Epidemiological and clinical characteristics of coronavirus disease (COVID-19) cases at a screening clinic during the early outbreak period: a single-centre study

Presenting characteristics, comorbidities, and outcomes among COVID-19 patients hospitalized in twin cities of Pakistan

Background

COVID-19 became a pandemic rapidly after its emergence in December 2019. It belongs to the coronavirus family of viruses, which have struck a few times before in history. Data based on previous research regarding etiology and epidemiology of other viruses from this family helped played a vital role in formulating prevention and precaution strategies during the initial stages of this pandemic. Data related to COVID-19 in Pakistan were not initially documented on a large scale. In addition, due to a weak health care system and low economic conditions, Pakistan’s population, in general, already suffers from many comorbidities, which can severely affect the outcome of patients infected with COVID-19.

Objective

COVID-19 infections are coupled with a manifestation of various notable outcomes that can be documented and characterized clinically. The aim of this study was to examine these clinical manifestations, which can serve as indicators for early detection as well as severity prognosis for COVID-19 infections, especially in high-risk groups.

Methods

A retrospective observational study involving abstraction of demographic features, presenting symptoms, and adverse clinical outcomes for 1812 patients with COVID-19 was conducted. Patients were admitted to the four major hospitals in the Rawalpindi-Islamabad region of Pakistan, and the study was conducted from February to August 2020. Multivariate regression analysis was carried out to identify significant indicators of COVID-19 severity, intensive care unit (ICU) admission, ventilator aid, and mortality. The study not only relates COVID-19 infection with comorbidities, but also examines other related factors, such as age and gender.

Results

This study identified fever (1592/1812, 87.9%), cough (1433/1812, 79.1%), and shortness of breath (998/1812, 55.1%) at the time of hospital admission as the most prevalent symptoms for patients with COVID-19. These symptoms were common but not conclusive of the outcome of infection. Out of 1812 patients, 24.4% (n=443) required ICU admission and 21.5% (n=390) required ventilator aid at some point of disease progression during their stay at the hospital; 25.9% (n=469) of the patients died. Further analysis revealed the relationship of the presented symptoms and comorbidities with the progression of disease severity in these patients. Older adult patients with comorbidities, such as hypertension, diabetes, chronic kidney disease, and asthma, were significantly affected in higher proportions, resulting in requirement of ICU admission and ventilator aid in some cases and, in many cases, even mortality.

Conclusions

Older adult patients with comorbidities, such as hypertension, diabetes, asthma, chronic obstructive pulmonary disorder, and chronic kidney disease, are at increased risk of developing severe COVID-19 infections, with an increased likelihood of adverse clinical outcomes.

Recombinant Protein Expression and Purification of N, S1, and RBD of SARS-CoV-2 from Mammalian Cells and Their Potential Applications

The coronavirus disease 2019 (COVID-19) pandemic has reached an unprecedented level. There is a strong demand for diagnostic and serological supplies worldwide, making it necessary for countries to establish their own technologies to produce high-quality biomolecules. The two main viral antigens used for the diagnostics for severe acute respiratory syndrome coronavirus (SARS-CoV-2) are the structural proteins spike (S) protein and nucleocapsid (N) protein. The spike protein of SARS-CoV-2 is cleaved into S1 and S2, in which the S1 subunit has the receptor-binding domain (RBD), which induces the production of neutralizing antibodies, whereas nucleocapsid is an ideal target for viral antigen-based detection. In this study, we designed plasmids, pcDNA3.1/S1 and pcDNA3.1/N, and optimized their expression of the recombinant S1 and N proteins from SARS-CoV-2 in a mammalian system. The RBD was used as a control. The antigens were successfully purified from Expi293 cells, with high yields of the S1, N, and RBD proteins. The immunogenic abilities of these proteins were demonstrated in a mouse model. Further, enzyme-linked immunosorbent assays with human serum samples showed that the SARS-CoV-2 antigens are a suitable alternative for serological assays to identify patients infected with COVID-19.

ACE2 Netlas: In silico Functional Characterization and Drug-Gene Interactions of ACE2 Gene Network to Understand Its Potential Involvement in COVID-19 Susceptibility

Angiotensin-converting enzyme-2 (ACE2) receptor has been identified as the key adhesion molecule for the transmission of the SARS-CoV-2. However, there is no evidence that human genetic variation in ACE2 is singularly responsible for COVID-19 susceptibility. Therefore, we performed an integrative multi-level characterization of genes that interact with ACE2 (ACE2-gene network) for their statistically enriched biological properties in the context of COVID-19. The phenome-wide association of 51 genes including ACE2 with 4,756 traits categorized into 26 phenotype categories, showed enrichment of immunological, respiratory, environmental, skeletal, dermatological, and metabolic domains (p < 4e-4). Transcriptomic regulation of ACE2-gene network was enriched for tissue-specificity in kidney, small intestine, and colon (p < 4.7e-4). Leveraging the drug-gene interaction database we identified 47 drugs, including dexamethasone and spironolactone, among others. Considering genetic variants within ± 10 kb of ACE2-network genes we identified miRNAs whose binding sites may be altered as a consequence of genetic variation. The identified miRNAs revealed statistical over-representation of inflammation, aging, diabetes, and heart conditions. The genetic variant associations in RORA, SLC12A6, and SLC6A19 genes were observed in genome-wide association study (GWAS) of COVID-19 susceptibility. We also report the GWAS-identified variant in 3p21.31 locus, serves as trans-QTL for RORA and RORC genes. Overall, functional characterization of ACE2-gene network highlights several potential mechanisms in COVID-19 susceptibility. The data can also be accessed at https://gpwhiz.github.io/ACE2Netlas/.

COVID-19 severity: Studying the clinical and demographic risk factors for adverse outcomes

BACKGROUND

The primary goal of the presented cross-sectional observational study was to determine the clinical and demographic risk factors for adverse coronavirus disease 2019 (COVID-19) outcomes in the Pakistani population.

