Covid-19: Do many people have pre-existing immunity?

Coronavirus disease-19 vaccine uptake, willingness for vaccination, and associated Factors among chronic follow patients attending in the two comprehensive specialized hospitals of Bahir Dar, Ethiopia

BACKGROUND

Even though the disease has spread throughout the world, with millions killed, global COVID-19 vaccination coverage remains low, particularly in developing countries. However, epidemiological data is lacking in the area. Hence, this study aimed to assess COVID-19 uptake, willingness for vaccination, and associated factors.

METHOD

A hospital-based cross-sectional study was conducted from May 1 to June 30, 2022, among patients attending chronic follow-up clinics in the two comprehensive specialized hospitals in Bahir Dar. The total sample size was 423. Participants were selected by a systematic random sampling technique. Data was gathered using a pre-tested questionnaire and analyzed using SPSS version 23. A descriptive analysis was performed. A binary logistic regression analysis was done to assess the association between variables. Variables with a p-value < 0.05 in the multi-variable logistic regression with a 95% confidence interval were considered statistically significant.

RESULTS

The analysis included 400 out of 423 participants, representing a 95% response rate. The COVID-19 vaccination uptake was 46.8%, while the acceptance was 60.5%. About 56% and 68% of the respondents had good knowledge and a favorable attitude, respectively. Elderly people were 2.7 times more likely to be vaccinated. Similarly, urban residents were 3.94 times more vaccinated. The probability of being vaccinated among respondents with good knowledge and favorable attitudes was 70% and 79%, respectively. The willingness for vaccination increased among those individuals with favorable attitudes (AOR: 1.82). Urban people were less likely to accept vaccination (AOR: 0.46). Some participants misunderstood that vaccination may aggravate their disease condition.

CONCLUSION

The overall COVID-19 vaccine uptake and acceptance for vaccination were low compared to what was estimated by the WHO. Age, residence, knowledge, and attitude were associated with COVID-19 vaccine uptake and acceptance of vaccination. Besides, there was a high level of rumor about the status of the vaccine and risk factors. Hence, special emphasis is warranted to deliver centrally trusted information. Moreover, further nationwide studies are warranted in the future.

The Effect of Mask Use on Seasonal Virus Diversity in SARS CoV-2 Negative Patients Treated as Inpatients During the 2021-2022 and 2022-2023 Seasonal Flu Period

The study aimed to explore the protective effect of mask use against respiratory tract viral agents during the pandemic. The study included patients with a COVID-19 negative test who were hospitalized in the pulmonary disease clinic with the diagnoses of asthma attack, chronic obstructive pulmonary disease (COPD) exacerbation, and pneumonia in two periods: during mandatory mask use (October 2021 - May 2022) and after the mask mandate was lifted (October 2022 - May 2023). Combined nose and throat swab samples taken from the patients were evaluated for viral agents by using the PCR test method. Viral agents isolated from the patients in the two periods were compared based on hospitalization diagnoses and periods. The study enrolled 1,335 patients, 483 female and 852 male. It was found that viral agents significantly increased during the period without a mask mandate compared to the period when the mask mandate was in effect (41.6% vs. 23.4%) (p < 0.001). During the period without mask mandate, influenza A, H1N1, and RSV/AB viruses significantly increased (p = 0.019, p = 0.003, p < 0.001, respectively). Our results indicated that mask use during the pandemic is protective against the transmission of respiratory tract viruses. Thus, it can be concluded that mask use is important not only in the coronavirus pandemic but also especially in influenza and RSV epidemics.

Excess Deaths in Korea During the COVID-19 Pandemic: 2020-2022

OBJECTIVES

Excess deaths, an indicator that compares total mortality rates before and during a pandemic, offer a comprehensive view of the pandemic's impact. However, discrepancies may arise from variations in estimating expected deaths. This study aims to compare excess deaths in Korea during the coronavirus disease 2019 pandemic using 3 methods and to analyze patterns using the most appropriate method.

METHODS

Expected deaths from 2020 to 2022 were estimated using mortality data from 2015-2019 as reference years. This estimation employed 3 approaches: (1) simple average, (2) age-adjusted average, and (3) age-adjusted linear regression. Excess deaths by age, gender, and cause of death were also presented.

RESULTS

The number of excess deaths varied depending on the estimation method used, reaching its highest point with the simple average and its lowest with the age-adjusted average. Age-adjusted linear regression, which accounts for both the aging population and declining mortality rates, was considered most appropriate. Using this model, excess deaths were estimated at 0.3% for 2020, 4.0% for 2021, and 20.7% for 2022. Excess deaths surged among individuals in their 20s throughout the pandemic, largely attributed to a rise in self-harm and suicide. Additionally, the results indicated sharp increases in deaths associated with "endocrine, nutritional, and metabolic diseases" and "symptoms, signs, and abnormal clinical and laboratory findings, not elsewhere classified."

CONCLUSIONS

Substantial variations in excess deaths were evident based on estimation method, with a notable increase in 2022. The heightened excess deaths among young adults and specific causes underscore key considerations for future pandemic responses.

The creativity of cells: aneural irrational cognition

Evidence of cognition in aneural cells is well-establish in the literature. This paper extends the exploration of the mechanisms of cognition by considering whether or not aneural cells may be capable of irrational cognition, making associations based on coincidental similarities and circumstantial factors. If aneural cells do harness such semiosic qualities, as with higher-level creativity, this might be how they are able to overcome old algorithms and invent tools for new situations. I will look at three examples of irrational learning in aneural systems in terms of semiotics: (1) generalisation in the immune system, based on viral molecular mimicry, whereby immune cells attack the self, which seems to be an overgeneralisation of an icon sign based on mere similarity, not identity, (2) the classical conditioning of pea plants to trope toward wind as a sign of light, which seems to be an association of an index sign based on mere temporal proximity, and (3) a pharmaceutical intervention to prevent pregnancy, using a conjugate to encrypt self with non-self, which seems to be an example of symbol use. We identify irrational cognition easily when it leads to 'wrong' outcomes, but, if it occurs, it may also lead to favourable outcomes and 'creative' solutions.

Pandemic fatigue, behavioral intention and predictors of COVID-19 vaccination among individuals living with HIV in Bench Sheko Zone, in Southern Ethiopia, application of TBP: a facility based cross sectional study

Introduction

People living with HIV often face inequalities and negative outcomes, which make them vulnerable. To protect this population and achieve herd immunity, it is crucial for COVID-19 vaccination efforts to prioritize and encourage vaccination among people living with HIV (PLWH). However, in Ethiopia, there is a lack of motivation in this regard. To tackle this issue, a study was conducted in the Bench Sheko Zone of Southwest Ethiopia. The study aimed to assess pandemic fatigue, behavioral intention to get vaccinated, and factors influencing COVID-19 vaccine acceptance among PLWH in that region.

Methods

A facility-based cross-sectional study was conducted among individuals living with HIV who were over 18 years old in Bench-Sheko Zone, located in Southwest Ethiopia. The study included a total of 590 participants from four ART healthcare facilities within the zone. The researchers utilized the Theory of Planned Behavior to examine the predictors of intention to use preconception care. Multiple linear regression analysis was employed to determine these predictors, with a p-value of less than 0.05 considered as indicative of a significant association. The final analysis of the study involved the use of linear regression analysis, and the measure of association was presented as the standardized B coefficient following a multivariable logistic regression analysis.

Result

In the conducted study, the response rate was an impressive 98%. The researchers aimed to investigate the behavioral intention toward the COVID-19 vaccine, which was found to be 55.7%. The average age of the participants in the study was 34.65 ± 6.67. The study was the assessment of pandemic fatigue, which had a mean value of 17.22 ± 5.28. During the multivariate linear regression analysis, four predictor variables were identified. Among these, three variables, namely subjective norm, pandemic fatigue, and age, positively influenced the behavioral intention toward the COVID-19 vaccine. Comprehending these factors can assist healthcare professionals and policymakers in formulating precise interventions and strategies aimed at enhancing the acceptance and adoption of vaccines.

Conclusion

The study indicates that individuals living with HIV have shown lower vaccine intention compared to previous research. The study identifies subjective norm, pandemic control measures, income, and age as predictors of individuals' intention to receive the COVID-19 vaccine.

Gene-based COVID-19 vaccines: Australian perspectives in a corporate and global context

Pandemic management requires societal coordination, global orchestration, respect for human rights and defence of ethical principles. Yet some approaches to the COVID-19 pandemic, driven by socioeconomic, corporate, and political interests, have undermined key pillars of ethical medical science. We explore significant mistakes that may have occurred in recent pandemic control, in order to better navigate the future. Within corporate and geopolitical infrastructure, we review the COVID-19 pandemic and novel mRNA and viral-vector DNA COVID-19 vaccines, deployed by wealthy western countries. The pandemic, together with rollouts of unconventional, gene-based vaccine technology, has provided experimental opportunity to engineer social control of entire populations. The haste and scale of development, production, and distribution of these new pharmaceuticals is unprecedented in history. Key phase III clinical trials for these products are yet to be fully completed, despite administration to billions of people. Mass vaccination of workforces has been mandated, and vaccine mandates correlate with excess mortality. Many independent data sets concur - we have experienced a pandemic of viral illness, followed by a pandemic of vaccine injury. For Australia, matters have operated the other way around. Vaccination followed later by the main viral wave. Australian excess mortality data correlates with this. Neither risk nor cost can justify these products for the vast majority of people. Lack of efficacy against infection and transmission, and the equivalent benefits of natural immunity, obviate mandatory therapeutics. With the many gene-based pharmaceuticals planned, a new era of pathology lies ahead. We should pause, reflect, and reaffirm essential freedoms, welcome the end of the COVID-19 pandemic, embrace natural immunity, and lift all mandated medical therapy.

