Severe Acute Respiratory Syndrome by SARS-CoV-2 Infection or Other Etiologic Agents Among Brazilian Indigenous Population: An Observational Study from the First Year of Coronavirus Disease (COVID)-19 Pandemic

Background

Indigenous peoples are vulnerable to pandemics, including to the coronavirus disease (COVID)-19, since it causes high mortality and specially, the loss of elderly Indigenous individuals.

Methods

The epidemiological data of severe acute respiratory syndrome (SARS) by SARS-CoV-2 infection or other etiologic agents (OEA) among Brazilian Indigenous peoples during the first year of COVID-19 pandemic was obtained from a Brazilian Ministry of Health open-access database to perform an observational study. Considering only Indigenous individuals diagnosed with SARS by COVID-19, the epidemiology data were also evaluated as risk of death. The type of sample collection for virus screening, demographic profile, clinical symptoms, comorbidities, and clinical evolution were evaluated. The primary outcome was considered the death in the Brazilian Indigenous individuals and the secondary outcome, the characteristics of Brazilian Indigenous infected by SARS-CoV-2 or OEA, as the need for intensive care unit admission or the need for mechanical ventilation support. The statistical analysis was done using Logistic Regression Model. Alpha of 0.05.

Findings

A total of 3,122 cases of Indigenous individuals with SARS in Brazil were reported during the first year of the COVID-19 pandemic. Of these, 1,994 were diagnosed with COVID-19 and 730/1,816 (40.2%) of them died. The death rate among individuals with SARS-CoV-2 was three-fold increased when compared to the group of individuals with OEA. Several symptoms (myalgia, loss of smell, and sore throat) and comorbidities (cardiopathy, systemic arterial hypertension, and diabetes mellitus) were more prevalent in the COVID-19 group when compared to Indigenous individuals with OEA. Similar profile was observed considering the risk of death among the Indigenous individuals with COVID-19 who presented several symptoms (oxygen saturation <95%, dyspnea, and respiratory distress) and comorbidities (renal disorders, cardiopathy, and diabetes mellitus). The multivariate analysis was significant in differentiating between the COVID-19-positive and non-COVID-19 patients [X²₍₇₎=65.187; P-value<0.001]. Among the patients’ features, the following contributed in relation to the diagnosis of COVID-19: age [≥43 years-old [y.o.]; OR=1.984 (95%CI=1.480-2.658)]; loss of smell [OR=2.373 (95%CI=1.461-3.854)]; presence of previous respiratory disorders [OR=0.487; 95%CI=0.287-0.824)]; and fever [OR=1.445 (95%CI=1.082-1.929)]. Also, the multivariate analysis was able to predict the risk of death [X²₍₉₎=293.694; P-value<0.001]. Among the patients’ features, the following contributed in relation to the risk of death: male gender [OR=1.507 (95%CI=1.010-2.250)]; age [≥60 y.o.; OR=3.377 (95%CI=2.292-4.974)]; the need for ventilatory support [invasive mechanical ventilation; OR=24.050 (95%CI=12.584-45.962) and non-invasive mechanical ventilation; OR=2.249 (95%CI=1.378-3.671)]; dyspnea [OR=2.053 (95%CI=1.196-3.522)]; oxygen saturation <95% [OR=1.691 (95%CI=1.050-2.723)]; myalgia [OR=0.423 (95%CI=0.191-0.937)]; and the presence of kidney disorders [OR=3.135 (95%CI=1.144-8.539)].

Interpretation

The Brazilian Indigenous peoples are in a vulnerable situation during the COVID-19 pandemic and presented an increased risk of death due to COVID-19. Several factors were associated with enhanced risk of death, as male sex, older age (≥60 y.o.), and need for ventilatory support; also, other factors might help to differentiate SARS by COVID-19 or by OEA, as older age (≥43 y.o.), loss of smell, and fever.

Funding

Fundação de Amparo à Pesquisa do Estado de São Paulo (Foundation for Research Support of the State of São Paulo; #2021/05810-7).

