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Aya Pastrana N, Agudelo-Londoño S, Franco-Suarez O, Otero Machuca J, Guzman-Tordecilla DN, López Sánchez MC, Rodriguez-Patarroyo M, Rivera-Sánchez CA, Castro-Barbudo D, Trujillo AJ, Maniar V, Vecino-Ortiz AI. Improving COVID-19 vaccine uptake: a message co-design process for a national mHealth intervention in Colombia. Glob Health Action 2023; 16:2242670. [PMID: 37643136 PMCID: PMC10467523 DOI: 10.1080/16549716.2023.2242670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 07/23/2023] [Indexed: 08/31/2023] Open
Abstract
BACKGROUND COVID-19 vaccination is a global priority. Latin American countries have some of the highest COVID-19 death rates worldwide with vaccination hampered by a variety of reasons, including mis- and disinformation, vaccine hesitancy, and vaccine supply constraints. Addressing vaccine hesitancy through effective messages has been found to help increase vaccine uptake. Participatory processes could be used to co-design health messages for this purpose. OBJECTIVE This article describes the methodology used to co-design evidence-based audio messages to be deployed in a cohort of individuals through an interactive voice response (IVR) mobile phone survey intervention, aimed towards increasing vaccination uptake in an adult population in Colombia. METHODS Participants of the COVID-19 vaccination message co-design process included a sample of the general population of the country, representatives of the funder organisation, and research team members. The co-design process consisted of four phases: (1) formative quantitative and qualitative research, (2) message drafting based on the results of the formative research, (3) message content evaluation, and (4) evaluation of the voices to deliver the audio messages; and was informed by reflexive meetings. RESULTS Three categories of evidence-based audio messages were co-designed, each corresponding to an arm of the mHealth intervention: (1) factual messages, (2) narrative messages, and (3) mixed messages. An additional fourth arm with no message was proposed for control. The iterative co-design process ended with a total of 14 audio messages recorded to be deployed via the intervention. CONCLUSIONS Co-developing health messages in response to health emergencies is possible. Adopting more context-relevant, participatory, people-centred, and reflexive multidisciplinary approaches could help develop solutions that are more responsive to the needs of populations and public health priorities. Investing resources in message co-design is deemed to have a greater potential for influencing behaviours and improving health outcomes.
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Affiliation(s)
- Nathaly Aya Pastrana
- IMEK Centro de Investigación en Mercadeo & Desarrollo, Santiago de Cali, Colombia
- Instituto de Salud Pública, Pontificia Universidad Javeriana, Bogotá, Colombia
| | | | - Oscar Franco-Suarez
- Instituto de Salud Pública, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Jessica Otero Machuca
- Instituto de Salud Pública, Pontificia Universidad Javeriana, Bogotá, Colombia
- Health Behavior, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | | | | | | | | | - Antonio J. Trujillo
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Vidhi Maniar
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Andres I. Vecino-Ortiz
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
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2
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Álvarez-Díaz DA, Ruiz-Moreno HA, Zapata-Bedoya S, Franco-Muñoz C, Laiton-Donato K, Ferro C, Sepulveda MTH, Pacheco-Montealegre M, Walteros DM, Carrero-Galindo LC, Mercado-Reyes M. Clinical outcomes associated with Mu variant infection during the third epidemic peak of COVID-19 in Colombia. Int J Infect Dis 2022; 125:149-152. [PMID: 36332905 PMCID: PMC9625851 DOI: 10.1016/j.ijid.2022.10.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 10/07/2022] [Accepted: 10/18/2022] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND The higher number of cases and deaths caused by COVID-19 in Colombia occurred during the third epidemic peak, where the Mu variant was associated with 50% of the cases. OBJECTIVE To evaluate the association between the clinical outcome of COVID-19 with health conditions and SARS-CoV-2 lineages. METHODS In this study, clinical metadata and SARS-CoV-2 lineages from 535 patients with different degrees of COVID-19 severity were obtained after the SARS-CoV-2 genomic surveillance in Colombia. Then, the associations between these variables were determined using a multidimensional unfolding analysis. RESULTS Asymptomatic, symptomatic, severe, and deceased outcomes represented 15.2%, 29.7%, 7.3%, and 47.8% of the cases, respectively. Males tend to develop more serious COVID-19, and severe or fatal outcomes were typically observed in patients aged >60 years with comorbidities, including chronic obstructive pulmonary disease, heart disease, kidney disease, obesity, asthma, and smoking history. The SARS-CoV-2 Mu and Gamma variants dominated the third epidemic peak and accounted for most fatal cases with odd ratio values of 128.2 (CI 53.0-310.1) and 18.6 (CI 8.294-41.917). CONCLUSION This study shows the high impact of SARS-CoV-2 lineages with higher prevalence on public health and the importance of monitoring COVID-19 risk factors to control the associated mortality.
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Affiliation(s)
- Diego A Álvarez-Díaz
- Genómica de Microorganismos Emergentes. Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá, Colombia.
