COVID-19 in Latin America: Novel transmission dynamics for a global pandemic?

Social influence, performance expectancy, and price value as determinants of telemedicine services acceptance in Chile

Medicine is a discipline based on and nurtured by scientific research and technological development. The use of health services supported by information technology is increasing worldwide, and Latin America is no exception. Factors such as needing more specialists in peripheral cities, large geographic areas, and socio-cultural aspects limit the possibility of receiving timely and quality medical care services. Information Technology (IT) for health purposes, such as e-health, is a cost-effective solution for equitable access to quality healthcare services and optimization of the rising associated costs. As an e-health service, telemedicine facilitates and mediates distance communication between the patient and medical staff. Even though Latin America is at the beginning of the development of telemedicine, it would have a relevant impact, given the geographic and socioeconomic conditions of the population in this part of the world. Drawing on the extended Unified Theory of Acceptance and Use of Technology (UTAUT2) theory, we developed a theoretical model to identify the latent factors influencing the public acceptance of telemedicine and examined their interrelationships. A survey questionnaire was designed and administered to 391 residents in Antofagasta, a mine region of Chile. After that, structural equation modeling was employed to analyze the survey data. The results reveal that the UTAUT2 factors' performance expectancy, social influence, and price value significantly impact the intention to use (R 2 = 0.693). Additionally, the model presented a good fit. This study enriches the existing theoretical research on the acceptance of telemedicine services and offers insights into understanding and managing technology in the Chilean health sector.

Risk factors for COVID-19 in-hospital mortality in Argentina: A competing risk survival analysis

COVID-19 poses dire threats for low and middle-income countries (LMICs). Yet, there remains limited rigorous evidence describing the characteristics and outcomes of hospitalized patients for LMICs, and often the evidence was based on small samples and/or unicentric. The objective of this study was to examine risk factors of COVID-19 mortality in Argentina, a hard-hit middle-income Latin American country. We analyze data on 5,146 COVID-19 patients from 11 centers across 10 cities in Argentina, making this one of the largest multi-centric retrospective observational descriptive studies in the LMICs. Information on demographics and co-morbidities was extracted from medical records. Outcomes of relevance consisted of whether the patient was discharged or deceased (as established in medical records), along with date of each event. We use survival models that account for competing risks. Median age was 60 years (IQR: 48-72), there were fewer women (40.8%) hospitalized than men (59.2%), and the most prevalent comorbidities were hypertension (40.9%), diabetes (20.0%) and obesity (19.1%). Patients were hospitalized for a median duration of 8 days (IQR: 5-13), and in-hospital mortality was 18.1%, though it varied substantially across health centers (95%CI: 17.1%-19.2%). Baseline characteristics most associated with in-hospital mortality were respiratory rate (adjusted HR = 3.6, 95%CI: 2.5-5.4 for ≥ 26 breathes/min), older age (adjusted HR = 2.5, 95%CI: 2.0-3.3 for the 80+ age group), and chronic kidney disease (adjusted HR = 2.2, 95%CI: 1.8-2.8). Associations were attenuated when survival models did not account for the competing risk of being discharged. We document lower mortality rates than those in prior studies, likely due to a lower prevalence of comorbidities amongst patients in our sample. Compared with standard Cox models, we find that, when using competing risk models, risk factors have a larger role in explaining COVID-19 mortality. Overall, we provide rigorous evidence describing the characteristics and outcomes of hospitalized patients for LMICs. Thus, our findings are useful to conduct a more accurate in-hospital monitoring of patient subgroups who may be at greater risk. They also provide valuable guidance for public health and policy efforts in Argentina and other developing countries.

A comprehensive review of discovery and development of drugs discovered from 2020-2022

To fully evaluate and define the new drug molecule for its pharmacological characteristics and toxicity profile, pre-clinical and clinical studies are conducted as part of the drug research and development process. The average time required for all drug development processes to finish various regulatory evaluations ranges from 11.4 to 13.5 years, and the expense of drug development is rising quickly. The development in the discovery of newer novel treatments is, however, largely due to the growing need for new medications. Methods to identify Hits and discovery of lead compounds along with pre-clinical studies have advanced, and one example is the introduction of computer-aided drug design (CADD), which has greatly shortened the time needed for the drug to go through the drug discovery phases. The pharmaceutical industry will hopefully be able to address the present and future issues and will continue to produce novel molecular entities (NMEs) to satisfy the expanding unmet medical requirements of the patients as the success rate of the drug development processes is increasing. Several heterocyclic moieties have been developed and tested against many targets and proved to be very effective. In-depth discussion of the drug design approaches of newly found drugs from 2020 to 2022, including their pharmacokinetic and pharmacodynamic profiles and in-vitro and in-vivo assessments, is the main goal of this review. Considering the many stages these drugs are going through in their clinical trials, this investigation is especially pertinent. It should be noted that synthetic strategies are not discussed in this review; instead, they will be in a future publication.

The bibliometric landscape of infectious disease research in Panama (1990-2019)

Background

This work aims to analyze the landscape of scientific publications on subjects related to One Health and infectious diseases in Panama. The research questions are: How does the One Health research landscape look like in Panama? Are historical research efforts aligned with the One Health concept? What infectious diseases have received more attention from the local scientific community since 1990?

Methods

Boolean searches on the Web of Science, SCOPUS and PubMed were undertaken to evaluate the main trends of publications related to One Health and infectious disease research in the country of Panama, between 1990 and 2019.

Results

4546 publications were identified since 1990, including 3564 peer-reviewed articles interconnected with One Health related descriptors, and 211 articles focused particularly on infectious diseases. A pattern of exponential growth in the number of publications with various contributions from Panamanian institutions was observed. The rate of multidisciplinary research was moderate, whereas those of interinstitutional and intersectoral research ranged from low to very low. Research efforts have centered largely on protozoan, neglected and arthropod-borne diseases with a strong emphasis on malaria, Chagas and leishmaniasis.

Conclusion

Panama has scientific capabilities on One Health to tackle future infectious disease threats, but the official collaboration schemes and strategic investment to develop further competencies need to be conciliated with modern times, aka the pandemics era. The main proposition here, addressed to the government of Panama, is to launch a One Health regional center to promote multidisciplinary, interinstitutional and intersectoral research activities in Panama and beyond.

A tool for the cheap and rapid screening of SARS-CoV-2 variants of concern (VoCs) by Sanger sequencing

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an emerging virus that, since March 2020, has been responsible for a global and ongoing pandemic. Its rapid spread over the past nearly 3 years has caused novel variants to arise. To monitor the circulation and emergence of SARS-CoV-2 variants, surveillance systems based on nucleotide mutations are required. In this regard, we searched in the spike, ORF8, and nucleocapsid genes to detect variable sites among SARS-CoV-2 variants. We describe polymorphic genetic regions that enable us to differentiate between the Alpha, Beta, Gamma, Delta, and Omicron variants of concern (VoCs). We found 21 relevant mutations, 13 of which are unique for Omicron lineages BA.1/BA.1.1, BA.2, BA.3, BA.4, and BA.5. This genetic profile enables the discrimination between VoCs using only four reverse transcription PCR fragments and Sanger sequencing, offering a cheaper and faster alternative to whole-genome sequencing for SARS-CoV-2 surveillance. IMPORTANCE Our work describes a new (Sanger sequencing-based) screening methodology for SARS-CoV-2, performing PCR amplifications of a few target regions to detect diagnostic mutations between virus variants. Using the methodology developed in this work, we were able to discriminate between the following VoCs: Alpha, Beta, Gamma, Delta, and Omicron (BA.1/BA.1.1, BA.2, BA.3, BA.4, and BA.5). This becomes important, especially in low-income countries where current methodologies like next-generation sequencing have prohibitive costs. Furthermore, rapid detection would allow sanitary authorities to take rapid measures to limit the spread of the virus and therefore reduce the probability of new virus dispersion. With this methodological approach, 13 previously unreported diagnostic mutations among several Omicron lineages were found.