Influenza-A mediated pre-existing immunity levels to SARS-CoV-2 could predict early COVID-19 outbreak dynamics

Susceptibility to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections is highly variable and could be mediated by a cross-protective pre-immunity. We identified 14 cross-reactive peptides between SARS-CoV-2 and influenza A H1N1, H3N2, and human herpesvirus (HHV)-6A/B with potential relevance. The H1N1 peptide NGVEGF was identical to a peptide in the most critical receptor binding motif in SARS-CoV-2 spike protein that interacts with the angiotensin converting enzyme 2 receptor. About 62%-73% of COVID-19-negative blood donors in Stockholm had antibodies to this peptide in the early pre-vaccination phase of the pandemic. Seasonal flu vaccination enhanced neutralizing capacity to SARS-CoV-2 and T cell immunity to this peptide. Mathematical modeling taking the estimated pre-immunity levels to flu into account could fully predict pre-Omicron SARS-CoV-2 outbreaks in Stockholm and India. This cross-immunity provides mechanistic explanations to the epidemiological observation that influenza vaccination protected people against early SARS-CoV-2 infections and implies that flu-mediated cross-protective immunity significantly dampened the first SARS-CoV-2 outbreaks.

Potential use of endemic human coronaviruses to stimulate immunity against pathogenic SARS-CoV-2 and its variants

While severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes significant morbidity and mortality in humans, there is a wide range of disease outcomes following virus exposures. Some individuals are asymptomatic while others develop complications within a few days after infection that can lead to fatalities in a smaller portion of the population. In the present study, we have analyzed the factors that may influence the outcome of post-SARS-CoV-2 infection. One factor that may influence virus control is pre-existing immunity conferred by an individual's past exposures to endemic coronaviruses (eCOVIDs) which cause the common cold in humans and generally, most children are exposed to one of the four eCOVIDs before 2 years of age. Here, we have carried out protein sequence analyses to show the amino acid homologies between the four eCOVIDs (i.e. OC43, HKU1, 229E, and NL63) as well as examining the cross-reactive immune responses between SARS-CoV-2 and eCOVIDs by epidemiologic analyses. Our results show that the nations where continuous exposures to eCOVIDs are very high due to religious and traditional causes showed significantly lower cases and low mortality rates per 100,000. We hypothesize that in the areas of the globe where Muslims are in majority and due to religious practices are regularly exposed to eCOVIDs they show a significantly lower infection, as well as mortality rate, and that is due to pre-existing cross-immunity against SARS-CoV-2. This is due to cross-reactive antibodies and T-cells that recognize SARS-CoV-2 antigens. We also have reviewed the current literature that has also proposed that human infections with eCOVIDs impart protection against disease caused by subsequent exposure to SARS-CoV-2. We propose that a nasal spray vaccine consisting of selected genes of eCOVIDs would be beneficial against SARS-CoV-2 and other pathogenic coronaviruses.

Reproduction number projection for the COVID-19 pandemic

The recently derived Hybrid-Incidence Susceptible-Transmissible-Removed (HI-STR) prototype is a deterministic compartment model for epidemics and an alternative to the Susceptible-Infected-Removed (SIR) model. The HI-STR predicts that pathogen transmission depends on host population characteristics including population size, population density and social behaviour common within that population.

The HI-STR prototype is applied to the ancestral Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV2) to show that the original estimates of the Coronavirus Disease 2019 (COVID-19) basic reproduction number $\mathcal{R}_{0}$ R 0 for the United Kingdom (UK) could have been projected onto the individual states of the United States of America (USA) prior to being detected in the USA.

The Imperial College London (ICL) group’s estimate of $\mathcal{R}_{0}$ R 0 for the UK is projected onto each USA state. The difference between these projections and the ICL’s estimates for USA states is either not statistically significant on the paired Student t-test or not epidemiologically significant.

The SARS-CoV2 Delta variant’s $\mathcal{R}_{0}$ R 0 is also projected from the UK to the USA to prove that projection can be applied to a Variant of Concern (VOC). Projection provides both a localised baseline for evaluating the implementation of an intervention policy and a mechanism for anticipating the impact of a VOC before local manifestation.

Hybrid molecules based on an emodin scaffold. Synthesis and activity against SARS-CoV-2 and Plasmodium

Since the Covid-19 epidemic, it has been clear that the availability of small and affordable drugs that are able to efficiently control viral infections in humans is still a challenge in medicinal chemistry. The synthesis and biological activities of a series of hybrid molecules that combine an emodin moiety and other structural moieties expected to act as possible synergistic pharmacophores in a single molecule were studied. Emodin has been reported to block the entry of the SARS-CoV-2 virus into human cells and might also inhibit cytokine production, resulting in the reduction of pulmonary injury induced by SARS-CoV-2. The pharmacophore associated with emodin was either a polyamine residue (emodin-PA series), a choice driven by the fact that a natural alkyl PA like spermine and spermidine play regulatory roles in immune cell functions, or a diphenylmethylpiperazine derivative of the norchlorcyclizine series (emoxyzine series). In fact, diphenylmethylpiperazine antagonists of the H1 histamine receptor display activity against several viruses by multiple interrelated mechanisms. In the emoxyzine series, the most potent drug against SARS-CoV-2 was (R)-emoxyzine-2, with an EC50 value = 1.9 μM, which is in the same range as that of the reference drug remdesivir. However, the selectivity index was rather low, indicating that the dissociation of antiviral potency and cytotoxicity remains a challenge. In addition, since emodin was also reported to be a relatively high-affinity inhibitor of the virulence regulator FIKK kinase from the malaria parasite Plasmodium vivax, the antimalarial activity of the synthesized hybrid compounds has been evaluated. However, these molecules cannot efficiently compete with the currently used antimalarial drugs.

Innate and Adaptive Immunity during SARS-CoV-2 Infection: Biomolecular Cellular Markers and Mechanisms

The coronavirus 2019 (COVID-19) pandemic was caused by a positive sense single-stranded RNA (ssRNA) severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, other human coronaviruses (hCoVs) exist. Historical pandemics include smallpox and influenza, with efficacious therapeutics utilized to reduce overall disease burden through effectively targeting a competent host immune system response. The immune system is composed of primary/secondary lymphoid structures with initially eight types of immune cell types, and many other subtypes, traversing cell membranes utilizing cell signaling cascades that contribute towards clearance of pathogenic proteins. Other proteins discussed include cluster of differentiation (CD) markers, major histocompatibility complexes (MHC), pleiotropic interleukins (IL), and chemokines (CXC). The historical concepts of host immunity are the innate and adaptive immune systems. The adaptive immune system is represented by T cells, B cells, and antibodies. The innate immune system is represented by macrophages, neutrophils, dendritic cells, and the complement system. Other viruses can affect and regulate cell cycle progression for example, in cancers that include human papillomavirus (HPV: cervical carcinoma), Epstein-Barr virus (EBV: lymphoma), Hepatitis B and C (HB/HC: hepatocellular carcinoma) and human T cell Leukemia Virus-1 (T cell leukemia). Bacterial infections also increase the risk of developing cancer (e.g., Helicobacter pylori). Viral and bacterial factors can cause both morbidity and mortality alongside being transmitted within clinical and community settings through affecting a host immune response. Therefore, it is appropriate to contextualize advances in single cell sequencing in conjunction with other laboratory techniques allowing insights into immune cell characterization. These developments offer improved clarity and understanding that overlap with autoimmune conditions that could be affected by innate B cells (B1+ or marginal zone cells) or adaptive T cell responses to SARS-CoV-2 infection and other pathologies. Thus, this review starts with an introduction into host respiratory infection before examining invaluable cellular messenger proteins and then individual immune cell markers.

Transitioning the COVID-19 response in the WHO African region: a proposed framework for rethinking and rebuilding health systems

The onset of the pandemic revealed the health system inequities and inadequate preparedness, especially in the African continent. Over the past months, African countries have ensured optimum pandemic response. However, there is still a need to build further resilient health systems that enhance response and transition from the acute phase of the pandemic to the recovery interpandemic/preparedness phase. Guided by the lessons learnt in the response and plausible pandemic scenarios, the WHO Regional Office for Africa has envisioned a transition framework that will optimise the response and enhance preparedness for future public health emergencies. The framework encompasses maintaining and consolidating the current response capacity but with a view to learning and reshaping them by harnessing the power of science, data and digital technologies, and research innovations. In addition, the framework reorients the health system towards primary healthcare and integrates response into routine care based on best practices/health system interventions. These elements are significant in building a resilient health system capable of addressing more effectively and more effectively future public health crises, all while maintaining an optimal level of essential public health functions. The key elements of the framework are possible with countries following three principles: equity (the protection of all vulnerable populations with no one left behind), inclusiveness (full engagement, equal participation, leadership, decision-making and ownership of all stakeholders using a multisectoral and transdisciplinary, One Health approach), and coherence (to reduce the fragmentation, competition and duplication and promote logical, consistent programmes aligned with international instruments).

SARS-CoV-2-The Role of Natural Immunity: A Narrative Review

BACKGROUND

Both natural immunity and vaccine-induced immunity to COVID-19 may be useful to reduce the mortality/morbidity of this disease, but still a lot of controversy exists.

AIMS

This narrative review analyzes the literature regarding these two immunitary processes and more specifically: (a) the duration of natural immunity; (b) cellular immunity; (c) cross-reactivity; (d) the duration of post-vaccination immune protection; (e) the probability of reinfection and its clinical manifestations in the recovered patients; (f) the comparisons between vaccinated and unvaccinated as to the possible reinfections; (g) the role of hybrid immunity; (h) the effectiveness of natural and vaccine-induced immunity against Omicron variant; (i) the comparative incidence of adverse effects after vaccination in recovered individuals vs. COVID-19-naïve subjects.

MATERIAL AND METHODS

through multiple search engines we investigated COVID-19 literature related to the aims of the review, published since April 2020 through July 2022, including also the previous articles pertinent to the investigated topics.

