Genomic Surveillance Enables the Identification of Co-infections With Multiple SARS-CoV-2 Lineages in Equatorial Guinea

COVID-19 disease caused by SARS-CoV-2 represents an ongoing global public health emergency. Rapid identification of emergence, evolution, and spread of SARS-CoV-2 variants of concern (VOC) would enable timely and tailored responses by public health decision-making bodies. Yet, global disparities in current SARS-CoV-2 genomic surveillance activities reveal serious geographical gaps. Here, we discuss the experiences and lessons learned from the SARS-CoV-2 monitoring and surveillance program at the Public Health Laboratory on Bioko Island, Equatorial Guinea that was implemented as part of the national COVID-19 response and monitoring activities. We report how three distinct SARS-CoV-2 variants have dominated the epidemiological situation in Equatorial Guinea since March 2020. In addition, a case of co-infection of two SARS-CoV-2 VOC, Beta and Delta, in a clinically asymptomatic and fully COVID-19 vaccinated man living in Equatorial Guinea is presented. To our knowledge, this is the first report of a person co-infected with Beta and Delta VOC globally. Rapid identification of co-infections is relevant since these might provide an opportunity for genetic recombination resulting in emergence of novel SARS-CoV-2 lineages with enhanced transmission or immune evasion potential.

A systematic review of vitamin D status and dietary intake in various Slovenian populations

Aim Vitamin D (VitD) is involved in calcium and phosphate homeostasis, bone health, and normal functioning of the immune system. VitD status is monitored using serum 25-hydroxy-vitamin D (25(OH)D) as a biomarker. Serum 25(OH)D concentrations below 30 nmol/L indicate VitD deficiency and below 50 nmol/L indicate insufficiency. VitD can be synthesised endogenously in human skin when exposed to ultraviolet B (UVB) radiation. In the absence of sufficient UVB-light exposure, VitD intake becomes the main source of VitD, with a recommended daily intake of 20 μg. The aim of this study was to conduct a review and meta-analysis on the abovementioned topics, focusing on scientific studies in various Slovenian populations. Methods We conducted a systematic review and meta-analysis of published scientific papers, academic theses, or conference contributions reporting serum 25(OH)D status and VitD intake across various Slovenian populations. A search was carried out using Web of Science, Scopus, Medline, and the Slovenian library database. Results We identified 43 pertinent studies that addressed 25(OH)D status and 16 that addressed VitD intake. Serum 25(OH)D status was generally low across all populations, and notable seasonal variability was observed. VitD intakes were below 5 μg in all studies. Conclusions A general observation is that various population groups across Slovenia are at high risk of vitamin D insufficiency and deficiency, particularly during wintertime. Regarding vitamin D intake, all included studies reported daily intakes below the recommended level. We also identified key research gaps that need to be addressed to support further public health decision-making.

Antimicrobial Usage and Resistance in Makkah Region Hospitals: A Regional Point Prevalence Survey of Public Hospitals

(1) Background: Inappropriate use of antimicrobials and subsequently rise of antimicrobial resistance (AMR) remains a major public health priority. Over-prescribing of broad-spectrum antibiotics is one of the main contributing factors for the emergence of AMR. We sought to describe antimicrobial prescribing trends among patients in public hospitals in Makkah hospitals. (2) Method: We undertook a point prevalence survey (PPS) in six hospitals in Makkah, Saudi Arabia, from January 2019 to July 2019. The survey included all the inpatients receiving antimicrobials on the day of PPS. Data was collected using the Global point prevalence survey (PPS) tool developed by the University of Antwerp, Belgium. (3) Results: Of 710 hospitalized patients, 447 patients (61.9%) were treated with one or more antimicrobials during the study period. The average bed occupancy among six hospitals was 74.4%. The majority of patients received antimicrobials parenterally (90.3%). Of the total prescribed antimicrobials, 415 (53.7%) antimicrobials were used in medical departments, 183 (23.7%) in surgical departments, and 175 (22.6%) in ICUs. Pneumonia (17.3%), skin and soft tissue infections (10.9%), and sepsis (6.6.%) were three common clinical indications. Ceftriaxones were the most commonly used antibiotics that were prescribed in 116 (15%) of patients, followed by piperacillin, with an enzyme inhibitor in 84 (10.9%). (4) Conclusion: There was a high prevalence of antibiotic use in the hospitals of Makkah, which could be a potential risk factor for the incidence of resistant strains, particularly MRSA infection. Public health decision-makers should take these findings into consideration to update national policies for antibiotic use in order to reduce the risks of further increases of AMR.