| | - Hector A Ruiz-Moreno
- Genómica de Microorganismos Emergentes. Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá, Colombia
| | - Silvana Zapata-Bedoya
- Genómica de Microorganismos Emergentes. Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá, Colombia
| | - Carlos Franco-Muñoz
- Genómica de Microorganismos Emergentes. Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá, Colombia; Grupo de Parasitología. Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá, Colombia
| | - Katherine Laiton-Donato
- Genómica de Microorganismos Emergentes. Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá, Colombia
| | - Carolina Ferro
- Dirección de Vigilancia y Análisis del Riesgo en Salud Pública, Instituto Nacional de Salud, Bogotá, Colombia
| | - Maria T Herrera Sepulveda
- Genómica de Microorganismos Emergentes. Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá, Colombia
| | - Mauricio Pacheco-Montealegre
- Genómica de Microorganismos Emergentes. Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá, Colombia
| | - Diana M Walteros
- Dirección de Vigilancia y Análisis del Riesgo en Salud Pública, Instituto Nacional de Salud, Bogotá, Colombia
| | | | - Marcela Mercado-Reyes
- Genómica de Microorganismos Emergentes. Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá, Colombia; Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá, Colombia
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3
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Wang X, Stelzer-Braid S, Scotch M, Rawlinson WD. Detection of respiratory viruses directly from clinical samples using next-generation sequencing: A literature review of recent advances and potential for routine clinical use. Rev Med Virol 2022; 32:e2375. [PMID: 35775736 PMCID: PMC9539958 DOI: 10.1002/rmv.2375] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 06/01/2022] [Accepted: 06/20/2022] [Indexed: 11/15/2022]
Abstract
Acute respiratory infection is the third most frequent cause of mortality worldwide, causing over 4.25 million deaths annually. Although most diagnosed acute respiratory infections are thought to be of viral origin, the aetiology often remains unclear. The advent of next‐generation sequencing (NGS) has revolutionised the field of virus discovery and identification, particularly in the detection of unknown respiratory viruses. We systematically reviewed the application of NGS technologies for detecting respiratory viruses from clinical samples and outline potential barriers to the routine clinical introduction of NGS. The five databases searched for studies published in English from 01 January 2010 to 01 February 2021, which led to the inclusion of 52 studies. A total of 14 different models of NGS platforms were summarised from included studies. Among these models, second‐generation sequencing platforms (e.g., Illumina sequencers) were used in the majority of studies (41/52, 79%). Moreover, NGS platforms have proven successful in detecting a variety of respiratory viruses, including influenza A/B viruses (9/52, 17%), SARS‐CoV‐2 (21/52, 40%), parainfluenza virus (3/52, 6%), respiratory syncytial virus (1/52, 2%), human metapneumovirus (2/52, 4%), or a viral panel including other respiratory viruses (16/52, 31%). The review of NGS technologies used in previous studies indicates the advantages of NGS technologies in novel virus detection, virus typing, mutation identification, and infection cluster assessment. Although there remain some technical and ethical challenges associated with NGS use in clinical laboratories, NGS is a promising future tool to improve understanding of respiratory viruses and provide a more accurate diagnosis with simultaneous virus characterisation.
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Affiliation(s)
- Xinye Wang
- Virology Research Laboratory, Serology and Virology Division (SAViD), NSW Health Pathology, Prince of Wales Hospital, University of New South Wales, Sydney, New South Wales, Australia.,School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
| | - Sacha Stelzer-Braid
- Virology Research Laboratory, Serology and Virology Division (SAViD), NSW Health Pathology, Prince of Wales Hospital, University of New South Wales, Sydney, New South Wales, Australia.,School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
| | - Matthew Scotch
- Kirby Institute, University of New South Wales, Sydney, New South Wales, Australia.,Biodesign Center for Environmental Health Engineering, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - William D Rawlinson
- Virology Research Laboratory, Serology and Virology Division (SAViD), NSW Health Pathology, Prince of Wales Hospital, University of New South Wales, Sydney, New South Wales, Australia.,School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
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4
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Ospina J, Hincapié-Palacio D, Ochoa J, Velásquez C, Almanza Payares R. Monitoring COVID-19 in Colombia during the first year of the pandemic. J Public Health Res 2022; 11:22799036221115770. [PMID: 36052098 PMCID: PMC9425916 DOI: 10.1177/22799036221115770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 07/09/2022] [Indexed: 11/16/2022] Open
Abstract
Background: COVID-19 cases in Medellín, the second largest city in Colombia, were monitored during the first year of the pandemic using both mathematical models based on transmission theory and surveillance from each observed epidemic phase. Design and Methods: Expected cases were estimated using mandatory reporting data from Colombia’s national epidemiological surveillance system from March 7, 2020 to March 7, 2021. Initially, the range of daily expected cases was estimated using a Borel-Tanner stochastic model and a deterministic Susceptible-Infected-Removed (SIR) model. A subsequent expanded version of the SIR model was used to include asymptomatic cases, severe cases and deaths. The moving average, standard deviation, and goodness of fit of estimated cases relative to confirmed reported cases were assessed, and local transmission in Medellin was contrasted with national transmission in Colombia. Results: The initial phase was characterized by imported case detection and the later phase by community transmission and increases in case magnitude and severity. In the initial phase, a maximum range of expected cases was obtained based on the stochastic model, which even accounted for the reduction of new imported cases following the closure of international airports. The deterministic estimate achieved an adequate fit with respect to accumulated cases until the conclusion of the mandatory national quarantine and gradual reopening, when reported cases increased. The estimated new cases were reasonably fit with the maximum reported incidence. Conclusion: Adequate model fit was obtained with the reported data. This experience of monitoring epidemic trajectory can be extended using models adapted to local conditions.