Identification of Mpro inhibitors of SARS-CoV-2 using structure based computational drug repurposing

The recent outbreak of COVID-19, caused by the novel pathogen SARS-coronavirus 2 (SARS-CoV-2) is a severe health emergency. In this pandemic, drug repurposing seems to be the most promising alternative to identify effective therapeutic agents for immediate treatment of infected patients. The present study aimed to evaluate all the drugs present in drug bank as potential novel SARS-CoV-2 inhibitors, using computational drug repurposing studies. Docking-based virtual screening and binding energy prediction were performed, followed by Absorption Distribution Metabolism Excretion calculation. Hydroxychloroquine and Nelfinavir have been identified as the best potential inhibitor against the SARS-CoV-2, therefore, they were used as reference compounds in computational DR studies. The docking study revealed 13 best compounds based on their highest binding affinity, binding energy, and dock score concerning the other screened compounds. Out of 13, only 4 compounds were further shortlisted based on their binding energy and best ADME properties. The hierarchical virtual screening yielded the best 04 drugs, DB07042 (compound 2), DB13035 (compound 3), DB13604 (compound 5) and DB08253 (compound 6), with commendable binding energies in kcal/mol, i.e. −65.45, −62.01, −52.09 and −51.70 respectively. Further, Molecular dynamics simulation with 04 best-retrieved hits has confirmed stable trajectories in protein in terms of root mean square deviation and root mean square fluctuation. During 30 ns simulation, the interactions were also found similar to the docking-based studies. However, clinical studies are necessary to investigate their therapeutic use against this outbreak.

Nano-size dependence in the adsorption by the SARS-CoV-2 spike protein over gold colloid

Gold nano-particles were coated with the spike protein (S protein) of SARS-CoV-2 and exposed to increasingly acidic conditions. Their responses were investigated by monitoring the surface plasmon resonance (SPR) band shift. As the external pH was gradually changed from neutral pH to pH ∼2 the peak of the SPR band showed a significant red-shift, with a sigmoidal feature implying the formation of the gold-protein aggregates. The coating of S protein changed the surface property of the gold enough to extract the coverage fraction of protein over nano particles, Θ, which did not exhibit clear nano-size dependence. The geometrical simulation to explain Θ showed the average axial length to be a = 7. 25 nm and b =8.00 nm when the S-protein was hypothesized as a prolate shape with spiking-out orientation. As the pH value externally hopped between pH∼3 and pH∼10, a behavior of reversible protein folding was observed for particles with diameters >30 nm. It was concluded that S protein adsorption conformation was impacted by the size (diameter, d) of a core nano-gold, where head-to-head dimerized S protein was estimated for d ≤ 80 nm and a parallel in opposite directions formation for d = 100 nm.

A review of the COVID-19 pandemic and its interaction with environmental media

Viruses are biologically active parasites that only exist inside a host they are submicroscopic level. The novel coronavirus disease, or COVID-19, is generally caused by the SARS-CoV-2 virus and is comparable to severe acute respiratory syndrome (SARS). As a result of globalization, natural alterations or changes in the SARS-CoV-2 have created significant risks to human health over time. These viruses can live and survive in different ways in the atmosphere unless they reach another host body. At this stage, we will discuss the details of the transmission and detection of this deadly SARS-CoV-2 virus via certain environmental media, such as the atmosphere, water, air, sewage water, soil, temperature, relative humidity, and bioaerosol, to better understand the diffusion, survival, infection potential and diagnosis of COVID-19.

