and central linker regions were associated with increased risk of ICU admission, whereas the N-arm region was associated with reduced ICU admission risk. Some SARS-CoV-2 nucleocapsid amino acid mutations may enhance viral infection and COVID-19 disease severity.

The gray swan: model-based assessment of the risk of sudden failure of hybrid immunity to SARS-CoV-2 (preprint)

In the fourth year of the COVID-19 pandemic, public health authorities worldwide have adopted a strategy of learning to live with SARS-CoV-2. This has involved the removal of measures for limiting viral spread, resulting in a large burden of recurrent SARS-CoV-2 infections. Crucial for managing this burden is the concept of the so-called wall of hybrid immunity, through repeated reinfections and vaccine boosters, to reduce the risk of severe disease and death. Protection against both infection and severe disease is provided by the induction of neutralizing antibodies (nAbs) against SARS-CoV-2. However, pharmacokinetic (PK) waning and rapid viral evolution both degrade nAb binding titers. The recent emergence of variants with strongly immune evasive potential against both the vaccinal and natural immune responses raises the question of whether the wall of population-level immunity can be maintained in the face of large jumps in nAb binding potency. Here we use an agent-based simulation to address this question. Our findings suggest large jumps in viral evolution may cause failure of population immunity resulting in sudden increases in mortality. As a rise in mortality will only become apparent in the weeks following a wave of disease, reactive public health strategies will not be able to provide meaningful risk mitigation. Learning to live with the virus could thus lead to large death tolls with very little warning. Our work points to the importance of proactive management strategies for the ongoing pandemic, and to the need for multifactorial approaches to COVID-19 disease control.

COVID-19 adenoviral vector vaccination elicits a robust memory B cell response with the capacity to recognize Omicron BA.2 and BA.5 variants (preprint)

Following the COVID-19 pandemic caused by SARS-CoV-2, novel vaccines have successfully reduced severe disease and death. Despite eliciting lower antibody responses, adenoviral vector vaccines are nearly as effective as mRNA vaccines. Therefore, protection against severe disease may be mediated by immune memory cells. We here evaluated plasma antibody and memory B cells (Bmem) targeting the Spike receptor binding domain (RBD) elicited by the adenoviral vector vaccine ChAdOx1 (AstraZeneca), their capacity to bind Omicron subvariants, and compared this to the response elicited by the mRNA vaccine BNT162b2 (Pfizer-BioNTech). Whole blood was sampled from 31 healthy adults pre-vaccination, and four weeks after dose one and dose two of ChAdOx1. Neutralizing antibodies (NAb) against SARS-CoV-2 were quantified at each timepoint. Recombinant RBDs of the Wuhan-Hu-1 (WH1), Delta, BA.2, and BA.5 variants were produced for ELISA-based quantification of plasma IgG and incorporated separately into fluorescent tetramers for flow cytometric identification of RBD-specific Bmem. NAb and RBD-specific IgG levels were over eight times lower following ChAdOx1 vaccination than BNT162b2. In ChAdOx1-vaccinated individuals, median plasma IgG recognition of BA.2 and BA.5 as a proportion of WH1-specific IgG was 26% and 17%, respectively. All donors generated resting RBD-specific Bmem, which were boosted after the second dose of ChAdOx1, and were similar in number to those produced by BNT162b2. The second dose of ChAdOx1 boosted Bmem that recognized VoC, and 37% and 39% of WH1-specific Bmem recognized BA.2 and BA.5, respectively. These data uncover mechanisms by which ChAdOx1 elicits immune memory to confer effective protection against severe COVID-19.