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Affiliation(s)
- Juan Ospina
- Logic and Computing Group, School of Sciences, Eafit University, Medellín, Colombia
| | - Doracelly Hincapié-Palacio
- Theoretical Epidemiology, Epidemiology Group, University of Antioquia, "Héctor Abad Gomez" National Faculty of Public Health, Universidad de Antioquia, Medellín, Colombia
| | - Jesús Ochoa
- Theoretical Epidemiology, Epidemiology Group, University of Antioquia, "Héctor Abad Gomez" National Faculty of Public Health, Universidad de Antioquia, Medellín, Colombia
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García-Garro PA, Aibar-Almazán A, Rivas-Campo Y, Vega-Ávila GC, Afanador-Restrepo DF, Martínez-Amat A, Afanador-Rodríguez MI, Hita-Contreras F. Factors Associated with the Level of Physical Activity in Middle-Aged Colombian People during Lockdown in Response to COVID-19: A Cross-Sectional Study. Healthcare (Basel) 2022; 10:healthcare10061050. [PMID: 35742101 PMCID: PMC9223190 DOI: 10.3390/healthcare10061050] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 05/27/2022] [Accepted: 06/02/2022] [Indexed: 02/06/2023] Open
Abstract
(1) Background: Due to the pandemic caused by COVID-19, mandatory confinement was declared, which generated a decrease in the practice of physical activity (PA). Based on this problem, it was proposed to study the associations between PA in relation to depressive symptoms, quality of sleep, and the quality of life of middle-aged people who work in the university context during compulsory confinement as a result of COVID-19. (2) Methods: A total of 336 middle-aged people (48 ± 6.67) participated in this analytical cross-sectional study. The variable levels of PA, quality of sleep, symptoms of depression, and quality of life were measured with the International Physical Activity Questionary (IPAQ), the Pittsburgh Sleep Quality Index (PSQI), the Zung Self-Rating Depression Scale (ZSDS), and the SF-12v2 questionnaire, respectively. (3) Results: A logistic regression model was used to analyze the relationships between the level of PA and depressive symptoms (OR = 2.053), total sleep duration (OR = 0.495), sleep disturbances (OR = 2.414), quality of sleep (OR = 2.471), use of sleep medication (OR = 0.348), daytime dysfunction (OR = 1.809), general health (OR = 0.949), and physical functioning (OR = 0.987). (4) Conclusions: In middle-aged people, during compulsory confinement, being insufficiently active is a risk for depressive symptoms and disturbances in sleep quality.
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Affiliation(s)
- Patricia Alexandra García-Garro
- GIP Pedagogy Research Group, Faculty of Distance and Virtual Education, Antonio José Camacho University Institution, Santiago de Cali 760016, Colombia; (P.A.G.-G.); (Y.R.-C.); (G.C.V.-Á.); (D.F.A.-R.); (M.I.A.-R.)
| | - Agustín Aibar-Almazán
- Department of Health Sciences, Faculty of Health Sciences, University of Jaén, 23071 Jaén, Spain; (A.M.-A.); (F.H.-C.)
- Correspondence:
| | - Yulieth Rivas-Campo
- GIP Pedagogy Research Group, Faculty of Distance and Virtual Education, Antonio José Camacho University Institution, Santiago de Cali 760016, Colombia; (P.A.G.-G.); (Y.R.-C.); (G.C.V.-Á.); (D.F.A.-R.); (M.I.A.-R.)
| | - Gloria Cecilia Vega-Ávila
- GIP Pedagogy Research Group, Faculty of Distance and Virtual Education, Antonio José Camacho University Institution, Santiago de Cali 760016, Colombia; (P.A.G.-G.); (Y.R.-C.); (G.C.V.-Á.); (D.F.A.-R.); (M.I.A.-R.)
| | - Diego Fernando Afanador-Restrepo
- GIP Pedagogy Research Group, Faculty of Distance and Virtual Education, Antonio José Camacho University Institution, Santiago de Cali 760016, Colombia; (P.A.G.-G.); (Y.R.-C.); (G.C.V.-Á.); (D.F.A.-R.); (M.I.A.-R.)
| | - Antonio Martínez-Amat
- Department of Health Sciences, Faculty of Health Sciences, University of Jaén, 23071 Jaén, Spain; (A.M.-A.); (F.H.-C.)
| | - María Isabel Afanador-Rodríguez
- GIP Pedagogy Research Group, Faculty of Distance and Virtual Education, Antonio José Camacho University Institution, Santiago de Cali 760016, Colombia; (P.A.G.-G.); (Y.R.-C.); (G.C.V.-Á.); (D.F.A.-R.); (M.I.A.-R.)
| | - Fidel Hita-Contreras
- Department of Health Sciences, Faculty of Health Sciences, University of Jaén, 23071 Jaén, Spain; (A.M.-A.); (F.H.-C.)
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Ortiz-Pineda PA, Sierra-Torres CH. Evolutionary Traits and Genomic Surveillance of SARS-CoV-2 in South America. Glob Health Epidemiol Genom 2022; 2022:8551576. [PMID: 35655960 PMCID: PMC9132712 DOI: 10.1155/2022/8551576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 03/12/2022] [Accepted: 04/24/2022] [Indexed: 11/18/2022] Open
Abstract
Since the zoonotic event from which SARS-CoV-2 started infecting humans late in 2019, the virus has caused more than 5 million deaths and has infected over 500 million people around the world. The pandemic has had a severe impact on social and economic activities, with greater repercussions in low-income countries. South America, with almost 5% of the world's population, has reckoned with almost a fifth of the total people infected and more than 26% (>1/4) of the deceased. Fortunately, the full genome structure and sequence of SARS-CoV-2 have been rapidly obtained and studied thanks to all the scientific efforts and data sharing around the world. Such molecular analysis of SARS-CoV-2 dynamics showed that rates of mutation, similar to other members of the Coronaviridae family, along with natural selection forces, could result in the emergence of new variants; few of them might be of high consequence. However, this is a serious threat to controlling the pandemic and, of course, enduring the process of returning to normalization with the implicit monetary cost of such a contingency. The lack of updated knowledge in South America justifies the need to develop a structured genomic surveillance program of current and emerging SARS-CoV-2 variants. The modeling of the molecular events and microevolution of the virus will contribute to making better decisions on public health management of the pandemic and developing accurate treatments and more efficient vaccines.