Exploratory study on the spatial relationship between emerging infectious diseases and urban characteristics: Cases from Korea

In the modern global context of interconnected populations, the recent emergence of infectious diseases involves complex interactions. The purpose of this study is to investigate the spatial correlations between urban characteristics, taking into account the socio-ecological aspects, and the emergence of infectious diseases. Using exploratory spatial data analysis and spatial regression between the infectious disease emergence data and 14 urban characteristics, we analyzed 225 spatial units in South Korea, where there was a re-emergence of measles and a 2015 outbreak of Middle East Respiratory Syndrome. As results of exploratory spatial data analysis, the emerging infectious diseases had spatial dependence and showed spatial clusters. Spatial regression models showed that urban characteristic factors had different effects according to the type of infectious disease. Common factors were characteristics related to low socioeconomic status in water or food-borne diseases and manageable infectious diseases. Intermittent infections disease epidemics are related to high-quality residential environments and the response capacity of the local government. New infectious diseases are different than other infectious diseases, which are related to the ecological environment. This study suggests spatial policies for preventing infectious diseases considering the spatial relationships between urban characteristics and infectious diseases as well as the management of public health.

Fast track triage for COVID-19 based on a population study: The soda score

BACKGROUND

Healthcare systems are under prominent stress due to the COVID-19 pandemic. A fast and simple triage is mandatory to screen patients who will benefit from early hospitalization, from those that can be managed as outpatients. There is a lack of all-comers scores, and no score has been proposed for western-world population.

AIMS

To develop a fast-track risk score valid for every COVID-19 patient at diagnosis.

METHODS

Single-center, retrospective study based on all the inhabitants of a healthcare area. Logistic regression was used to identify simple and wide-available risk factors for adverse events (death, intensive care admission, invasive mechanical ventilation, bleeding > BARC3, acute renal injury, respiratory insufficiency, myocardial infarction, acute heart failure, pulmonary emboli, or stroke).

RESULTS

Of the total healthcare area population, 447.979 inhabitants, 965 patients (0.22%), were diagnosed with COVID-19. A total of 124 patients (12.85%) experienced adverse events. The novel SODA score (based on sex, peripheral O2 saturation, presence of diabetes, and age) demonstrated good accuracy for adverse events prediction (area under ROC curve 0.858, CI: 0.82-0.98). A cut-off value of ≤2 points identifies patients with low risk (positive predictive value [PPV] for absence of events: 98.9%) and a cut-off of ≥5 points, high-risk patients (PPV 58.8% for adverse events).

CONCLUSIONS

This quick and easy score allows fast-track triage at the moment of diagnosis for COVID-19 using four simple variables: age, sex, SpO2, and diabetes. SODA score could improve preventive measures taken at diagnosis in high-risk patients and also relieve resources by identifying very low-risk patients.

A comparative genomics-based study of positive strand RNA viruses emphasizing on SARS-CoV-2 utilizing dinucleotide signature, codon usage and codon context analyses

The novel corona virus disease or COVID-19 caused by a positive strand RNA virus (PRV) called SARS-CoV-2 is plaguing the entire planet as we conduct this study. In this study a multifaceted analysis was carried out employing dinucleotide signature, codon usage and codon context to compare and unravel the genomic as well as genic characteristics of the SARS-CoV-2 isolates and how they compare to other PRVs which represents some of the most pathogenic human viruses. The main emphasis of this study was to comprehend the codon biology of the SARS-CoV-2 in the backdrop of the other PRVs like Poliovirus, Japanese encephalitis virus, Hepatitis C virus, Norovirus, Rubella virus, Semliki Forest virus, Zika virus, Dengue virus, Human rhinoviruses and the Betacoronaviruses since codon usage pattern along with the nucleotide composition prevalent within the viral genome helps to understand the biology and evolution of viruses. Our results suggest discrete genomic dinucleotide signature within the PRVs. Some of the genes from the different SARS-CoV-2 isolates were also found to demonstrate heterogeneity in terms of their dinucleotide signature. The SARS-CoV-2 isolates also demonstrated a codon context trend characteristically dissimilar to the other PRVs. The findings of this study are expected to contribute to the developing global knowledge base in countering COVID-19.

