Résumé
The Omicron variant of SARS-CoV-2 is the latest pandemic lineage causing COVID-19. Despite having a vaccination rate ≥ 85% Ecuador recorded a high incidence of Omicron from December 2021 to March 2022. Since Omicron emerged it is evolving into multiple sublineages with distinct prevalence in different regions. In this work, we use all Omicron sequences from Ecuador available at GISAID until March 2022 and the software Nextclade and Pangolin to identify which lineages circulate in this country. We detected 12 different sublineages (BA.1, BA.1.1, BA.1.1.1, BA.1.1.14, BA.1.1.2, BA.1.14, BA.1.15, BA.1.16, BA.1.17, BA.1.6, BA.2, BA.2.3), which has been reported in Africa, America, Europe, and Asia suggesting multiple introduction events. Sublineages BA.1.1 and BA.1 were the most prevalent. Genomic surveillance must continue to evaluate the dynamic of current sublineages, early introduction of new ones and vaccine efficacy against evolving SARS-CoV-2.
Sujets)
COVID-19Résumé
behavior with health campaigns. We examine Guayaquil, Ecuador which was hit particularly hard in the first few months of the pandemic. As lockdowns and social distancing led families to rely on others to secure food or medical assistance, perceptions on trust and the dynamics of social capital during the initial (and worst) months of the pandemic were particularly important. Methods: : This paper uses a unique dataset of people receiving a COVID test after suspicion of infection. People in our dataset were active during the height of the pandemic and faced the possibility of needing to rely on others in the case of testing positive. We use regression analysis to study the relation between compliance with mobility restrictions and institutional and relational trust. Results: : We find that trusting that close relations (such as family) will be there for you in the case of falling ill is associated with a significant increase in the probability of complying with health campaigns. Additionally, we find that trust in the government has a weak relationship to compliance. However, compliance decreases when examining increased trust in the police but increases with trust in the military. Conclusions: : The findings show that enhancing trust may improve compliance with social distancing measures. However, increasing trust in specific groups could have negative consequences. Importantly, compliance could be increased by emphasizing in campaigns that your behavior could influence the health of those who you care about.
Sujets)
COVID-19Résumé
Characterisation of SARS-CoV-2 genetic diversity through space and time can reveal trends in virus importation and domestic circulation, and permit the exploration of questions regarding the early transmission dynamics. Here we present a detailed description of SARS-CoV-2 genomic epidemiology in Ecuador, one of the hardest hit countries during the early stages of the COVID-19 pandemic. We generate and analyse 160 whole genome sequences sampled from all provinces of Ecuador in 2020. Molecular clock and phylgeographic analysis of these sequences in the context of global SARS-CoV-2 diversity enable us to identify and characterise individual transmission lineages within Ecuador, explore their spatiotemporal distributions, and consider their introduction and domestic circulation. Our results reveal a pattern of multiple international importations across the country, with apparent differences between key provinces. Transmission lineages were mostly introduced before the implementation of non-pharmaceutical interventions (NPIs), with differential degrees of persistence and national dissemination.
Sujets)
COVID-19Résumé
SARS-CoV-2, the etiological agent of COVID-19, was first described in Wuhan, China in December 2019 and has now spread globally. Ecuador was the second country in South America to confirm cases and Guayaquil was one of the first cities in the world to experience high mortality due to COVID-19. The aim of this study was to describe the lineages circulating throughout the country and to compare the mutations in local variants, to the reference strain. In this work we used the MinION platform (Oxford Nanopore Technologies) to sequence the whole SARS-CoV-2 genomes of 119 patients from all provinces of Ecuador, using the ARTIC network protocols. Our data from lineage assignment of the one hundred and nineteen whole genomes revealed twenty different lineages. All genomes presented differences in the S gene compared to the Wuhan reference strain, being the D614G amino acid replacement the most common change. The B.1.1.119 lineage was the most frequent and was found in several locations in the Coast and Andean region. Three sequences were assigned to the new B.1.1.7 lineage. Our work is an important contribution to the understanding of the epidemiology of SARS- CoV-2 in Ecuador and South America.