Spatio-temporal multidisciplinary analysis of socio-environmental conditions to explore the COVID-19 early evolution in urban sites in South America

This study aimed to analyse how socio-environmental conditions affected the early evolution of COVID-19 in 14 urban sites in South America based on a spatio-temporal multidisciplinary approach. The daily incidence rate of new COVID-19 cases with symptoms as the dependent variable and meteorological-climatic data (mean, maximum, and minimum temperature, precipitation, and relative humidity) as the independent variables were analysed. The study period was from March to November of 2020. We inquired associations of these variables with COVID-19 data using Spearman's non-parametric correlation test, and a principal component analysis considering socio economic and demographic variables, new cases, and rates of COVID-19 new cases. Finally, an analysis using non-metric multidimensional scale ordering by the Bray-Curtis similarity matrix of meteorological data, socio economic and demographic variables, and COVID-19 was performed. Our findings revealed that the average, maximum, and minimum temperatures and relative humidity were significantly associated with rates of COVID-19 new cases in most of the sites, while precipitation was significantly associated only in four sites. Additionally, demographic variables such as the number of inhabitants, the percentage of the population aged 60 years and above, the masculinity index, and the GINI index showed a significant correlation with COVID-19 cases. Due to the rapid evolution of the COVID-19 pandemic, these findings provide strong evidence that biomedical, social, and physical sciences should join forces in truly multidisciplinary research that is critically needed in the current state of our region.

A systematic review of the impact of corruption in Latin America during the spread of the first wave of COVID-19

As the Covid-19 pandemic crisis raged in Latin America, numerous acts of corruption affected containment strategies and weakened institutional systems. A systematic review was conducted during the first wave of contagion in 2020 to analyse the relationship between corruption and Covid-19 in Latin American countries, highlighting its components and the institutions involved. Following the PRISMA guidelines, scientific databases and prepublications were searched using the terms (((SARS-CoV-2) OR (Covid-19)) AND ((Corruption [Mesh]) AND (Latin America))). Seventy-two studies were included in the initial search, 36 in MEDLINE/PubMed, 20 in Scielo, and 11 prepublications. Of the 25 eligible studies, none met the required standard for inclusion. Although corruption is endemic in Latin America, its levels and impact during the first wave of Covid-19 contagion have not been quantified.

Water, sanitation, hygiene practices, health and nutritional status among children before and during the COVID-19 pandemic: longitudinal evidence from remote areas of Dailekh and Achham districts in Nepal

Background

The COVID-19 pandemic drew hygiene to the center of disease prevention. The provision of adequate water, sanitation, and hygiene (WASH) services is crucial to protect public health during a pandemic. Yet, access to levels of water supply that support adequate hygiene measures are deficient in many areas in Nepal. We examined WASH practices and their impact on child health and nutritional status in two districts before and during the COVID-19 pandemic.

Methods

A longitudinal and mixed method study was conducted in March–May 2018 and November–December 2021. In total, 715 children aged 0–10 years were surveyed at baseline. Of these, 490 children were assessed at endline. Data collection methods included observations, a questionnaire, stool analysis, anthropometric measurements, water quality analysis, and an assessment of clinical signs of nutritional deficiencies. We conducted 10 in-depth interviews to understand major problems related to COVID-19.

Results

Most respondents (94.2%) had heard about COVID-19; however, they did not wear face masks or comply with any social distancing protocols. Almost 94.2% of the households self-reported handwashing with soap 5–10 times per day at endline, especially after defecation, compared to 19.6% at baseline. Water quality was better at endline than at baseline with median 12 to 29 CFU Escherichia coli/100 mL (interquartile range at baseline [IQR] = 4–101) at the point of collection and 34 to 51.5 CFU Escherichia coli/100 mL (IQR = 8–194) at the point of consumption. Fever (41.1–16.8%; p = 0.01), respiratory illness (14.3–4.3%; p = 0.002), diarrhea (19.6–9.5%; p = 0.01), and Giardia lamblia infections (34.2–6.5%, p = 0.01) decreased at endline. In contrast, nutritional deficiencies such as bitot’s spots (26.7–40.2%; p = 0.01), pale conjunctiva (47.0–63.3%; p = 0.01), and dermatitis (64.8–81.4%; p = 0.01) increased at endline. The inadequacy of the harvest and the lack of household income to meet households’ nutritional needs increased drastically (35.0–94.2%; p = 0.01).

Conclusion

We found that improved water quality and handwashing practices were associated with a decrease in infectious diseases. However, food security also decreased resulting in a high prevalence of nutritional deficiencies. Our findings underline that disaster preparedness should consider access to adequate WASH, nutrition, and health supplies.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12889-022-14346-8.

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.

High mortality among hospitalized adult patients with COVID-19 pneumonia in Peru: A single centre retrospective cohort study

Background

Peru is the country with the world’s highest COVID-19 death rate per capita. Characteristics associated with increased mortality among adult patients with COVID-19 pneumonia in this setting are not well described.

Methods

Retrospective, single-center cohort study including 1537 adult patients hospitalized with a diagnosis of SARS-CoV-2 pneumonia between May 2020 and August 2020 at a national hospital in Lima, Peru. The primary outcome measure was in-hospital mortality.

Results

In-hospital mortality was 49.71%. The mean age was 60 ± 14.25 years, and 68.38% were males. We found an association between mortality and inflammatory markers, mainly leukocytes, D-dimer, lactate dehydrogenase, C-reactive protein and ferritin. A multivariate model adjusted for age, hypertension, diabetes mellitus, and corticosteroid use demonstrated that in-hospital mortality was associated with greater age (RR: 2.01, 95%CI: 1.59–2.52) and a higher level of oxygen requirement (RR: 2.77, 95%CI: 2.13–3.62). Conclusions: In-hospital mortality among COVID-19 patients in Peru is high and is associated with greater age and higher oxygen requirements.

Statistical Modeling of Deaths from COVID-19 Influenced by Social Isolation in Latin American Countries

Social isolation is extremely important to minimize the effects of a pandemic. Latin American countries have similar socioeconomic characteristics and health system infrastructures. These countries face difficulties in dealing with the COVID-19 pandemic, and some of them have very high death rates. The government stringency index (GSI) of 12 Latin American countries was gathered from the Oxford COVID-19 Government Response Tracker project. The GSI is calculated by considering nine social distancing and isolation measures. Population data from the United Nations Population Fund and number-of-deaths data were collected from the dashboard of the WHO. We performed an analysis of the data collected from March through December 2020 using a mixed linear model. Peru, Brazil, Chile, Bolivia, Colombia, Argentina, and Ecuador had the highest death rates, with an increasing trend over time. Suriname, Venezuela, Uruguay, Paraguay, and Guyana had the lowest death rates, and these rates remained steady. The GSI in most countries followed the same pattern during the months analyzed. In other words, high indices at the beginning of the pandemic and lower indices in the latter months, whereas the number of deaths increased during the entire period. Almost no country kept its GSI high for a long time, especially from October to December. Time and GSI, as well as their interaction, were highly significant. As their interaction increases, the death rate decreases. In conclusion, a greater GSI at the start of the COVID-19 pandemic was associated with a decrease in the number of deaths over time in Latin American countries.