METHODS

We examined the individuals (n = 6331) that consulted two private diagnostic centers in Lahore, Pakistan, for COVID-19 testing between May 1, 2020, and November 30, 2020. The attending nurse collected clinical and demographic information. A confirmed case of COVID-19 was defined as having a positive result through real-time reverse transcriptase polymerase chain reaction (RT-PCR) assay of nasopharyngeal swab specimens.

RESULTS

RT-PCR testing was positive in 1094 cases. Out of which, 5.2% had severe, and 20.8% had mild symptoms. We observed a strong association of COVID-19 severity with the number and type of comorbidities. The severity of the disease intensified as the number of comorbidities increased. The most vulnerable groups for the poor outcome are patients with diabetes and hypertension. Increasing age was also associated with PCR positivity and the severity of the disease.

CONCLUSIONS

Most cases of COVID-19 included in this study developed mild symptoms or were asymptomatic. Risk factors for adverse outcomes included older age and the simultaneous presence of comorbidities.

Evaluation of the Pharmacologic Treatment of COVID-19 Pandemic in Iraq

The impact of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2, or COVID-19) has been detrimental to human health, economy, and wellbeing. Little information is known on the epidemiology and outcome of the disease in a localized community within Iraq. We carried out an audit of confirmed cases of COVID-19 in the Kirkuk General Hospital. Data from the 20th of June to the 31st of July, 2020, were collected and analyzed. Suspected COVID-19 cases were confirmed by real-time polymerase chain reaction (RT-PCR). Data on clinical symptoms, age, and treatment protocols were analyzed concerning the outcome. Our study included a total of 200 individual confirmed COVID-19 patients. The majority of cases 55% (n = 110) displayed severe symptoms, while 32.5% (65 cases) and 12.5% (25 cases) of patients displayed moderate to mild symptoms, respectively. The rate of death in the referred patients was 5%. Most patients admitted to the hospital for treatment recovered and were discharged from the hospital within 5 to 30 days post-diagnosis. Statistical analysis revealed that patients treated with oseltamivir, hydroxychloroquine, and azithromycin in combination with vitamins C and D have shorter hospital stay compared to patients receiving the same therapeutic protocol in combination with steroids. Moreover, a higher mortality rate (4.5%) was observed in patients treated with oseltamivir, hydroxychloroquine, ceftriaxone, and steroids. This study highlights a significant relationship between age, secondary ailments, and the choice of medications as simple predictors of the outcome of COVID-19.

Factors Affecting the Antibody Immunogenicity of Vaccines against SARS-CoV-2: A Focused Review

Vaccines are a crucial part of the global anti-pandemic effort against COVID-19. The effects of vaccines, as well as their common influencing factors, are the most important issues that we should focus on at this time. To this end, we review statistics on immunogenicity after vaccination, using neutralizing antibodies as the main reference index. Age, infection history, and virus variants are compared, and vaccination program recommendations are made accordingly. Suggestions are made to address concerns raised by the vaccines' shortened development cycle, as well as the emergence of immunity escape of viral variants. Finally, a brief description and future prospects are provided based on the principle of the ADE effect and previous experience with similar viruses.

Neurological Manifestations in COVID-19 Patients: A Meta-Analysis

Common symptoms such as dizziness, headache, olfactory dysfunction, nausea, vomiting, etc. in COVID-19 patients have indicated the involvement of the nervous system. However, the exact association of the nervous system with COVID-19 infection is still unclear. Thus, we have conducted a meta-analysis of clinical studies associated with neurological problems in COVID-19 patients. We have searched for electronic databases with MeSH terms, and the studies for analysis were selected based on inclusion and exclusion criteria and quality assessment. The Stats Direct (version 3) was used for the analysis. The pooled prevalence with 95% confidence interval of various neurological manifestations reported in the COVID-19 patients was found to be headache 14.6% (12.2-17.2), fatigue 33.6% (29.5-37.8), olfactory dysfunction 26.4% (21.8-31.3), gustatory dysfunction 27.2% (22.3-32.3), vomiting 6.7% (5.5-8.0), nausea 9.8% (8.1-11.7), dizziness 6.7% (4.7-9.1), myalgia 21.4% (18.8-24.1), seizure 4.05% (2.5-5.8), cerebrovascular diseases 9.9% (6.8-13.4), sleep disorders 14.9% (1.9-36.8), altered mental status 17.1% (12.3-22.5), neuralgia 2.4% (0.8-4.7), arthralgia 19.9% (15.3-25.0), encephalopathy 23.5% (14.3-34.1), encephalitis 0.6% (0.2-1.3), malaise 38.3% (24.7-52.9), confusion 14.2% (6.9-23.5), movement disorders 5.2% (1.7-10.4), and Guillain-Barre syndrome 6.9% (2.3-13.7). However, the heterogeneity among studies was found to be high. Various neurological manifestations related to the central nervous system (CNS) and peripheral nervous system (PNS) are associated with COVID-19 patients.

Aging & COVID-19 susceptibility, disease severity, and clinical outcomes: The role of entangled risk factors

The emergence of Severe Acute Respiratory Syndrome Corona Virus 2 (SARS-CoV-2) in late 2019 has been associated with a high rate of mortality and morbidity. It has been determined that the old population are not only at an increased risk for affliction with COVID-19 infection, but also atypical presentations, severe forms of the disease, and mortality are more common in this population. A plethora of mechanisms and risk factors contribute to the higher risk of infection in the old population. For instance, aging is associated with an increment in the expression of Angiotensin-Converting Enzyme-2 (ACE-2), the receptor for SARS-CoV-2 spike protein, which precipitates replication of the virus in the old population. On the other hand, immune dysregulation and changes in gut microbiota as a result of aging can contribute to the cytokine storm, one of the main indicators of disease severity. Decrement in sex steroids, especially in women, as well as growth hormone, both of which have crucial roles in immune regulation, is a key contributor to disease severity in old age. Senescence-associated oxidative stress and mitochondrial dysfunction in both pneumocytes and immune cells contribute to the severity of infection in an exacerbative manner. In addition, lifestyle-associated factors such as nutrition and physical activity, which are compromised in old age, are known as important factors in COVID-19 infection. Aging-associated comorbidities, especially cardiovascular diseases and diabetes mellitus, also put older adults at an increased risk of complications, and disease severity.

