Change in Psychoactive Substance Consumption in Relation to Psychological Distress During the COVID-19 Pandemic in Uruguay.

Objectives: This study aimed to analyse how the health crisis associated with the COVID-19 pandemic affected psychoactive substance consumption in Uruguay. Methods: An online survey was answered by 1,916 Uruguayan citizens between March and April 2020 regarding psychoactive substance use before and after the instauration of a recommended quarantine, increases in frequency and volume of use (during the quarantine) of the psychoactive substance they reported as having consumed the most in the year prior to the quarantine and psychological distress experienced during the last month. Results: The main substances consumed during the quarantine were alcohol, tobacco, marijuana and psychopharmaceuticals. Approximately 28% of respondents increased the volume (and 17.7%, the frequency) of use of the substance they had consumed the most the year before the instauration of the quarantine. Moreover, 5.7% initiated the consumption of a new psychoactive substance during the quarantine, mostly marijuana and psychopharmaceuticals. Psychological distress was significantly higher among women, participants under 30 and among those that increased the volume of their most or second preferred psychoactive substance. The group reporting an increase in the volume of use exhibited greater psychological distress. Conclusion: These results indicate an association between the instauration of the recommended quarantine in Uruguay and greater psychoactive substance use during the period as well as an association between increased psychoactive substance use during this period and levels of psychological stress. These results are relevant in terms of public health and policies.

Consecutive deletions in a unique Uruguayan SARS-CoV-2 lineage evidence the genetic variability potential of accessory genes.

Deletions frequently occur in the six accessory genes of SARS-CoV-2, but most genomes with deletions are sporadic and have limited spreading capability. Here, we analyze deletions in the ORF7a of the N.7 lineage, a unique Uruguayan clade from the Brazilian B.1.1.33 lineage. Thirteen samples collected during the early SARS-CoV-2 wave in Uruguay had deletions in the ORF7a. Complete genomes were obtained by Illumina next-generation sequencing, and deletions were confirmed by Sanger sequencing and capillary electrophoresis. The N.7 lineage includes several individuals with a 12-nucleotide deletion that removes four amino acids of the ORF7a. Notably, four individuals underwent an additional 68-nucleotide novel deletion that locates 44 nucleotides downstream in the terminal region of the same ORF7a. The simultaneous occurrence of the 12 and 68-nucleotide deletions fuses the ORF7a and ORF7b, two contiguous accessory genes that encode transmembrane proteins with immune-modulation activity. The fused ORF retains the signal peptide and the complete Ig-like fold of the 7a protein and the transmembrane domain of the 7b protein, suggesting that the fused protein plays similar functions to original proteins in a single format. Our findings evidence the remarkable dynamics of SARS-CoV-2 and the possibility that single and consecutive deletions occur in accessory genes and promote changes in the genomic organization that help the virus explore genetic variations and select for new, higher fit changes.

Transmission cluster of COVID-19 cases from Uruguay: emergence and spreading of a novel SARS-CoV-2 ORF6 deletion.

BACKGROUND: Evolutionary changes in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) include indels in non-structural, structural, and accessory open reading frames (ORFs) or genes. OBJECTIVES: We track indels in accessory ORFs to infer evolutionary gene patterns and epidemiological links between outbreaks. METHODS: Genomes from Coronavirus disease 2019 (COVID-19) case-patients were Illumina sequenced using ARTIC_V3. The assembled genomes were analysed to detect substitutions and indels. FINDINGS: We reported the emergence and spread of a unique 4-nucleotide deletion in the accessory ORF6, an interesting gene with immune modulation activity. The deletion in ORF6 removes one repeat unit of a two 4-nucleotide repeat, which shows that directly repeated sequences in the SARS-CoV-2 genome are associated with indels, even outside the context of extended repeat regions. The 4-nucleotide deletion produces a frameshifting change that results in a protein with two inserted amino acids, increasing the coding information of this accessory ORF. Epidemiological and genomic data indicate that the deletion variant has a single common ancestor and was initially detected in a health care outbreak and later in other COVID-19 cases, establishing a transmission cluster in the Uruguayan population. MAIN CONCLUSIONS: Our findings provide evidence for the origin and spread of deletion variants and emphasise indels' importance in epidemiological studies, including differentiating consecutive outbreaks occurring in the same health facility.

A deletion in SARS-CoV-2 ORF7 identified in COVID-19 outbreak in Uruguay.