Effectiveness of COVID-19 Vaccines against Delta (B.1.617.2) Variant: A Systematic Review and Meta-Analysis of Clinical Studies

The high transmissibility, mortality, and morbidity rate of the SARS-CoV-2 Delta (B.1.617.2) variant have raised concerns regarding vaccine effectiveness (VE). To address this issue, all publications relevant to the effectiveness of vaccines against the Delta variant were searched in the Web of Science, Scopus, EMBASE, and Medline (via PubMed) databases up to 15 October 2021. A total of 15 studies (36 datasets) were included in the meta-analysis. After the first dose, the VE against the Delta variant for each vaccine was 0.567 (95% CI 0.520–0.613) for Pfizer-BioNTech, 0.72 (95% CI 0.589–0.822) for Moderna, 0.44 (95% CI 0.301–0.588) for AstraZeneca, and 0.138 (95% CI 0.076–0.237) for CoronaVac. Meta-analysis of 2,375,957 vaccinated cases showed that the Pfizer-BioNTech vaccine had the highest VE against the infection after the second dose, at 0.837 (95% CI 0.672–0.928), and third dose, at 0.972 (95% CI 0.96–0.978), as well as the highest VE for the prevention of severe infection or death, at 0.985 (95% CI 0.95–0.99), amongst all COVID-19 vaccines. The short-term effectiveness of vaccines, especially mRNA-based vaccines, for the prevention of the Delta variant infection, hospitalization, severe infection, and death is supported by this study. Limitations include a lack of long-term efficacy data, and under-reporting of COVID-19 infection cases in observational studies, which has the potential to falsely skew VE rates. Overall, this study supports the decisions by public health decision makers to promote the population vaccination rate to control the Delta variant infection and the emergence of further variants.

Adapting serosurveys for the SARS-CoV-2 vaccine era

Population-level immune surveillance, which includes monitoring exposure and assessing vaccine-induced immunity, is a crucial component of public health decision-making during a pandemic. Serosurveys estimating the prevalence of SARS-CoV-2 antibodies in the population played a key role in characterizing SARS-CoV-2 epidemiology during the early phases of the pandemic. Existing serosurveys provide infrastructure to continue immune surveillance, but must be adapted to remain relevant in the SARS-CoV-2 vaccine era. Here, we delineate how SARS-CoV-2 serosurveys should be designed to distinguish infection- and vaccine-induced humoral immune responses to efficiently monitor the evolution of the pandemic. We discuss how serosurvey results can inform vaccine distribution to improve allocation efficiency in countries with scarce vaccine supplies and help assess the need for booster doses in countries with substantial vaccine coverage.

Using stated preference methods to inform public health decision making

Croatia has recognised the importance of prevention programmes in the field of public health, although their effectiveness is not satisfactory due to the low population response, which has a negative impact on the rationalisation of public spending. One of the possible solutions is to consider the stated preferences of the target population. Therefore, the main objective of this study is to evaluate the use of stated preference methods in improving public health prevention programmes. For the purpose of the study, a questionnaire was designed using three different methods - Discrete Choice Experiment (DCE), Contingent Rating method (CR) and Best-Worst Scaling method (BWS). This study shows that the attributes of the Croatian cervical cancer screening programme are significantly associated with the respondents' utility level, which in turn is related to women's response. Since BWS, DCE, and CR measure the same construct - utility - we can say that convergent validity partially confirms the external validity of the methods. The author concludes that it is necessary to implement market principles, i.e. the demand-side analysis using stated preference methods, in the planning, implementation and re-evaluation of public health programmes.