RESULTS

nearly 900 studies were collected, and 246 pertinent articles were included. It was highlighted that the vast majority of the individuals after suffering from COVID-19 develop a natural immunity both of cell-mediated and humoral type, which is effective over time and provides protection against both reinfection and serious illness. Vaccine-induced immunity was shown to decay faster than natural immunity. In general, the severity of the symptoms of reinfection is significantly lower than in the primary infection, with a lower degree of hospitalizations (0.06%) and an extremely low mortality.

CONCLUSIONS

this extensive narrative review regarding a vast number of articles highlighted the valuable protection induced by the natural immunity after COVID-19, which seems comparable or superior to the one induced by anti-SARS-CoV-2 vaccination. Consequently, vaccination of the unvaccinated COVID-19-recovered subjects may not be indicated. Further research is needed in order to: (a) measure the durability of immunity over time; (b) evaluate both the impacts of Omicron BA.5 on vaccinated and healed subjects and the role of hybrid immunity.

Preexisting antibodies targeting SARS-CoV-2 S2 cross-react with commensal gut bacteria and impact COVID-19 vaccine induced immunity

The origins of preexisting SARS-CoV-2 cross-reactive antibodies and their potential impacts on vaccine efficacy have not been fully clarified. In this study, we demonstrated that S2 was the prevailing target of the preexisting S protein cross-reactive antibodies in both healthy human and SPF mice. A dominant antibody epitope was identified on the connector domain of S2 (1147-SFKEELDKYFKNHT-1160, P144), which could be recognized by preexisting antibodies in both human and mouse. Through metagenomic sequencing and fecal bacteria transplant, we demonstrated that the generation of S2 cross-reactive antibodies was associated with commensal gut bacteria. Furthermore, six P144 reactive monoclonal antibodies were isolated from naïve SPF mice and were proven to cross-react with commensal gut bacteria collected from both human and mouse. A variety of cross-reactive microbial proteins were identified using LC-MS, of which E. coli derived HSP60 and HSP70 proteins were confirmed to be able to bind to one of the isolated monoclonal antibodies. Mice with high levels of preexisting S2 cross-reactive antibodies mounted higher S protein specific binding antibodies, especially against S2, after being immunized with a SARS-CoV-2 S DNA vaccine. Similarly, we found that levels of preexisting S2 and P144-specific antibodies correlated positively with RBD binding antibody titers after two doses of inactivated SARS-CoV-2 vaccination in human. Collectively, our study revealed an alternative origin of preexisting S2-targeted antibodies and disclosed a previously neglected aspect of the impact of gut microbiota on host anti-SARS-CoV-2 immunity.

Prospects of animal models and their application in studies on adaptive immunity to SARS-CoV-2

The adaptive immune response induced by SARS-CoV-2 plays a key role in the antiviral process and can protect the body from the threat of infection for a certain period of time. However, owing to the limitations of clinical studies, the antiviral mechanisms, protective thresholds, and persistence of the immune memory of adaptive immune responses remain unclear. This review summarizes existing research models for SARS-CoV-2 and elaborates on the advantages of animal models in simulating the clinical symptoms of COVID-19 in humans. In addition, we systematically summarize the research progress on the SARS-CoV-2 adaptive immune response and the remaining key issues, as well as the application and prospects of animal models in this field. This paper provides direction for in-depth analysis of the anti-SARS-CoV-2 mechanism of the adaptive immune response and lays the foundation for the development and application of vaccines and drugs.

The 1968 Influenza Pandemic and COVID-19 Outcomes

Past pandemic experience can affect health outcomes in future pandemics. This paper focuses on the last major influenza pandemic in 1968 (H3N2), which killed up to 100,000 people in the US. We find that places with high influenza mortality in 1968 experienced 1-4% lower COVID-19 death rates. Our identification strategy isolates variation in COVID-19 rates across people born before and after 1968. In places with high 1968 influenza incidence, older cohorts experience lower COVID-19 death rates relative to younger ones. The relationship holds using county and patient-level data, as well as in hospital and nursing home settings. Results do not appear to be driven by systemic or policy-related factors, instead suggesting an individual-level response to prior influenza pandemic exposure. The findings merit investigation into potential biological and immunological mechanisms that account for these differences-and their implications for future pandemic preparedness.

Coordination and Management of COVID-19 in Africa through Health Operations and Technical Expertise Pillar: A Case Study from WHO AFRO One Year into Response

Background: following the importation of the first Coronavirus disease 2019 (COVID-19) case into Africa on 14 February 2020 in Egypt, the World Health Organisation (WHO) regional office for Africa (AFRO) activated a three-level incident management support team (IMST), with technical pillars, to coordinate planning, implementing, supervision, and monitoring of the situation and progress of implementation as well as response to the pandemic in the region. At WHO AFRO, one of the pillars was the health operations and technical expertise (HOTE) pillar with five sub-pillars: case management, infection prevention and control, risk communication and community engagement, laboratory, and emergency medical team (EMT). This paper documents the learnings (both positive and negative for consideration of change) from the activities of the HOTE pillar and recommends future actions for improving its coordination for future emergencies, especially for multi-country outbreaks or pandemic emergency responses. Method: we conducted a document review of the HOTE pillar coordination meetings’ minutes, reports, policy and strategy documents of the activities, and outcomes and feedback on updates on the HOTE pillar given at regular intervals to the Regional IMST. In addition, key informant interviews were conducted with 14 members of the HOTE sub pillar. Key Learnings: the pandemic response revealed that shared decision making, collaborative coordination, and planning have been significant in the COVID-19 response in Africa. The HOTE pillar’s response structure contributed to attaining the IMST objectives in the African region and translated to timely support for the WHO AFRO and the member states. However, while the coordination mechanism appeared robust, some challenges included duplication of coordination efforts, communication, documentation, and information management. Recommendations: we recommend streamlining the flow of information to better understand the challenges that countries face. There is a need to define the role and responsibilities of sub-pillar team members and provide new team members with information briefs to guide them on where and how to access internal information and work under the pillar. A unified documentation system is important and could help to strengthen intra-pillar collaboration and communication. Various indicators should be developed to constantly monitor the HOTE team’s deliverables, performance and its members.

COVID-19: Pathophysiology, transmission, and drug development for therapeutic treatment and vaccination strategies

COVID-19, a dreaded and highly contagious pandemic, is flagrantly known for its rapid prevalence across the world. Till date, none of the treatments are distinctly accessible for this life-threatening disease. Under the prevailing conditions of medical emergency, one creative strategy for the identification of novel and potential antiviral agents gaining momentum in research institutions and progressively being leveraged by pharmaceutical companies is target-based drug repositioning/repurposing. A continuous monitoring and recording of results offer an anticipation that this strategy may help to reveal new medications for viral infections. This review recapitulates the neoteric illation of COVID-19, its genomic dispensation, molecular evolution via phylogenetic assessment, drug targets, the most frequently worldwide used repurposed drugs and their therapeutic applications, and a recent update on vaccine management strategies. The available data from solidarity trials exposed that the treatment with several known drugs, viz. lopinavir-ritonavir, chloroquine, hydroxychloroquine, etc had displayed various antagonistic effects along with no impactful result in diminution of mortality rate. The drugs like remdesivir, favipiravir, and ribavirin proved to be quite safer therapeutic options for treatment against COVID-19. Similarly, dexamethasone, convalescent plasma therapy and oral administration of 2DG are expected to reduce the mortality rate of COVID-19 patients.

The Impact of the Highly Virulent SARS-CoV-2 Gamma Variant on Young Adults in the State of São Paulo: Was It Inevitable?

Background

The coronavirus disease 2019 (COVID-19) pandemic had and is still having a tremendous impact on people all over the world, but it has been particularly harsh in South America. Nine out of 13 South American countries are among the 50 countries with the highest COVID-19 death rates. The gamma severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant that emerged by the end of 2020 in the Brazilian Amazon quickly spread throughout the country causing the harsh COVID-19 second wave. This variant displayed high viral loads, high transmissibility, and increased virulence as compared to previous variants.

Aims

The aim of this retrospective study is to revisit and analyse the epidemiology of the COVID-19 second wave in the state of São Paulo, the most populous Brazilian state. In addition to examining the possible factors that led to the emergence and propagation of the gamma variant, measures that could have prevented its spread and that of other highly virulent variants were also investigated.

Materials and methods

Data from São Paulo's official sources on morbidity, mortality, age distribution, and testing prior to and during the COVID-19 second wave (February - June 2021) and data regarding the distribution of SARS-CoV-2 variants in the country were parsed, analyzed, and compared to the period that anteceded the eruption of the second COVID-19 wave.

Results

In the state of São Paulo, the toll of the COVID-19 second wave surpassed that of the first 11 months of the pandemic (from March 2020 to January 2021), as 56% of the deaths occurred in the five months of the second wave between February and June 2021. The mean age of COVID-19 victims, which was already below life expectancy in the state dropped even further in the pandemic's second wave, reaching an average of 60 years of age. The years of life lost per death per month doubled and the case-fatality rate (CFR) of young adults (20-39 years old) more than trebled during this period. A number of hypotheses have been raised that might explain the emergence and spread of the gamma variant and the measures that could have been taken to prevent it and minimise its impact on the population.

Conclusions

Over 142,000 people died as a result of the SARS-CoV-2 gamma variant sweep in São Paulo in the first semester of 2021. Due to its high viral load, the gamma variant displayed high transmissibility and a high degree of virulence resulting in increased case fatality rates across most age tiers. Notably, this second wave was marked by a very significant increase in deaths among young adults. This increase was at least partially due to a deterioration in general health provoked by non-pharmaceutical interventions. In hindsight, a safer and more effective measure might have been to allow the free spread of the virus among the young and healthy in the first wave, thus conferring immunity against more virulent variants that emerged later on.