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Affiliation(s)
- Pablo A. Ortiz-Pineda
- Laboratory of Molecular Biology and Genomics, InnovaGen Foundation, Popayán, Colombia
| | - Carlos H. Sierra-Torres
- Laboratory of Molecular Biology and Genomics, InnovaGen Foundation, Popayán, Colombia
- Human Genetics Laboratory, Department of Physiological Sciences, Faculty of Health Sciences, University of Cauca, Popayán, Colombia
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7
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Mercado-Reyes M, Malagón-Rojas J, Rodríguez-Barraquer I, Zapata-Bedoya S, Wiesner M, Cucunubá Z, Toloza-Pérez YG, Hernández-Ortiz JP, Acosta-Reyes J, Parra-Barrera E, Ibáñez-Beltrán E, Quinche GG, Muñoz-Galindo L, Rubio V, Galindo-Borda M, Osorio-Velázquez EG, Bermúdez-Forero A, Pinto-Chacón N, Puerto-Castro G, Franco-Muñoz C, Estupiñan MI, Villar LÁ, Gore-Saravia N, Miranda-Montoya MC, Castellanos J, Valle EM, Navarro-Lechuga E, Oviedo JD, Ospina-Martínez M. Seroprevalence of anti-SARS-CoV-2 antibodies in Colombia, 2020: A population-based study. LANCET REGIONAL HEALTH. AMERICAS 2022; 9:100195. [PMID: 35156075 PMCID: PMC8817632 DOI: 10.1016/j.lana.2022.100195] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Background Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to cause very high morbidity and mortality throughout Latin American countries. However, few population-based seroprevalence surveys have been conducted to quantify attack rates and characterize drivers of transmission. Methods We conducted a population-based cross-sectional study to assess the seroprevalence of antibodies against SARS-CoV-2 in ten cities in Colombia between September and December 2020. The study involved multi-stage cluster sampling at each city. Participants provided a serum sample and answered a demographic and risk factor questionnaire. Prior infection by SARS-CoV-2 was ascertained using the "SARS-CoV-2 Total (COV2T) Advia Centaur - Siemens" chemiluminescence assay. Findings A total of 17863 participants from 7320 households participated in the study. Seroprevalence varied substantially between cities, ranging from 26% (95%CI 23–29 %) in Medellín to 68% (95%CI 62–74 %) in Guapi. There were no differences in seroprevalence by sex, but seropositivity was higher in certain ethnic groups. There was substantial heterogeneity in seroprevalence within cities, driven to a large extent by a strong association between socioeconomic stratum and seropositivity. Interpretation Colombia has been one of the Latin American countries most affected by the COVID-19 pandemic. This study documented very high attack rates in several Colombian cities by the end of 2020 and identified key drivers of heterogeneities including ethnicity and socioeconomic stratum. Few studies of seroprevalence of SARS-CoV-2 have been conducted in Latin America, and therefore this study contributes to the fundamental understanding of the pandemic in the region. Funding The study was sponsored by, Ministerio de Ciencia y Tecnología e Innovación –CT361/2020, Ministerio de Salud y Protección Social, Fundación Universitaria del Norte, Imperial College of London, Universidad Nacional de Colombia (Sede Medellín), Universidad de Córdoba, California University, Unidad Nacional de Gestión del Riesgo, Centro de Atención y Diagnóstico de Enfermedades Infecciosas -CDI-, Centro Internacional de Entrenamiento e Investigaciones Médicas -CIDEIM-, Departamento Administrativo Nacional de Estadística - DANE, Fondo Nacional de Turismo -FONTUR-, Secretarías de Salud Departamentales, Distritales y Municipales and Instituto Nacional de Salud.
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Affiliation(s)
| | | | | | | | - Magdalena Wiesner
- Instituto Nacional de Salud, Avenida Calle 26 51 -20, Bogotá, Colombia
| | | | | | | | - Jorge Acosta-Reyes
- School of Medicine, Universidad del Norte de Barranquilla, Barranquilla, Colombia
| | | | | | - Gianni G Quinche
- Instituto Nacional de Salud, Avenida Calle 26 51 -20, Bogotá, Colombia
| | | | - Vivian Rubio
- Instituto Nacional de Salud, Avenida Calle 26 51 -20, Bogotá, Colombia
| | | | | | | | | | | | | | - María Isabel Estupiñan
- Centro de Atención y Diagnóstico de Enfermedades Infecciosas - CDI, Bucaramanga, Colombia
| | - Luis Ángel Villar
- Centro de Atención y Diagnóstico de Enfermedades Infecciosas - CDI, Bucaramanga, Colombia
| | - Nancy Gore-Saravia
- Centro Internacional de Entrenamiento e Investigaciones Medicas - CIDEIM, Cali, Colombia
| | | | | | | | | | - Juan Daniel Oviedo
- Departamento Administrativo Nacional de Estadística - DANE, Bogotá, Colombia
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8
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Musa SS, Tariq A, Yuan L, Haozhen W, He D. Infection fatality rate and infection attack rate of COVID-19 in South American countries. Infect Dis Poverty 2022; 11:40. [PMID: 35382879 PMCID: PMC8983329 DOI: 10.1186/s40249-022-00961-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 03/14/2022] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND The ongoing COVID-19 pandemic hit South America badly with multiple waves. Different COVID-19 variants have been storming across the region, leading to more severe infections and deaths even in places with high vaccination coverage. This study aims to assess the spatiotemporal variability of the COVID-19 pandemic and estimate the infection fatality rate (IFR), infection attack rate (IAR) and reproduction number ([Formula: see text]) for twelve most affected South American countries. METHODS We fit a susceptible-exposed-infectious-recovered (SEIR)-based model with a time-varying transmission rate to the reported COVID-19 deaths for the twelve South American countries with the highest mortalities. Most of the epidemiological datasets analysed in this work are retrieved from the disease surveillance systems by the World Health Organization, Johns Hopkins Coronavirus Resource Center and Our World in Data. We investigate the COVID-19 mortalities in these countries, which could represent the situation for the overall South American region. We employ COVID-19 dynamic model with-and-without vaccination considering time-varying flexible transmission rate to estimate IFR, IAR and [Formula: see text] of COVID-19 for the South American countries. RESULTS We simulate the model in each scenario under suitable parameter settings and yield biologically reasonable estimates for IFR (varies between 0.303% and 0.723%), IAR (varies between 0.03 and 0.784) and [Formula: see text] (varies between 0.7 and 2.5) for the 12 South American countries. We observe that the severity, dynamical patterns of deaths and time-varying transmission rates among the countries are highly heterogeneous. Further analysis of the model with the effect of vaccination highlights that increasing the vaccination rate could help suppress the pandemic in South America. CONCLUSIONS This study reveals possible reasons for the two waves of COVID-19 outbreaks in South America. We observed reductions in the transmission rate corresponding to each wave plausibly due to improvement in nonpharmaceutical interventions measures and human protective behavioral reaction to recent deaths. Thus, strategies coupling social distancing and vaccination could substantially suppress the mortality rate of COVID-19 in South America.
