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  1. Article ; Online: Occurrence of SARS-CoV-2 reinfections at regular intervals in Ecuador.

    Guevara, Rommel / Prado-Vivar, Belén / Márquez, Sully / Muñoz, Erika B / Carvajal, Mateo / Guadalupe, Juan José / Becerra-Wong, Mónica / Proaño, Stefanie / Bayas-Rea, Rosa / Coloma, Josefina / Grunauer, Michelle / Trueba, Gabriel / Rojas-Silva, Patricio / Barragán, Verónica / Cárdenas, Paúl

    Frontiers in cellular and infection microbiology

    2022  Volume 12, Page(s) 951383

    Abstract: SARS-CoV-2 reinfection is defined as a new infection with a different virus variant in an individual who has already recovered from a previous episode of COVID-19. The first case of reinfection in the world was described in August 2020, since then, ... ...

    Abstract SARS-CoV-2 reinfection is defined as a new infection with a different virus variant in an individual who has already recovered from a previous episode of COVID-19. The first case of reinfection in the world was described in August 2020, since then, reinfections have increased over time and their incidence has fluctuated with specific SARS-CoV-2 variant waves. Initially, reinfections were estimated to represent less than 1% of total COVID-19 infections. With the advent of the Omicron variant, reinfections became more frequent, representing up to 10% of cases (based on data from developed countries). The frequency of reinfections in Latin America has been scarcely reported. The current study shows that in Ecuador, the frequency of reinfections has increased 10-fold following the introduction of Omicron, after 22 months of surveillance in a single center of COVID-19 diagnostics. Suspected reinfections were identified retrospectively from a database of RT-qPCR-positive patients. Cases were confirmed by sequencing viral genomes from the first and second infections using the ONT MinION platform. Monthly surveillance showed that the main incidence peaks of reinfections were reached within four to five months, coinciding with the increase of COVID-19 cases in the country, suggesting that the emergence of reinfections is related to higher exposure to the virus during outbreaks. This study performed the longest monitoring of SARS-CoV-2 reinfections, showing an occurrence at regular intervals of 4-5 months and confirming a greater propensity of Omicron to cause reinfections.
    MeSH term(s) COVID-19/diagnosis ; COVID-19/epidemiology ; Ecuador/epidemiology ; Humans ; Reinfection ; Retrospective Studies ; SARS-CoV-2/genetics
    Language English
    Publishing date 2022-09-09
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2619676-1
    ISSN 2235-2988 ; 2235-2988
    ISSN (online) 2235-2988
    ISSN 2235-2988
    DOI 10.3389/fcimb.2022.951383
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: SARS-CoV-2 detection and sequencing in heart tissue associated with myocarditis and persistent arrhythmia: A case report.

    Egas, Diego / Guadalupe, Juan José / Prado-Vivar, Belén / Becerra-Wong, Mónica / Márquez, Sully / Castillo, Stalin / Latta, Johanna / Rodriguez, Francisco / Escorza, Giovanni / Trueba, Gabriel / Grunauer, Michelle / Barragán, Verónica / Rojas-Silva, Patricio / Cárdenas, Paúl

    IDCases

    2021  Volume 25, Page(s) e01187

    Abstract: Background: SARS-CoV-2 uses the human cell receptor angiotensin-converting enzyme (ACE2). ACE2 is widely present in the cardiovascular system including the myocardium and the conduction system. COVID-19 patients that present severe symptoms have been ... ...

    Abstract Background: SARS-CoV-2 uses the human cell receptor angiotensin-converting enzyme (ACE2). ACE2 is widely present in the cardiovascular system including the myocardium and the conduction system. COVID-19 patients that present severe symptoms have been reported to have complications involving myocardial injuries caused by the virus. Here we report the detection of SARS-CoV-2 by whole genome sequencing in the endocardium of a patient with severe bradycardia.
    Case presentation: We report a case of a 34-year-old male patient with COVID-19 tested by PCR, he started with gastrointestinal symptoms, however, he quickly deteriorated his hemodynamic state by means of myocarditis and bradycardia. After performing an endocardium biopsy, it was possible to identify the presence of SARS-CoV-2 in the heart tissue and to sequence its whole genome using the ARTIC-Network protocol and a modified tissue RNA extraction method. The patient's outcome was improved after a permanent pacemaker was implanted.
    Conclusions: It was possible to identify a SARS-CoV-2 clade 20A in the endocardium of the reported patient.
    Language English
    Publishing date 2021-06-11
    Publishing country Netherlands
    Document type Case Reports
    ZDB-ID 2745454-X
    ISSN 2214-2509
    ISSN 2214-2509
    DOI 10.1016/j.idcr.2021.e01187
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Metagenome of a Bronchoalveolar Lavage Fluid Sample from a Confirmed COVID-19 Case in Quito, Ecuador, Obtained Using Oxford Nanopore MinION Technology.