Nicotinic cholinergic system and COVID-19: In silico evaluation of nicotinic acetylcholine receptor agonists as potential therapeutic interventions

SARS-CoV-2 infection was announced as a pandemic in March 2020. Since then, several scientists have focused on the low prevalence of smokers among hospitalized COVID-19 patients. These findings led to our hypothesis that the Nicotinic Cholinergic System (NCS) plays a crucial role in the manifestation of COVID-19 and its severe symptoms. Molecular modeling revealed that the SARS-CoV-2 Spike glycoprotein might bind to nicotinic acetylcholine receptors (nAChRs) through a cryptic epitope homologous to snake toxins, substrates well documented and known for their affinity to the nAChRs. This binding model could provide logical explanations for the acute inflammatory disorder in patients with COVID-19, which may be linked to severe dysregulation of NCS. In this study, we present a series of complexes with cholinergic agonists that can potentially prevent SARS-CoV-2 Spike glycoprotein from binding to nAChRs, avoiding dysregulation of the NCS and moderating the symptoms and clinical manifestations of COVID-19. If our hypothesis is verified by in vitro and in vivo studies, repurposing agents currently approved for smoking cessation and neurological conditions could provide the scientific community with a therapeutic option in severe COVID-19.

Chloroquine, hydroxychloroquine, and COVID-19: Systematic review and narrative synthesis of efficacy and safety

The COVID-19 pandemic has required clinicians to urgently identify new treatment options or the re-purposing of existing drugs. Of particular interest are chloroquine (CQ) and hydroxychloroquine (HCQ). The aims of this systematic review are to systematically identify and collate 24 studies describing the use of CQ and HCQ in human clinical trials and to provide a detailed synthesis of evidence of its efficacy and safety. Of clinical trials, 100% showed no significant difference in the probability of viral transmission or clearance in prophylaxis or therapy, respectively, compared to the control group. Among observational studies employing an endpoint specific to efficacy, 58% concurred with the finding of no significant difference in the attainment of outcomes. Three-fifths of clinical trials and half of observational studies examining an indicator unique to drug safety discovered a higher probability of adverse events in those treated patients suspected of, and diagnosed with, COVID-19. Of the total papers focusing on cardiac side-effects, 44% found a greater incidence of QTc prolongation and/or arrhythmias, 44% found no evidence of a significant difference, and 11% mixed results. The strongest available evidence points towards the inefficacy of CQ and HCQ in prophylaxis or in the treatment of hospitalised COVID-19 patients.

Pneumothorax in patients with prior or current COVID-19 pneumonia

As the number of COVID-19 cases emerge, new complications associated with the disease are recognized. We present three cases of spontaneous pneumothorax in patients with COVID-19. They show that a pneumothorax can occur during different phases of disease, in patients without a pulmonary disease history and is not necessarily associated to positive pressure ventilation or severity of COVID-19. Although the exact causative mechanisms remain unknown, this observation might imply that extensive alveolar destruction due to COVID-19 may lead to bulla formation resulting in subsequent pneumothorax.

Awareness and Concerns Among Adult Liver Transplant Recipients in the Current Pandemic Caused by Novel Coronavirus (COVID-19): Strategies to Safeguard a High-risk Population

BACKGROUND

The coronavirus disease 2019 (COVID-19) virus is spreading rapidly, and there are obvious concerns for the immunocompromised patient population including transplant recipients. Creating awareness and understanding patient concerns will play an important role in protecting this vulnerable group in developing timely and appropriate healthcare interventions.

METHODS

A cross-sectional online survey was conducted between 23rd March 2020 and 1st April 2020 among 154 liver transplant recipients, transplanted between October 2018 and February 2020. An 18-point questionnaire explored their knowledge of COVID-19, awareness of recipient's high-risk status, interventions to minimize cross-infections, and concerns of this patient group regarding the pandemic.

