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1.
PLoS One ; 17(2): e0263563, 2022.
Article in English | MEDLINE | ID: covidwho-1793526

ABSTRACT

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.


Subject(s)
COVID-19/virology , Cell Lineage , Gene Deletion , Genome, Viral , Open Reading Frames/genetics , SARS-CoV-2/genetics , Viral Proteins/genetics , Adult , Aged , COVID-19/epidemiology , COVID-19/genetics , Child , Female , High-Throughput Nucleotide Sequencing , Humans , Male , Middle Aged , Phylogeny , SARS-CoV-2/classification , SARS-CoV-2/isolation & purification , Uruguay/epidemiology
2.
Transbound Emerg Dis ; 68(6): 3075-3082, 2021 Nov.
Article in English | MEDLINE | ID: covidwho-1526429

ABSTRACT

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.


Subject(s)
COVID-19 , SARS-CoV-2 , Sequence Deletion , COVID-19/virology , Disease Outbreaks , Genome, Viral , Humans , Phylogeny , SARS-CoV-2/genetics , Uruguay/epidemiology
3.
Int J Environ Res Public Health ; 18(19)2021 Sep 23.
Article in English | MEDLINE | ID: covidwho-1438596

ABSTRACT

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.


Subject(s)
COVID-19 , Pandemics , Humans , Latin America/epidemiology , Pandemics/prevention & control , SARS-CoV-2 , Uruguay/epidemiology
4.
MEDICC Rev ; 23(3-4): 65-73, 2021.
Article in English | MEDLINE | ID: covidwho-1399829

ABSTRACT

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.


Subject(s)
COVID-19 , Epidemics , Cuba/epidemiology , Humans , Latin America , SARS-CoV-2 , Uruguay/epidemiology
5.
Emerg Infect Dis ; 27(11): 2957-2960, 2021 Nov.
Article in English | MEDLINE | ID: covidwho-1374226

ABSTRACT

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.


Subject(s)
COVID-19 , SARS-CoV-2 , Genomics , Humans , Uruguay/epidemiology
6.
Appetite ; 167: 105651, 2021 12 01.
Article in English | MEDLINE | ID: covidwho-1356129

ABSTRACT

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.


Subject(s)
COVID-19 , Pandemics , Cross-Sectional Studies , Diet, Healthy , Feeding Behavior , Humans , SARS-CoV-2 , Surveys and Questionnaires , Uruguay/epidemiology
8.
J Cancer Res Ther ; 17(2): 547-550, 2021.
Article in English | MEDLINE | ID: covidwho-1268381

ABSTRACT

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.


Subject(s)
Breast Neoplasms/drug therapy , COVID-19/epidemiology , Continuity of Patient Care/statistics & numerical data , Delivery of Health Care/statistics & numerical data , Medical Oncology/statistics & numerical data , Adult , Aged , Aged, 80 and over , Antineoplastic Combined Chemotherapy Protocols/adverse effects , Bone Marrow/drug effects , Breast Neoplasms/complications , Breast Neoplasms/diagnosis , Breast Neoplasms/immunology , COVID-19/immunology , COVID-19/prevention & control , COVID-19/transmission , Communicable Disease Control/standards , Continuity of Patient Care/organization & administration , Delivery of Health Care/organization & administration , Delivery of Health Care/standards , Electronic Health Records/statistics & numerical data , Female , Granulocyte Colony-Stimulating Factor/administration & dosage , Hematopoiesis/drug effects , Hematopoiesis/immunology , Humans , Medical Oncology/organization & administration , Medical Oncology/standards , Middle Aged , Pandemics/prevention & control , Referral and Consultation/standards , Referral and Consultation/statistics & numerical data , Retrospective Studies , Telemedicine/organization & administration , Telemedicine/standards , Telemedicine/statistics & numerical data , Triage/organization & administration , Triage/standards , Uruguay/epidemiology
9.
Methods ; 195: 15-22, 2021 11.
Article in English | MEDLINE | ID: covidwho-1243244

ABSTRACT

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.


Subject(s)
Asymptomatic Infections/epidemiology , COVID-19 Testing/methods , COVID-19 Testing/standards , COVID-19/diagnosis , COVID-19/epidemiology , Argentina/epidemiology , Bolivia/epidemiology , COVID-19/prevention & control , COVID-19 Testing/trends , Chile/epidemiology , Cuba/epidemiology , Epidemics/prevention & control , Humans , Mexico/epidemiology , Mortality/trends , Uruguay/epidemiology
10.
Methods ; 195: 72-76, 2021 11.
Article in English | MEDLINE | ID: covidwho-1142318

ABSTRACT

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.


Subject(s)
COVID-19 Testing/statistics & numerical data , COVID-19 Testing/trends , COVID-19/epidemiology , Data Interpretation, Statistical , Research Design/statistics & numerical data , Research Design/trends , Bayes Theorem , Bolivia/epidemiology , COVID-19/diagnosis , Humans , Republic of Korea/epidemiology , United States/epidemiology , Uruguay/epidemiology
11.
Emerg Microbes Infect ; 10(1): 51-65, 2021 Dec.
Article in English | MEDLINE | ID: covidwho-1066197

ABSTRACT

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.


Subject(s)
COVID-19/complications , Mutation , SARS-CoV-2/genetics , Adolescent , Adult , Aged , Aged, 80 and over , COVID-19/epidemiology , COVID-19/virology , Disease Outbreaks , Female , Humans , Male , Middle Aged , Phylogeny , Polymorphism, Single Nucleotide , SARS-CoV-2/classification , SARS-CoV-2/isolation & purification , Uruguay/epidemiology , Young Adult
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