Seasonal coronaviruses and SARS-CoV-2: effects of preexisting immunity during the COVID-19 pandemic

Although the coronavirus disease 2019 (COVID-19) epidemic is still ongoing, vaccination rates are rising slowly and related treatments and drugs are being developed. At the same time, there is increasing evidence of preexisting immunity against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in humans, mainly consisting of preexisting antibodies and immune cells (including T cells and B cells). The presence of these antibodies is mainly due to the seasonal prevalence of four common coronavirus types, especially OC43 and HKU1. The accumulated relevant evidence has suggested that the target of antibodies is mainly the S2 subunit of S protein, followed by evolutionary conservative regions such as the nucleocapsid (N) protein. Additionally, preexisting memory T and B cells are also present in the population. Preexisting antibodies can help the body protect against SARS-CoV-2 infection, reduce the severity of COVID-19, and rapidly increase the immune response post-infection. These multiple effects can directly affect disease progression and even the likelihood of death in certain individuals. Besides the positive effects, preexisting immunity may also have negative consequences, such as antibody-dependent enhancement (ADE) and original antigenic sin (OAS), the prevalence of which needs to be further established. In the future, more research should be focused on evaluating the role of preexisting immunity in COVID-19 outcomes, adopting appropriate policies and strategies for fighting the pandemic, and vaccine development that considers preexisting immunity.

Coordination mechanisms for COVID-19 in the WHO Regional office for Africa

Aim

This study describes the coordination mechanisms that have been used for management of the COVID 19 pandemic in the WHO AFRO region; relate the patterns of the disease (length of time between onset of coordination and first case; length of the wave of the disease and peak attack rate) to coordination mechanisms established at the national level, and document best practices and lessons learned.

Method

We did a retrospective policy tracing of the COVID-19 coordination mechanisms from March 2020 (when first cases of COVID-19 in the AFRO region were reported) to the end of the third wave in September 2021. Data sources were from document and Literature review of COVID-19 response strategies, plans, regulations, press releases, government websites, grey and peer-reviewed literature. The data was extracted to Excel file database and coded then analysed using Stata (version 15). Analysis was done through descriptive statistical analysis (using measures of central tendencies (mean, SD, and median) and measures of central dispersion (range)), multiple linear regression, and thematic analysis of qualitative data.

Results

There are three distinct layered coordination mechanisms (strategic, operational, and tactical) that were either implemented singularly or in tandem with another coordination mechanism. 87.23% (n = 41) of the countries initiated strategic coordination, and 59.57% (n = 28) initiated some form of operational coordination. Some of countries (n = 26,55.32%) provided operational coordination using functional Public Health Emergency Operation Centres (PHEOCs) which were activated for the response. 31.91% (n = 15) of the countries initiated some form of tactical coordination which involved the decentralisation of the operations at the local/grassroot level/district/ county levels. Decentralisation strategies played a key role in coordination, as was the innovative strategies by the countries; some coordination mechanisms built on already existing coordination systems and the heads of states were effective in the success of the coordination process. Financing posed challenge to majority of the countries in initiating coordination.

Conclusion

Coordinating an emergency is a multidimensional process that includes having decision-makers and institutional agents define and prioritise policies and norms that contain the spread of the disease, regulate activities and behaviour and citizens, and respond to personnel who coordinate prevention.

HLA-dependent variation in SARS-CoV-2 CD8 + T cell cross-reactivity with human coronaviruses

The conditions and extent of cross-protective immunity between severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and common-cold human coronaviruses (HCoVs) remain open despite several reports of pre-existing T cell immunity to SARS-CoV-2 in individuals without prior exposure. Using a pool of functionally evaluated SARS-CoV-2 peptides, we report a map of 126 immunogenic peptides with high similarity to 285 MHC-presented peptides from at least one HCoV. Employing this map of SARS-CoV-2-non-homologous and homologous immunogenic peptides, we observe several immunogenic peptides with high similarity to human proteins, some of which have been reported to have elevated expression in severe COVID-19 patients. After combining our map with SARS-CoV-2-specific TCR repertoire data from COVID-19 patients and healthy controls, we show that public repertoires for the majority of convalescent patients are dominated by TCRs cognate to non-homologous SARS-CoV-2 peptides. We find that for a subset of patients, >50% of their public SARS-CoV-2-specific repertoires consist of TCRs cognate to homologous SARS-CoV-2-HCoV peptides. Further analysis suggests that this skewed distribution of TCRs cognate to homologous or non-homologous peptides in COVID-19 patients is likely to be HLA-dependent. Finally, we provide 10 SARS-CoV-2 peptides with known cognate TCRs that are conserved across multiple coronaviruses and are predicted to be recognized by a high proportion of the global population. These findings may have important implications for COVID-19 heterogeneity, vaccine-induced immune responses, and robustness of immunity to SARS-CoV-2 and its variants.

Modeling SARS-CoV-2 spike/ACE2 protein-protein interactions for predicting the binding affinity of new spike variants for ACE2, and novel ACE2 structurally related human protein targets, for COVID-19 handling in the 3PM context

Aims

The rapid spread of new SARS-CoV-2 variants has highlighted the crucial role played in the infection by mutations occurring at the SARS-CoV-2 spike receptor binding domain (RBD) in the interactions with the human ACE2 receptor. In this context, it urgently needs to develop new rapid tools for quickly predicting the affinity of ACE2 for the SARS-CoV-2 spike RBD protein variants to be used with the ongoing SARS-CoV-2 genomic sequencing activities in the clinics, aiming to gain clues about the transmissibility and virulence of new variants, to prevent new outbreaks and to quickly estimate the severity of the disease in the context of the 3PM.

Methods

In our study, we used a computational pipeline for calculating the interaction energies at the SARS-CoV-2 spike RBD/ACE2 protein-protein interface for a selected group of characterized infectious variants of concern/interest (VoC/VoI). By using our pipeline, we built 3D comparative models of the SARS-CoV-2 spike RBD/ACE2 protein complexes for the VoC B.1.1.7-United Kingdom (carrying the mutations of concern/interest N501Y, S494P, E484K at the RBD), P.1-Japan/Brazil (RBD mutations: K417T, E484K, N501Y), B.1.351-South Africa (RBD mutations: K417N, E484K, N501Y), B.1.427/B.1.429-California (RBD mutations: L452R), the B.1.141 (RBD mutations: N439K), and the recent B.1.617.1-India (RBD mutations: L452R; E484Q) and the B.1.620 (RBD mutations: S477N; E484K). Then, we used the obtained 3D comparative models of the SARS-CoV-2 spike RBD/ACE2 protein complexes for predicting the interaction energies at the protein-protein interface.

Results

Along SARS-CoV-2 mutation database screening and mutation localization analysis, it was ascertained that the most dangerous mutations at VoC/VoI spike proteins are located mainly at three regions of the SARS-CoV-2 spike "boat-shaped" receptor binding motif, on the RBD domain. Notably, the P.1 Japan/Brazil variant present three mutations, K417T, E484K, N501Y, located along the entire receptor binding motif, which apparently determines the highest interaction energy at the SARS-CoV-2 spike RBD/ACE2 protein-protein interface, among those calculated. Conversely, it was also observed that the replacement of a single acidic/hydrophilic residue with a basic residue (E484K or N439K) at the "stern" or "bow" regions, of the boat-shaped receptor binding motif on the RBD, appears to determine an interaction energy with ACE2 receptor higher than that observed with single mutations occurring at the "hull" region or with other multiple mutants. In addition, our pipeline allowed searching for ACE2 structurally related proteins, i.e., THOP1 and NLN, which deserve to be investigated for their possible involvement in interactions with the SARS-CoV-2 spike protein, in those tissues showing a low expression of ACE2, or as a novel receptor for future spike variants. A freely available web-tool for the in silico calculation of the interaction energy at the SARS-CoV-2 spike RBD/ACE2 protein-protein interface, starting from the sequences of the investigated spike and/or ACE2 variants, was made available for the scientific community at: https://www.mitoairm.it/covid19affinities.

Conclusion

In the context of the PPPM/3PM, the employment of the described pipeline through the provided webservice, together with the ongoing SARS-CoV-2 genomic sequencing, would help to predict the transmissibility of new variants sequenced from future patients, depending on SARS-CoV-2 genomic sequencing activities and on the specific amino acid replacement and/or on its location on the SARS-CoV-2 spike RBD, to put in play all the possible counteractions for preventing the most deleterious scenarios of new outbreaks, taking into consideration that a greater transmissibility has not to be necessarily related to a more severe manifestation of the disease.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13167-021-00267-w.

Limited Recognition of Highly Conserved Regions of SARS-CoV-2

Understanding the immune response to severe acute respiratory syndrome coronavirus (SARS-CoV-2) is critical to overcome the current coronavirus disease (COVID-19) pandemic. Efforts are being made to understand the potential cross-protective immunity of memory T cells, induced by prior encounters with seasonal coronaviruses, in providing protection against severe COVID-19. In this study we assessed T-cell responses directed against highly conserved regions of SARS-CoV-2. Epitope mapping revealed 16 CD8⁺ T-cell epitopes across the nucleocapsid (N), spike (S), and open reading frame (ORF)3a proteins of SARS-CoV-2 and five CD8⁺ T-cell epitopes encoded within the highly conserved regions of the ORF1ab polyprotein of SARS-CoV-2. Comparative sequence analysis showed high conservation of SARS-CoV-2 ORF1ab T-cell epitopes in seasonal coronaviruses. Paradoxically, the immune responses directed against the conserved ORF1ab epitopes were infrequent and subdominant in both convalescent and unexposed participants. This subdominant immune response was consistent with a low abundance of ORF1ab encoded proteins in SARS-CoV-2 infected cells. Overall, these observations suggest that while cross-reactive CD8⁺ T cells likely exist in unexposed individuals, they are not common and therefore are unlikely to play a significant role in providing broad preexisting immunity in the community.

IMPORTANCE T cells play a critical role in protection against SARS-CoV-2. Despite being highly topical, the protective role of preexisting memory CD8⁺ T cells, induced by prior exposure to circulating common coronavirus strains, remains less clear. In this study, we established a robust approach to specifically assess T cell responses to highly conserved regions within SARS-CoV-2. Consistent with recent observations we demonstrate that recognition of these highly conserved regions is associated with an increased likelihood of milder disease. However, extending these observations we observed that recognition of these conserved regions is rare in both exposed and unexposed volunteers, which we believe is associated with the low abundance of these proteins in SARS-CoV-2 infected cells. These observations have important implications for the likely role preexisting immunity plays in controlling severe disease, further emphasizing the importance of vaccination to generate the immunodominant T cells required for immune protection.