    Márquez, Sully / Prado-Vivar, Belén / Guadalupe, Juan José / Gutierrez, Bernardo / Becerra-Wong, Mónica / Jibaja, Manuel / Tobar, Milton / Barragán, Verónica / Rojas-Silva, Patricio / Coloma, Josefina / Trueba, Gabriel / Grunauer, Michelle / Cárdenas, Paúl

    Microbiology resource announcements

    2020  Volume 9, Issue 41

    Abstract: We report the metagenome analysis of a bronchoalveolar lavage (BAL) fluid sample from a confirmed coronavirus disease 2019 (COVID-19) case in Quito, Ecuador. Sequencing was performed using MinION technology. ...

    Abstract We report the metagenome analysis of a bronchoalveolar lavage (BAL) fluid sample from a confirmed coronavirus disease 2019 (COVID-19) case in Quito, Ecuador. Sequencing was performed using MinION technology.
    Keywords covid19
    Language English
    Publishing date 2020-10-08
    Publishing country United States
    Document type Journal Article
    ISSN 2576-098X
    ISSN (online) 2576-098X
    DOI 10.1128/MRA.00996-20
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: A case of SARS-CoV-2 reinfection in Ecuador.

    Prado-Vivar, Belén / Becerra-Wong, Mónica / Guadalupe, Juan José / Márquez, Sully / Gutierrez, Bernardo / Rojas-Silva, Patricio / Grunauer, Michelle / Trueba, Gabriel / Barragán, Verónica / Cárdenas, Paúl

    The Lancet. Infectious diseases

    2020  Volume 21, Issue 6, Page(s) e142

    MeSH term(s) Antibodies, Viral ; COVID-19/immunology ; COVID-19/virology ; Ecuador ; Humans ; Mutation ; Reinfection ; SARS-CoV-2/genetics ; SARS-CoV-2/immunology
    Chemical Substances Antibodies, Viral
    Language English
    Publishing date 2020-11-23
    Publishing country United States
    Document type Letter
    ZDB-ID 2061641-7
    ISSN 1474-4457 ; 1473-3099
    ISSN (online) 1474-4457
    ISSN 1473-3099
    DOI 10.1016/S1473-3099(20)30910-5
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article: SARS-CoV-2 genome sequencing from COVID-19 in Ecuadorian patients: a whole country analysis.

    Márquez, Sully / Prado-Vivar, Belén / Guadalupe, Juan José / Becerra-Wong, Mónica / Gutierrez, Bernardo / Fernández-Cadena, Juan Carlos / Andrade-Molina, Derly / Morey-Leon, Gabriel / Moncayo, Miguel / Guevara, Rommel / Coloma, Josefina / Trueba, Gabriel / Grunauer, Michelle / Barragán, Verónica / Rojas-Silva, Patricio / Cárdenas, Paúl

    medRxiv : the preprint server for health sciences

    2021  

    Abstract: 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 ... ...

    Abstract 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.
    Language English
    Publishing date 2021-03-24
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2021.03.19.21253620
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Metagenome of a Bronchoalveolar Lavage Fluid Sample from a Confirmed COVID-19 Case in Quito, Ecuador, Obtained Using Oxford Nanopore MinION Technology

    Márquez, Sully / Prado-Vivar, Belén / Guadalupe, Juan José / Gutierrez, Bernardo / Becerra-Wong, Mónica / Jibaja, Manuel / Tobar, Milton / Barragán, Verónica / Rojas-Silva, Patricio / Coloma, Josefina / Trueba, Gabriel / Grunauer, Michelle / Cárdenas, Paúl

    Microbiology Resource Announcements

    2020  Volume 9, Issue 41

    Abstract: ABSTRACT We report the metagenome analysis of a bronchoalveolar lavage (BAL) fluid sample from a confirmed coronavirus disease 2019 (COVID-19) case in Quito, Ecuador. Sequencing was performed using MinION technology. ...

    Abstract ABSTRACT We report the metagenome analysis of a bronchoalveolar lavage (BAL) fluid sample from a confirmed coronavirus disease 2019 (COVID-19) case in Quito, Ecuador. Sequencing was performed using MinION technology.
    Keywords covid19
    Language English
    Publisher American Society for Microbiology
    Publishing country us
    Document type Article ; Online
    ISSN 2576-098X
    DOI 10.1128/mra.00996-20
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article ; Online: COVID-19 Re-Infection by a Phylogenetically Distinct SARS-CoV-2 Variant, First Confirmed Event in South America.