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Affiliation(s)
- Salihu Sabiu Musa
- Department of Applied Mathematics, Hong Kong Polytechnic University, Hong Kong, China
- Department of Mathematics, Kano University of Science and Technology, Wudil, Nigeria
| | - Amna Tariq
- Department of Population Health Sciences, School of Public Health, Georgia State University, Atlanta, GA USA
| | - Liu Yuan
- Department of Applied Mathematics, Hong Kong Polytechnic University, Hong Kong, China
| | - Wei Haozhen
- Department of Applied Mathematics, Hong Kong Polytechnic University, Hong Kong, China
| | - Daihai He
- Department of Applied Mathematics, Hong Kong Polytechnic University, Hong Kong, China
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9
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Stoddard G, Black A, Ayscue P, Lu D, Kamm J, Bhatt K, Chan L, Kistler AL, Batson J, Detweiler A, Tan M, Neff N, DeRisi JL, Corrigan J. Using genomic epidemiology of SARS-CoV-2 to support contact tracing and public health surveillance in rural Humboldt County, California. BMC Public Health 2022; 22:456. [PMID: 35255849 PMCID: PMC8900115 DOI: 10.1186/s12889-022-12790-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 01/03/2022] [Indexed: 11/12/2022] Open
Abstract
Background During the COVID-19 pandemic within the United States, much of the responsibility for diagnostic testing and epidemiologic response has relied on the action of county-level departments of public health. Here we describe the integration of genomic surveillance into epidemiologic response within Humboldt County, a rural county in northwest California. Methods Through a collaborative effort, 853 whole SARS-CoV-2 genomes were generated, representing ~58% of the 1,449 SARS-CoV-2-positive cases detected in Humboldt County as of March 12, 2021. Phylogenetic analysis of these data was used to develop a comprehensive understanding of SARS-CoV-2 introductions to the county and to support contact tracing and epidemiologic investigations of all large outbreaks in the county. Results In the case of an outbreak on a commercial farm, viral genomic data were used to validate reported epidemiologic links and link additional cases within the community who did not report a farm exposure to the outbreak. During a separate outbreak within a skilled nursing facility, genomic surveillance data were used to rule out the putative index case, detect the emergence of an independent Spike:N501Y substitution, and verify that the outbreak had been brought under control. Conclusions These use cases demonstrate how developing genomic surveillance capacity within local public health departments can support timely and responsive deployment of genomic epidemiology for surveillance and outbreak response based on local needs and priorities. Supplementary Information The online version contains supplementary material available at 10.1186/s12889-022-12790-0.
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Affiliation(s)
- Gunnar Stoddard
- Humboldt County Department of Health and Human Services - Public Health, CA, Eureka, USA
| | | | | | - Dan Lu
- Chan Zuckerberg Initiative, CA, San Francisco, USA
| | - Jack Kamm
- Chan Zuckerberg Biohub, CA, San Francisco, USA
| | - Karan Bhatt
- Chan Zuckerberg Biohub, CA, San Francisco, USA
| | - Lienna Chan
- Chan Zuckerberg Biohub, CA, San Francisco, USA
| | | | | | | | | | - Norma Neff
- Chan Zuckerberg Biohub, CA, San Francisco, USA
| | - Joseph L DeRisi
- Chan Zuckerberg Biohub, CA, San Francisco, USA.,Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Jeremy Corrigan
- Humboldt County Department of Health and Human Services - Public Health, CA, Eureka, USA. .,Humboldt County Public Health Laboratory, CA, Eureka, USA.
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10
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Sivaranjanee R, Kumar PS. The unfurl of the coronavirus and its thwack on humans and the environment: a review. CURRENT OPINION IN ENVIRONMENTAL SCIENCE & HEALTH 2021; 24:100289. [PMID: 34222734 PMCID: PMC8233452 DOI: 10.1016/j.coesh.2021.100289] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
The new coronavirus disease 2019 (COVID-19) severe acute respiratory syndrome coronavirus 2 was first discovered in Wuhan (China) in December 2019 and belongs to the same family as that of the severe acute respiratory syndrome coronavirus 1. On January 30, 2020, the World Health Organization announced the outbreak as a Public Health Emergency of International Concern. Diagnosis of this disease is carried out by using special molecular tests. It is mandatory to identify the individual with COVID-19 symptoms, and isolation is necessary to prevent further transmission of this virus. This review highlights the formation, prodrome, transmission and survival mechanism of COVID-19 and shows that the pandemic circumstance fundamentally improves the air quality in various urban areas across the globe, decreases water contamination and commotion and diminishes the tension on the traveller objections, which may facilitate the reclamation of the natural framework. The worldwide effect of this new outbreak is still dubious.
