ABSTRACT
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.
Subject(s)
COVID-19ABSTRACT
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.
Subject(s)
COVID-19ABSTRACT
The permanence of rt-PCR positivity after a long time in COVID-19 patients has prompted the question of whether SARS-CoV-2 could cause a persistent infection or patients can become re-infected by this virus. Both possibilities could have critical implications for the management and control of COVID-19. Here we present the first confirmed case of SARS-CoV-2 reinfection in Ecuador and South America. Materials and methods: Our diagnostic laboratory detected a potential re-infection in one patient who was SARS-COv2 rt-PCR positive twice (in May and July 2020). The first laboratory-confirmed infection presented with mild symptoms and full recovery, reaffirmed by a negative RT-PCR test result obtained two weeks after symptom onset. More severe COVID-19-like symptoms presented again four weeks after the first event, and a third RT-PCR test was performed which resulted positive. The total RNA extraction (from the samples collected on both occasions) was sequenced in an Oxford Nanopore MinION using a tilling PCR protocol developed by the ARTIC-Network, and the reads were analyzed using the artic-medaka consensus generation tool. Anti SARS-CoV-2 IgM and IgG antibodies were investigated. Results: different SARS-CoV-2 variants were identified in each infection event. For the first infection, the genome was assigned to the B1.p9 GISAID clade while the variant associated with the second episode was assigned to the A.1.1 GISAID clade. High levels of both SARS-CoV-2 specific IgM and IgG were observed during the second event.Discussion: a patient with two COVID-19 events presented two different SARS-CoV-2 variants on each event, confirming reinfection. This phenomenon is still considered rare.
Subject(s)
COVID-19ABSTRACT
SARS-CoV-2, the etiological agent of COVID-19 was first described in Wuhan in December 2019 and has now spread globally. Ecuador was the second country in South America to report confirmed cases. The first case reported in Quito, the capital city of Ecuador, was a tourist who came from the Netherlands and presented symptoms on March 10th, 2020 (index case). In this work we used the MinION platform (Oxford Nanopore Technologies) to sequence the metagenome of the bronchoalveolar lavage (BAL) from this case reported, and subsequently we sequenced the whole genome of the index case and other three patients using the ARTIC network protocols. Our data from the metagenomic approach confirmed the presence of SARS-CoV-2 coexisting with pathogenic bacteria suggesting coinfection. Relevant bacteria found in the BAL metagenome were Streptococcus pneumoniae, Mycobacterium tuberculosis, Staphylococcus aureus and Chlamydia spp. Lineage assignment of the four whole genomes revealed three different origins. The variant HEE-01 was imported from the Netherlands and was assigned to B lineage, HGSQ-USFQ-018, belongs to the B.1 lineage showing nine nucleotide differences with the reference strain and grouped with sequences from the United Kingdom, and HGSQ-USFQ-007 and HGSQ-USFQ-010 belong to the B lineage and grouped with sequences from Scotland. All genomes show mutations in their genomes compared to the reference strain, which could be important to understand the virulence, severity and transmissibility of the virus. Our findings also suggest that there were at least three independent introductions of SARS-CoV-2 to Ecuador.
Subject(s)
COVID-19 , TuberculosisABSTRACT
ObjectiveThis living systematic review aims to provide a timely, rigorous and continuously updated summary of the available evidence on the role of cell-based therapies in the treatment of patients with COVID-19. Data sourcesWe conducted searches in PubMed/Medline, Embase, Cochrane Central Register of Controlled Trials (CENTRAL), grey literature and in a centralised repository in L-OVE (Living OVerview of Evidence). L-OVE is a platform that maps PICO questions to evidence from Epistemonikos database. In response to the COVID-19 emergency, L-OVE was adapted to expand the range of evidence it covers and customised to group all COVID-19 evidence in one place. All the searches covered the period until April 23, 2020 (one day before submission). Eligibility criteria for selecting studies and methodsWe adapted an already published common protocol for multiple parallel systematic reviews to the specificities of this question. We searched for randomised trials evaluating the effect of cell-based therapies versus placebo or no treatment in patients with COVID-19. Anticipating the lack of randomised trials directly addressing this question, we also searched for trials evaluating other coronavirus infections, such as MERS-CoV and SARS-CoV, and non-randomised studies in COVID-19. Two reviewers independently screened each study for eligibility. A living, web-based version of this review will be openly available during the COVID-19 pandemic. We will resubmit it every time the conclusions change or whenever there are substantial updates. ResultsWe screened 1,043 records but no study was considered eligible. We identified 61 ongoing studies, including 39 randomised trials evaluating different types of cell-based therapies in COVID-19. ConclusionsWe did not find any studies that met our inclusion criteria and hence there is no evidence to support or refute the use of cell-based therapies in the treatment of patients with COVID-19. A substantial number of ongoing studies should provide valuable evidence to inform researchers and decision makers in the near future. PROSPERO Registration numberCRD42020179711 O_TEXTBOXO_TEXTBOXNOBox 1C_TEXTBOXNO Linked resources in this Living Systematic Review Common protocolCommon protocol for the systematic reviews and overviews of systematic reviews being conducted by the COVID-19 L{middle dot}OVE Working Group. Available here Living reviewWeb version of this systematic review, presented in a living systematic review format. This means it is continuously updated as soon as new evidence emerges. Available here Living OVerview of Evidence - L{middle dot}OVEAn open platform that uses artificial intelligence and a broad network of contributors to identify all of the evidence relevant to this and other healthcare questions, including those related to COVID-19. Available here C_TEXTBOX
Subject(s)
COVID-19ABSTRACT
OBJECTIVE: To determine the impact of mesenchymal stromal cells outcomes important to patients with COVID-19. DESIGN: This is the protocol of a living systematic review. DATA SOURCES: We will conduct searches in PubMed/Medline, Embase, Cochrane Central Register of Controlled Trials (CENTRAL), grey literature and in a centralised repository in L-OVE (Living OVerview of Evidence). L-OVE is a platform that maps PICO questions to evidence from Epistemonikos database. In response to the COVID-19 emergency, L-OVE was adapted to expand the range of evidence it covers and customised to group all COVID-19 evidence in one place. The search will cover the period until the day before submission to a journal. ELIGIBILITY CRITERIA FOR SELECTING STUDIES AND METHODS: We adapted an already published common protocol for multiple parallel systematic reviews to the specificities of this question. We will include randomised trials evaluating the effect of mesenchymal stromal cells versus placebo or no treatment in patients with COVID-19. Randomised trials evaluating other coronavirus infections, such as MERS-CoV and SARS-CoV, and non-randomised studies in COVID-19 will be searched in case we find no direct evidence from randomised trials, or if the direct evidence provides low- or very low-certainty for critical outcomes. Two reviewers will independently screen each study for eligibility, extract data, and assess the risk of bias. We will pool the results using meta-analysis and will apply the GRADE system to assess the certainty of the evidence for each outcome. A living, web-based version of this review will be openly available during the COVID-19 pandemic. We will resubmit it every time the conclusions change or whenever there are substantial updates. ETHICS AND DISSEMINATION: No ethics approval is considered necessary. The results of this review will be widely disseminated via peer-reviewed publications, social networks and traditional media. PROSPERO Registration Submitted to PROSPERO (awaiting ID allocation).