Incidence of SARS-CoV-2 infection among previously infected or vaccinated employees

INTRODUCTION

We aimed to determine the incidence of SARS-CoV-2 infection among individuals with a previous SARS-CoV-2 infection versus vaccinated individuals.

METHODS

In March 2020, a SARS-CoV-2 testing company began routinely screening its workforce for SARS-CoV-2 with a PCR test. On December 15, 2020, vaccination with either the BNT162b2 or mRNA-1273 vaccines became available. Routine screening has continued through July 2021. We compared the incidence of SARS-CoV-2 infection between people who were SARS-CoV-2 naïve and unvaccinated, people with prior COVID-19 without vaccination, and people vaccinated without prior COVID-19. Incidence in 100 person-years with 95% confidence intervals (95% CIs) was calculated with the Poisson Exact equation. The incidence rate ratio (IRR), the ratio of confirmed COVID-19 cases per 100 person-years of follow-up with 95% CIs, was used as a measure of association between groups. Analyses were performed on StataSE.

RESULTS

The median age of employees was 29.0 years (interquartile range: 23.6, 39.9). During the observation period, 258 SARS-CoV-2 incident infections were identified. The naïve, unvaccinated group had a SARS-CoV-2 incidence of 25.9 per 100 person-years (95% CI: 22.8-29.3). The previously infected, unvaccinated group had an incidence of 0 per 100 person-years (95% CI: 0-5.0). The vaccinated group had an incidence of 1.6 per 100 person-years (95% CI: 0.04-4.2).

CONCLUSION

We found a strong association between prior SARS-CoV-2 infection and/or vaccination for SARS-CoV-2 with either the BNT162b2 or mRNA-1273 vaccines and the reduced incidence of SARS-CoV-2 infection when compared with those naïve and/or unvaccinated to SARS-CoV-2.

Comparison of T-cell immune responses to SARS-CoV-2 spike (S) and nucleocapsid (N) protein using an in-house flow-cytometric assay in laboratory employees with and without previously confirmed COVID-19 in South Africa: nationwide cross-sectional study

AIMS

To compare specific T-cell responses between laboratory employees in South Africa with and without previously diagnosed SARS-CoV-2 infection.

METHODS

Employees at a private pathology laboratory in South Africa were invited to participate in a nationwide cross-sectional study. T-cell proliferation to SARS-CoV-2 nucleocapsid (N)-proteins and spike (S)-proteins was measured by flow cytometry and compared between participants.

RESULTS

Based on classification according to SARS-CoV-2 reverse transcription (RT)-PCR results, a total of 81% (42/52) of positive participants demonstrated T-cell proliferation to SARS-CoV-2 N-proteins or S-proteins (95% CI 67.5% to 90.4%), while 62% (68/110) of negative participants also had detectable T-cell responses to SARS-CoV-2 proteins (95% CI 52.1% to 70.9%). When classified according to SARS-CoV-2 serology results, 92.6% (50/54) of positive participants demonstrated T-cell proliferation to SARS-CoV-2 proteins (95% CI 82.1 to 97,9 %), while 56% (60/108) of negative participants demonstrated T-cell proliferation (95% CI 45.7% to 65.1%). The magnitude of the T-cell responses as determined by a stimulation index, was significantly higher in the group previously infected by SARS-CoV-2 than in the negative group. A statistically significant difference in T-cell proliferation was noted between high risk and low risk groups for exposure to SARS-CoV-2 within the negative group, but no significant difference in magnitude of the response.

CONCLUSIONS

A significant proportion of South African laboratory employees who were not previously diagnosed with COVID-19 demonstrated T-cell reactivity to SARS-CoV-2 N-proteins and S-proteins. The pre-existing T-cell proliferation responses may be attributable to cross-reactive immune responses to other human coronaviruses, or possibly asymptomatic infection.

An update on host immunity correlates and prospects of re-infection in COVID-19

Reinfection with SARS-CoV-2 is not frequent yet the incidence rate of it is increasing globally owing to the slow emergence of drift variants that pose a perpetual threat to vaccination strategies and have a greater propensity for disease reoccurrence. Long-term protection against SARS-CoV-2 reinfection relies on the induction of the innate as well as the adaptive immune response endowed with immune memory. However, a multitude of factors including the selection pressure, the waning immunity against SARS-CoV-2 over the first year after infection possibly favors evolution of more infectious immune escape variants, amplifying the risk of reinfection. Additionally, the correlates of immune protection, the novel SARS-CoV-2 variants of concern (VOC), the durability of the adaptive and mucosal immunity remain major challenges for the development of therapeutic and prophylactic interventions. Interestingly, a recent body of evidence indicated that the gastrointestinal (GI) tract is another important target organ for SARS-CoV-2 besides the respiratory system, potentially increasing the likelihood of reinfection by impacting the microbiome and the immune response via the gut-lung axis. In this review, we summarized the latest development in SARS-CoV-2 reinfection, and explored the untapped potential of trained immunity. We also highlighted the immune memory kinetics of the humoral and cell-mediated immune response, genetic drift of the emerging viral variants, and discussed the current challenges in vaccine development. Understanding the dynamics and the quality of immune response by unlocking the power of the innate, humoral and cell-mediated immunity during SARS-CoV-2 reinfection would open newer avenues for drug discovery and vaccine designs.

COVID-19 Vaccination: The Mainspring of Challenges and the Seed of Remonstrance

As of March 2020, the time when the coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) became a pandemic, our existence has been threatened and the lives of millions have been claimed. With this ongoing global issue, vaccines are considered of paramount importance in curtailing the outbreak and probably a prime gamble to bring us back to 'ordinary life'. To date, more than 200 vaccine candidates have been produced, many of which were approved by the Food and Drug Administration (FDA) for emergency use, with the research and discovery phase of their production process passed over. Capering such a chief practice in COVID-19 vaccine development, and manufacturing vaccines at an unprecedented speed brought many challenges into play and raised COVID-19 vaccine remonstrance. In this review, we highlight relevant challenges to global COVID-19 vaccine development, dissemination, and deployment, particularly at the level of large-scale production and distribution. We also delineate public perception on COVID-19 vaccination and outline the main facets affecting people's willingness to get vaccinated.

Cross-Reactive Antibodies to SARS-CoV-2 and MERS-CoV in Pre-COVID-19 Blood Samples from Sierra Leoneans

Many countries in sub-Saharan Africa have experienced lower COVID-19 caseloads and fewer deaths than countries in other regions worldwide. Under-reporting of cases and a younger population could partly account for these differences, but pre-existing immunity to coronaviruses is another potential factor. Blood samples from Sierra Leonean Lassa fever and Ebola survivors and their contacts collected before the first reported COVID-19 cases were assessed using enzyme-linked immunosorbent assays for the presence of antibodies binding to proteins of coronaviruses that infect humans. Results were compared to COVID-19 subjects and healthy blood donors from the United States. Prior to the pandemic, Sierra Leoneans had more frequent exposures than Americans to coronaviruses with epitopes that cross-react with severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), SARS-CoV, and Middle Eastern respiratory syndrome coronavirus (MERS-CoV). The percentage of Sierra Leoneans with antibodies reacting to seasonal coronaviruses was also higher than for American blood donors. Serological responses to coronaviruses by Sierra Leoneans did not differ by age or sex. Approximately a quarter of Sierra Leonian pre-pandemic blood samples had neutralizing antibodies against SARS-CoV-2 pseudovirus, while about a third neutralized MERS-CoV pseudovirus. Prior exposures to coronaviruses that induce cross-protective immunity may contribute to reduced COVID-19 cases and deaths in Sierra Leone.

Differential pre-pandemic breast milk IgA reactivity against SARS-CoV-2 and circulating human coronaviruses in Ugandan and American mothers

OBJECTIVE

Uganda has registered fewer coronavirus disease 2019 (COVID-19) cases and deaths per capita than Western countries. The lower numbers of cases and deaths might be due to pre-existing cross-immunity induced by circulating common cold human coronaviruses (HCoVs) before the COVID-19 pandemic. To investigate pre-existing mucosal antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19, a comparison was performed of IgA reactivity to SARS-CoV-2 and HCoVs in milk from mothers collected in 2018.

METHODS

Ugandan and United States milk samples were run on an ELISA to measure specific IgA to SARS-CoV-2 and HCoVs NL63, OC43, HKU1, and 229E spike proteins. Pooled plasma from United States SARS-CoV-2-positive and negative cases were positive and negative controls, respectively.

RESULTS

One Ugandan mother had high milk IgA reactivity against all HCoVs and SARS-CoV-2 spike proteins. Ugandan mothers had significantly higher IgA reactivity against the betacoronavirus HCoV-OC43 than United States mothers (P = 0.018). By contrast, United States mothers had significantly higher IgA reactivity against the alphacoronaviruses HCoV-229E and HCoV-NL63 than Ugandan mothers (P < 0.0001 and P = 0.035, respectively).

CONCLUSION

Some Ugandan mothers have pre-existing HCoV-induced IgA antibodies against SARS-CoV-2, which may be passed to infants via breastfeeding.

International comparisons of COVID-19 case and mortality data and the effectiveness of non-pharmaceutical interventions: a plea for reconsideration

International comparisons of the effectiveness of coronavirus disease 2019 (COVID-19) non-pharmaceutical interventions (NPIs) based on national case and mortality data are fraught with underestimated complexity. This article calls for stronger attention to just how extensive is the multifactorial nature of national case and mortality data, and argues that, unless a globally consistent benchmark of measurement can be devised, such comparisons are facile, if not misleading. This can lead to policy decisions and public support for the adoption of potentially harmful NPIs that are ineffective in combating the COVID-19 pandemic and damaging to mental health, social cohesion, human rights and economic development. The unscientific use of international comparisons of case and mortality data in public discourse, media reporting and policymaking on NPI effectiveness should be subject to greater scrutiny.