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Affiliation(s)
- R Sivaranjanee
- Department of Chemical Engineering, St. Joseph's College of Engineering, Chennai 600119, India
| | - P Senthil Kumar
- Department of Chemical Engineering, Sri Sivasubramaniya Nadar College of Engineering, Chennai 603110, India
- Centre of Excellence in Water Research (CEWAR), Sri Sivasubramaniya Nadar College of Engineering, Chennai 603110, India
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11
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Wagatsuma K, Sato R, Yamazaki S, Iwaya M, Takahashi Y, Nojima A, Oseki M, Abe T, Phyu WW, Tamura T, Sekizuka T, Kuroda M, Matsumoto HH, Saito R. Genomic Epidemiology Reveals Multiple Introductions of Severe Acute Respiratory Syndrome Coronavirus 2 in Niigata City, Japan, Between February and May 2020. Front Microbiol 2021; 12:749149. [PMID: 34777297 PMCID: PMC8581661 DOI: 10.3389/fmicb.2021.749149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 10/04/2021] [Indexed: 01/19/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) has caused a serious disease burden and poses a tremendous public health challenge worldwide. Here, we report a comprehensive epidemiological and genomic analysis of SARS-CoV-2 from 63 patients in Niigata City, a medium-sized Japanese city, during the early phase of the pandemic, between February and May 2020. Among the 63 patients, 32 (51%) were female, with a mean (±standard deviation) age of 47.9 ± 22.3 years. Fever (65%, 41/63), malaise (51%, 32/63), and cough (35%, 22/63) were the most common clinical symptoms. The median Ct value after the onset of symptoms lowered within 9 days at 20.9 cycles (interquartile range, 17–26 cycles), but after 10 days, the median Ct value exceeded 30 cycles (p < 0.001). Of the 63 cases, 27 were distributed in the first epidemic wave and 33 in the second, and between the two waves, three cases from abroad were identified. The first wave was epidemiologically characterized by a single cluster related to indoor sports activity spread in closed settings, which included mixing indoors with families, relatives, and colleagues. The second wave showed more epidemiologically diversified events, with most index cases not related to each other. Almost all secondary cases were infected by droplets or aerosols from closed indoor settings, but at least two cases in the first wave were suspected to be contact infections. Results of the genomic analysis identified two possible clusters in Niigata City, the first of which was attributed to clade S (19B by Nexstrain clade) with a monophyletic group derived from the Wuhan prototype strain but that of the second wave was polyphyletic suggesting multiple introductions, and the clade was changed to GR (20B), which mainly spread in Europe in early 2020. These findings depict characteristics of SARS-CoV-2 transmission in the early stages in local community settings during February to May 2020 in Japan, and this integrated approach of epidemiological and genomic analysis may provide valuable information for public health policy decision-making for successful containment of chains of infection.
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Affiliation(s)
- Keita Wagatsuma
- Division of International Health (Public Health), Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Ryosuke Sato
- Niigata City Public Health and Sanitation Center, Niigata, Japan
| | - Satoru Yamazaki
- Niigata City Public Health and Sanitation Center, Niigata, Japan
| | - Masako Iwaya
- Niigata City Public Health and Sanitation Center, Niigata, Japan
| | | | - Akiko Nojima
- Niigata City Public Health and Sanitation Center, Niigata, Japan
| | - Mitsuru Oseki
- Division of Health Science, Niigata City Institute of Public Health and Environment, Niigata, Japan
| | - Takashi Abe
- Division of Bioinformatics, Graduate School of Science and Technology, Niigata University, Niigata, Japan
| | - Wint Wint Phyu
- Division of International Health (Public Health), Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Tsutomu Tamura
- Virology Section, Niigata Prefectural Institute of Public Health and Environmental Science, Niigata, Japan
| | - Tsuyoshi Sekizuka
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Makoto Kuroda
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Haruki H Matsumoto
- Division of Health and Welfare, Niigata Prefectural Government Office, Niigata, Japan
| | - Reiko Saito
- Division of International Health (Public Health), Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
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12
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Reduced levels of convalescent neutralizing antibodies against SARS-CoV-2 B.1+L249S+E484K lineage. Virus Res 2021; 308:198629. [PMID: 34780883 PMCID: PMC8585963 DOI: 10.1016/j.virusres.2021.198629] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 10/20/2021] [Accepted: 11/10/2021] [Indexed: 12/11/2022]
Abstract
The E484K mutation at the SARS-CoV-2 Spike protein emerged independently in different variants around the world and has been widely associated with immune escape from neutralizing antibodies generated during previous infection or vaccination. In this work, the B.1 + L249S+E484K lineage was isolated along with A.1, B.1.420, and B.1.111 SARS-CoV-2 lineages without the E484K mutation and the neutralizing titer of convalescent sera was compared using microneutralization assays. While no significant differences in the neutralizing antibody titers were found between A.1 and B.lineages without the E484K mutation, the neutralizing titers against B.1 + L249S+E484K were 1.5, 1.9, 2.1, and 1.3-fold lower than against A.1, B.1.420, B.1.111-I, and B.1.111-II, respectively. However, molecular epidemiological data indicate that there is no increase in the transmissibility rate associated with this new lineage. This study supports the capability of new variants with the E484K mutation to be resistant to neutralization by humoral immunity, and therefore the need to intensify surveillance programs to determine if these lineages represent a risk for public health.