The analysis of genetic diversity in SARS-CoV-2 is the focus of several studies, providing insights into how the virus emerged and evolves. Most common changes in SARS-CoV-2 are single or point nucleotide substitutions; meanwhile, insertions and deletions (indels) have been identified as a less frequent source of viral genetic variability. Here, we report the emergence of a 12-nucleotide deletion in ORF7a, resulting in a 4-amino acid in-frame deletion. The Δ12 variant was identified in viruses from patients of a single outbreak and represents the first report of this deletion in South American isolates. Phylogenetic analysis revealed that Δ12 strains belong to the lineage B.1.1 and clustered separated from the remaining Uruguayan strains. The ∆12 variant was detected in 14 patients of this outbreak by NGS sequencing and/or two rapid and economic methodologies: Sanger amplicon sequencing and capillary electrophoresis. The presence of strong molecular markers as the deletion described here are useful for tracking outbreaks and reveal a significant aspect of the SARS-CoV-2 evolution on the robustness of the virus to keep its functionality regardless loss of genetic material.

Using Systems Dynamics for Capturing the Multicausality of Factors Affecting Health System Capacity in Latin America while Responding to the COVID-19 Pandemic.

Similar interventions to stop the spread of COVID-19 led to different outcomes in Latin American countries. This study aimed to capture the multicausality of factors affecting HS-capacity that could help plan a more effective response, considering health as well as social aspects. A facilitated GMB was constructed by experts and validated with a survey from a wider population. Statistical analyses estimated the impact of the main factors to the HS-capacity and revealed the differences in its mechanisms. The results show a similar four-factor structure in all countries that includes public administration, preparedness, information, and collective self-efficacy. The factors are correlated and have mediating effects with HS-capacity; this is the base for differences among countries. HS-capacity has a strong relation with public administration in Bolivia, while in Nicaragua and Uruguay it is related through preparedness. Nicaragua lacks information as a mediation effect with HS-capacity whereas Bolivia and Uruguay have, respectively, small and large mediation effects with it. These outcomes increase the understanding of the pandemic based on country-specific context and can aid policymaking in low-and middle-income countries by including these factors in future pandemic response models.

A Year in the COVID-19 Epidemic: Cuba and Uruguay in the Latin American Context.

INTRODUCTION: One year after WHO declared COVID-19 a pandemic, we found it useful to carry out a diagnosis of the situation in Latin America. OBJECTIVE: Examine the prevailing epidemiological panorama in mid-March 2021 in 16 countries in Latin America and the performance, over time, in the two countries with the best responses to their respective epidemics. METHODS: Using morbidity and mortality data, we compared the relative performance of each country under review and identified the two countries with the most successful responses to the pandemic. We used five indicators to analyze the course of each country's performance during the pandemic throughout 2020: prevalence of active cases per million population; cumulative incidence rate in 7 days per 100,000 population; positivity rate over a 7-day period; percentage of recovered patients and crude mortality rate per 1,000,000 population. RESULTS: According to the performance indicators, Cuba was ranked highest, followed by Uruguay. Although figures remained within acceptable margins, both nations experienced notable setbacks in the first weeks of 2021, especially sharp in Uruguay. CONCLUSIONS: Any characterization of the situation is condemned to be short-lived due to the emergence of mutational variants; however, this analysis identified favorable sociodemographic characteristics in both nations, and in their health systems, which may offer possible explanations for the results we obtained.

Real-Time Genomic Surveillance for SARS-CoV-2 Variants of Concern, Uruguay.

We developed a genomic surveillance program for real-time monitoring of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) in Uruguay. We report on a PCR method for SARS-CoV-2 VOCs, the surveillance workflow, and multiple independent introductions and community transmission of the SARS-CoV-2 P.1 VOC in Uruguay.

Is COVID-19 a threat or an opportunity for healthy eating? An exploration of the factors that moderate the impact of the pandemic on eating habits in Uruguay.

In May 2020, Uruguay was one of the few Latin American countries that had managed to control the outbreak of COVID-19 without mandatory curfews or quarantines. However, several social distancing measures created a major disruption in different aspects of the daily life of Uruguayan citizens. In this context, the objectives of the present work were i) to identify changes in eating habits perceived by Uruguayan citizens as a consequence of the COVID-19 pandemic, and ii) to explore factors associated with different perceived changes on eating habits. A cross-sectional online study was conducted with 891 participants, recruited using an advertisement on Facebook and Instagram. Fifty-one percent of the participants indicated that their eating habits had changed since the detection of the first cases of COVID-19 in Uruguay. Large heterogeneity in the categorization of the changes existed: 45% of the participants regarded the changes as positive, 32% as negative and 23% as neither positive nor negative. A multinomial logistic regression analysis was used to study the influence of explanatory variables in the likelihood of belonging to groups who reported different changes in eating habits (no changes, positive, negative, or neither positive nor negative changes). Household income and reliance on instrumental and emotional support increased the likelihood of reporting positive changes in eating habits, whereas negative changes were associated with a reduction in household income due to COVID-19 and the coping strategies self-distraction and self-blaming. Insights for policy making to reinforce positive effects and minimize threats to healthy eating are discussed.