COVID-19 seen from a syndemic perspective: Impact of unhealthy habits and future perspectives to combat these negative interactions in Latin America

COVID-19 has to this point led to more than 5 million deaths and has imposed numerous measures restricting populations worldwide, including Latin America (LA). However, analyzing COVID-19 from the perspective of a syndemic, it demonstrates the relationship between the interaction of multiple comorbidities and the increase of contagion in people who are socially vulnerable. The number of deaths by COVID-19 in LA is strongly associated with multi-morbidities (diabetes, obesity, sedentary, smoking, among others) and disproportionately attacks communities located in poorer, low-income regions and ethnic minorities. This review aims to revisit the relationship between COVID-19 and both unhealthy living habits (i.e., sedentary lifestyle, poor nutritional habits, overweight and obesity, smoking) and cardiovascular disease in Latin American countries. In addition, this review aims to introduce strategies and policies that combat social inequalities and enable healthy living behaviors in LA countries. If LA countries do not work on public policies that decrease multi-morbidities and social inequalities, we will be unable to eliminate COVID-19, as well as possible other outbreaks that may arise in the future.

Wastewater, waste, and water-based epidemiology (WWW-BE): A novel hypothesis and decision-support tool to unravel COVID-19 in low-income settings?

Traditional wastewater-based epidemiology (W-BE) relying on SARS-CoV-2 RNA detection in wastewater is attractive for understanding COVID-19. Yet traditional W-BE based on centralized wastewaters excludes putative SARS-CoV-2 reservoirs such as: (i) wastewaters from shared on-site sanitation facilities, (ii) solid waste including faecal sludge from non-flushing on-site sanitation systems, and COVID-19 personal protective equipment (PPE), (iii) raw/untreated water, and (iv) drinking water supply systems in low-income countries (LICs). A novel hypothesis and decision-support tool based on Wastewater (on-site sanitation, municipal sewer systems), solid Waste, and raw/untreated and drinking Water-based epidemiology (WWW-BE) is proposed for understanding COVID-19 in LICs. The WWW-BE conceptual framework, including components and principles is presented. Evidence on the presence of SARS-CoV-2 and its proxies in wastewaters, solid materials/waste (papers, metals, fabric, plastics), and raw/untreated surface water, groundwater and drinking water is discussed. Taken together, wastewaters from municipal sewer and on-site sanitation systems, solid waste such as faecal sludge and COVID-19 PPE, raw/untreated surface water and groundwater, and drinking water systems in LICs act as potential reservoirs that receive and harbour SARS-CoV-2, and then transmit it to humans. Hence, WWW-BE could serve a dual function in estimating the prevalence and potential transmission of COVID-19. Several applications of WWW-BE as a hypothesis and decision support tool in LICs are discussed. WWW-BE aggregates data from various infected persons in a spatial unit, hence, putatively requires less resources (analytical kits, personnel) than individual diagnostic testing, making it an ideal decision-support tool for LICs. The novelty, and a critique of WWW-BE versus traditional W-BE are presented. Potential challenges of WWW-BE include: (i) biohazards and biosafety risks, (ii) lack of expertise, analytical equipment, and accredited laboratories, and (iii) high uncertainties in estimates of COVID-19 cases. Future perspectives and research directions including key knowledge gaps and the application of novel and emerging technologies in WWW-BE are discussed.

Latin American registry of renal involvement in COVID-19 disease. The relevance of assessing proteinuria throughout the clinical course

The Latin American Society of Nephrology and Hypertension conducted a prospective cohort, multinational registry of Latin American patients with kidney impairment associated to COVID-19 infection with the objective to describe the characteristics of acute kidney disease under these circumstances. The study was carried out through open invitation in order to describe the characteristics of the disease in the region. Eight-hundred and seventy patients from 12 countries were included. Median age was 63 years (54-74), most of patients were male (68.4%) and with diverse comorbidities (87.2%). Acute kidney injury (AKI) was hospital-acquired in 64.7% and non-oliguric in 59.9%. Multiorgan dysfunction syndrome (MODS) due to COVID-19 and volume depletion were the main factors contributing to AKI (59.2% and 35.7% respectively). Kidney replacement therapy was started in 46.2%. Non-recovery of renal function was observed in 65.3%. 71.5% of patients were admitted to ICU and 72.2% underwent mechanical ventilation. Proteinuria at admission was present in 62.4% of patients and proteinuria during hospital-stay occurred in 37.5%. Those patients with proteinuria at admission had higher burden of comorbidities, higher baseline sCr, and MODS was severe. On the other hand, patients with de novo proteinuria had lower incidence of comorbidities and near normal sCr at admission, but showed adverse course of disease. COVID-19 MODS was the main cause of AKI in both groups. All-cause mortality of the general population was 57.4%, and it was associated to age, sepsis as cause of AKI, severity of condition at admission, oliguria, mechanical ventilation, non-recovery of renal function, in-hospital complications and hospital stay. In conclusion, our study contributes to a better knowledge of this condition and highlights the relevance of the detection of proteinuria throughout the clinical course.

Cross-cultural validation of the new version of the Coronavirus Anxiety Scale in twelve Latin American countries

The Coronavirus Anxiety Scale (CAS) was recently developed to assess dysfunctional anxiety related to COVID-19. Although different studies reported that the CAS is psychometrically sound, it is unclear whether it is invariant across countries. Therefore, the present study aimed to examine the measurement invariance of the CAS in twelve Latin American countries (Argentina, Bolivia, Chile, Colombia, Cuba, Ecuador, El Salvador, Guatemala, Mexico, Paraguay, Peru, and Uruguay). A total of 5196 people participated, with a mean age of 34.06 (SD = 26.54). Multigroup confirmatory factor analysis (CFA) was used to examine the measurement invariance of the CAS across countries and gender. Additionally, the graded response model (GRM) was used to provide a global representation of the representativeness of the scale with respect to the COVID-19 dysfunctional anxiety construct. The unidimensional structure of the five-item CAS was not confirmed in all countries. Therefore, it was suggested that a four-item model of the CAS (CAS-4) provides a better fit across the twelve countries and reliable scores. Multigroup CFA showed that the CAS-4 exhibits scalar invariance across all twelve countries and all genders. In addition, the CAS-4 items are more informative at average and high levels of COVID-19 dysfunctional anxiety than at lower levels. According to the results, the CAS-4 is an instrument with strong cross-cultural validity and is suitable for cross-cultural comparisons of COVID-19 dysfunctional anxiety symptoms in the general population of the twelve Latin American countries evaluated.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s12144-021-02563-0.

High mortality among patients with cancer and COVID-19 infection: the experience of a Brazilian cancer center

Objective

To evaluate the severity of COVID-19 in cancer patients to describe clinical and epidemiological factors associated with poor outcomes (mortality and need of intensive care unit admission or mechanical ventilation).

Methods

Retrospective data from patients with cancer and laboratory diagnosis of COVID-19, obtained between March 16 and May 29, 2020, were retrieved out of a cancer center database. Data analyzed included patient history, age, sex, comorbidities, types of cancer and anticancer therapy.

Results

This sample comprised 105 patients aged 18-92 years, 80.9% of whom were females. Dyspnea was the most prevalent initial symptom (30.4%) among patients who died (p<0.0001). Overall, 57.1% of patients had metastatic disease and 60% had poor performance status (Eastern Cooperative Oncologic Group ≥2) at the time of COVID-19 diagnosis. The overall mortality rate was 40.95%. Mortality rates were higher in male patients and those with poor performance status (p<0.0001).