Experience from a COVID-19 screening centre of a tertiary care institution: A retrospective hospital-based study

BACKGROUND

The COVID-19 pandemic continues to be a significant public health concern across the whole world, including India. In the absence of any specific treatment or vaccine against COVID-19, the role of efficient testing and reporting has been uncontested so far as the number of cases is rising daily. In order to strengthen the screening activities and to prevent nosocomial infection, facility-based screening centres have been designed and operated at various levels of healthcare, including tertiary care institutions.

METHODS

The present study has been planned with an objective to understand the patient profile and evaluate the functioning of COVID-19 screening OPD (CS-OPD) at a tertiary care hospital. In this hospital-based retrospective study, data from individuals visiting the COVID-19 screening OPD during the period from 17th March 2020 to 31st July 2020 were collected. We documented and analysed relevant demographic, epidemiological and clinical characteristics of the patients.

RESULTS

A total of 10,735 patients visited the COVID-19 screening OPD during the defined study period of which 3652 individuals were tested. The majority of the patients, i.e., 65.67% (7050) were male and in the 15-59 years age group (84.68%). The most common symptoms among patients visiting CS-OPD was cough (9.86%). Of the total, 17.17% (1843) of patients reported to the CS-OPD with a contact history of COVID-19-positive patient. On the other hand, 13.49% (1448) of patients were with either domestic or international travel history. The overall testing rate and positivity rate for CS-OPD during this period were found to be 34.02% and 7.94%, respectively.

CONCLUSION

The clinical, demographic and epidemiological characteristics of patients visiting CS-OPD varied across the study period depending upon the containment and testing strategy. The CS-OPD played a crucial role in preventing nosocomial infection and maintaining non-COVID care at the tertiary care hospital.

Immunometabolic bases of type 2 diabetes in the severity of COVID-19

The outbreak of coronavirus disease 2019 (COVID-19) is caused by the novel severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). COVID-19 and type 2 diabetes (T2D) have now merged into an ongoing global syndemic that is threatening the lives of millions of people around the globe. For this reason, there is a deep need to understand the immunometabolic bases of the main etiological factors of T2D that affect the severity of COVID-19. Here, we discuss how hyperglycemia contributes to the cytokine storm commonly associated with COVID-19 by stimulating monocytes and macrophages to produce interleukin IL-1β, IL-6, and TNF-α in the airway epithelium. The main mechanisms through which hyperglycemia promotes reactive oxygen species release, inhibition of T cell activation, and neutrophil extracellular traps in the lungs of patients with severe SARS-CoV-2 infection are also studied. We further examine the molecular mechanisms by which proinflammatory cytokines induce insulin resistance, and their deleterious effects on pancreatic β-cell exhaustion in T2D patients critically ill with COVID-19. We address the effect of excess glucose on advanced glycation end product (AGE) formation and the role of AGEs in perpetuating pneumonia and acute respiratory distress syndrome. Finally, we discuss the contribution of preexisting endothelial dysfunction secondary to diabetes in the development of neutrophil trafficking, vascular leaking, and thrombotic events in patients with severe SARS-CoV-2 infection. As we outline here, T2D acts in synergy with SARS-CoV-2 infection to increase the progression, severity, and mortality of COVID-19. We think a better understanding of the T2D-related immunometabolic factors that contribute to exacerbate the severity of COVID-19 will improve our ability to identify patients with high mortality risk and prevent adverse outcomes.

An update review of globally reported SARS-CoV-2 vaccines in preclinical and clinical stages

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the rapidly spreading pandemic COVID-19 in the world. As an effective therapeutic strategy is not introduced yet and the rapid genetic variations in the virus, there is an emerging necessity to design, evaluate and apply effective new vaccines. An acceptable vaccine must elicit both humoral and cellular immune responses, must have the least side effects and the storage and transport systems should be available and affordable for all countries. These vaccines can be classified into different types: inactivated vaccines, live-attenuated virus vaccines, subunit vaccines, virus-like particles (VLPs), nucleic acid-based vaccines (DNA and RNA) and recombinant vector-based vaccines (replicating and non-replicating viral vector). According to the latest update of the WHO report on April 2nd, 2021, at least 85 vaccine candidates were being studied in clinical trial phases and 184 candidate vaccines were being evaluated in pre-clinical stages. In addition, studies have shown that other vaccines, including the Bacillus Calmette-Guérin (BCG) vaccine and the Plant-derived vaccine, may play a role in controlling pandemic COVID-19. Herein, we reviewed the different types of COVID-19 candidate vaccines that are currently being evaluated in preclinical and clinical trial phases along with advantages, disadvantages or adverse reactions, if any.

The COVID-19 epidemic in Madagascar: clinical description and laboratory results of the first wave, march-september 2020

BACKGROUND

Following the first detection of SARS-CoV-2 in passengers arriving from Europe on 19 March 2020, Madagascar took several mitigation measures to limit the spread of the virus in the country.

METHODS

Nasopharyngeal and/or oropharyngeal swabs were collected from travellers to Madagascar, suspected SARS-CoV-2 cases and contact of confirmed cases. Swabs were tested at the national reference laboratory using real-time RT-PCR. Data collected from patients were entered in an electronic database for subsequent statistical analysis. All distribution of laboratory-confirmed cases were mapped, and six genomes of viruses were fully sequenced.

RESULTS

Overall, 26,415 individuals were tested for SARS-CoV-2 between 18 March and 18 September 2020, of whom 21.0% (5,553/26,145) returned positive. Among laboratory-confirmed SARS-CoV-2-positive patients, the median age was 39 years (IQR: 28-52), and 56.6% (3,311/5,553) were asymptomatic at the time of sampling. The probability of testing positive increased with age with the highest adjusted odds ratio of 2.2 [95% CI: 1.9-2.5] for individuals aged 49 years and more. Viral strains sequenced belong to clades 19A, 20A and 20B indicative of several independent introduction of viruses.

