COVID, Volume 2, Issue 8 (August 2022) – 11 articles

When confronted with a public health emergency, significant innovative treatment protocols can sometimes be discovered by medical doctors at the front lines based on repurposed medications. We propose a statistical framework for analyzing the case series of patients treated with such new protocols, that enables a comparison with our prior knowledge of expected outcomes, in the absence of treatment. The goal of the proposed methodology is not to provide a precise measurement of treatment efficacy, but to establish the existence of treatment efficacy, in order to facilitate the binary decision of whether the treatment protocol should be adopted on an emergency basis. The methodology consists of a frequentist component that compares a treatment group against the probability of an adverse outcome in the absence of treatment, and calculates an efficacy threshold that has to be exceeded by this probability, in order to control the corresponding p-value and reject the null hypothesis. The efficacy threshold is further adjusted with a Bayesian technique, in order to also control the false positive rate. A random selection bias threshold is then calculated from the efficacy threshold to control for random selection bias. Exceeding the efficacy threshold establishes the existence of treatment efficacy by the preponderance of evidence, and exceeding the more demanding random selection bias threshold establishes the existence of treatment efficacy by the clear and convincing evidentiary standard. The combined techniques are applied to case series of high-risk COVID-19 outpatients that were treated using the early Zelenko protocol and the more enhanced McCullough protocol. Full article

Monitoring students’ risk perception forms part of emergency management during public health emergencies. Thus, public risk perception generally triggers attitudes, emotional responses, and prevention behaviors, which affect the evolution of emergencies and disease control strategies. However, research has paid less attention to the COVID-19 risk perception of students in Ghana. This study assessed the prevalence of COVID-19 risk perception and further identified its correlates among university students. In this study, 882 students from two public universities in Ghana were conveniently recruited. The data were analysed using frequency counts, percentages, and ordered logistic regression. The study revealed the prevalence of a high degree of COVID-19 risk perception among almost half (47.4%) of the sampled students. Results from ordered logistic regression analysis showed that age, sex, religion, use of professional and social media platforms, level (years) of study, and COVID-19 knowledge were significant correlates of COVID-19 risk perception. The dissemination of appropriate COVID-19 information and behavior-change communication to such relatively high-risk behavior sub-groups could help counter the debilitative effects of non-altruistic attitudes because of COVID-19 risk perception. Full article

The coronavirus disease 2019 (COVID-19) is a contagious disease caused by a new coronavirus called SARS-CoV-2. The first case was discovered in Wuhan, China, in December 2019, raising concerns about the emergence of a new coronavirus that poses a significant public health risk. The objective of this study, based on data collected and sequenced at the Institut de Recherche en Santé, de Surveillance Epidémiologique et de Formations (IRESSEF), is to characterize the pandemic evolution, establish a relationship between the different strains in each wave, and finally determine the phylodynamic evolution of the pandemic, utilizing microreact simulations. The study shows that SARS-CoV-2 strains have evolved over time and the variability of the virus is characterized by sequencing during each wave, as is its contagiousness (the speed at which it spreads). The pandemic has spread at a rate of 44.34 cases/week during the first wave. Twelve weeks later it has risen to 185.33 cases/week during the second wave. Twenty-three weeks into the pandemic, the numbers have reached 681.77 cases/week during the third wave. During the fourth wave, the rate of infection was found to decrease slightly at 646 cases/week between early December 2021 and mid-January 2022. Data collected during this study also provided us with a geographical distribution of COVID-19, indicating that the epidemic started in Dakar before spreading inland. Full article

Background: Acute Respiratory Distress Syndrome (ARDS) is caused by non-cardiogenic pulmonary edema and occurs in critically ill patients. It is one of the fatal complications observed among severe COVID-19 cases managed in intensive care units (ICU). Supportive lung-protective ventilation and prone positioning remain the mainstay interventions. Purpose: We describe the severity of ARDS, clinical outcomes, and management of ICU patients with laboratory-confirmed COVID-19 infection in multiple Saudi hospitals. Methods: A multicenter retrospective cohort study was conducted of critically ill patients who were admitted to the ICU with COVID-19 and developed ARDS. Results: During our study, 1154 patients experienced ARDS: 591 (51.2%) with severe, 415 (36.0%) with moderate, and 148 (12.8%) with mild ARDS. The mean sequential organ failure assessment (SOFA) score was significantly higher in severe ARDS with COVID-19 (6 ± 5, p = 0.006). Kaplan–Meier survival analysis showed COVID-19 patients with mild ARDS had a significantly higher survival rate compared to COVID-19 patients who experienced severe ARDS (p = 0.023). Conclusion: ARDS is a challenging condition complicating COVID-19 infection. It carries significant morbidity and results in elevated mortality. ARDS requires protective mechanical ventilation and other critical care supportive measures. The severity of ARDS is associated significantly with the rate of death among the patients. Full article