Conclusion

This cohort is one of the largest Brazilian studies describing clinical and epidemiological features of patients with cancer and concurrent COVID-19. Findings of this study emphasize the vulnerability of cancer patients in the current pandemic, and indicate high mortality from COVID-19 among male cancer patients and cancer patients with poor performance status. This analysis may assist the selection of patients who may benefit from strict isolation and eventual discontinuation of anticancer therapy to reduce exposure to infection.

Socio-Demographic Variables, Fear of COVID-19, Anxiety, and Depression: Prevalence, Relationships and Explanatory Model in the General Population of Seven Latin American Countries

The COVID-19 pandemic has gravely impacted Latin America. A model was tested that evaluated the contribution of socio-demographic factors and fear of COVID-19 on anxiety and depression in samples of residents in seven Latin American countries (Argentina, Ecuador, Mexico, Paraguay, Uruguay, Colombia, and El Salvador). A total of 4,881 individuals, selected by convenience sampling, participated in the study. Moderate and severe levels of depressive symptoms and anxiety were identified, as well as a moderate average level of fear of COVID-19. In addition, it was observed that about a quarter of the participants presented symptoms of generalized anxiety disorder and a major depressive episode. Fear of COVID-19 significantly and positively predicted anxiety and depressive symptoms, whereas the effects of socio-demographic variables are generally low [χ2(287) = 5936.96, p < 0.001; RMSEA = 0.064 [0.062, 0.065]; CFI = 0.947; and SRMR = 0.050]. This suggests the need for the implementation of preventive actions in the general population of these countries, with the aim of reducing the prevalence of depressive, anxious and fearful symptoms related to COVID-19.

Factors Associated With a Persistent Seronegative Status 1 Year After a SARS-CoV-2 Massive Infection Outbreak in Community Dwellers Living in Rural Ecuador: A Prospective Population-based Study

Background

The SARS-CoV-2 pandemic is affecting millions of people living in rural areas of Low- and Middle-Income Countries and is causing an already anticipated devastating effect on the health and economics of these populations. More information is needed to modify behaviors that may counterbalance the consequences of mass spread of the virus in these underserved communities. This study aimed to identify factors associated with a persistent SARS-CoV-2 seronegative status 1 year after a massive infection outbreak in middle-aged and older adults living in rural Ecuador.

Methods

Individuals enrolled in the Atahualpa Project Cohort as of March 2020 received 5 rounds of tests for determination of SARS-CoV-2 antibodies in blood. Individuals who remained seronegative up to April 2021 were considered “persistently seronegative.” An adjusted Poisson regression model was fitted to estimate the incidence risk ratio of factors directly or inversely associated with a persistent seronegative status.

Results

A total of 673 individuals received baseline tests. Thirty-one declined consent or died and 429 seroconverted, leaving 213 seronegative subjects. Average SARS-CoV-2 incidence rate was 9.87 events (95% C.I.: 8.91-10.83) per 100 person-months of observation. The use of flushing toilet systems (instead of open latrines) increased 1.5 times the possibility of remaining seronegative. Likewise, every additional bedroom in the house increased by 15% the possibility of remaining seronegative. In contrast, every additional person in the house and having high cholesterol levels significantly reduced the possibility of remaining seronegative.

Conclusions

The use of flushing toilet systems and the number of bedrooms in the house directly influenced the possibility of remaining seronegative among individuals living in this rural setting. Study results also demonstrated a sustained transmission of the virus even after a significant proportion of the population has been infected. Our findings reinforce the mass spread of SARS-CoV-2 in rural communities.

A Comprehensive Meta-Analysis of COVID-19 in Latin America

BACKGROUND

Latin America has become the epicenter of the coronavirus disease 2019 (COVID-19) pandemic. We aim to perform a systematic comparative review of the clinical characteristics that are associated with this disease in Latin American countries.

METHODS

We conducted a systematic review of published articles, journal and/or epidemiological reports of confirmed COVID-19 cases in Latin America. Data were obtained either through publicly available information from Ministries of Health, published journal reports and/or unpublished datasets. We analyzed data from SARS-CoV-2 positive patients evaluated at healthcare centers and hospitals of 8 countries including Brazil, Peru, Mexico, Argentina, Colombia, Venezuela, Ecuador, and Bolivia, between March 1^st and July 30^th, 2020. These countries consist of a total population that exceeds 519 million. Demographics, comorbidities, and clinical symptoms were collected. Statistical descriptive analysis and correlation analyses of symptoms, comorbidities and mortality were performed.

RESULTS

A total of 728,282 COVID-19 patients were included in this study. Of these, 52.6% were female. The average age was 48.4 years. Peru had the oldest cohort with 56.8 years and highest rate of females (56.8%) while Chile had the youngest cohort (39 years old). Venezuela had the highest male prevalence (56.7%). Most common symptoms were cough with 60.1% (Bolivia had the highest rate 78%), fatigue/tiredness with 52.0%, sore throat with 50.3%, and fever with 44.2%. Bolivian patients had fever as the top symptom (83.3%). GI symptoms included diarrhea which was highest in Mexico with 22.9%. Hypertension was among the top (12.1%) comorbidities, followed by diabetes with 8.3% and obesity at 4.5%. In multivariate analyses, the leading and significant comorbidities were hypertension (r = 0.83, p = 0.02), diabetes (r = 0.91, p = 0.01), and obesity (r = 0.86, p = 0.03). Mortality was highest in Mexico (16.6%) and lowest in Venezuela (0.9%) among the analyzed cohorts.

CONCLUSION

Overall, COVID-19 patients in Latin America display cough, fatigue, and fever as main symptoms. Up to 53% of patients with COVID-19 have GI manifestations. Different clinical symptoms were associated with COVID-19 in Latin American countries. Metabolic syndrome components were the main comorbidities associated with poor outcome. Country-specific management and prevention plans are needed and can be established from this meta-analysis.

The association between initial COVID-19 spread and meteorological factors in Indonesia

On March 2, 2020, the first Coronavirus Disease (COVID-19) case was reported in Jakarta, Indonesia. One and a half months later (15/05/2020), the cumulative number of infection cases was 16,496, with a total of 1076 mortalities. This study investigates the possible role of weather in the early cases of COVID-19 in six selected cities in Indonesia. Daily temperature and relative humidity data from weather stations nearby in each city were collected from March 3 to April 30, 2020, corresponding with COVID-19 incidence. Correlation tests and regression analysis were performed to examine the association of those two data series. Moreover, we analyzed the distribution of COVID-19 referring the weather data to estimate the effective range of weather data supporting the COVID-19 incidence. Our result reveals that weather data is generally associated with COVID-19 incidence. The daily average temperature (T-ave) and relative humidity (RH) present significant positive and negative correlation with COVID-19 data, respectively. However, the correlation coefficients are weak, with the strongest correlations found at the 5-day lag, i.e., 0.37 (- 0.41) for T-ave (RH). The regression analysis consistently confirmed this relation. The distribution analysis reveals that most COVID-19 cases in Indonesia occurred in the daily temperature range of 25-31 °C and relative humidity of 74-92%. Our findings suggest that COVID-19 incidence in Indonesia has a weak association with weather conditions. Therefore, non-meteorological factors seem to play a more prominent role and should be given greater consideration in preventing the spread of COVID-19.

Graphic abstract

Supplementary Information

The online version contains supplementary material available at 10.1007/s42398-021-00202-9.