CONCLUSIONS

Our study describes the first wave of the COVID-19 in Madagascar. Despite early strategies in place Madagascar could not avoid the introduction and spread of the virus. More studies are needed to estimate the true burden of disease and make public health recommendations for a better preparation to another wave.

COVID-19 Testing Experience in a Resource-Limited Setting: The Use of Existing Facilities in Public Health Emergency Management

Introduction: Coronavirus disease 2019 (COVID-19) is a public health emergency with little testing and treatment experiences at its occurrence. Diagnostic and treatment rapidly changed in the world including Ethiopia. Haramaya University has strived to change its diagnostic capacity using existing facilities in response to the national call to the pandemic.

Objective: This summary aims to detail experiences of setting up COVID-19 testing in Haramaya University laboratories, Eastern Ethiopia.

Methods: Desktop exercise was conducted to understand the start-up and implementations of COVID-19 testing in two Haramaya University laboratories, Hararghe Health Research Partnership and Campylobacter Genomics and Environmental Enteric Dysfunction laboratories. Communication, formats, guidelines, and standards were reviewed and summarized. Discussion with those involved in the start-up and implementation of the testing were also held. Ideas were summarized to learn the experiences the COVID-19 testing exercises.

Lesson Learned: This is a huge experience for Haramaya University to participate in the national call to increase the testing platform in the management of COVID19. Close work relationship with the public health authorities at all levels demonstrated the university's commitment to public service. The university has used the opportunity to advance its molecular testing capability by training its staff and students. The University has also contributed to the capacity development for laboratories in the surrounding areas of Harar, Somali, Oromia, and Dire Dawa. The pandemic has been an opportunity in harnessing existing resource for the benefit of the public during such times of dire needs to provide critical public health laboratory interventions.

Abnormal pulmonary function and imaging studies in critical COVID-19 survivors at 100 days after the onset of symptoms

Background

The long-term repercussions of critical COVID-19 on pulmonary function and imaging studies remains unexplored. In this study, we investigated the pulmonary function and computed tomography (CT) findings of critical COVID-19 patients approximately 100 days after symptom onset.

Methods

We retrospectively extracted data on critical COVID-19 patients who received invasive mechanical ventilation during hospitalization from April to December 2020 and evaluated their pulmonary function, residual respiratory symptoms and radiographic abnormalities on CT.

Results

We extracted 17 patients whose median age was 63 (interquartile range [IQR], 59–67) years. The median lengths of hospitalization and mechanical ventilation were 23 (IQR, 18–38) and 9 (IQR, 6–13) days, respectively. At 100 days after symptom onset, the following pulmonary function abnormalities were noted in 8 (47%) patients: a diffusion capacity of the lung for carbon monoxide (%DL_CO) of <80% for 6 patients (35%); a percent vital capacity (%VC) of <80% for 4 patients (24%); and a forced expiratory volume in one second/forced vital capacity (FEV₁%) of <70% for 1 patient (6%) who also presented with %DL_CO and %VC abnormalities. Twelve (71%) patients reported residual respiratory symptoms and 16 (94%) showed abnormalities on CT.

Conclusions

Over 90% of the critical COVID-19 patients who underwent invasive mechanical ventilation continued presenting with abnormal imaging studies and 47% of the patients presented with abnormal pulmonary function 100 days after symptom onset. The extent of the residual CT findings might be associated with the degree of abnormal pulmonary function in critical COVID-19 survivors.

A Bittersweet Response to Infection in Diabetes; Targeting Neutrophils to Modify Inflammation and Improve Host Immunity

Chronic and recurrent infections occur commonly in both type 1 and type 2 diabetes (T1D, T2D) and increase patient morbidity and mortality. Neutrophils are professional phagocytes of the innate immune system that are critical in pathogen handling. Neutrophil responses to infection are dysregulated in diabetes, predominantly mediated by persistent hyperglycaemia; the chief biochemical abnormality in T1D and T2D. Therapeutically enhancing host immunity in diabetes to improve infection resolution is an expanding area of research. Individuals with diabetes are also at an increased risk of severe coronavirus disease 2019 (COVID-19), highlighting the need for re-invigorated and urgent focus on this field. The aim of this review is to explore the breadth of previous literature investigating neutrophil function in both T1D and T2D, in order to understand the complex neutrophil phenotype present in this disease and also to focus on the development of new therapies to improve aberrant neutrophil function in diabetes. Existing literature illustrates a dual neutrophil dysfunction in diabetes. Key pathogen handling mechanisms of neutrophil recruitment, chemotaxis, phagocytosis and intracellular reactive oxygen species (ROS) production are decreased in diabetes, weakening the immune response to infection. However, pro-inflammatory neutrophil pathways, mainly neutrophil extracellular trap (NET) formation, extracellular ROS generation and pro-inflammatory cytokine generation, are significantly upregulated, causing damage to the host and perpetuating inflammation. Reducing these proinflammatory outputs therapeutically is emerging as a credible strategy to improve infection resolution in diabetes, and also more recently COVID-19. Future research needs to drive forward the exploration of novel treatments to improve infection resolution in T1D and T2D to improve patient morbidity and mortality.

Gastrointestinal Manifestations of Pediatric Coronavirus Disease and Their Relationship with a Severe Clinical Course: A Systematic Review and Meta-analysis

BACKGROUND

Data on the gastrointestinal (GI) manifestations of Pediatric Corona Virus Disease (COVID-19) are conflicting and the relationship between GI involvement and the severity of COVID-19 disease has not been evaluated. The objectives of this systematic review were to determine the GI manifestations of pediatric COVID-19 and to evaluate their role as risk factors for a severe clinical course.

METHODS

: A systematic literature search was carried out in PubMed and Scopus for studies published before 31 December 2020 with information about the GI manifestations of pediatric COVID-19. Patients with a severe and nonsevere clinical course were compared using the inverse variance heterogeneity model and odds ratio (OR) as the effect size. A sensitivity analysis was performed if the heterogeneity was high among studies.