Estimated prevalence of COVID-19 in Brazil with probabilistic bias correction

Using data collected by the Brazilian National Household Sample Survey - COVID-19 (PNAD-COVID19) and semi-Bayesian modelling developed by Wu et al., we have estimated the effect of underreporting of COVID-19 cases in Brazil as of December 2020. The total number of infected individuals is about 3 to 8 times the number of cases reported, depending on the state. Confirmed cases are at 3.1% of the total population and our estimate of total cases is at almost 15% of the approximately 212 million Brazilians as of 2020. The method we adopted from Wu et al., with slight modifications in prior specifications, applies bias corrections to account for incomplete testing and imperfect test accuracy. Our estimates, which are comparable to results obtained by Wu et al. for the United States, indicate that projections from compartmental models (such as SEIR models) tend to overestimate the number of infections and that there is considerable regional heterogeneity (results are presented by state).

National population prevalence of antibodies to SARS-CoV-2 in Scotland during the first and second waves of the COVID-19 pandemic

Objectives

Studies that measure the prevalence of antibodies to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (‘seroprevalence’) are essential to understand population exposure to SARS-CoV-2 among symptomatic and asymptomatic individuals. We aimed to measure seroprevalence in the Scottish population over the course of the COVID-19 pandemic – from before the first recorded case in Scotland through to the second pandemic wave.

Study design

The study design of this study is serial cross sectional.

Methods

We tested 41,477 residual samples retrieved from primary and antenatal care settings across Scotland for SARS-CoV-2 antibodies over a 12-month period from December 2019-December 2020 (before rollout of COVID-19 vaccination). Five-weekly rolling seroprevalence estimates were adjusted for the sensitivity and specificity of the assays and weighted to reference populations. Temporal trends in seroprevalence estimates and weekly SARS-CoV-2 notifications were compared.

Results

Five-weekly rolling seroprevalence rates were 0% until the end of March, when they increased contemporaneously with the first pandemic wave. Seroprevalence rates remained stable through the summer (range: 3%–5%) during a period of social restrictions, after which they increased concurrently with the second wave, reaching 9.6% (95% confidence interval [CI]: 8.4%–10.8%) in the week beginning 28th December in 2020. Seroprevalence rates were lower in rural vs. urban areas (adjusted odds ratio [AOR]: 0.70, 95% CI: 0.61–0.79) and among individuals aged 20–39 years and 60 years and older (AOR: 0.74, 95% CI: 0.64–0.86; AOR: 0.80, 95% CI: 0.69–0.91, respectively) relative to those aged 0–19 years.

Conclusions

After two waves of the COVID-19 pandemic, less than one in ten individuals in the Scottish population had antibodies to SARS-CoV-2. Seroprevalence may underestimate the true population exposure as a result of waning antibodies among individuals who were infected early in the first wave.

A spatial and dynamic solution for allocation of COVID-19 vaccines when supply is limited

Background

Since most of the global population needs to be vaccinated to reduce COVID-19 transmission and mortality, a shortage of COVID-19 vaccine supply is inevitable. We propose a spatial and dynamic vaccine allocation solution to assist in the allocation of limited vaccines to people who need them most.

Methods

We developed a weighted kernel density estimation (WKDE) model to predict daily COVID-19 symptom onset risk in 291 Tertiary Planning Units in Hong Kong from 18 January 2020 to 22 December 2020. Data of 5,409 COVID-19 onset cases were used. We then obtained spatial distributions of accumulated onset risk under three epidemic scenarios, and computed the vaccine demands to form the vaccine allocation plan. We also compared the vaccine demand under different real-time effective reproductive number (R_t) levels.

Results

The estimated vaccine usages in three epidemiologic scenarios are 30.86% - 45.78% of the Hong Kong population, which is within the total vaccine availability limit. In the sporadic cases or clusters of onset cases scenario, when 6.26% of the total population with travel history to high-risk areas can be vaccinated, the COVID-19 transmission between higher- and lower-risk areas can be reduced. Furthermore, if the current R_t is increased to double, the vaccine usages needed will be increased by more than 7%.

Conclusions

The proposed solution can be used to dynamically allocate limited vaccines in different epidemic scenarios, thereby enabling more effective protection. The increased vaccine usages associated with increased R_t indicates the necessity to maintain appropriate control measures even with vaccines available.

The supply of COVID-19 vaccines is limited in many parts of the world, particularly in low-income countries. To assist in the allocation of limited vaccines, a spatial and dynamic solution was proposed, based on a new model to predict risk of COVID-19 onset in urban communities. A case study in Hong Kong indicated that the estimated vaccine usage (30.86–45.78%) under three epidemiologic scenarios was within the total vaccine availability limit. Vaccine usage would need to be increased by more than 7% if the current rate of viral spread was doubled. The proposed solution has the potential to help countries to allocate limited vaccines spatially and dynamically in different epidemic scenarios, thereby enabling more effective protection.

Shi et al. propose a weighted kernel density estimation model to estimate COVID-19 risk across communities in Hong Kong. The authors use this data to evaluate potential COVID-19 vaccine allocation strategies in different epidemic scenarios.

Cross-Reactive Immune Responses toward the Common Cold Human Coronaviruses and Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2): Mini-Review and a Murine Study

While severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes serious morbidity and mortality in humans (coronavirus disease 2019, COVID-19), there is an enormous range of disease outcomes following virus exposures. Some individuals are asymptomatic while others succumb to virus infection within days. Presently, the factors responsible for disease severity are not fully understood. One factor that may influence virus control is pre-existing immunity conferred by an individual's past exposures to common cold human coronaviruses (HCoVs). Here, we describe previous literature and a new, murine study designed to examine cross-reactive immune responses between SARS-CoV-2 and common cold HCoVs (represented by prototypes OC43, HKU1, 229E, and NL63). Experimental results have been mixed. In SARS-CoV-2-unexposed humans, cross-reactive serum antibodies were identified toward nucleocapsid (N) and the spike subunit S2. S2-specific antibodies were in some cases associated with neutralization. SARS-CoV-2-unexposed humans rarely exhibited antibody responses to the SARS-CoV-2 spike subunit S1, and when naïve mice were immunized with adjuvanted S1 from either SARS-CoV-2 or common cold HCoVs, S1-specific antibodies were poorly cross-reactive. When humans were naturally infected with SARS-CoV-2, cross-reactive antibodies that recognized common cold HCoV antigens increased in magnitude. Cross-reactive T cells, like antibodies, were present in humans prior to SARS-CoV-2 exposures and increased following SARS-CoV-2 infections. Some studies suggested that human infections with common cold HCoVs afforded protection against disease caused by subsequent exposures to SARS-CoV-2. Small animal models are now available for the testing of controlled SARS-CoV-2 infections. Additionally, in the United Kingdom, a program of SARS-CoV-2 human challenge experiments has received regulatory approval. Future, controlled experimental challenge studies may better define how pre-existing, cross-reactive immune responses influence SARS-CoV-2 infection outcomes.

COVID-19, Alcohol Consumption and Stockpiling Practises in Midlife Women: Repeat Surveys During Lockdown in Australia and the United Kingdom

Introduction: This project examined the impact of COVID-19 and associated restrictions on alcohol practises (consumption and stockpiling), and perceptions of health risk among women in midlife (those aged 45–64 years).

Methods: We collected online survey data from 2,437 midlife women in the United Kingdom (UK) and Australia in May 2020, recruited using a commercial panel, in the early days of mandated COVID-19 related restrictions in both countries. Participants were surveyed again (N = 1,377) in July 2020, at a time when COVID-19 restrictions were beginning to ease. The surveys included the Alcohol Use Disorder Identification Test—Consumption (AUDIT-C) and questions alcohol stockpiling. Analysis involved a range of univariate and multivariate techniques examining the impact of demographic variables and negative affect on consumption and acquisition outcomes.

Results: In both surveys (May and July), UK women scored higher than Australian women on the AUDIT-C, and residence in the UK was found to independently predict stockpiling of alcohol (RR: 1.51; 95% CI: 1.20, 1.91). Developing depression between surveys (RR: 1.53; 95% CI: 1.14, 2.04) and reporting pessimism (RR: 1.42; 95% CI: 1.11, 1.81), and fear/anxiety (RR: 1.33; 95% CI: 1.05, 1.70) at the beginning of the study period also predicted stockpiling by the end of the lockdown. Having a tertiary education was protective for alcohol stockpiling at each time point (RR: 0.69; 95% CI: 0.54, 0.87).

Conclusions: COVID-19 was associated with increases in risky alcohol practises that were predicted by negative emotional responses to the pandemic. Anxiety, pessimism and depression predicted stockpiling behaviour in UK and Australian women despite the many demographic and contextual differences between the two cohorts. Given our findings and the findings of others that mental health issues developed or were exacerbated during lockdown and may continue long after that time, urgent action is required to address a potential future pandemic of alcohol-related harms.

Retracted: The Safety of COVID-19 Vaccinations-We Should Rethink the Policy

Background: COVID-19 vaccines have had expedited reviews without sufficient safety data. We wanted to compare risks and benefits. Method: We calculated the number needed to vaccinate (NNTV) from a large Israeli field study to prevent one death. We accessed the Adverse Drug Reactions (ADR) database of the European Medicines Agency and of the Dutch National Register (lareb.nl) to extract the number of cases reporting severe side effects and the number of cases with fatal side effects. Result: The NNTV is between 200-700 to prevent one case of COVID-19 for the mRNA vaccine marketed by Pfizer, while the NNTV to prevent one death is between 9000 and 50,000 (95% confidence interval), with 16,000 as a point estimate. The number of cases experiencing adverse reactions has been reported to be 700 per 100,000 vaccinations. Currently, we see 16 serious side effects per 100,000 vaccinations, and the number of fatal side effects is at 4.11/100,000 vaccinations. For three deaths prevented by vaccination we have to accept two inflicted by vaccination. Conclusions: This lack of clear benefit should cause governments to rethink their vaccination policy.