COVID-19 in medium-sized municipalities in the 14 health macro-regions of Minas Gerais, Brazil

The present study focused on the scenario of confirmed cases of SARS-CoV-2 infection in the state of Minas Gerais (MG), Brazil, from March 2020 to March 2021. We evaluated the evolution of COVID-19 prevalence and death in one municipality from each of the 14 health macro-regions of MG state. Socio-demographic characteristics and variables related to the municipalities were analyzed. The raw dataset used in this study was freely sourced from the website Brasil.io. From the raw dataset, two time series were extracted: the cumulative confirmed cases of COVID-19 and cumulative death counts, and they were compared to the state data using a nowcasting approach. In order to make time series comparisons possible, all data was normalized per 100,000 inhabitants. When analyzing in light of colored wave code interventions initiated in August 2020 in MG, for the majority of the municipalities, there was an absence of clear influence on prevalence and deaths. The national holidays in the first semester of 2020 had a small impact on the COVID-19 prevalence of the municipalities, but the holidays in the second semester of 2020 and beginning of 2021 caused important impacts on COVID-19 prevalence. The low number of ICU beds in some municipalities contributed to the higher number of deaths. The analysis showed here is expected to contribute to the improvement of decision making of the MG government, as it opened a huge possibility to have the total macro-regions and state data analyzed.

SARS-CoV-2 in Rural Latin America. A Population-based Study in Coastal Ecuador

Antibodies to SARS-CoV-2 were detected in 303/673 rural Ecuadorian adults (45%), 77% of whom had compatible clinical manifestations. Seropositivity was associated with the use of open latrines. Our findings support the fears of mass spread of SARS-CoV-2 in rural Latin America and cannot exclude a contributing role for fecal-oral transmission.

COVID-19 in chronic myeloid leukemia patients in Latin America

This observational, multicenter study aimed to report the clinical evolution of COVID-19 in patients with chronic myeloid leukemia in Latin America. A total of 92 patients presented with COVID-19 between March and December 2020, 26% of whom were severe or critical. The median age at COVID-19 diagnosis was 48 years (22-79 years), 32% were 60 years or older, and 61% were male. Thirty-nine patients presented with at least one comorbidity (42.3%). Eighty-one patients recovered (88%), and 11 (11.9%) died from COVID-19. There was one case of reinfection. Patients with a major molecular response presented superior overall survival compared to patients with no major molecular response (91 vs. 61%, respectively; p = 0.004). Patients in treatment-free remission and receiving tyrosine kinase inhibitors showed higher survival rates than patients who underwent hematopoietic stem cell transplantation and those who did not receive tyrosine kinase inhibitors (100, 89, 50, and 33%, respectively; p < 0.001).

A critical review on SARS-CoV-2 infectivity in water and wastewater. What do we know?

The COVID-19 outbreak circulating the world is far from being controlled, and possible contamination routes are still being studied. There are no confirmed cases yet, but little is known about the infection possibility via contact with sewage or contaminated water as well as with aerosols generated during the pumping and treatment of these aqueous matrices. Therefore, this article presents a literature review on the detection of SARS-CoV-2 in human excreta and its pathways through the sewer system and wastewater treatment plants until it reaches the water bodies, highlighting their occurrence and infectivity in sewage and natural water. Research lines are still indicated, which we believe are important for improving the detection, quantification, and mainly the infectivity analyzes of SARS-CoV-2 and other enveloped viruses in sewage and natural water. In fact, up till now, no case of transmission via contact with sewage or contaminated water has been reported and the few studies conducted with these aqueous matrices have not detected infectious viruses. On the other hand, studies are showing that SARS-CoV-2 can remain viable, i.e., infectious, for up to 4.3 and 6 days in sewage and water, respectively, and that other species of coronavirus may remain viable in these aqueous matrices for more than one year, depending on the sample conditions. These are strong pieces of evidence that the contamination mediated by contact with sewage or contaminated water cannot be ruled out, even because other more resistant and infectious mutations of SARS-CoV-2 may appear.

Latin America and the Caribbean SARS-CoV-2 Surveillance: Longitudinal Trend Analysis

Background

The COVID-19 pandemic has placed unprecedented stress on economies, food systems, and health care resources in Latin America and the Caribbean (LAC). Existing surveillance provides a proxy of the COVID-19 caseload and mortalities; however, these measures make it difficult to identify the dynamics of the pandemic and places where outbreaks are likely to occur. Moreover, existing surveillance techniques have failed to measure the dynamics of the pandemic.

Objective

This study aimed to provide additional surveillance metrics for COVID-19 transmission to track changes in the speed, acceleration, jerk, and persistence in the transmission of the pandemic more accurately than existing metrics.

Methods

Through a longitudinal trend analysis, we extracted COVID-19 data over 45 days from public health registries. We used an empirical difference equation to monitor the daily number of cases in the LAC as a function of the prior number of cases, the level of testing, and weekly shift variables based on a dynamic panel model that was estimated using the generalized method of moments approach by implementing the Arellano–Bond estimator in R. COVID-19 transmission rates were tracked for the LAC between September 30 and October 6, 2020, and between October 7 and 13, 2020.

Results

The LAC saw a reduction in the speed, acceleration, and jerk for the week of October 13, 2020, compared to the week of October 6, 2020, accompanied by reductions in new cases and the 7-day moving average. For the week of October 6, 2020, Belize reported the highest acceleration and jerk, at 1.7 and 1.8, respectively, which is particularly concerning, given its high mortality rate. The Bahamas also had a high acceleration at 1.5. In total, 11 countries had a positive acceleration during the week of October 6, 2020, whereas only 6 countries had a positive acceleration for the week of October 13, 2020. The TAC displayed an overall positive trend, with a speed of 10.40, acceleration of 0.27, and jerk of –0.31, all of which decreased in the subsequent week to 9.04, –0.81, and –0.03, respectively.

Conclusions

Metrics such as new cases, cumulative cases, deaths, and 7-day moving averages provide a static view of the pandemic but fail to identify where and the speed at which SARS-CoV-2 infects new individuals, the rate of acceleration or deceleration of the pandemic, and weekly comparison of the rate of acceleration of the pandemic indicate impending explosive growth or control of the pandemic. Enhanced surveillance will inform policymakers and leaders in the LAC about COVID-19 outbreaks.

Dissemination and evolution of SARS-CoV-2 in the early pandemic phase in South America

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) pandemic spread rapidly and this scenario is concerning in South America, mainly in Brazil with more than seven million cases of infection. Three major pandemic lineages/clades could be identified along with SARS-CoV-2 dissemination (G, GR, and GH) in the Americas. These clades differ according to their genomic characteristics, virulence, and spreading times. The present study describes the main clades and the respective temporal spreading analyses based on SARS-CoV-2 whole-genome sequences (WGS) from South America, obtained in the early pandemic phase (from March 1 to May 31 in 2020). SARS-CoV-2 WGSs with available information from country and year of sampling were obtained from different countries and the main clades were identified and analyzed independently with a Bayesian approach. The results demonstrated the prevalence of clades GR (n = 842; 54.6%), G (n = 529; 34.3%), and GH (n = 171; 11.1%). The frequencies of the clades were significantly different between South American countries. Clade G was the most prevalent in Ecuador, Suriname, and Uruguay, clade GR in Argentina, Brazil, and Peru, and clade GH in Colombia. The phylodynamic analysis indicated that all these main lineages increased viral spreading from February to early March and after an evolutionary stationary phase was observed. The decrease observed in the virus dissemination was directly associated to the reduction of social movement after March. In conclusion, these data demonstrated the current predominance of clades G, GR, and GH in South America because of the early dissemination of them in the first pandemic phase in South America.