RESULTS

A total of 811 studies were identified through a systematic search of which 55 studies (4369 patients) were included in this systematic review. The commonest GI symptoms were diarrhea-19.08% [95% confidence interval (CI) 10.6-28.2], nausea/vomiting 19.7% (95% CI 7.8-33.2) and abdominal pain 20.3% (95% CI 3.7-40.4). The presence of diarrhea was significantly associated with a severe clinical course with a pooled OR of 3.97 (95% CI 1.80-8.73; p < 0.01). Abdominal pain and nausea/vomiting were not associated with disease severity.

CONCLUSIONS

Diarrhea, nausea/vomiting or abdominal pain are present in nearly one-fifth of all children with COVID-19. The presence of diarrhea portends a severe clinical course.

Fat-Soluble Vitamins and the Current Global Pandemic of COVID-19: Evidence-Based Efficacy from Literature Review

The outbreak of pneumonia caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), later named COVID-19 by the World Health Organization (WHO), was initiated at Wuhan, Hubei, China, and there was a rapid spread of novel SARS-CoV-2 and the disease COVID-19 in late 2019. The entire world is now experiencing the challenge of COVID-19 infection. However, still very few evidence-based treatment options are available for the prevention and treatment of COVID-19 disease. The present review aims to summarize the publicly available information to give a comprehensive yet balanced scientific overview of all the fat-soluble vitamins concerning their role in SARS-CoV-2 virus infection. The roles of different fat-soluble vitamins and micronutrients in combating SARS-CoV-2 infection have been recently explored in several studies. There are various hypotheses to suggest their use to minimize the severity of COVID-19 infection. These vitamins are pivotal in the maintenance and modulation of innate and cell-mediated, and antibody-mediated immune responses. The data reported in recent literature demonstrate that deficiency in one or more of these vitamins compromises the patients' immune response and makes them more vulnerable to viral infections and perhaps worse disease prognosis. Vitamins A, D, E, and K boost the body's defense mechanism against COVID-19 infection and specifically prevent its complications such as cytokine storm and other inflammatory processes, leading to increased morbidity and mortality overemphasis. However, more detailed randomized double-blind clinical pieces of evidence are required to define the use of these supplements in preventing or reducing the severity of the COVID-19 infection.

RT-qPCR Assays for Rapid Detection of the N501Y, 69-70del, K417N, and E484K SARS-CoV-2 Mutations: A Screening Strategy to Identify Variants With Clinical Impact

Background

Several variants of the SARS-CoV-2 have been documented globally during the current COVID-19 pandemic. The N501Y, 69-70del, K417N, and E484K SARS-CoV-2 mutations have been documented among the most relevant due to their potential pathogenic biological effects. This study aimed to design, validate, and propose a fast real-time RT-qPCR assay to detect SARS-CoV-2 mutations with possible clinical and epidemiological relevance in the Mexican population.

Methods

Targeting spike (S) gene mutations of SARS-CoV-2 (N501Y, 69-70del, K417N, and E484K), specific primers, and probes for three specific quantitative reverse transcription PCR (RT-qPCR) assays were designed, and validated using Sanger sequencing. These assays were applied in clinical samples of 1060 COVID-19 patients from Jalisco Mexico.

Results

In silico analyzes showed high specificity of the three assays. Amplicons of samples were confirmed through sequencing. The screening of samples of COVID-19 patients allowed the identification of the E484K mutation in nine individuals and the identification of P.2 Brazilian variant in Mexico.

Conclusion

This work provides low-cost RT-qPCR assays for rapid screening and molecular surveillance of mutations with potential clinical impact. This strategy allowed the detection of E484K mutation and P.2 variant for the first time in samples from the Mexican population.

The Escalating Magnitude of COVID-19 Infections among the Northeastern Ethiopia Region: A Community-Based Cross-Sectional Study

Background

The novel coronavirus disease (COVID-19) is lethal and extremely contagious, with a rapidly rising global prevalence. The World Health Organization has declared the outbreak a global pandemic; it is reported to have spread to nearly every country in the world. However, the prevalence varies across developed and developing countries, as well as within different regions of the same country. It is not hidden that estimating the magnitude of COVID-19 infection from the community surveys is critical for public health policymakers to make decisions to deal with the outbreak, optimize measures, and design mitigation plans.

Methods

A community-based cross-sectional study was conducted from 01 July to 31 August 2020 in the northeastern Ethiopia region. A simple random sampling technique was used to select study participants from the community survey, contact traces from confirmed cases, and infection suspects. After extraction of viral nucleic acid from oropharyngeal specimen, the real-time fluorescent polymerase chain reaction (RT-PCR) kit was used for detecting novel coronavirus.

Results

A total of 8752 study participants were included in this study. About 63.6% were males and 36.4% were females. Out of the total 8752 study participants, 291 (3.3%) were found to be infected with the virus. The first laboratory-confirmed cases of COVID-19 were detected in the fourth week of the study period, that is, from July 24 to July 31, 2020, and the peak prevalence was observed in the last two weeks. The COVID-19 infection was more prevalent among males and in the age group of 36–52 years. Participants tested via contact trace had 1.65 times (AOR = 1.65, 95% CI = 1.09–2.51, P=0.018) the likelihood of COVID-19 infection in comparison to the other forms of community surveys.

Conclusion

The trend in the prevalence of COVID-19 infection in the northeastern region has shown increment, and increasing testing capacity has a greater benefit in identifying early infection for the prevention, treatment, and control of the international pandemic.