Effect of the unfavorable maternal-fetal environment cause by mitigation measures of the covid-19 pandemic in the public maternity of reference of Uruguay.

INTRODUCTION: The mitigation measures to face the health emergency due to the COVID 19 pandemic generated a deep economic, social, and psychological crisis at the community level. This effect is greater in the people, who are the most violated in their rights. In relation to the social crisis and gender perspective, women are particularly affected by the pandemic. Given the disadvantaged situation of women socially, economically, and politically, their self-care is diminished. OBJECTIVE: To identify whether there is an association between the classic risk factors for prematurity and fetal growth restriction and the increase in these pathologies in the period March-September 2020, in a maternity hospital that assists women from low resources. MATERIALS AND METHODS: A retrospective study, with a comparative analysis of the periods between 15 March and 30 September 2019 and the same period in 2020. The data were obtained from an electronic clinical database. The prevalence of preterm birth and small-for-gestational age newborn was analyzed. Indicators available in the database that reflect maternal conditions that lead to an unfavorable maternal environment were selected and they were classified into categories. RESULTS: In the period of 2019, 3225 births were registered and in the period of 2020, 3036 births. In the 2019 period, 12.2% of prematurity was evidenced, while in the 2020 period, 14.5% (RR = 1.19, IC 95% = 1.05-1.35, p = .005). In relation to PEG 5.5% in the first period versus 6.9% in the second (RR = 1.26, CI 95% = 1.04-1.53, p = .01). No increases were found in the indicators that are traditionally related to the etiologies proposed to explain the increase in prematurity and small-for-age gestational, there was no evidence of an increase in inflammatory or vascular conditions. CONCLUSION: The economic, psychological and social crises, in the 1st semester of the health emergency, seriously affected the social determinants of the health of pregnant women who use the Public Maternity of reference in Uruguay. This situation is at the base of the poor perinatal results in the period of the maximum mediated mitigation of the pandemic.

Impact of the COVID-19 pandemic on health care activities at a Uruguayan mastology unit.

PURPOSE: Health emergency due to COVID-19 started in Uruguay on March 13, 2020; our mastology unit tried to ensure adequate oncological care, and protect patients from the virus infection and complications. OBJECTIVE: To assess the health care activities in the "peak" of the pandemic during 3 months. MATERIALS AND METHODS: we collected data from the electronic health record. RESULTS: There were a total of 293 medical appointments from 131 patients (221 face-to-face), that decreased by 16.7% compared to the same period in 2019 (352 appointments). The medical appointments were scheduled to evaluate the continuity of systemic treatment or modifications (95 patients; 72.5%), follow-up (17; 12.9%), first-time consultation (12; 9.1%), and assess paraclinical studies (7; 5.3%). The patients were on hormone therapy (81 patients; 74%), chemotherapy (CT) (21; 19%), and anti-HER2 therapies (9; 8%). New twenty treatments were initiated. Of the 14 patients that were on adjuvant/neoadjuvant CT, 9 (64.3%) continued with the same regimen with the addition of prophylactic granulocyte-colony-stimulating factors (G-CSF), and 5 (35.7%), who were receiving weekly paclitaxel, continued the treatment with no changes. Of the seven patients that were on palliative CT, 2 (28.5%) continued the treatment with the addition of G-CSF, 3 (42.8%) continued with weekly capecitabine or paclitaxel with no treatment changes, and 2 (28.5%) changed their treatment regimen (a less myelosuppressive regimen was selected for one and due to progression of the disease in the other patient). The ninety patients who were receiving adjuvant, neoadjuvant, or palliative criteria hormone therapy and/or anti-HER2 therapies, continued the treatment with no changes. CONCLUSIONS: The evidence suggests that, although medical appointments decreased by approximately 17%, we could maintain healthcare activities, continued most of the treatments while the most modified was CT with G-CSF to avoid myelosuppression.

Test positivity - Evaluation of a new metric to assess epidemic dispersal mediated by non-symptomatic cases.