For the first time in history, we have witnessed the origin and development of a pandemic. To handle the accelerated accumulation of viral mutations and to comprehend the virus’ evolutionary adaptation in humans, an unparalleled program of genetic sequencing and monitoring of SARS-CoV-2 variants has been undertaken. Several scientists have theorized that, with the Omicron surge producing a more contagious but less severe disease, the end of COVID-19 is near. However, by analyzing the behavior shown by this virus for 2 years, we have noted that pandemic viruses do not always show decreased virulence. Instead, it appears there is an evolutionary equilibrium between transmissibility and virulence. We have termed this concept “intermittent virulence”. The present work analyzes the temporal and epidemiological behavior of SARS-CoV-2 and suggests that there is a high possibility that new virulent variants will arise in the near future, although it is improbable that SARS-CoV-2’s virulence will be the same as was seen during the alpha or delta waves, due to the fact that the human population has reached a sufficient level of herd immunity through natural infection or due to the vaccination programs. The most recent global mortality data raised a question whether this pandemic is really over. Furthermore, it is uncertain when the endemic phase will begin. Darwin’s words: “the survival of the fittest” are still valid, and the virus will continue killing nonvaccinated old people, vaccinated old people, and those with comorbidities. We have underestimated the SARS-CoV-2 mastery of immune escape and have not yet seen the full adaptive potential this virus can develop through natural selection. Full article

The application of extremum seeking control is investigated to mitigate the spread of the COVID-19 pandemic, maximizing social distancing while limiting the number of infections. The procedure does not rely on the accurate knowledge of an epidemiological model and takes realistic constraints into account, such as hospital capacities, the observation horizon of the pandemic evolution and the quantized government sanitary policy decisions. Based on the bifurcation analysis of a SEIARD compartmental model providing two possible types of equilibria, numerical simulation reveals the transient behaviour of the extremum of the constrained cost function, which, if rapidly caught by the algorithm, slowly drifts to the steady-state optimum. Specific features are easily incorporated in the real-time optimization procedure, such as quantized sanitary condition levels and long actuation (decision) periods (usually several weeks), requiring processing of the discrete control signal saturation and quantization. The performance of the proposed method is numerically assessed, considering the convergence rate and accuracy (quantization bias). Full article

A complete response to the challenge of COVID-19 requires diagnosis, prevention, and treatment strategies. Until recently, the treatment arm has included largely ineffective, often unproven medications with minimal impact on disease outcomes. The earlier experimental therapies are now giving way to approved antiviral drugs with a demonstrated capacity for SARS-CoV-2 suppression, and more are on the way. New oral antiviral drugs will expand treatment options for persons with COVID-19 and, if used early, become the first line of defense for reducing hospitalization, mortality, and virus spread. Several oral medications have been approved for treating COVID-19 on an emergency use basis in the United States (US), European Union (EU), United Kingdom (UK), China, Russia, and India, with other countries now facilitating regulatory reviews and approvals. Here, we compare the risk/benefit profiles of three leading oral antiviral drugs: Favipiravir, Molnupiravir, and Paxlovid. These compounds have distinct features supporting their targeted use by persons with COVID-19 disease. Full article

Background: With the worldwide outbreak of the COVID-19 pandemic, an important question about virus transmission via contaminated surfaces is arising; therefore, research is needed to prove the persistence of viable viruses on surfaces. The purpose of the study was to determine the level of surface contamination with SARS-CoV-2 in a university clinical center. Methods: A study of environmental viral contamination in the rooms of an acute COVID department was performed. Rapid qualitative antigen tests, real-time RT-PCR, and virus isolation in cell cultures were used for virus detection. Results: None of the taken samples were antigen positive. The SARS-CoV-2 RNA was detected in 10% of samples: one positive sample in an empty room after cleaning and disinfection; nine positive samples in occupied rooms. No viable virus was recovered on cell cultures. Conclusions: In our research, the rapid antigen tests did not prove to be effective for environmental samples, but we were able to detect SARS-CoV-2 RNA in 10% of samples using the RT-PCR method. The highest proportion of PCR-positive samples was from unused items in occupied multi-bed rooms. No viable virus was detected, therefore, infection by surface transmission is unlikely, but it remains prudent to maintain strict hand and environmental hygiene and the use of personal protective equipment. Full article