Non-standard bioinformatics characterization of SARS-CoV-2

A non-standard bioinformatics method, 4D-Dynamic Representation of DNA/RNA Sequences, aiming at an analysis of the information available in nucleotide databases, has been formulated. The sequences are represented by sets of "material points" in a 4D space - 4D-dynamic graphs. The graphs representing the sequences are treated as "rigid bodies" and characterized by values analogous to the ones used in the classical dynamics. As the graphical representations of the sequences, the projections of the graphs into 2D and 3D spaces are used. The method has been applied to an analysis of the complete genome sequences of the 2019 novel coronavirus. As a result, 2D and 3D classification maps are obtained. The coordinate axes in the maps correspond to the values derived from the exact formulas characterizing the graphs: the coordinates of the centers of mass and the 4D moments of inertia. The points in the maps represent sequences and their coordinates are used as the classifiers. The main result of this work has been derived from the 3D classification maps. The distribution of clusters of points which emerged in these maps, supports the hypothesis that SARS-CoV-2 may have originated in bat and in pangolin. Pilot calculations for Zika virus sequence data prove that the proposed approach is also applicable to a description of time evolution of genome sequences of viruses.

COVID-19: Epidemiological Situation of Argentina and its Neighbor Countries after Three Months of Pandemic

OBJECTIVE

In this work, in order to establish a better comprehension of the association between Argentina and its neighbor countries' capacity, and COVID-19 burden during the first 3 months, different indicators were evaluated.

METHOD

We analyzed the association between GHSI, INFORM index and COVID-19 burden (number of confirmed cases and deaths), also the number of tests, lethality and the stringency of Governmental policies were evaluated.

RESULTS

Uruguay, Paraguay, and Bolivia started earlier different prevention measures. The number of tests differs, as Chile is the 1 that makes more. Uruguay and Paraguay register fewer positive cases and deaths from COVID-19. The GHS index is led by Brazil, followed by Argentina, and then Chile. However, the INFORM index is led by Uruguay followed by Argentina, while Chile and Paraguay are on par.

CONCLUSION

The countries that took preventive measures earlier and carried out a more tests are the ones that are obtaining the best results against COVID-19.

Social Determinants of Health and Risk of SARS-CoV-2 Infection in Community-Dwelling Older Adults Living in a Rural Latin American Setting

High social risk, as measured by the social determinants of health (SDH), may increase the risk of SARS-CoV-2 infection. However, this association has not been studied in rural communities. Using the Atahualpa Project cohort, we aimed to assess the association between SDH and SARS-CoV-2 seropositivity in community-dwelling older adults living in rural Ecuador. SARS-CoV-2 antibodies were determined in 319 individuals aged ≥ 60 years that completed a validated field instrument to assess their social risk before the introduction of this novel pandemic. Multivariate models were fitted to assess the independent association between SDH-and each of their components-and SARS-CoV-2 seropositivity, after adjusting for relevant covariates. According to the Gijon scale, 102 (32%) individuals had a high social risk (≥ 10 points). A total of 141 (44%) individuals were seropositive to SARS-CoV-2. A fully-adjusted logistic regression model showed an independent) association between social risk and SARS-CoV-2 positivity (OR 1.15; 95% CI 1.04-1.27; p = 0.008). For every unit of the total SDH score, the odds of SARS-CoV-2 seropositivity increased 15% (95% CI 3.7-27%). In addition, multivariate models showed that the individual component of SDH more strongly associated with SARS-CoV-2 seropositivity was housing, which suggested that lack of basic home facilities may increase the risk of SARS-CoV-2 infection. Knowledge on the association between high social risk and SARS-CoV-2 infection is indispensable for the development of cost-effective preventive strategies for controlling modifiable factors that are in the path of SARS-CoV-2 infection among older adults living in underserved communities.

Public health matters: why is Latin America struggling in addressing the pandemic?

This article examines how Argentina, Brazil, Chile, Colombia, Mexico, and Peru addressed the COVID-19 pandemic and the effectiveness of these policy responses from the date each country declared a sanitary emergency, between middle and late March 2020 to the most recent available measurement on 23 September 2020. To analyze how governments responded to the COVID-19 pandemic in these six Latin American countries, we use an index of government response, created by the University of Oxford. To explore the effects of these governmental mitigation policies on reducing social mobility, we use Google mobility reports. We also analyze how these policies may have influenced COVID-19 mortality rates. Overall, the results showed that both timelier and more stringent implementation of the public policies analyzed to address the COVID-19 pandemic seem to be associated with higher mobility reductions and lower mortality rates. We draw five policy lessons from the way each country implemented these mitigation policies. KEY MESSAGE: Timelier and more stringent implementation of these public policies may contribute to a higher mobility reduction in several public spaces and to lower mortality rates. The effectiveness of the closure and containment policies in each Latin American country seem to depend on the degree of compliance of their respective populations and to their socioeconomic living conditions. Economic and social policies of income support and debt relief provided by governments allowed people to comply with closure and containment policies. Health systems should maintain high levels of policy stringency together with effective surveillance through testing policy and contact tracing.

Obesity and COVID-19 in Latin America: A tragedy of two pandemics-Official document of the Latin American Federation of Obesity Societies

In May 2020, Latin America became the epicenter of the COVID-19 pandemic, a region already afflicted by social disparities, poor healthcare access, inadequate nutrition and a large prevalence of noncommunicable chronic diseases. Obesity and its comorbidities are increasingly prevalent in Latin America, with a more rapid growth in individuals with lower income, and currently a disease associated with COVID-19 severity, complications and death. In this document, the Latin American Association of Obesity Societies and collaborators present a review of the burden of two pandemics in Latin America, discuss possible mechanisms that explain their relationship with each other and provide public health and individual recommendations, as well as questions for future studies.

SARS-CoV-2 RNA in Swabbed Samples from Latrines and Flushing Toilets: A Case-Control Study in a Rural Latin American Setting

Information about factors potentially favoring the spread of SARS-CoV-2 in rural settings is limited. Following a case–control study design in a rural Ecuadorian village that was severely struck by the pandemic, SARS-CoV-2 RNA were detected by real-time PCR in swabs obtained from inner and upper walls in 24/48 randomly selected latrines from case-houses and in 12/48 flushing toilets from paired control-houses (P = 0.014; McNemar’s test). This association persisted in a conditional logistic regression model adjusted for relevant covariates (OR: 4.82; 95% CI: 1.38–16.8; P = 0.014). In addition, SARS-CoV-2–seropositive subjects were more often identified among those living in houses with a latrine (P = 0.002). Latrines have almost five times the odds of containing SARS-CoV-2 RNA than their paired flushing toilets. Latrines are reservoirs of SARS-CoV-2 RNA, and it cannot be ruled out that latrines could contribute to viral transmission in rural settings. Frequent disinfection of latrines should be recommended to reduce the likelihood of fecal contamination.

Poor sanitation and transmission of COVID-19 in Brazil

Coronavirus is a family of viruses that cause respiratory infections. From cases first recorded in China at the end of 2019, a new type of virus in this family, named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was discovered. The disease caused by this virus, COVID-19, was brought into Brazil by people in social classes with greater purchasing power, but groups with larger demographic dimensions have tended to become more affected over time. Poor sanitation can generate risky situations and behavior among people who live in spaces with characteristics that limit their quality of life. Installation of piped water in homes and basic education for the population are fundamental measures for disease control, including in relation to COVID-19. In this updating article, the COVID-19 pandemic was analyzed in the context of iniquities in Brazil (comparing these with the situation in other countries). A bibliographic search of texts relating to basic sanitation, socioeconomic development and transmission of COVID-19 in Brazil and worldwide was conducted.