Long-COVID and Post-COVID Health Complications: An Up-to-Date Review on Clinical Conditions and Their Possible Molecular Mechanisms

The COVID-19 pandemic has infected millions worldwide, leaving a global burden for long-term care of COVID-19 survivors. It is thus imperative to study post-COVID (i.e., short-term) and long-COVID (i.e., long-term) effects, specifically as local and systemic pathophysiological outcomes of other coronavirus-related diseases (such as Middle East Respiratory Syndrome (MERS) and Severe Acute Respiratory Syndrome (SARS)) were well-cataloged. We conducted a comprehensive review of adverse post-COVID health outcomes and potential long-COVID effects. We observed that such adverse outcomes were not localized. Rather, they affected different human systems, including: (i) immune system (e.g., Guillain-Barré syndrome, rheumatoid arthritis, pediatric inflammatory multisystem syndromes such as Kawasaki disease), (ii) hematological system (vascular hemostasis, blood coagulation), (iii) pulmonary system (respiratory failure, pulmonary thromboembolism, pulmonary embolism, pneumonia, pulmonary vascular damage, pulmonary fibrosis), (iv) cardiovascular system (myocardial hypertrophy, coronary artery atherosclerosis, focal myocardial fibrosis, acute myocardial infarction, cardiac hypertrophy), (v) gastrointestinal, hepatic, and renal systems (diarrhea, nausea/vomiting, abdominal pain, anorexia, acid reflux, gastrointestinal hemorrhage, lack of appetite/constipation), (vi) skeletomuscular system (immune-mediated skin diseases, psoriasis, lupus), (vii) nervous system (loss of taste/smell/hearing, headaches, spasms, convulsions, confusion, visual impairment, nerve pain, dizziness, impaired consciousness, nausea/vomiting, hemiplegia, ataxia, stroke, cerebral hemorrhage), (viii) mental health (stress, depression and anxiety). We additionally hypothesized mechanisms of action by investigating possible molecular mechanisms associated with these disease outcomes/symptoms. Overall, the COVID-19 pathology is still characterized by cytokine storm that results to endothelial inflammation, microvascular thrombosis, and multiple organ failures.

Epidemiological and Clinical Characteristics of COVID-19: A Retrospective Multi-Center Study in Pakistan

The emergence of a pathogen responsible for a mysterious respiratory disease was identified in China and later called a novel coronavirus. This disease was named COVID-19. The present study seeks to determine the epidemiological and clinical characteristics of COVID-19 in Pakistan. This report will exhibit a linkage between epidemiology and clinical aspects which in turn can be helpful to prevent the transmission of the virus in Pakistan. A retrospective, multiple center study was performed by collecting the data from patients' with their demographics, epidemiological status, history of co-morbid conditions, and clinical manifestations of the disease. The data was collected from 31 public-sector and 2 private hospitals across Pakistan by on-field healthcare workers. A Chi-square test was applied to assess the relationship between categorical data entries. A total of 194 medical records were examined. The median age of these patients was found to be 34 years. A total of 53.6% active cases were present including 41.2% males and 12.4% females till the end of the study. Adults accounted for most of the cases (94.3%) of COVID-19. Fever (86.60%), cough (85.05%), fatigue (36.60%), dyspnea (24.74%), and gastrointestinal discomfort (10.31%) were among the most frequently reported signs and symptoms by the patients. However, 4.12% of the total patient population remained asymptomatic. The median duration of hospital stay was found to be 14 (0-19) days. The earliest source of the spread of the virus may be linked to the foreigners traveling to Pakistan. Spread among men was more as compared to women. A few cases were found to be positive, due to the direct contact with pets or livestock. Hypertension (7.73%), diabetes (4.64%), cardiovascular conditions (2.58%) were the most common co-morbidities. The percentage mortality was 2.50% with the highest mortality among elders.

Viral Clearance Course of COVID-19 Outbreaks

Background

Coronavirus disease 2019 (COVID-19) viral course and behavior remain unpredictable. This study describes incubation time and viral clearance of COVID-19 hospitalized cases in Northern Jordan.

Methods

All COVID-19 confirmed cases hospitalized from March 15 to June 09, 2020, were included. Nasopharyngeal swabs were collected, and COVID-19 reverse transcription-polymerase chain reaction (RT-PCR) was performed every two days in all cases. The viral cure was defined when two negative RT-PCR tests were obtained ≥ 24 hours apart. Viral clearance time (VCT) reflects the time from the first positive nasopharyngeal swab to the first of two consecutive negative tests.

Results

In this cohort, a total of 157 patients were included. Most cases resulted from two major outbreaks. The median incubation period was 6 days (IQR, 3-10) and ranged from 1 to 17 days. The median VCT was 13 days (IQR, 7-2) and ranged from 1 to 40 days. Symptomatic presentation and abnormal chest radiograph were predictors for a prolonged VCT (p=0.015 and p=0.014, respectively). The median time of resolution of symptoms was 7 days (IQR, 3-10 days). Most symptomatic cases (91.7%) remained RT-PCR positive for up to 20 days after symptoms resolution, with a median of 13.5 days. VCT significantly correlated with the incubation period (p=0.013).

Conclusion

Viral cure lagged for as long as 20 days after resolution of symptoms. Continuing with social-distancing, frequent hand hygiene, and wearing facial mask remains essential and is recommended even after clinical resolution of symptoms.

A narrative review on characterization of acute respiratory distress syndrome in COVID-19-infected lungs using artificial intelligence

COVID-19 has infected 77.4 million people worldwide and has caused 1.7 million fatalities as of December 21, 2020. The primary cause of death due to COVID-19 is Acute Respiratory Distress Syndrome (ARDS). According to the World Health Organization (WHO), people who are at least 60 years old or have comorbidities that have primarily been targeted are at the highest risk from SARS-CoV-2. Medical imaging provides a non-invasive, touch-free, and relatively safer alternative tool for diagnosis during the current ongoing pandemic. Artificial intelligence (AI) scientists are developing several intelligent computer-aided diagnosis (CAD) tools in multiple imaging modalities, i.e., lung computed tomography (CT), chest X-rays, and lung ultrasounds. These AI tools assist the pulmonary and critical care clinicians through (a) faster detection of the presence of a virus, (b) classifying pneumonia types, and (c) measuring the severity of viral damage in COVID-19-infected patients. Thus, it is of the utmost importance to fully understand the requirements of for a fast and successful, and timely lung scans analysis. This narrative review first presents the pathological layout of the lungs in the COVID-19 scenario, followed by understanding and then explains the comorbid statistical distributions in the ARDS framework. The novelty of this review is the approach to classifying the AI models as per the by school of thought (SoTs), exhibiting based on segregation of techniques and their characteristics. The study also discusses the identification of AI models and its extension from non-ARDS lungs (pre-COVID-19) to ARDS lungs (post-COVID-19). Furthermore, it also presents AI workflow considerations of for medical imaging modalities in the COVID-19 framework. Finally, clinical AI design considerations will be discussed. We conclude that the design of the current existing AI models can be improved by considering comorbidity as an independent factor. Furthermore, ARDS post-processing clinical systems must involve include (i) the clinical validation and verification of AI-models, (ii) reliability and stability criteria, and (iii) easily adaptable, and (iv) generalization assessments of AI systems for their use in pulmonary, critical care, and radiological settings.

