Massive SARS-CoV-2 RT-PCR Testing on Rural Communities in Manabi Province (Ecuador) Reveals Severe COVID-19 Outbreaks

COVID-19 preparedness and response in rural and remote areas: A scoping review

This scoping review used the Arksey and O'Malley approach to explore COVID-19 preparedness and response in rural and remote areas to identify lessons to inform future health preparedness and response planning. A search of scientific and grey literature for rural COVID-19 preparedness and responses identified 5 668 articles published between 2019 and early 2022. A total of 293 articles were included, of which 160 (54.5%) were from high income countries and 106 (36.2%) from middle income countries. Studies focused mostly on the Maintenance of Essential Health Services (63; 21.5%), Surveillance, epidemiological investigation, contact tracing and adjustment of public health and social measures (60; 20.5%), Coordination and Planning (32; 10.9%); Case Management (30; 10.2%), Social Determinants of Health (29; 10%) and Risk Communication (22; 7.5%). Rural health systems were less prepared and national COVID-19 responses were often not adequately tailored to rural areas. Promising COVID-19 responses involved local leaders and communities, were collaborative and multisectoral, and engaged local cultures. Non-pharmaceutical interventions were applied less, support for access to water and sanitation at scale was weak, and more targeted approaches to the isolation of cases and quarantine of contacts were preferable to blanket lockdowns. Rural pharmacists, community health workers and agricultural extension workers assisted in overcoming shortages of health professionals. Vaccination coverage was hindered by weaker rural health systems. Digital technology enabled better coordination, communication, and access to health services, yet for some was inaccessible. Rural livelihoods and food security were affected through disruptions to local labour markets, farm produce markets and input supply chains. Important lessons include the need for rural proofing national health preparedness and response and optimizing synergies between top-down planning with localised planning and coordination. Equity-oriented rural health systems strengthening and action on rural social determinants is essential to better prepare for and respond to future outbreaks.

A report on SARS-CoV-2 first wave in Ecuador: drug consumption dynamics

Introduction: The first COVID-19 wave in Ecuador started in March 2020 and extended until November. Several types of drugs have been proposed as a potential treatment during this period, and some affected people have self-medicated. Method: A retrospective study was conducted with 10,175 individuals who underwent RT-PCR tests for SARS-CoV-2 from July to November 2020. We compared the number of positive and negative cases in Ecuador with symptoms and drug consumption. The Chi-square test of independence compared clinical and demographic data and PCR test results. Odds ratios analyzed drug consumption dynamics. Results: Of 10,175 cases, 570 were positive for COVID-19, while 9,605 were negative. In positive cases, there was no association between the RT-PCR result and sex, age, or comorbidities. When considering demographic data, Cotopaxi and Napo had the highest rates of positive cases (25.7% and 18.8%, respectively). Manabí, Santa Elena, and Guayas regions had fewer than 10% positive cases. The Drug consumption dynamic analysis showed that negative COVID-19 cases presented higher drug consumption than positive cases. In both groups, the most consumed medication was acetaminophen. Acetaminophen and Antihistamines had higher odds of consumption in positive PCR cases than in negative. Symptoms like fever and cough were more related to positive RT-PCR results. Conclusion: The first COVID-19 wave in Ecuador has affected the provinces differently. At a national level, the consumption of drugs has been highly associated with self-medication.

Social deprivation and SARS-CoV-2 testing: a population-based analysis in a highly contrasted southern France region

Background

Testing was the cornerstone of the COVID-19 epidemic response in most countries until vaccination became available for the general population. Social inequalities generally affect access to healthcare and health behaviors, and COVID-19 was rapidly shown to impact deprived population more drastically. In support of the regional health agency in Provence-Alpes-Côte d'Azur (PACA) in South-Eastern France, we analyzed the relationship between testing rate and socio-demographic characteristics of the population, to identify gaps in testing coverage and improve targeting of response strategies.

Methods

We conducted an ecological analysis of SARS-CoV-2/COVID-19 testing rate in the PACA region, based on data aggregated at the finest spatial resolution available in France (IRIS) and by periods defined by public health implemented measures and major epidemiological changes. Using general census data, population density, and specific deprivation indices, we used principal component analysis followed by hierarchical clustering to define profiles describing local socio-demographic characteristics. We analyzed the association between these profiles and testing rates in a generalized additive multilevel model, adjusting for access to healthcare, presence of a retirement home, and the age profile of the population.

Results

We identified 6 socio-demographic profiles across the 2,306 analyzed IRIS spatial units: privileged, remote, intermediate, downtown, deprived, and very deprived (ordered by increasing social deprivation index). Profiles also ranged from rural (remote) to high density urban areas (downtown, very deprived). From July 2020 to December 2021, we analyzed SARS-CoV-2/COVID-19 testing rate over 10 periods. Testing rates fluctuated strongly but were highest in privileged and downtown areas, and lowest in very deprived ones. The lowest adjusted testing rate ratios (aTRR) between privileged (reference) and other profiles occurred after implementation of a mandatory healthpass for many leisure activities in July 2021. Periods of contextual testing near Christmas displayed the largest aTRR, especially during the last periods of 2021 after the end of free convenience testing for unvaccinated individuals.