Consumer fear and healthy eating during COVID-19 pandemic

PurposeThis study aims to contribute to the healthy eating literature by analyzing whether fear of coronavirus disease 2019 (COVID-19), ability to prepare food and the safety-seeking are antecedents of the intention to consume healthy foods during COVID-19 pandemic.Design/methodology/approachThe authors conducted two studies. The first study was done with a sample of 546 valid respondents. Partial Least Squares Structural Equation Modeling (PLS-SEM) was used to analyze data. The second study was qualitative, in which 40 subjects took part. Data were analyzed using thematic analysis.FindingsThe main findings reveal that ability to prepare food and the safety-seeking are strong antecedents of the intention to consume healthy foods. In addition, safety-seeking mediates the relationship between fear of COVID-19 and intention to consume healthy eating. However, high levels of fear did not influence the ability to prepare food and intention to consume healthy foods. Also, the ability to prepare food does not mediate the relation between fear of COVID-19 and intention to consume healthy food.Originality/valueThis study is among the first to consider terror management propositions to analyze the intention to consume healthy foods during COVID-19 pandemic. From a scientific point of view, it has several contributions to the literature. First, this study provides advances and innovation in the field by identifying new explanatory relations. Second, this study extends the scope of terror management health model (TMHM) by analyzing it in the pandemic context. Third, the findings seem to provide empirical support for recent criticism of TMHM assumptions. Moreover, practical implications are outlined to public health decision-makers and healthy food businesses on increasing consumers’ intention to healthy eating.

SARS-COV-2 Omicron variant predicted to exhibit higher affinity to ACE-2 receptor and lower affinity to a larger range of neutralizing antibodies, using a rapid assessment platform

Rapid assessment of whether a pandemic pathogen may have increased transmissibility or be capable of evading existing vaccines and therapeutics is critical to mounting an effective public health response. Over the period of seven days, we utilized rapid computational prediction methods to evaluate potential public health implications of the emerging SARS-CoV-2 Omicron variant. Specifically, we modeled the structure of the Omicron variant, examined its interface with human angiotensin converting enzyme 2 (ACE-2) and evaluated the change in binding affinity between Omicron, ACE-2 and publicly known neutralizing antibodies. We also compared the Omicron variant to known Variants of Concern (VoC). Seven of the 15 Omicron mutations occurring in the spike protein receptor binding domain (RBD) occur at the ACE-2 cell receptor interface, and therefore may play a critical role in enhancing binding to ACE-2. Our estimates of Omicron RBD-ACE-2 binding affinities indicate that at least two of RBD mutations, Q493K/R and N501Y, contribute to enhanced ACE-2 binding, nearly doubling delta-delta-G (ddG) free energies calculated for other variants. Binding affinity estimates also were calculated for 54 known neutralizing SARS-CoV-2 antibodies. Analysis of the results showed that Omicron substantially degrades binding for more than half of these neutralizing SARS-CoV-2 antibodies, and for roughly twice as many of the antibodies than the currently dominant Delta variant. This early study lends support to use of rapid computational risk assessments to inform public health decision-making while awaiting detailed experimental characterization and confirmation.

Can auxiliary indicators improve COVID-19 forecasting and hotspot prediction?

Short-term forecasts of traditional streams from public health reporting (such as cases, hospitalizations, and deaths) are a key input to public health decision-making during a pandemic. Since early 2020, our research group has worked with data partners to collect, curate, and make publicly available numerous real-time COVID-19 indicators, providing multiple views of pandemic activity in the United States. This paper studies the utility of five such indicators—derived from deidentified medical insurance claims, self-reported symptoms from online surveys, and COVID-related Google search activity—from a forecasting perspective. For each indicator, we ask whether its inclusion in an autoregressive (AR) model leads to improved predictive accuracy relative to the same model excluding it. Such an AR model, without external features, is already competitive with many top COVID-19 forecasting models in use today. Our analysis reveals that 1) inclusion of each of these five indicators improves on the overall predictive accuracy of the AR model; 2) predictive gains are in general most pronounced during times in which COVID cases are trending in “flat” or “down” directions; and 3) one indicator, based on Google searches, seems to be particularly helpful during “up” trends.