Modelling of hypothetical SARS-CoV-2 point of care tests for routine testing in residential care homes: rapid cost-effectiveness analysis

BACKGROUND

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the virus that causes coronavirus disease 2019 (COVID-19), which at the time of writing (January 2021) was responsible for more than 2.25 million deaths worldwide and over 100,000 deaths in the UK. SARS-CoV-2 appears to be highly transmissible and could rapidly spread in residential care homes.

OBJECTIVE

The work undertaken aimed to estimate the clinical effectiveness and cost-effectiveness of viral detection point-of-care tests for detecting SARS-CoV-2 compared with laboratory-based tests in the setting of a hypothetical care home facility for elderly residents.

PERSPECTIVE/SETTING

The perspective was that of the NHS in 2020. The setting was a hypothetical care home facility for elderly residents. Care homes with en suite rooms and with shared facilities were modelled separately.

METHODS

A discrete event simulation model was constructed to model individual residents and simulate the spread of SARS-CoV-2 once it had entered the residential care facility. The numbers of COVID-19-related deaths and critical cases were recorded in addition to the number of days spent in isolation. Thirteen strategies involving different hypothetical SARS-CoV-2 tests were modelled. Recently published desirable and acceptable target product profiles for SARS-CoV-2 point-of-care tests and for hospital-based SARS-CoV-2 tests were modelled. Scenario analyses modelled early release from isolation based on receipt of a negative SARS-CoV-2 test result and the impact of vaccination. Incremental analyses were undertaken using both incremental cost-effectiveness ratios and net monetary benefits.

RESULTS

Cost-effectiveness results depended on the proportion of residential care facilities penetrated by SARS-CoV-2. SARS-CoV-2 point-of-care tests with desirable target product profiles appear to have high net monetary benefit values. In contrast, SARS-CoV-2 point-of-care tests with acceptable target product profiles had low net monetary benefit values because of unnecessary isolations. The benefit of allowing early release from isolation depended on whether or not the facility had en suite rooms. The greater the assumed efficacy of vaccination, the lower the net monetary benefit values associated with SARS-CoV-2 point-of-care tests, when assuming that a vaccine lowers the risk of contracting SARS-CoV-2.

LIMITATIONS

There is considerable uncertainty in the values for key parameters within the model, although calibration was undertaken in an attempt to mitigate this. Some degree of Monte Carlo sampling error persists because of the timelines of the project. The example care home simulated will also not match those of decision-makers deciding on the clinical effectiveness and cost-effectiveness of introducing SARS-CoV-2 point-of-care tests. Given these limitations, the results should be taken as indicative rather than definitive, particularly the cost-effectiveness results when the relative cost per SARS-CoV-2 point-of-care test is uncertain.

CONCLUSIONS

SARS-CoV-2 point-of-care tests have considerable potential for benefit for use in residential care facilities, but whether or not this materialises depends on the diagnostic accuracy and costs of forthcoming SARS-CoV-2 point-of-care tests.

FUTURE WORK

More accurate results would be obtained when there is more certainty on the diagnostic accuracy of and the reduction in time to test result associated with SARS-CoV-2 point-of-care tests when used in the context of residential care facilities, the proportion of care home penetrated by SARS-CoV-2 and the levels of immunity once vaccination is administered. These parameters are currently uncertain.

FUNDING

This report was commissioned by the National Institute for Health Research (NIHR) Evidence Synthesis programme as project number 132154. This project was funded by the NIHR Health Technology Assessment programme and will be published in full in Health Technology Assessment; Vol. 25, No. 39. See the NIHR Journals Library website for further project information.

Dynamic causal modelling of immune heterogeneity

An interesting inference drawn by some COVID-19 epidemiological models is that there exists a proportion of the population who are not susceptible to infection-even at the start of the current pandemic. This paper introduces a model of the immune response to a virus. This is based upon the same sort of mean-field dynamics as used in epidemiology. However, in place of the location, clinical status, and other attributes of people in an epidemiological model, we consider the state of a virus, B and T-lymphocytes, and the antibodies they generate. Our aim is to formalise some key hypotheses as to the mechanism of resistance. We present a series of simple simulations illustrating changes to the dynamics of the immune response under these hypotheses. These include attenuated viral cell entry, pre-existing cross-reactive humoral (antibody-mediated) immunity, and enhanced T-cell dependent immunity. Finally, we illustrate the potential application of this sort of model by illustrating variational inversion (using simulated data) of this model to illustrate its use in testing hypotheses. In principle, this furnishes a fast and efficient immunological assay-based on sequential serology-that provides a (1) quantitative measure of latent immunological responses and (2) a Bayes optimal classification of the different kinds of immunological response (c.f., glucose tolerance tests used to test for insulin resistance). This may be especially useful in assessing SARS-CoV-2 vaccines.

A phenomenological estimate of the true scale of CoViD-19 from primary data

Estimation of the prevalence of undocumented SARS-CoV-2 infections is critical for understanding the overall impact of CoViD-19, and for implementing effective public policy intervention strategies. We discuss a simple yet effective approach to estimate the true number of people infected by SARS-CoV-2, using raw epidemiological data reported by official health institutions in the largest EU countries and the USA.

Effects of Age, Gender, Health Status, and Political Party on COVID-19-Related Concerns and Prevention Behaviors: Results of a Large, Longitudinal Cross-sectional Survey

Background

With conflicting information about COVID-19, the general public may be uncertain about how to proceed in terms of precautionary behavior and decisions about whether to return to activity.

Objective

The aim of this study is to determine the factors associated with COVID-19–related concerns, precautionary behaviors, and willingness to return to activity.

Methods

National survey data were obtained from the Democracy Fund + UCLA Nationscape Project, an ongoing cross-sectional weekly survey. The sample was provided by Lucid, a web-based market research platform. Three outcomes were evaluated: (1) COVID-19–related concerns, (2) precautionary behaviors, and (3) willingness to return to activity. Key independent variables included age, gender, race or ethnicity, education, household income, political party support, religion, news consumption, number of medication prescriptions, perceived COVID-19 status, and timing of peak COVID-19 infections by state.

Results

The data included 125,508 responses from web-based surveys conducted over 20 consecutive weeks during the COVID-19 pandemic (comprising approximately 6250 adults per week), between March 19 and August 5, 2020, approved by the University of California, Los Angeles (UCLA) Institutional Review Board for analysis. A substantial number of participants were not willing to return to activity even after the restrictions were lifted. Weighted multivariate logistic regressions indicated the following groups had different outcomes (all P<.001): individuals aged ≥65 years (COVID-19–related concerns: OR 2.05, 95% CI 1.93-2.18; precautionary behaviors: OR 2.38, 95% CI 2.02-2.80; return to activity: OR 0.41, 95% CI 0.37-0.46 vs 18-40 years); men (COVID-19–related concerns: OR 0.73, 95% CI 0.70-0.75; precautionary behaviors: OR 0.74, 95% CI 0.67-0.81; return to activity: OR 2.00, 95% CI 1.88-2.12 vs women); taking ≥4 medications (COVID-19–related concerns: OR 1.47, 95% CI 1.40-1.54; precautionary behaviors: OR 1.36, 95% CI 1.20-1.555; return to activity: OR 0.75, 95% CI 0.69-0.81 vs <3 medications); Republicans (COVID-19–related concerns: OR 0.40, 95% CI 0.38-0.42; precautionary behaviors: OR 0.45, 95% CI 0.40-0.50; return to activity: OR 2.22, 95% CI 2.09-2.36 vs Democrats); and adults who reported having COVID-19 (COVID-19–related concerns: OR 1.24, 95% CI 1.12-1.39; precautionary behaviors: OR 0.65, 95% CI 0.52-0.81; return to activity: OR 3.99, 95% CI 3.48-4.58 vs those who did not).

Conclusions

Participants’ age, party affiliation, and perceived COVID-19 status were strongly associated with their COVID-19–related concerns, precautionary behaviors, and willingness to return to activity. Future studies need to develop and test targeted messaging approaches and consider political partisanship to encourage preventative behaviors and willingness to return to activities.

Nano-Enabled COVID-19 Vaccines: Meeting the Challenges of Durable Antibody Plus Cellular Immunity and Immune Escape

At the time of preparing this Perspective, large-scale vaccination for COVID-19 is in progress, aiming to bring the pandemic under control through vaccine-induced herd immunity. Not only does this vaccination effort represent an unprecedented scientific and technological breakthrough, moving us from the rapid analysis of viral genomes to design, manufacture, clinical trial testing, and use authorization within the time frame of less than a year, but it also highlights rapid progress in the implementation of nanotechnology to assist vaccine development. These advances enable us to deliver nucleic acid and conformation-stabilized subunit vaccines to regional lymph nodes, with the ability to trigger effective humoral and cellular immunity that prevents viral infection or controls disease severity. In addition to a brief description of the design features of unique cationic lipid and virus-mimicking nanoparticles for accomplishing spike protein delivery and presentation by the cognate immune system, we also discuss the importance of adjuvancy and design features to promote cooperative B- and T-cell interactions in lymph node germinal centers, including the use of epitope-based vaccines. Although current vaccine efforts have demonstrated short-term efficacy and vaccine safety, key issues are now vaccine durability and adaptability against viral variants. We present a forward-looking perspective of how vaccine design can be adapted to improve durability of the immune response and vaccine adaptation to overcome immune escape by viral variants. Finally, we consider the impact of nano-enabled approaches in the development of COVID-19 vaccines for improved vaccine design against other infectious agents, including pathogens that may lead to future pandemics.

Lack of antibodies against seasonal coronavirus OC43 nucleocapsid protein identifies patients at risk of critical COVID-19

BACKGROUND

The vast majority of COVID-19 patients experience a mild disease. However, a minority suffers from critical disease with substantial morbidity and mortality.