Conclusion

We characterized in-depth local heterogeneity and temporal trends in testing rates and identified areas and circumstances associated with low testing rates, which the regional health agency targeted specifically for the deployment of health mediation activities.

High SARS-CoV-2 infection rates and viral loads in community-dwelling individuals from rural indigenous and mestizo communities from the Andes during the first wave of the COVID-19 pandemic in Ecuador

Background

Neglected indigenous groups and underserved rural populations in Latin America are highly vulnerable to COVID-19 due to poor health infrastructure and limited access to SARS-CoV-2 diagnosis. The Andean region in Ecuador includes a large number of isolated rural mestizo and indigenous communities living under poverty conditions.

Objective

We herein present a retrospective analysis of the surveillance SARS-CoV-2 testing in community-dwelling populations from four provinces in the Ecuadorian Andes, carried out during the first weeks after the national lockdown was lifted in June 2020.

Results

A total number of 1,021 people were tested for SARS-CoV-2 by RT-qPCR, resulting in an overall high infection rate of 26.2% (268/1,021, 95% CI: 23.6-29%), which was over 50% in several communities. Interestingly, community-dwelling super spreaders with viral loads over 10⁸ copies/mL represented 7.46% (20/268, 95% CI: 4.8-11.1%) of the SARS-CoV-2 infected population.

Conclusion

These results support that COVID-19 community transmission in rural communities from the Andean region was happening at the early stages of the COVID-19 pandemic in Ecuador and point out the weakness of the COVID-19 control program. Community-dwelling individuals in neglected rural and indigenous communities should be considered for a successful control and surveillance program in future pandemics in low- and middle-income countries.

The deadly impact of COVID-19 among children from Latin America: The case of Ecuador

Background

The SARS-CoV-2 pandemic remains a critical global health concern, with older adults being the most vulnerable group. Nonetheless, it is crucial to recognize that COVID-19 has caused numerous deaths in children worldwide. Emerging evidence indicates that infants and breastfeeding children, particularly those aged below one year, face a greater risk of hospitalization and mortality than older children with COVID-19.

Objective

This study aimed to describe the epidemiology of COVID-19 among children during the early phase of the pandemic in Ecuador.

Methods

We conducted a country-wide population-based analysis of the epidemiology of COVID-19, using incidence and mortality data reported from Ecuador between February 15, 2020 and May 14 2021. Measurements of frequency, central tendency, dispersion, and absolute differences were calculated for all categorical and continuous variables.

Results

At least 34,001 cases (23,587 confirmed cases, 5,315 probable and 5,099 suspected) and 258 COVID-19 related deaths have been reported among children in Ecuador during the first 16 months of the pandemic. The overall incidence rate was 612 cases per 100,000 children, the mortality rate was 3 per 100,000, while the case fatality rate was 0.76%. The highest risk group for infection was children and adolescents between 15 and 19 years of age; however, the highest mortality rate occurred in children under one year of age. The largest provinces, such as Pichincha, Guavas and Manabí, were the ones that reported the highest number of cases, 27%, 12.1% and 10.8%, respectively.

Conclusions

This study is the first to report on COVID-19 epidemics among children in Ecuador. Our findings reveal that younger children have a lower risk of SARS-CoV-2 infection, but a higher risk of mortality compared to older children and adolescents. Additionally, we observed significant disparities in infection rates and outcomes among children living in rural areas, those with comorbidities, and those from indigenous ethnic groups.

High rates of SARS-CoV-2 infection in funeral home workers in Ecuador: Is it an occupational risk for COVID-19?

Aim

The COVID-19 outbreak has already caused more than 6.5 million deaths, overwhelming health systems worldwide. The unusual demand for funeral home services could make these workers a potential risk group for occupational exposure to SARS-CoV-2 associated with corpses management for COVID-19 patients.

Methodology

This is a cross-sectional study aimed to describe the infection rate of SARS-CoV-2 in funeral home staff by testing them with RT-qPCR in Quito, Ecuador. A total of 232 funeral home workers, representing more than 40% of funeral home personnel in Quito, were included in the study, in June 2020, immediately after the population lockdown was lifted in Ecuador.

Results

A total of 48 individuals tested positive for SARS-CoV-2, yielding an infection rate of 20.7%. The SARS-CoV-2 infection rate was 18.1 and 20.0% among personnel managing corpses or not managing corpses, respectively. Among the SARS-CoV-2 positive patients, 81.3% reported no symptoms related to COVID-19, and 3 individuals had high viral loads over 10⁸ copies/ml.

Conclusion

The high SARS-CoV-2 infection rate in funeral home staff suggested a potential occupational risk for COVID-19 but not related to corpses management. Public health guidelines for safe corpses management for COVID-19 victims and safe funeral services should be reinforced.

Sustained COVID-19 community transmission and potential super spreading events at neglected afro-ecuadorian communities assessed by massive RT-qPCR and serological testing of community dwelling population

Background

Neglected ethnic minorities from underserved rural populations in Latin America are highly vulnerable to coronavirus disease 2019 (COVID-19) due to poor health infrastructure and limited access to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) diagnosis. Esmeraldas is a mainly rural province of the Coastal Region of Ecuador characterized by a high presence of Afro-Ecuadorian population living under poverty conditions.