This paper presents the findings of an exploratory study on the continuously generating Big Data on Twitter related to the sharing of information, news, views, opinions, ideas, knowledge, feedback, and experiences about the COVID-19 pandemic, with a specific focus on the Omicron variant, which is the globally dominant variant of SARS-CoV-2 at this time. A total of 12,028 tweets about the Omicron variant were studied, and the specific characteristics of the tweets that were analyzed include sentiment, language, source, type, and embedded URLs. The findings of this study are manifold. First, from sentiment analysis, it was observed that 50.5% of tweets had a ‘neutral’ emotion. The other emotions—‘bad’, ‘good’, ‘terrible’, and ‘great’—were found in 15.6%, 14.0%, 12.5%, and 7.5% of the tweets, respectively. Second, the findings of language interpretation showed that 65.9% of the tweets were posted in English. It was followed by Spanish or Castillian, French, Italian, Japanese, and other languages, which were found in 10.5%, 5.1%, 3.3%, 2.5%, and <2% of the tweets, respectively. Third, the findings from source tracking showed that “Twitter for Android” was associated with 35.2% of tweets. It was followed by “Twitter Web App”, “Twitter for iPhone”, “Twitter for iPad”, “TweetDeck”, and all other sources that accounted for 29.2%, 25.8%, 3.8%, 1.6%, and <1% of the tweets, respectively. Fourth, studying the type of tweets revealed that retweets accounted for 60.8% of the tweets, it was followed by original tweets and replies that accounted for 19.8% and 19.4% of the tweets, respectively. Fifth, in terms of embedded URL analysis, the most common domain embedded in the tweets was found to be twitter.com, which was followed by biorxiv.org, nature.com, wapo.st, nzherald.co.nz, recvprofits.com, science.org, and other domains. Finally, to support research and development in this field, we have developed an open-access Twitter dataset that comprises Tweet IDs of more than 500,000 tweets about the Omicron variant, posted on Twitter since the first detected case of this variant on 24 November 2021. Full article

While vaccine acceptance changes over time, and factors determining vaccine acceptance differ depending on disease and region, limited studies have evaluated vaccine acceptance in Nepal. We conducted an online, cross-sectional study to assess COVID-19 vaccine acceptance among Nepalese. Data were collected before and after the vaccine approval in Nepal, during which 576 and 241 responses were obtained, respectively. We found that vaccine acceptance was generally high among Nepalese (93%) and increased after the safety of vaccine was examined by the regulatory bodies (98%). This indicated the role of the national drug regulatory authority to convey drug safety. In addition, we analyzed the predictor(s) of vaccine acceptance. We found that the people who believe that vaccine is an effective measure in preventing and controlling the disease were highly likely to accept vaccination. Given that Nepal had just passed the most devastating wave of COVID-19 during our post-approval data collection, we assume that this might have also played a role in the belief that vaccination is an appropriate approach to combat the pandemic. Likewise, the number of people willing to vaccinate as soon as possible increased from 43% to 86% after approval. Therefore, our results indicate that the government needs to focus on assuring the safety and effectiveness of a vaccine to enhance acceptance. Although fewer responses obtained after vaccine approval might have affected our results, overall, our findings indicate vaccine acceptance is likely to be affected by socio-demographic factors and the attitudes of respondents. This should be carefully considered in the rollout of the vaccination plans in Nepal and countries alike in future. Full article

In this work we present an updated version of “Safe University”, a protocol aimed to ensure the safe operation of academic institutions during the SARS-CoV-2 pandemic. The protocol is detailed, addressing all aspects of the actions that are required, ranging from controlled access to the university premises and tracking of immunity status to air quality provisions and organization of classes and teaching methods and more. A step-by-step guide and a sample timeline are included, to facilitate practical implementation. The protocol was first developed in the summer of 2021, when the Delta variant had first emerged but not yet dominated, with the aim to support the operation of Greek universities at the beginning of the 2021–2022 academic year. Since then, it has been updated to reflect the evolution of the virus and the pandemic, as well as the developments in the relevant scientific knowledge and additional monitoring, safeguarding and treatment tools that humanity now possesses. It has also been given a more generic form, making it suitable and adjustable for other countries and cultural/political environments as well as other respiratory viruses. With some additional adjustments, it can also be suitable to deal with epidemics from non-respiratory viruses that may arise in the future. Full article