SARS-CoV-2 in wastewater: Challenges for developing countries

The COVID-19 pandemic that has engulfed the world, has affected the human lives in several aspects. The detection of SARS-CoV-2 in faeces and urine of the infected person, even after viral clearance in the respiratory tract, and its presence in untreated wastewater raises the possibility of fecal-oral transmission in future. The situation is likely to be more aggravated in developing and least developed countries struggling with the problem of ineffective waste disposal system, open defecation, poor sanitation, and limited access to clean drinking water. In this review, the available data on wastewater treatment, sanitation status and healthcare infrastructure from middle- and low-income countries is collected and correlated with the risk associated with the fecal-oral transmission of SARS-CoV-2. The review also highlights the limitation of COVID-19 surveillance through sewage monitoring in these countries owing to the absence of proper sewerage system. An inclusive approach of awareness, prevention, and mitigation from global to the local levels is required to overcome this challenging situation in developing countries.

Late incidence of SARS-CoV-2 infection in a highly-endemic remote rural village. A prospective population-based cohort study

Data on SARS-CoV-2 transmission in rural communities is scarce or non-existent. A previous cross-sectional study in middle-aged and older adults enrolled in the Atahualpa Project Cohort demonstrated that 45% of participants had SARS-CoV-2 antibodies, 77% of whom were symptomatic. Here, we assessed the incidence of SARS-CoV-2 infection in the above-mentioned rural population. One month after baseline testing, 362 of 370 initially seronegative individuals were re-tested to assess incidence of seroconversion and associated risk factors. Twenty-eight of them (7.7%) became seropositive. The overall incidence rate ratio was 7.4 per 100 person months of potential virus exposure (95% C.I.: 4.7-10.2). Six seroconverted individuals (21.4%) developed SARS-CoV-2-related symptomatology. The only covariate significantly associated with seroconversion was the use of an open latrine. Predictive margins showed that these individuals were 2.5 times more likely to be infected (95% C.I.: 1.03-6.1) than those using a flushing toilet. Therefore, along one month, approximately 8% of seronegative individuals became infected, even after almost half of the population was already seropositive. Nevertheless, a smaller proportion of incident cases were symptomatic (21% versus 77% of the earlier cases), and no deaths were recorded. Whether this decreased clinical expression resulted from a lower viral load in new infections cannot be determined. Increased seroconversion in individuals using latrines is consistent with a contributory role of fecal-oral transmission, although we cannot rule out the possibility that latrines are acting as a proxy for poverty or other unknown interacting variables.

SARS-CoV-2 spread across the Colombian-Venezuelan border

INTRODUCTION

Venezuela and Colombia both adopted measures of containment early in response to the COVID-19 pandemic. However, Venezuela's ongoing humanitarian crisis has decimated its health care system, and forced millions of Venezuelans to flee through its porous border with Colombia. The extensive shared border, and illegal cross-border transit through improvised trails between the two countries are major challenges for public health authorities. We report the first SARS-CoV-2 genomes from Venezuela, and present a snapshot of the SARS-CoV-2 epidemiologic landscape in the Colombian-Venezuelan border region.

METHODS

We sequenced and assembled viral genomes from total RNA extracted from nasopharyngeal (NP) clinical specimens using a custom reference-based analysis pipeline. Three assemblies obtained were subjected to typing using the Phylogenetic Assignment of Named Global Outbreak LINeages 'Pangolin' tool. A total of 376 publicly available SARS-CoV-2 genomes from South America were obtained from the GISAID database to perform comparative genomic analyses. Additionally, the Wuhan-1 strain was used as reference.

RESULTS

We found that two of the SARS-CoV-2 genomes from Venezuela belonged to the B1 lineage, and the third to the B.1.13 lineage. We observed a point mutation in the Spike protein gene (D614G substitution), previously reported to be associated with increased infectivity, in all three Venezuelan genomes. Additionally, three mutations (R203K/G204R substitution) were present in the nucleocapsid (N) gene of one Venezuelan genome.

CONCLUSIONS

Genomic sequencing demonstrates similarity between SARS-CoV-2 lineages from Venezuela and viruses collected from patients in bordering areas in Colombia and from Brazil, consistent with cross-border transit despite administrative measures including lockdowns. The presence of mutations associated with increased infectivity in the 3 Venezuelan genomes we report and Colombian SARS-CoV-2 genomes from neighboring borders areas may pose additional challenges for control of SARS-CoV-2 spread in the complex epidemiological landscape in Latin American countries. Public health authorities should carefully follow the progress of the pandemic and its impact on displaced populations within the region.

COVID-19 in the least developed, fragile, and conflict-affected countries - How can the most vulnerable be protected?

The relentless spread of coronavirus disease 2019 (COVID-19) and its penetration into the least developed, fragile, and conflict-affected countries (LDFCAC) is a certainty. Expansion of the pandemic will be expedited by factors such as an abundance of at-risk populations, inadequate COVID-19 mitigation efforts, sheer inability to comply with community mitigation strategies, and constrained national preparedness. This situation will reduce the benefits achieved through decades of disease control and health promotion measures, and the economic progress made during periods of global development. Without interventions, and as soon as international travel and trade resume, reservoirs of COVID-19 and other vaccine-preventable diseases in LDFCAC will continue ‘feeding’ developed countries with repeated infection seeds. Assuring LDFCAC equity in access to medical countermeasures, funds to mitigate the pandemic, and a paradigm change in the global development agenda, similar to the post-World War II Marshall Plan for Europe, are urgently needed. We argue for a paradigm change in strategy, including a new global pandemic financing mechanism for COVID-19 and other future pandemics. This approach should assist LDFCAC in gaining access to and membership of a global interdisciplinary pandemic taskforce to enable in-country plans to train, leverage, and maintain essential functioning and also to utilize and enhance surveillance and early detection capabilities. Such a task force will be able to build on and expand research into the management of pandemics, protect vulnerable populations through international laws/treaties, and reinforce and align the development agenda to prevent and mitigate future pandemics. Lifting LDFCAC from COVID-related failure will offer the global community the best economic dividends of the century.

SARS-CoV-2 sequencing: The technological initiative to strengthen early warning systems for public health emergencies in Latin America and the Caribbean

The COVID-19 pandemic caused by SARS-CoV-2 is a public health problem on a scale unprecedented in the last 100 years, as has been the response focused on the rapid genomic characterization of SARS-CoV-2 in virtually all regions of the planet. This pandemic emerged during the era of genomic epidemiology, a science fueled by continued advances in next-generation sequencing. Since its recent appearance, genomic epidemiology included the precise identification of new lineages or species of pathogens and the reconstruction of their genetic variability in real time, evidenced in past outbreaks of influenza H1N1, MERS, and SARS. However, the global and uncontrolled scale of this pandemic created a scenario where genomic epidemiology was put into practice en masse, from the rapid identification of SARS-CoV-2 to the registration of new lineages and their active surveillance throughout the world. Prior to the COVID-19 pandemic, the availability of genomic data on circulating pathogens in several Latin America and the Caribbean countries was scarce or nil. With the arrival of SARS-CoV-2, this scenario changed significantly, although the amount of available information remains scarce and, in countries such as Colombia, Brazil, Argentina, and Chile, the genomic information of SARS-CoV-2 was obtained mainly by research groups in genomic epidemiology rather than the product of a public health surveillance policy or program. This indicates the need to establish public health policies aimed at implementing genomic epidemiology as a tool to strengthen surveillance and early warning systems against threats to public health in the region.