RESULTS

There were 112 (73%) respondents, with median age of 53 years (81% males). There was no difference in demographics between those who responded (n = 112) and those who did not respond to the survey (n = 42). Most of the recipients were aware of the main symptoms of COVID-19, such as fever (92%), breathlessness (86%), and dry cough (87%), but less than half were aware of diarrhea (39%) as a symptom. Awareness about spread from asymptomatic individuals was limited (26%). Majority (95%) understood their high-risk status, but worryingly, 23% of the respondents felt that there was no risk in visiting the hospital for routine clinic visit and blood tests. Concerns were raised by the recipients mostly regarding the uncertainties of COVID-19 infection and its treatment options, the quality of information on social messaging platforms, and lack of access to routine tests/immunosuppression levels because of lockdown/social distancing.

CONCLUSIONS

Our liver transplant recipients have a reasonable awareness regarding COVID-19. Problems in accessing the healthcare system during prolonged periods of lockdown was a major concern. It is important for each transplant unit to educate, support, and remain accessible to this vulnerable patient cohort as the pandemic continues to progress worldwide.

Ebola in the Eastern Democratic Republic of Congo: One Health approach to infectious disease control

The Democratic Republic of Congo (DRC) is facing its tenth outbreak of Ebola virus disease (EVD), in North-Kivu and Ituri provinces. This is the second most deadly EVD outbreak in history, after the one that occurred in West Africa in 2014. The DRC Ministry of Health (MoH), supported by the World Health Organization (WHO) and a range of regional and international partners, are implementing EVD response plans in these affected areas such as screening of suspect cases at points of entry, case detection, contact tracing, laboratory testing, case management and infection prevention and control, safe and dignified burials, ring vaccination (this involves vaccination of infected individuals, direct contacts of infected individuals and contacts of their contacts), and therapeutics, community mobilization and free access to healthcare services. Despite these efforts, there has been a sharp rise in the number of confirmed cases within the identified affected areas, and due to a number of challenges unique to DRC, there has been an expansion in the geographical extent of transmission. The significance of the proximity of these regions to wildlife and the Virunga National Park is questionable in the EVD transmission dynamics. The close interaction between human, animal, and environmental factors, in combination with high population movement due to regular rebel attacks in these regions, suggest the need for the integration of the One Health approach in the holistic response plans for control and prevention of EVD. This paper seeks to highlight the implications and importance of a One Health–based approach into the infectious diseases control program implementation in DRC.

Evidence of prenatal toxicity of herbal based indigenous formulations for sex selection in rat models

Indigenous preparations(IPs) for a male child is reported from some parts of India. The present study aims to explore the effects of IPs for sex selection or sex selection drugs (SSDs) on pregnancy outcomes in rat models. SSDs contain Bryonia laciniosa, Quercus infectoria and Putranjiva roxburghii along with other ingredients.

Methods

An experimental design with successfully mated female rats were randomized into control and treatment groups. Phase 1 had 2 interventional arms while phase 2 had 3 interventional arms (12 rats/arm) besides control arm. In phase-1, pregnant females were dosed two SSDs(1000 mg/kg) on gestation days 1–5 whereas, in phase-2, on gestation days 6–19 to correlate the effect of the SSDs (500/1000/1500 mg/kg) consumption during different stages of pregnancy. Pregnant females were observed for clinical signs following treatment. The rats were sacrificed one day before expected day of delivery for evaluation. Pregnancy rate, gestation index, number of corpora lutea, and litter size were assessed. Foetuses were examined for sex, skeletal and soft tissue alterations.

Discussion and conclusion

In phase 1, no appreciable findings were there with SSD exposure. In phase 2, intrauterine growth and survival of foetuses were affected when SSDs were administered during organogenesis period. Decreased number of live foetuses and increased incidence of early and late resorption, reduced fetal growth with significant alteration in skeleton and viscera were found in treatment groups in a dose-dependent manner. This correlates well with findings from observational studies in pregnant women. However, such treatment at any dose did not effect sex differentiation.

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Indigenous preparations for sex selection consumed during organogenesis period of pregnancy lead to fetal resorptions.