Epidemic control may be hampered when the percentage of asymptomatic cases is high. Seeking remedies for this problem, test positivity was explored between the first 60 to 90 epidemic days in six countries that reported their first COVID-19 case between February and March 2020: Argentina, Bolivia, Chile, Cuba, Mexico, and Uruguay. Test positivity (TP) is the percentage of test-positive individuals reported on a given day out of all individuals tested the same day. To generate both country-specific and multi-country information, this study was implemented in two stages. First, the epidemiologic data of the country infected last (Uruguay) were analyzed. If at least one TP-related analysis yielded a statistically significant relationship, later assessments would investigate the six countries. The Uruguayan data indicated (i) a positive correlation between daily TP and daily new cases (r = 0.75); (ii) a negative correlation between TP and the number of tests conducted per million inhabitants (TPMI, r = -0.66); and (iii) three temporal stages, which differed from one another in both TP and TPMI medians (p < 0.01) and, together, revealed a negative relationship between TPMI and TP. No significant relationship was found between TP and the number of active or recovered patients. The six countries showed a positive correlation between TP and the number of deaths/million inhabitants (DMI, r = 0.65, p < 0.01). With one exception -a country where isolation was not pursued-, all countries showed a negative correlation between TP and TPMI (r = 0.74). The temporal analysis of country-specific policies revealed four patterns, characterized by: (1) low TPMI and high DMI, (2) high TPMI and low DMI; (3) an intermediate pattern, and (4) high TPMI and high DMI. Findings support the hypothesis that test positivity may guide epidemiologic policy-making, provided that policy-related factors are considered and high-resolution geographical data are utilized.

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.

Statistical methods for comparing test positivity rates between countries: Which method should be used and why?

The test positivity (TP) rate has emerged as an important metric for gauging the illness burden due to COVID-19. Given the importance of COVID-19 TP rates for understanding COVID-related morbidity, researchers and clinicians have become increasingly interested in comparing TP rates across countries. The statistical methods for performing such comparisons fall into two general categories: frequentist tests and Bayesian methods. Using data from Our World in Data (ourworldindata.org), we performed comparisons for two prototypical yet disparate pairs of countries: Bolivia versus the United States (large vs. small-to-moderate TP rates), and South Korea vs. Uruguay (two very small TP rates of similar magnitude). Three different statistical procedures were used: two frequentist tests (an asymptotic z-test and the 'N-1' chi-square test), and a Bayesian method for comparing two proportions (TP rates are proportions). Results indicated that for the case of large vs. small-to-moderate TP rates (Bolivia versus the United States), the frequentist and Bayesian approaches both indicated that the two rates were substantially different. When the TP rates were very small and of similar magnitude (values of 0.009 and 0.007 for South Korea and Uruguay, respectively), the frequentist tests indicated a highly significant contrast, despite the apparent trivial amount by which the two rates differ. The Bayesian method, in comparison, suggested that the TP rates were practically equivalent-a finding that seems more consistent with the observed data. When TP rates are highly similar in magnitude, frequentist tests can lead to erroneous interpretations. A Bayesian approach, on the other hand, can help ensure more accurate inferences and thereby avoid potential decision errors that could lead to costly public health and policy-related consequences.

SARS-CoV-2 genomic characterization and clinical manifestation of the COVID-19 outbreak in Uruguay.

COVID-19 is a respiratory illness caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and declared by the World Health Organization a global public health emergency. Among the severe outbreaks across South America, Uruguay has become known for curtailing SARS-CoV-2 exceptionally well. To understand the SARS-CoV-2 introductions, local transmissions, and associations with genomic and clinical parameters in Uruguay, we sequenced the viral genomes of 44 outpatients and inpatients in a private healthcare system in its capital, Montevideo, from March to May 2020. We performed a phylogeographic analysis using sequences from our cohort and other studies that indicate a minimum of 23 independent introductions into Uruguay, resulting in five major transmission clusters. Our data suggest that most introductions resulting in chains of transmission originate from other South American countries, with the earliest seeding of the virus in late February 2020, weeks before the borders were closed to all non-citizens and a partial lockdown implemented. Genetic analyses suggest a dominance of S and G clades (G, GH, GR) that make up >90% of the viral strains in our study. In our cohort, lethal outcome of SARS-CoV-2 infection significantly correlated with arterial hypertension, kidney failure, and ICU admission (FDR < 0.01), but not with any mutation in a structural or non-structural protein, such as the spike D614G mutation. Our study contributes genetic, phylodynamic, and clinical correlation data about the exceptionally well-curbed SARS-CoV-2 outbreak in Uruguay, which furthers the understanding of disease patterns and regional aspects of the pandemic in Latin America.