Clinical manifestation and maternal complications and neonatal outcomes in pregnant women with COVID-19: a comprehensive evidence synthesis and meta-analysis

OBJECTIVES

There is little known about pregnancy-related complications and comorbidity in this group of women. Therefore, this systematic review and meta-analysis were performed to find out whether COVID-19 may cause different manifestations and outcomes in the antepartum and postpartum period or not.

MATERIAL AND METHODS

We searched databases, including Medline (PubMed), Embase, Scopus, Web of sciences, Cochrane library, Ovid, and CINHAL to retrieve all articles reporting the prevalence of maternal and neonatal complications, in addition to clinical manifestations, in pregnant women with COVID-19 that published with English language January to November 2020.

RESULTS

Seventy-four studies with total 5560 pregnant women included in this systematic review. The results show that the pooled prevalence of neonatal mortality, lower birth weight, stillbirth, premature birth, and intrauterine fetal distress in women with COVID-19 was 4% (95% Cl: 1 - 9%), 21% (95% Cl: 11 - 31%), 2% (95% Cl: 1 - 6%), 28% (95% Cl: 13 - 43%), and 14% (95% Cl: 4 - 25%); respectively. Moreover, the pooled prevalence of fever, cough, diarrhea, and dyspnea were 56% (95% Cl: 32 - 81%), 29% (95% Cl: 21 - 38%), 9% (95% Cl: 2 - 16%), and 3% (95% Cl: 1 - 6%) in pregnant women with COVID-19. Two studies reported that pregnant women with severe COVID pneumonia have higher levels of d-dimer. Also, COVID pneumonia is more common in pregnant women than non-pregnant.

CONCLUSION

According to this meta-analysis, pregnant women with COVID-19 with or without pneumonia, are at a higher risk of preeclampsia, preterm birth, miscarriage and cesarean delivery. Furthermore, the risk of LBW and intrauterine fetal distress seems to be increased in neonates. In addition, our evaluations are investigative of higher risk of COVID-19 in the third trimester in pregnant women comparing to the first and second trimester. It can be due to higher BMI in the third trimester causing to increase the likelihood of disease deterioration, which can trigger a cascade of side effects starting with coagulation, pneumonia, hypoxemia affecting the placenta leading to ICU admission, fetal distress, premature birth and higher rates of C-section.

First report on prevalence of SARS-CoV-2 infection among health-care workers in Nicaragua

The Nicaraguan COVID-19 situation is exceptional for Central America. The government restricts testing and testing supplies, and the true extent of the coronavirus crisis remains unknown. Dozens of deaths have been reported among health-care workers. However, statistics on the crisis' effect on health-care workers and their risk of being infected with SARS-CoV-2 are lacking. We aimed to estimate the prevalence of SARS-CoV-2 infection in health-care workers and to examine correlations with risk factors such as age, sex and comorbidities. Study participants (N = 402, median age 38.48 years) included physicians, nurses and medical assistants, from public and private hospitals, independent of symptom presentation. SARS-CoV-2 was detected on saliva samples using the loop-mediated isothermal amplification assay. A questionnaire was employed to determine subjects' COVID-19-associated symptoms and their vulnerability to complications from risk factors such as age, sex, professional role and comorbidities. The study was performed five weeks into the exponential growth period in Nicaragua. We discovered that 30.35% of health-care workers participating in our study had been infected with SARS-CoV-2. A large percentage (54.92%) of those who tested positive were asymptomatic and were still treating patients. Nearly 50% of health-care workers who tested positive were under 40, an astonishing 30.33% reported having at least one comorbidity. In our study, sex and age are important risk factors for the probability of testing positive for SARS-CoV-2 with significance being greatest among those between 30 and 40 years of age. In general, being male resulted in higher risk. Our data are the first non-governmental data obtained in Nicaragua. They shed light on several important aspects of COVID-19 in an underdeveloped nation whose government has implemented a herd-immunity strategy, while lacking an adequate healthcare system and sufficient PPE for health-care workers. These data are important for creating policies for containing the spread of SARS-CoV-2.

Leveraging technology for health services continuity in times of COVID-19 pandemic: Patient follow-up, and mitigation of worse patient outcomes

BACKGROUND

Since the outbreak of the COVID-19 pandemic in Wuhan, China, which has now spread globally, the health systems continue to face challenges in the provision of health care, there is a risk of exposure for both the physicians and the patients. While there is significant progress in the adoption of technology in health care. This study sought to examine the adverse effects of the measures put in place by the government to curb the spread of COVID-19 and come up with an intervention to prevent worse outcomes for chronic conditions.

METHODS

Booking registers for four specialty clinics in Machakos Level 5 Hospital were reviewed to identify patients who missed clinic appointments for follow-up. An automated data collection tool (ODK-collect) was used for data collection. COVID-19 Machakos App was developed to facilitate follow-up and referral of patients to the nearest facilities, capturing and posting of information in real-time to a central database. The mobile App also facilitated the tracking of patients and aided doctors to give feedback on whether the patients reported to the referred facilities. The doctors were also able to capture doctors' notes on the patients' status while ensuring the confidentiality and privacy of the patients. An interactive dashboard was developed to generate analytics reports and summaries to monitor clinic attendance and trends in the provision of health care during the pandemic period.