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13
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Buitrago SP, Garzón-Ospina D. Genetic diversity of SARS-CoV-2 in South America: demographic history and structuration signals. Arch Virol 2021; 166:3357-3371. [PMID: 34604926 PMCID: PMC8487618 DOI: 10.1007/s00705-021-05258-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 08/19/2021] [Indexed: 11/24/2022]
Abstract
In 2020, the emergence of SARS-CoV-2 caused a global public health crisis with significant mortality rates and a large socioeconomic burden. The rapid spread of this new virus has led to the appearance of new variants, making the characterization and monitoring of genetic diversity necessary to understand the population dynamics and evolution of the virus. Here, a population-genetics-based study was performed starting with South American genome sequences available in the GISAID database to investigate the genetic diversity of SARS-CoV-2 on this continent and the evolutionary mechanisms that modulate it.
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Affiliation(s)
- Sindy P Buitrago
- PGAME-Population Genetics and Molecular Evolution, Fundación Scient, Tunja, Boyacá, Colombia. .,GEBIMOL, School of Biological Sciences, Universidad Pedagógica y Tecnológica de Colombia-UPTC, Tunja, Boyacá, Colombia. .,GEO, School of Biological Sciences, Universidad Pedagógica y Tecnológica de Colombia-UPTC, Tunja, Boyacá, Colombia.
| | - Diego Garzón-Ospina
- PGAME-Population Genetics and Molecular Evolution, Fundación Scient, Tunja, Boyacá, Colombia.,GEBIMOL, School of Biological Sciences, Universidad Pedagógica y Tecnológica de Colombia-UPTC, Tunja, Boyacá, Colombia.,GEO, School of Biological Sciences, Universidad Pedagógica y Tecnológica de Colombia-UPTC, Tunja, Boyacá, Colombia
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14
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Characterization of the emerging B.1.621 variant of interest of SARS-CoV-2. INFECTION GENETICS AND EVOLUTION 2021; 95:105038. [PMID: 34403832 PMCID: PMC8364171 DOI: 10.1016/j.meegid.2021.105038] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 07/21/2021] [Accepted: 08/11/2021] [Indexed: 12/25/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genetic diversity has the potential to impact the virus transmissibility and the escape from natural infection- or vaccine-elicited neutralizing antibodies. Here, representative samples from circulating SARS-CoV-2 in Colombia between January and April 2021, were processed for genome sequencing and lineage determination following the nanopore amplicon ARTIC network protocol and PANGOLIN pipeline. This strategy allowed us to identify the emergence of the B.1.621 lineage, considered a variant of interest (VOI) with the accumulation of several substitutions affecting the Spike protein, including the amino acid changes I95I, Y144T, Y145S and the insertion 146 N in the N-terminal domain, R346K, E484K and N501Y in the Receptor binding Domain (RBD) and P681H in the S1/S2 cleavage site of the Spike protein. The rapid increase in frequency and fixation in a relatively short time in Magdalena, Atlantico, Bolivar, Bogotá D.C, and Santander that were near the theoretical herd immunity suggests an epidemiologic impact. Further studies will be required to assess the biological and epidemiologic roles of the substitution pattern found in the B.1.621 lineage.
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15
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Juscamayta-López E, Carhuaricra D, Tarazona D, Valdivia F, Rojas N, Maturrano L, Gavilán R. Phylogenomics reveals multiple introductions and early spread of SARS-CoV-2 into Peru. J Med Virol 2021; 93:5961-5968. [PMID: 34185310 PMCID: PMC8426889 DOI: 10.1002/jmv.27167] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 06/23/2021] [Accepted: 06/25/2021] [Indexed: 12/12/2022]
Abstract
Peru has become one of the countries with the highest mortality rates from the current coronavirus disease 2019 (COVID‐19) pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2). To investigate early transmission events and the genomic diversity of SARS‐CoV‐2 isolates circulating in Peru in the early COVID‐19 pandemic, we analyzed 3472 viral genomes, of which 149 were from Peru. Phylogenomic analysis revealed multiple and independent introductions of the virus likely from Europe and Asia and a high diversity of genetic lineages circulating in Peru. In addition, we found evidence for community‐driven transmission of SARS‐CoV‐2 as suggested by clusters of related viruses found in patients living in different regions of Peru. This is the first snapshot of the sources of epidemic transmission and genomic diversity of SARS‐CoV‐2 lineages circulating in Peru during the early COVID‐19 pandemic. Phylogenomic analysis revealed multiple and independent introductions of the virus likely from Europe and Asia, and high diversity of genetic lineages circulating in Peru with predominance of the G614G variant (S gene,n= 136/149). We found evidence that early spread of the virus in Lima City was sustained by community transmission.
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Affiliation(s)
- Eduardo Juscamayta-López
- Laboratorio de Infecciones Respiratorias Agudas, Centro Nacional de Salud Pública, Instituto Nacional de Salud, Lima, Peru.,Laboratorio de Biología y Genética Molecular, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Dennis Carhuaricra
- Laboratorio de Biología y Genética Molecular, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - David Tarazona
- Laboratorio de Infecciones Respiratorias Agudas, Centro Nacional de Salud Pública, Instituto Nacional de Salud, Lima, Peru.,Laboratorio de Biología y Genética Molecular, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Faviola Valdivia
- Laboratorio de Infecciones Respiratorias Agudas, Centro Nacional de Salud Pública, Instituto Nacional de Salud, Lima, Peru
| | - Nancy Rojas
- Laboratorio de Virus Respiratorios, Centro Nacional de Salud Pública, Instituto Nacional de Salud, Lima, Peru
| | - Lenin Maturrano
- Laboratorio de Biología y Genética Molecular, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Ronnie Gavilán
- Laboratorio de Enteropatógenos, Centro Nacional de Salud Pública, Instituto Nacional de Salud, Lima, Peru.,Escuela Profesional de Medicina Humana, Universidad Privada San Juan Bautista, Lima, Peru
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16
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Laiton-Donato K, Usme-Ciro JA, Franco-Muñoz C, Álvarez-Díaz DA, Ruiz-Moreno HA, Reales-González J, Prada DA, Corchuelo S, Herrera-Sepúlveda MT, Naizaque J, Santamaría G, Wiesner M, Walteros DM, Ospina Martínez ML, Mercado-Reyes M. Novel Highly Divergent SARS-CoV-2 Lineage With the Spike Substitutions L249S and E484K. Front Med (Lausanne) 2021; 8:697605. [PMID: 34262921 PMCID: PMC8273171 DOI: 10.3389/fmed.2021.697605] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 05/31/2021] [Indexed: 12/02/2022] Open
Abstract
COVID-19 pandemics has led to genetic diversification of SARS-CoV-2 and the appearance of variants with potential impact in transmissibility and viral escape from acquired immunity. We report a new and highly divergent lineage containing 21 distinctive mutations (10 non-synonymous, eight synonymous, and three substitutions in non-coding regions). The amino acid changes L249S and E484K located at the CTD and RBD of the Spike protein could be of special interest due to their potential biological role in the virus-host relationship. Further studies are required for monitoring the epidemiologic impact of this new lineage.
