Detection and genome characterisation of SARS-CoV-2 P.6 lineage in dogs and cats living with Uruguayan COVID-19 patients.

BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections in domestic animals have occurred from the beginning of the pandemic to the present time. Therefore, from the perspective of One Health, investigating this topic is of global scientific and public interest. OBJECTIVES: The present study aimed to determine the presence of SARS-CoV-2 in domestic animals whose owners had coronavirus disease 2019 (COVID-19). METHODS: Nasopharyngeal and faecal samples were collected in Uruguay. Using quantitative polymerase chain reaction (qPCR), we analysed the presence of the SARS-CoV-2 genome. Complete genomes were obtained using ARTIC enrichment and Illumina sequencing. Sera samples were used for virus neutralisation assays. FINDINGS: SARS-CoV-2 was detected in an asymptomatic dog and a cat. Viral genomes were identical and belonged to the P.6 Uruguayan SARS-CoV-2 lineage. Only antiserum from the infected cat contained neutralising antibodies against the ancestral SARS-CoV-2 strain and showed cross-reactivity against the Delta but not against the B.A.1 Omicron variant. MAIN CONCLUSIONS: Domestic animals and the human SARS-CoV-2 P.6 variant comparison evidence a close relationship and gene flow between them. Different SARS-CoV-2 lineages infect dogs and cats, and no specific variants are adapted to domestic animals. This first record of SARS-CoV-2 in domestic animals from Uruguay supports regular surveillance of animals close to human hosts.

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.

Analytical sensitivity and clinical performance of "COVID-19 RT-PCR Real TM FAST (CY5) (ATGen, Uruguay) and "ECUGEN SARS-CoV-2 RT-qPCR" (UDLA-STARNEWCORP, Ecuador)": High quality-low cost local SARS-CoV-2 tests for South America.

BACKGROUND: Dozens of commercial RT-qPCR kits for SARS-CoV-2 detection are available with or without Emergency Use Authorization (EUA) by FDA or other regulatory agencies. OBJECTIVE: We evaluated the clinical performance of two SARS-CoV-2 RT-PCR kits designed and produced in South America, "COVID-19 RT-PCR Real TM FAST (CY5)" (ATGen, Uruguay) and "ECUGEN SARS-CoV-2 RT-qPCR" (UDLA-STARNEWCORP, Ecuador), for RT-qPCR SARS-CoV2 detection using "TaqMan 2019-nCoV Assay Kit v1" (Thermofisher, USA) as a gold standard technique. RESULTS: We report a great clinical performance and analytical sensitivity for the two South American kits with sensitivity values of 96.4 and 100%, specificity of 100% and limit of detection in the range of 10 copies/uL of RNA extraction. CONCLUSIONS: "COVID-19 RT-PCR Real TM FAST (CY5)" and "ECUGEN SARS-CoV-2 RT-qPCR" kits are reliable SARS-CoV-2 tests made in South America that have been extensively used in Uruguay, Argentina, Brazil, Bolivia and Ecuador. These locally produced SARS-CoV-2 tests have contributed to overcome supply shortages and reduce diagnosis cost, while maintaining the high quality standards of FDA EUA commercially available kits. This approach could be extended for other diagnostic products to improve infectious diseases surveillance at middle and low income countries beyond COVID-19 pandemic.

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.

The contributions of civil society to food security in the context of COVID-19: a qualitative exploration in Uruguay.

OBJECTIVE: The aim of this study was to explore and analyse the actions implemented by civil society to contribute to food security in the context of the COVID-19 outbreak in Uruguay, a high-income country in South America. DESIGN: An exploratory systematic approach was used to identify the contributions of civil society to food security through reports in news websites and Facebook posts. Data were analysed based on content analysis following a deductive-inductive approach. SETTING: Uruguay, Latin America. RESULTS: A total of 1220 civil society organisations were identified, which developed two main actions to increase access to food among the Uruguayan population: food baskets and 'community pots' (also known as 'common pots'). Most of the initiatives targeted citizens under socioeconomic vulnerability in the face of COVID-19, without specifying any specific requirement or population segment. Actions were mainly led by spontaneously organised community groups, and, to a lesser extent, by consolidated organisations. Interactions between organisations were identified. The foods provided by the organisations were mostly aligned with national dietary guidelines. Social media posts evidenced that the main challenge faced by organisations was related to the lack of funds or supplies. CONCLUSIONS: Results from this work suggest that the lack of funds or supplies poses challenges to the medium- and long-term contributions of civil society to food security and stresses the need for comprehensive governmental measures to guarantee food security amongst Uruguayan citizens.