RESULTS

Register data showed 977 (81.5%) out of a total of 1199 patients had missed their scheduled appointments. Among the 977, 746 (76%) were residents of Machakos County and qualified for follow-up. Missed appointments varied by clinic: Cancer Clinic 12 (1.6) %), Diabetes Clinic 212 (28.4%), Hypertension 293 (39.3%), and Paediatrics Clinic 229 (30.7%). Contact was made and follow-up was attempted for 746 patients, of which 453 patients (60.7%) were successful. The follow-up distribution of the 453 patients varied by the clinic as follows: Cancer Clinic 10, Diabetes Clinic 146, Hypertension 185, and Paediatrics Clinic 112. During the follow-up process, 331 patients from diabetes and hypertension clinics were requested to choose a preferred or nearby facility to be referred to. 191 (58%) patients chose Machakos Level 5 Hospital as their preferred facility and 137 (41%) patients chose to be referred to level 3 or 4 hospitals within the County. Three deaths were reported from the medical (Hypertension) clinic. Through the developed App, a total, 82 (60%) patients out of the 137 were reviewed at the referral facilities jointly with a specialist at Machakos Level 5 Hospital. For the duration of the study, some patients reported worse conditions by the time of review after missing scheduled appointments.

CONCLUSIONS

This intervention demonstrated that mobile phone technology could be leveraged to provide specialty treatment services remotely to mitigate against worse patient outcomes. The study reveals that there is a dire need to integrate technological interventions in the provision of health care services to ensure continuity.

RT-qPCR Assays for Rapid Detection of the N501Y, 69-70del, K417N, and E484K SARS-CoV-2 Mutations: A Screening Strategy to Identify Variants With Clinical Impact

BACKGROUND

Several variants of the SARS-CoV-2 have been documented globally during the current COVID-19 pandemic. The N501Y, 69-70del, K417N, and E484K SARS-CoV-2 mutations have been documented among the most relevant due to their potential pathogenic biological effects. This study aimed to design, validate, and propose a fast real-time RT-qPCR assay to detect SARS-CoV-2 mutations with possible clinical and epidemiological relevance in the Mexican population.

METHODS

Targeting spike (S) gene mutations of SARS-CoV-2 (N501Y, 69-70del, K417N, and E484K), specific primers, and probes for three specific quantitative reverse transcription PCR (RT-qPCR) assays were designed, and validated using Sanger sequencing. These assays were applied in clinical samples of 1060 COVID-19 patients from Jalisco Mexico.

RESULTS

In silico analyzes showed high specificity of the three assays. Amplicons of samples were confirmed through sequencing. The screening of samples of COVID-19 patients allowed the identification of the E484K mutation in nine individuals and the identification of P.2 Brazilian variant in Mexico.

CONCLUSION

This work provides low-cost RT-qPCR assays for rapid screening and molecular surveillance of mutations with potential clinical impact. This strategy allowed the detection of E484K mutation and P.2 variant for the first time in samples from the Mexican population.

Systematic Review on the Therapeutic Options for COVID-19: Clinical Evidence of Drug Efficacy and Implications

A novel coronavirus-2 (SARS-CoV-2) was first identified in Wuhan, China, and quickly spread globally. Several treatments have been proposed, many of which have proven ineffective. Consequently, there is a need to review the published evidence of drug clinical trials to guide future prescribing. A systematic review of published clinical trials and retrospective observational studies was carried out. The search was made using PubMed, Embase, MEDLINE, and China National Knowledge Infrastructure (CNKI) databases. Articles published between January 2020 and October 2020 and written in the English language were retrieved and included in the study. Researches that used traditional medicine, in-vitro and in-vivo animal studies, as well as reviews were excluded. Seventy-three relevant articles that fulfilled the inclusion criteria were finally selected and reviewed. Hydroxychloroquine, chloroquine, and azithromycin produced no clinical evidence of efficacy in randomized controlled clinical trials (RCT). However, retrospective observational studies reported the efficacy of remdesivir and lopinavir/ritonavir in reducing viral load, although there have been concerns with lopinavir/ritonavir and, more recently, remdesivir. Recently, tocilizumab, dexamethasone, and methylprednisolone significantly relieved lung inflammation and decreased mortality in patients with severe COVID-19. In addition, convalescent plasma was effective in boosting strong immunity among patients with mild COVID-19. There is currently no single worldwide approved therapeutic option for patients with COVID-19 despite the initial hype with medicines, including hydroxychloroquine. Nonetheless, dexamethasone has shown promise in symptomatic treatment and convalescent plasma in boosting immunity. New treatments are currently being researched, and the findings will be reported accordingly to provide evidence-based guidance for prescribers and policymakers.

ACE2 Netlas: In-silico functional characterization and drug-gene interactions of ACE2 gene network to understand its potential involvement in COVID-19 susceptibility

Angiotensin-converting enzyme-2 ( ACE2 ) receptor has been identified as the key adhesion molecule for the transmission of the SARS-CoV-2. However, there is no evidence that human genetic variation in ACE2 is singularly responsible for COVID-19 susceptibility. Therefore, we performed a multi-level characterization of genes that interact with ACE2 (ACE2-gene network) for their over-represented biological properties in the context of COVID-19. The phenome-wide association of 51 genes including ACE2 with 4,756 traits categorized into 26 phenotype categories, showed enrichment of immunological, respiratory, environmental, skeletal, dermatological, and metabolic domains (p<4e-4). Transcriptomic regulation of ACE2-gene network was enriched for tissue-specificity in kidney, small intestine, and colon (p<4.7e-4). Leveraging the drug-gene interaction database we identified 47 drugs, including dexamethasone and spironolactone, among others. Considering genetic variants within ± 10 kb of ACE2-network genes we characterized functional consequences (among others) using miRNA binding-site targets. MiRNAs affected by ACE2-network variants revealed statistical over-representation of inflammation, aging, diabetes, and heart conditions. With respect to variants mapped to the ACE2-network, we observed COVID-19 related associations in RORA, SLC12A6 and SLC6A19 genes. Overall, functional characterization of ACE2-gene network highlights several potential mechanisms in COVID-19 susceptibility. The data can also be accessed at https://gpwhiz.github.io/ACE2Netlas/.