    Prado-Vivar, Belen / Becerra-Wong, Monica / Guadalupe, Juan Jose / Marquez, Sully / Gutierrez, Bernardo / Rojas-Silva, Patricio / Grunauer, Michelle / Trueba, Gabriel / Barragan, Veronica / Cardenas, Paul

    SSRN Electronic Journal ; ISSN 1556-5068

    2020  

    Keywords covid19
    Language English
    Publisher Elsevier BV
    Publishing country us
    Document type Article ; Online
    DOI 10.2139/ssrn.3686174
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  8. Article ; Online: SARS-CoV-2 genome sequencing from COVID-19 in Ecuadorian patients: a whole country analysis.

    Marquez, Sully / Prado-Vivar, Belen / Guadalupe, Juan Jose / Becerra-Wong, Monica / Gutierrez, Bernardo / Clinical COVID-19 Ecuador Consortium / Fernandez-Cadena, Juan Carlos / Andrade-Molina, Derly / Morey, Gabriel / Barragan, Veronica / Rojas-Silva, Patricio / Trueba, Gabriel / Grunauer, Michelle / Cardenas, Paul

    medRxiv

    Abstract: 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 ... ...

    Abstract 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.
    Keywords covid19
    Language English
    Publishing date 2021-03-24
    Publisher Cold Spring Harbor Laboratory Press
    Document type Article ; Online
    DOI 10.1101/2021.03.19.21253620
    Database COVID19

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  9. Article: Genomic epidemiology of SARS-CoV-2 transmission lineages in Ecuador.

    Gutierrez, Bernardo / Márquez, Sully / Prado-Vivar, Belén / Becerra-Wong, Mónica / Guadalupe, Juan José / da Silva Candido, Darlan / Fernandez-Cadena, Juan Carlos / Morey-Leon, Gabriel / Armas-Gonzalez, Rubén / Andrade-Molina, Derly Madeleiny / Bruno, Alfredo / de Mora, Domenica / Olmedo, Maritza / Portugal, Denisse / Gonzalez, Manuel / Orlando, Alberto / Drexler, Jan Felix / Moreira-Soto, Andres / Sander, Anna-Lena /
    Brünink, Sebastian / Kühne, Arne / Patiño, Leandro / Carrazco-Montalvo, Andrés / Mestanza, Orson / Zurita, Jeannete / Sevillano, Gabriela / du Plessis, Louis / McCrone, John T / Coloma, Josefina / Trueba, Gabriel / Barragán, Verónica / Rojas-Silva, Patricio / Grunauer, Michelle / Kraemer, Moritz U G / Faria, Nuno R / Escalera-Zamudio, Marina / Pybus, Oliver G / Cárdenas, Paúl

    medRxiv : the preprint server for health sciences

    2021  

    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 ... ...

    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.
    Language English
    Publishing date 2021-04-05
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2021.03.31.21254685
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article: Genomic epidemiology of SARS-CoV-2 transmission lineages in Ecuador.

    Gutierrez, Bernardo / Márquez, Sully / Prado-Vivar, Belén / Becerra-Wong, Mónica / Guadalupe, Juan José / Candido, Darlan Da Silva / Fernandez-Cadena, Juan Carlos / Morey-Leon, Gabriel / Armas-Gonzalez, Rubén / Andrade-Molina, Derly Madeleiny / Bruno, Alfredo / De Mora, Domenica / Olmedo, Maritza / Portugal, Denisse / Gonzalez, Manuel / Orlando, Alberto / Drexler, Jan Felix / Moreira-Soto, Andres / Sander, Anna-Lena /
    Brünink, Sebastian / Kühne, Arne / Patiño, Leandro / Carrazco-Montalvo, Andrés / Mestanza, Orson / Zurita, Jeannete / Sevillano, Gabriela / Du Plessis, Louis / McCrone, John T / Coloma, Josefina / Trueba, Gabriel / Barragán, Verónica / Rojas-Silva, Patricio / Grunauer, Michelle / Kraemer, Moritz U G / Faria, Nuno R / Escalera-Zamudio, Marina / Pybus, Oliver G / Cárdenas, Paúl

    Virus evolution

    2021  Volume 7, Issue 2, Page(s) veab051

    Abstract: Characterisation of severe acute respiratory syndrome coronavirus-2 (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 ... ...

    Abstract Characterisation of severe acute respiratory syndrome coronavirus-2 (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 coronavirus-19 pandemic. We generated and analysed 160 whole genome sequences sampled from all provinces of Ecuador in 2020. Molecular clock and phylogeographic 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, with differential degrees of persistence and national dissemination.
    Language English
    Publishing date 2021-06-04
    Publishing country England
    Document type Journal Article
    ZDB-ID 2818949-8
    ISSN 2057-1577
    ISSN 2057-1577
    DOI 10.1093/ve/veab051
    Database MEDical Literature Analysis and Retrieval System OnLINE

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