SARS-CoV-2 in the Amazon region: A harbinger of doom for Amerindians

As the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) pandemic continues to expand, healthcare resources globally have been spread thin. Now, the disease is rapidly spreading across South America, with deadly consequences in areas with already weakened public health systems. The Amazon region is particularly susceptible to the widespread devastation from Coronavirus disease 2019 (COVID-19) because of its immunologically fragile native Amerindian inhabitants and epidemiologic vulnerabilities. Herein, we discuss the current situation and potential impact of COVID-19 in the Amazon region and how further spread of the epidemic wave could prove devastating for many Amerindian people living in the Amazon rainforest.

A multivariate analysis on spatiotemporal evolution of Covid-19 in Brazil

This data-driven work aims to analyze and classify the spatiotemporal distribution of all Brazilian states considering data so diverse as the number of Covid-19 cases, deaths, confirmed cases per 100 k inhabitants, mortality per 100 k inhabitants and case fatality rates as health indicators. We also considered population, area and population density as geographic indicators. Finally, GDP and HDI were taken into account as economic and social criteria. For this task data were collected from April 3rd until August 8th, 2020, corresponding to epidemiological weeks 14-32, reaching three million cases and a hundred thousand deaths. With this data it was possible to classify Brazilian states using multivariate methods into possible groups by means of non-hierarchical (k-means) cluster as well as factor analysis. It was possible to group all states plus the Federal District into five clusters, taking into account these 10 variables over the first five months of the epidemic. Group changes between states were observed over time and clusters, and between three and four factors were found. However, even with great difference on health indicators during days, the number of clusters remains fixed. Also, São Paulo and Rio de Janeiro states were ranked at top list taking into account all epidemiological weeks. Correlations were observed between variables, such as the number of Covid cases and deaths with GDP for most of epidemiological weeks. Some clusters were more critical due to specific variables, including cities that are main hotspots. These multivariate findings would provide a comprehensive description of the ongoing Covid-19 epidemic and may help to guide subsequent studies to understand and control virus transmission.

Strategic responses to the COVID-19 pandemic in Pacific Alliance countries

Purpose

The COVID-19 pandemic has forced governments of different countries to implement unprecedented strategies with the aim of reducing the rate of contagion and mitigating its economic and social effects. In this scenario, the purpose of this paper is to analyze four fundamental strategies, namely, testing and diagnosis, macroprudential, labor market and social assistance, based on the crisis management theory.

Design/methodology/approach

This research note is based on a review of the principal official legislations regarding the strategies implemented during the first 80 days from the first zero case registered in the Pacific Alliance countries.

Findings

The review shows that the Pacific Alliance countries have implemented similar strategies regarding macroprudential and labor market measures. On the other hand, there are differences among the strategies related to testing and diagnostic and social assistance.

Originality/value

The COVID-19 pandemic has significantly affected Latin American countries due to their economic and social problems. In this sense, the reporting and analysis of the principal strategies implemented by the Pacific Alliance countries constitute a baseline to understand the effectiveness of these strategies in mitigating the negative effects of the pandemic.

Household Clustering of SARS-CoV-2 in Community Settings: A Study from Rural Ecuador

The SARS-CoV-2 pandemic is now expanding into the developing world with devastating consequences. Departing from a population-based study in rural Ecuador where all adult individuals (aged 40 years or older) were tested for SARS-CoV-2 IgG and IgM antibodies, we expanded it to include a house-based case-control component assessing in-house clustering and other variables potentially associated with infection. We selected houses where exactly two study participants lived and were both seropositive (case-houses), and matched 1:1 to control-houses where both were seronegative. Younger household members had an antibody test performed. Infected household members were found in 33 (92%) case-houses and in only six (17%) control-houses. In 28/29 discordant house pairs, the case-house had seropositive household members and the control-house did not (odds ratio: 28; 95% CI: 4.6-1,144). Our data demonstrate strong in-house clustering of infection in community settings, stressing the importance of early case ascertainment and isolation for SARS-CoV-2 control.

Challenges of COVID-19 in children in low- and middle-income countries

As the coronavirus pandemic extends to low and middle income countries (LMICs), there are growing concerns about the risk of coronavirus disease (COVID-19) in populations with high prevalence of comorbidities, the impact on health and economies more broadly and the capacity of existing health systems to manage the additional burden of COVID-19. The direct effects of COVID are less of a concern in children, who seem to be largely asymptomatic or to develop mild illness as occurs in high income countries; however children in LMICs constitute a high proportion of the population and may have a high prevalence of risk factors for severe lower respiratory infection such as HIV or malnutrition. Further diversion of resources from child health to address the pandemic among adults may further impact on care for children. Poor living conditions in LMICs including lack of sanitation, running water and overcrowding may facilitate transmission of SARS-CoV-2. The indirect effects of the pandemic on child health are of considerable concern, including increasing poverty levels, disrupted schooling, lack of access to school feeding schemes, reduced access to health facilities and interruptions in vaccination and other child health programs. Further challenges in LMICs include the inability to implement effective public health measures such as social distancing, hand hygiene, timely identification of infected people with self-isolation and universal use of masks. Lack of adequate personal protective equipment, especially N95 masks is a key concern for health care worker protection. While continued schooling is crucial for children in LMICs, provision of safe environments is especially challenging in overcrowded resource constrained schools. The current crisis is a harsh reminder of the global inequity in health in LMICs. The pandemic highlights key challenges to the provision of health in LMICs, but also provides opportunities to strengthen child health broadly in such settings.

The arrival and spread of SARS-CoV-2 in Colombia

We performed phylogenomic analysis of severe acute respiratory syndrome coronavirus‐2 from 88 infected individuals across different regions of Colombia. Eleven different lineages were detected, suggesting multiple introduction events. Pangolin lineages B.1 and B.1.5 were the most frequent, with B.1 being associated with prior travel to high‐risk areas.

This is the first genomic epidemiology study of SARS‐CoV2 in Colombia.

SARS-CoV-2-related mortality in a rural Latin American population

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There is no evidence on mortality rates of SARS-CoV-2 in remote rural settings.

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We calculated SARS-CoV-2 mortality rate of adults living in Atahualpa (rural Ecuador).

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SARS-CoV-2 mortality rate was 15.7/1,000, which increased to 68.9/1,000 when only older adults were considered.

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Most deaths occurred over a two-month period, and markedly decreased subsequently.

A sudden increase in adult mortality associated with respiratory diseases was noticed in Atahualpa (a rural Ecuadorian village), coinciding with the introduction of SARS-CoV-2 in the region. From a total of 1,852 individuals aged ≥18 years, 40 deaths occurred between January and June, 2020. In addition, a seroprevalence survey showed that 45% of the adult population have SARS-CoV-2 antibodies. Verbal autopsies revealed SARS-CoV-2 as the most likely cause of death in 29 cases. The mean age of suspected or confirmed SARS-CoV-2 cases was 76.9 ± 12.1 years, while that of those dying from unrelated causes was 60.3 ± 20.4 years (p = 0.003). The overall mortality rate was 21.6 per 1,000 population (95% C.I.: 15.9 – 29.2), almost three-quarters of it due to SARS-CoV-2 (15.7 per 1,000; 95% C.I.: 11 – 22.4). This configures a 266% of excess mortality when compared to 5.9 per 1,000 (95% C.I.: 3.3 – 10.6) deaths from other causes. When SARS-CoV-2 mortality rate was calculated in individuals aged ≥60 years, it raised up to 68.9 per 1,000 (95% C.I.: 47.8 – 98.4). After peaking in April and May, mortality significantly decreased. It is possible that the high proportion of infected individuals and the resulting herd immunity contributed to the observed reduction in mortality.