Objective

We herein present a retrospective analysis of the surveillance SARS-CoV-2 testing in community-dwelling population from Esmeraldas carried out by our university laboratory in collaboration with regional health authorities during the first week of October 2020, in a region where no public SARS-CoV-2 detection laboratory was available at that time.

Results

A total number of 1,259 people were tested for SARS-CoV-2 by Reverse Transcription quantitative Polimerasa Chain Reaction (RT-qPCR), resulting in an overall infection rate of 7.7% (97/1259, 95% CI: [6.32–9.35%]) for SARS-CoV-2, up to 12.1% in some communities. Interestingly, community-dwelling super spreaders with viral loads over 10⁸ copies/ml represented 6.2% of the SARS-CoV-2-infected population. Furthermore, anti-SARS-CoV-2 IgG serological tests were applied to the same study group, yielding an overall seroprevalence of 11.68% (95% CI: [9.98–13.62%]) but as high as 24.47% at some communities.

Conclusion

These results support active COVID-19 community transmission in Esmeraldas province during the first semester of the COVID-19 pandemic as it has been shown for other rural communities in the Ecuadorian Coastal Region.

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).

SARS-CoV-2 infection in free roaming dogs from the Amazonian jungle

During the ongoing COVID-19 pandemic, there were several reports of SARS-CoV-2 transmission from human to animals, mostly to companion cats and dogs but also to free ranging wild species like minks and deers. Under this scenario, SARS-CoV-2 surveillance in domestic animals to assess the risk of transmission between species have been suggested by the OIE. Here we present a case report of SARS-CoV-2 infection in free roaming dogs, found at a rural indigenous community from the Ecuadorian Amazonia. Oral and nasal swabs samples were collected from three dogs found during a COVID-19 surveillance intervention in Amazonian indigenous communities where severe COVID-19 outbreaks were suspected. Total RNA was extracted from dog samples and detection of SARS-CoV-2 gene targets N, ORF1ab and S was performed. The three dogs tested positive for at least two SARS-CoV-2 viral targets. Moreover, there was a high SARS-CoV-2 infection rate of 87.2% within this community. Given that 17.1% of SARS-CoV-2 positive individuals had an ultra high load greater than 10⁸ copies/ml, transmission from humans to dogs likely occurred. To our knowledge, this study is the first report of SARS-CoV-2 positive free roaming dogs. Also, as those animals were found in the Amazonian forest, SARS-CoV-2 transmission to wild mammals is a potential concern. Given the high presence of free roaming dogs associated to rural and indigenous communities in South America, the potential role of these domestic animals on COVID-19 spread would deserve further surveillance studies involving SARS-CoV-2 detection by PCR and molecular epidemiology based on genome sequencing to confirm human to dog transmission.

Crucial contribution of the universities to SARS-CoV-2 surveillance in Ecuador: Lessons for developing countries

COVID-19 pandemic has challenged public health systems worldwide, particularly affecting developing countries in Latin America like Ecuador. In this report, we exposed the fundamental role of the Ecuadorian universities to improve COVID-19 surveillance in the country, with an overall contribution over 15% of the total SARS-CoV-2 RT-PCR tests done. We highlight the role of our university during the first semester of the COVID-19 pandemic, contributing to a massive free SARS-CoV-2 testing up to almost 10% of the total diagnosis completed in the country, mainly focus on underserved urban, rural and indigenous communities. Finally, we described our contribution to a high quality and low-cost SARS-CoV-2 RT-PCR diagnostic in Ecuador.

Perceived Risks of Infection, Hospitalization, and Death From COVID-19 at the Equator: Ecuador and Kenya

OBJECTIVES

This study's goal was to determine the perceived risks of infection as well as the perceived risks of hospitalization and death from COVID-19 in Ecuador and Kenya. It also assessed the factors associated with the risk-related perceptions.

METHODS

Cross-sectional studies with samples from the adult populations in both countries were conducted to assess the perceived risks of contracting COVID-19. Data were collected online using the Qualtrics platform (Qualtrics, Provo, Utah, United States) from samples of 1050 heads of households, aged 18 years or older, in each country. A total of 3 statistical analyses were conducted: summary statistics, correlation, and linear regression.

RESULTS

The average perceived risks of COVID-19 infection, hospitalization, and death in the Kenyan sample were 27.1%, 43.2%, and 17.2%, respectively, and the values for the Ecuadorian sample were 34%, 32.8%, and 23.3%, respectively. The Pearson's correlation coefficients between the risk measures in each country were less than 0.38. Risk measures were associated with several sociodemographic variables (e.g., income, gender, location), but not with age.

CONCLUSIONS

The perceived risks of COVID-19 infection, hospitalization, and death in Kenya and Ecuador were significantly higher relative to the statistics reported; however, no strong association existed between perceived risk and age, which is a key factor in adverse health outcomes, including death, among COVID-19 infected individuals.