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.

Emergence and Spread of a B.1.1.28-Derived P.6 Lineage with Q675H and Q677H Spike Mutations in Uruguay.

Uruguay controlled the viral dissemination during the first nine months of the SARS-CoV-2 pandemic. Unfortunately, towards the end of 2020, the number of daily new cases exponentially increased. Herein, we analyzed the country-wide genetic diversity of SARS-CoV-2 between November 2020 and April 2021. We identified that the most prevalent viral variant during the first epidemic wave in Uruguay (December 2020-February 2021) was a B.1.1.28 sublineage carrying Spike mutations Q675H + Q677H, now designated as P.6, followed by lineages P.2 and P.7. P.6 probably arose around November 2020, in Montevideo, Uruguay's capital department, and rapidly spread to other departments, with evidence of further local transmission clusters; it also spread sporadically to the USA and Spain. The more efficient dissemination of lineage P.6 with respect to P.2 and P.7 and the presence of mutations (Q675H and Q677H) in the proximity of the key cleavage site at the S1/S2 boundary suggest that P.6 may be more transmissible than other lineages co-circulating in Uruguay. Although P.6 was replaced by the variant of concern (VOC) P.1 as the predominant lineage in Uruguay since April 2021, the monitoring of the concurrent emergence of Q675H + Q677H in VOCs should be of worldwide interest.

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.

Disjoint and Functional Principal Component Analysis for Infected Cases and Deaths Due to COVID-19 in South American Countries with Sensor-Related Data.

In this paper, we group South American countries based on the number of infected cases and deaths due to COVID-19. The countries considered are: Argentina, Bolivia, Brazil, Chile, Colombia, Ecuador, Peru, Paraguay, Uruguay, and Venezuela. The data used are collected from a database of Johns Hopkins University, an institution that is dedicated to sensing and monitoring the evolution of the COVID-19 pandemic. A statistical analysis, based on principal components with modern and recent techniques, is conducted. Initially, utilizing the correlation matrix, standard components and varimax rotations are calculated. Then, by using disjoint components and functional components, the countries are grouped. An algorithm that allows us to keep the principal component analysis updated with a sensor in the data warehouse is designed. As reported in the conclusions, this grouping changes depending on the number of components considered, the type of principal component (standard, disjoint or functional) and the variable to be considered (infected cases or deaths). The results obtained are compared to the k-means technique. The COVID-19 cases and their deaths vary in the different countries due to diverse reasons, as reported in the conclusions.

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 blues: Lockdowns and mental health-related google searches in Latin America.

RATIONALE: Stress process theory considers that actual and perceived isolation, caused by mobility restrictions from attempted containment of the COVID-19 pandemic, deteriorates mental health. OBJECTIVE: We examine the relationship between the COVID-19 lockdowns and mental health-related Google searches in 11 Latin American countries. We include the following countries: Argentina, Bolivia, Chile, Colombia, Ecuador, Guatemala, Honduras, Mexico, Paraguay, Peru, and Uruguay. We also explore how changes in search patterns relate to income support policies and to COVID-19 death rates. METHOD: Using Google Trends data and an event-study design, as well as a difference-in-differences analysis, we investigate the association between country specific stay-at-home orders and internet searches including the following words: insomnia, stress, anxiety, sadness, depression, and suicide. RESULTS: We find three main patterns. First, searches for insomnia peak but then decline. Second, searches for stress, anxiety, and sadness increase and remain high throughout the lockdown. Third, there is no substantial change in depression-related or suicide-related searches after the lockdown. In terms of potential mechanisms, our results suggest that searches declined for suicide and insomnia following the passage of each country's income support, while in countries with higher COVID-19-related death rates, searches for insomnia, stress, and anxiety increased by more. CONCLUSIONS: Our results suggest that, in Latin America, Google searches for words associated with mild mental health disorders increased during the COVID-19 stay-at-home orders. Nonetheless, these conclusions should not be construed as a general population mental health deterioration, as we cannot verify that search indicators are accurately related to the users' current feelings and behaviors, and as internet users may not be representative of the population in this region.