OBJECTIVES

To identify individuals at risk of critical COVID-19, the relevance of a seroreactivity against seasonal human coronaviruses was analyzed.

METHODS

We conducted a multi-center non-interventional study comprising 296 patients with confirmed SARS-CoV-2 infections from four tertiary care referral centers in Germany and France. The ICU group comprised more males, whereas the outpatient group contained a higher percentage of females. For each patient, the serum or plasma sample obtained closest after symptom onset was examined by immunoblot regarding IgG antibodies against the nucleocapsid protein (NP) of HCoV 229E, NL63, OC43 and HKU1.

RESULTS

Median age was 60 years (range 18-96). Patients with critical disease (n=106) had significantly lower levels of anti-HCoV OC43 nucleocapsid protein (NP)-specific antibodies compared to other COVID-19 inpatients (p=0.007). In multivariate analysis (adjusted for age, sex and BMI), OC43 negative inpatients had an increased risk of critical disease (adjusted odds ratio (AOR) 2.68 [95% CI 1.09 - 7.05]), higher than the risk by increased age or BMI, and lower than the risk by male sex. A risk stratification based on sex and OC43 serostatus was derived from this analysis.

CONCLUSIONS

Our results suggest that prior infections with seasonal human coronaviruses can protect against a severe course of COVID-19. Therefore, anti-OC43 antibodies should be measured for COVID-19 inpatients and considered as part of the risk assessment for each patient. Hence, we expect individuals tested negative for anti-OC43 antibodies to particularly benefit from vaccination against SARS-CoV-2, especially with other risk factors prevailing.

Pre-existing T-cell immunity to SARS-CoV-2 in unexposed healthy controls in Ecuador, as detected with a COVID-19 Interferon-Gamma Release Assay

BACKGROUND

Studies of T-cell immune responses against SARS-CoV-2 are important in understanding the immune status of individuals or populations. Here, we use a simple, cheap, and rapid whole blood stimulation assay - an Interferon-Gamma Release Assay (IGRA) - to study T-cell immunity to SARS-CoV-2 in convalescent COVID-19 patients and in unexposed healthy contacts from Quito, Ecuador.

METHODS

Interferon-gamma (INF-γ) production was measured in the heparinized blood of convalescent and unexposed subjects after stimulation for 24 h with the SARS-CoV-2 Spike S1 protein, the Receptor Binding Domain (RBD) protein or the Nucleocapsid (NP) protein, respectively. The presence of IgG-RBD protein antibodies in both study groups was determined with an "in-house" ELISA.

RESULTS

As measured with INF-γ production, 80% of the convalescent COVID-19 patients, all IgG-RBD seropositive, had a strong T-cell response. However, unexpectedly, 44% of unexposed healthy controls, all IgG-RBD seronegative, had a strong virus-specific T-cell response with the COVID-19 IGRA, probably because of prior exposure to common cold-causing coronaviruses or other viral or microbial antigens.

CONCLUSION AND DISCUSSION

The high percentage of unexposed healthy subjects with a pre-existing immunity suggests that a part of the Ecuadorian population is likely to have SARS-CoV-2 reactive T-cells. Given that the IGRA technique is simple and can be easily scaled up for investigations where high numbers of patients are needed, this COVID-19 IGRA may serve to determine if the T-cell only response represents protective immunity to SARS-CoV-2 infection in a population-based study.

COVID-19 pandemic: Water, sanitation and hygiene (WASH) as a critical control measure remains a major challenge in low-income countries

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is responsible for the deadly respiratory disease called coronavirus disease of 2019 (COVID-19), an ongoing global public health emergency that has been declared a pandemic by the World Health Organization. We review literature on the transmission and control of SARS-CoV-2 and discuss the challenges of focusing on water, sanitation and hygiene (WASH) as critical control measures in low-income countries. A significantly higher prevalence of SARS-CoV-2 infection and COVID-19 related deaths has been reported for the United States of America and other high-income countries in Europe and Asia, regardless of advanced medical facilities in those countries. In contrast, much lower COVID-19 related morbidity and mortality rates have been documented in many low-income countries, despite having comparatively higher socioeconomic burdens and suboptimal medical facilities. By September 29, 2020 over one million deaths have been reported. On the same day, the cumulative total of COVID-19 related morbidity for Africa was 35,954 with 3.5% of the global COVID-19 related deaths. We present arguments for the relatively low COVID-19 morbidity and mortality rates in many low-income countries and discuss the critical importance of WASH for preventing the spread of infectious diseases like COVID-19. We observe that the key recommendations put forward by the World Health Organization to effectively control the pandemic have been difficult to implement in low-income countries. We conclude that the pandemic reinforces previous pronouncements that adequate and effective WASH measures are crucial for public health and recommend closer coordination between public health and WASH sectors.

Modelling of hypothetical SARS-CoV-2 point-of-care tests on admission to hospital from A&E: rapid cost-effectiveness analysis

BACKGROUND

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the virus that causes coronavirus disease 2019. At the time of writing (October 2020), the number of cases of COVID-19 had been approaching 38 million and more than 1 million deaths were attributable to it. SARS-CoV-2 appears to be highly transmissible and could rapidly spread in hospital wards.

OBJECTIVE

The work undertaken aimed to estimate the clinical effectiveness and cost-effectiveness of viral detection point-of-care tests for detecting SARS-CoV-2 compared with laboratory-based tests. A further objective was to assess occupancy levels in hospital areas, such as waiting bays, before allocation to an appropriate bay.

PERSPECTIVE/SETTING

The perspective was that of the UK NHS in 2020. The setting was a hypothetical hospital with an accident and emergency department.

METHODS

An individual patient model was constructed that simulated the spread of disease and mortality within the hospital and recorded occupancy levels. Thirty-two strategies involving different hypothetical SARS-CoV-2 tests were modelled. Recently published desirable and acceptable target product profiles for SARS-CoV-2 point-of-care tests were modelled. Incremental analyses were undertaken using both incremental cost-effectiveness ratios and net monetary benefits, and key patient outcomes, such as death and intensive care unit care, caused directly by COVID-19 were recorded.

RESULTS

A SARS-CoV-2 point-of-care test with a desirable target product profile appears to have a relatively small number of infections, a low occupancy level within the waiting bays, and a high net monetary benefit. However, if hospital laboratory testing can produce results in 6 hours, then the benefits of point-of-care tests may be reduced. The acceptable target product profiles performed less well and had lower net monetary benefits than both a laboratory-based test with a 24-hour turnaround time and strategies using data from currently available SARS-CoV-2 point-of-care tests. The desirable and acceptable point-of-care test target product profiles had lower requirement for patients to be in waiting bays before being allocated to an appropriate bay than laboratory-based tests, which may be of high importance in some hospitals. Tests that appeared more cost-effective also had better patient outcomes.

LIMITATIONS

There is considerable uncertainty in the values for key parameters within the model, although calibration was undertaken in an attempt to mitigate this. The example hospital simulated will also not match those of decision-makers deciding on the clinical effectiveness and cost-effectiveness of introducing SARS-CoV-2 point-of-care tests. Given these limitations, the results should be taken as indicative rather than definitive, particularly cost-effectiveness results when the relative cost per SARS-CoV-2 point-of-care test is uncertain.

CONCLUSIONS

Should a SARS-CoV-2 point-of-care test with a desirable target product profile become available, this appears promising, particularly when the reduction on the requirements for waiting bays before allocation to a SARS-CoV-2-infected bay, or a non-SARS-CoV-2-infected bay, is considered. The results produced should be informative to decision-makers who can identify the results most pertinent to their specific circumstances.

FUTURE WORK

More accurate results could be obtained when there is more certainty on the diagnostic accuracy of, and the reduction in time to test result associated with, SARS-CoV-2 point-of-care tests, and on the impact of these tests on occupancy of waiting bays and isolation bays. These parameters are currently uncertain.

FUNDING

This report was commissioned by the National Institute for Health Research (NIHR) Evidence Synthesis programme as project number 132154. This project was funded by the NIHR Health Technology Assessment programme and will be published in full in Health Technology Assessment; Vol. 25, No. 21. See the NIHR Journals Library website for further project information.

epitopepredict: a tool for integrated MHC binding prediction

A key step in the cellular adaptive immune response is the presentation of antigens to T cells. Computational prediction of T cell epitopes has many applications in vaccine design and immuno-diagnostics. This is the basis of immunoinformatics, which allows in silico screening of peptides before experiments are performed. With the availability of whole genomes for many microbial species it is now feasible to computationally screen whole proteomes for candidate peptides. epitopepredict is a programmatic framework and command line tool designed to aid this process. It provides access to multiple binding prediction algorithms under a single interface and scales for whole genomes using multiple target MHC alleles. A web interface is provided to assist visualization and filtering of the results. The software is freely available under an open-source license from https://github.com/dmnfarrell/epitopepredict.

COVID-19 and Dentistry in 72 Questions: An Overview of the Literature

The outbreak of Coronavirus Disease 2019 (COVID-19), caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), has significantly affected the dental care sector. Dental professionals are at high risk of being infected, and therefore transmitting SARS-CoV-2, due to the nature of their profession, with close proximity to the patient's oropharyngeal and nasal regions and the use of aerosol-generating procedures. The aim of this article is to provide an update on different issues regarding SARS-CoV-2 and COVID-19 that may be relevant for dentists. Members of the French National College of Oral Biology Lecturers ("Collège National des EnseignantS en Biologie Orale"; CNESBO-COVID19 Task Force) answered seventy-two questions related to various topics, including epidemiology, virology, immunology, diagnosis and testing, SARS-CoV-2 transmission and oral cavity, COVID-19 clinical presentation, current treatment options, vaccine strategies, as well as infection prevention and control in dental practice. The questions were selected based on their relevance for dental practitioners. Authors independently extracted and gathered scientific data related to COVID-19, SARS-CoV-2 and the specific topics using scientific databases. With this review, the dental practitioners will have a general overview of the COVID-19 pandemic and its impact on their practice.