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Such preparations are likely to cause skeletal and visceral malformations in babies.

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These have no impact on sex ratio.

Epidemic Models of Contact Tracing: Systematic Review of Transmission Studies of Severe Acute Respiratory Syndrome and Middle East Respiratory Syndrome

The emergence and reemergence of coronavirus epidemics sparked renewed concerns from global epidemiology researchers and public health administrators. Mathematical models that represented how contact tracing and follow-up may control Severe Acute Respiratory Syndrome (SARS) and Middle East Respiratory Syndrome (MERS) transmissions were developed for evaluating different infection control interventions, estimating likely number of infections as well as facilitating understanding of their likely epidemiology. We reviewed mathematical models for contact tracing and follow-up control measures of SARS and MERS transmission. Model characteristics, epidemiological parameters and intervention parameters used in the mathematical models from seven studies were summarized. A major concern identified in future epidemics is whether public health administrators can collect all the required data for building epidemiological models in a short period of time during the early phase of an outbreak. Also, currently available models do not explicitly model constrained resources. We urge for closed-loop communication between public health administrators and modelling researchers to come up with guidelines to delineate the collection of the required data in the midst of an outbreak and the inclusion of additional logistical details in future similar models.

Segmented regression analysis of emergency departments patient visits from Septicemia in Taiwan

Background

The protocol for early goal-directed therapy (EGDT) is effective for improving both the costs and outcomes of septicemia treatment, including a significant reduction in case fatality. However, this complicated protocol may have a downside. Furthermore, the Joint Taiwan Critical Care Medicine Committee has launched a nationwide educational program after the publication of the Surviving Sepsis Campaign (SSC) to improve the overall survival rate from septicemia in the emergency care system of Taiwan.

Objectives

To assess the impact of the EGDT protocol and SSC education programs on island-wide septicemia-related emergency department (ED) visits.

Methods

Segmented regression techniques were utilized to assess the differences in annual rates and changes in septicemia-related ED visits between 1998 and 2012. We considered annual incidence of two medical comorbidities as potential confounders: metastatic malignant neoplasms and malignant neoplasms of the lymphatic and hematopoietic tissues.

Results

The EGDT protocol was associated with decreased septicemia-related ED visits in 2002 (level change; p < 0.001), while the SSC education program led to a slight increase in septicemia-related ED visits in 2007 (slope change; p < 0.001). For the EGDT protocol, the number of patient visits decreased by 32.9% after the protocol was implemented in 2002 compared with the expected number without the intervention. For the SSC education program, the number of patient visits increased by 20.2% (compared with the predicted number) in 2007 after the education program was implemented.

Conclusions

The EGDT protocol and SSC education program were associated with significant immediate changes and lagged intervention effects on island-wide septicemia-related ED visits.

Knowledge, attitude and practice of secondary schools and university students toward Middle East Respiratory Syndrome epidemic in Saudi Arabia: A cross-sectional study

This study was aiming to investigate the knowledge, practice and attitudes of secondary school and university students toward MERS-CoV infection. This is a cross-sectional study conducted in Riyadh, Saudi Arabia. Study participants were recruited from several constituent colleges of King Saud University and secondary schools in Riyadh. Data were collected using self-administered, closed-ended questionnaires. Frequencies and proportions were computed for descriptive purposes. Chi square test was utilized to depict statistical difference between groups. Among the 1109 students who answered the questionnaires, 53.1% were male, and 46.9% were female. Level of knowledge about clinical presentation of MERS is generally similar among university and school students. The most frequently reported source of transmission is entering crowded spaces and being exposed to coughing and sneezing. Additionally, hand washing was the most commonly reported method of protection against the infection. The localized spread of MERS in Saudi Arabia and the number of fatalities associated with it might have increased public interest in understanding how to maintain proper precautionary measures both on a community and on an individual level. More emphasis should be placed on educating the student participants about preventive measures such as using tissues when sneezing and coughing and proper tissue disposal.