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Affiliation(s)
| | - Jose A. Usme-Ciro
- Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá, Colombia
- Centro de Investigación en Salud para el Trópico - CIST, Facultad de Medicina, Universidad Cooperativa de Colombia, Santa Marta, Colombia
| | - Carlos Franco-Muñoz
- Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá, Colombia
| | - Diego A. Álvarez-Díaz
- Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá, Colombia
| | | | | | - Diego Andrés Prada
- Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá, Colombia
| | - Sheryll Corchuelo
- Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá, Colombia
| | | | - Julian Naizaque
- Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá, Colombia
| | - Gerardo Santamaría
- Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá, Colombia
| | - Magdalena Wiesner
- Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá, Colombia
| | - Diana Marcela Walteros
- Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá, Colombia
| | | | - Marcela Mercado-Reyes
- Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá, Colombia
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17
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Gómez-Grosso LA, Mercado M, Ospina ML. In the grip of SARS-CoV-2: The scientific leadership of the Colombian Instituto Nacional de Salud. BIOMEDICA : REVISTA DEL INSTITUTO NACIONAL DE SALUD 2021; 41:195-200. [PMID: 34214259 PMCID: PMC8341952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Indexed: 11/09/2022]
Affiliation(s)
- Luis Alberto Gómez-Grosso
- Grupo de Fisiología Molecular, Instituto Nacional de Salud, Bogotá, D.C., ColombiaInstituto Nacional de SaludBogotáD.C.Colombia
| | - Marcela Mercado
- Directora de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá, D.C., ColombiaInstituto Nacional de SaludBogotáD.C.Colombia
| | - Martha Lucía Ospina
- Directora General, Instituto Nacional de Salud, Bogotá, D.C., ColombiaInstituto Nacional de SaludBogotáD.C.Colombia
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18
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Quiroga SA, Hernández C, Castañeda S, Jimenez P, Vega L, Gomez M, Martinez D, Ballesteros N, Muñoz M, Cifuentes C, Sierra N, Flórez C, Paniz-Mondolfi A, Ramírez JD. Contrasting SARS-CoV-2 RNA copies and clinical symptoms in a large cohort of Colombian patients during the first wave of the COVID-19 pandemic. Ann Clin Microbiol Antimicrob 2021; 20:39. [PMID: 34030702 PMCID: PMC8142070 DOI: 10.1186/s12941-021-00445-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Accepted: 05/11/2021] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND There is limited and controverting evidence looking at possible associations of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA copies and patient variables in large cohorts of symptomatic and asymptomatic patients. METHODS We studied 2275 symptomatic and asymptomatic patients from Colombia with coronavirus disease 2019 (COVID-19) and analyzed the associations between RT-PCR cycle threshold (Ct) value with gender, age, comorbidities, symptomatology, and disease severity. RESULTS 15.4 % of the samples (n = 428) reported at least one comorbidity. There were 2011 symptomatic cases (72.4 %), being the most common reported symptom cough (57.2 %, n = 1586). Respiratory distress was present in 21.4 % of patients (n = 595), and 435 patients (15.6 %) required hospital admission. We observed that patients with no prior medical history harbored higher RNA copies than patients with comorbidities (p = 0.02). No significant differences in RNA copies were observed between symptomatic and asymptomatic patients (p = 0.82). Strong correlations were detected between Ct values and the presence of odynophagia (p = 0.03), diarrhea (p = 0.04), and headache (p = 0.0008). An inverse association was found between RNA copy number and markers of disease severity, namely, respiratory distress (P < 0.0001) and hospitalization requirement (P < 0.0001). CONCLUSIONS SARS-CoV-2 RT-PCR cycle thresholds reveal strong associations with a prior medical history, specific symptomatology, and disease severity markers. Further research controlling potential confounding variables needs to be conducted to evaluate the nature and usefulness of these associations in managing COVID-19 patients.
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Affiliation(s)
- Santiago A Quiroga
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
- Escuela de Medicina y Ciencias de la Salud, Universidad del Rosario, Bogotá, Colombia
| | - Carolina Hernández
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Sergio Castañeda
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Paula Jimenez
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Laura Vega
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Marcela Gomez
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - David Martinez
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Nathalia Ballesteros
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Marina Muñoz
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Claudia Cifuentes
- Laboratorio de Salud Pública, Dirección de Salud Pública, Secretaria de Salud de Cundinamarca, Bogotá, Colombia
| | - Nathalia Sierra
- Laboratorio de Salud Pública, Dirección de Salud Pública, Secretaria de Salud de Cundinamarca, Bogotá, Colombia
| | | | - Alberto Paniz-Mondolfi
- Instituto de Investigaciones Biomédicas IDB/Incubadora Venezolana de la Ciencia, Barquisimeto, Venezuela
- Icahn School of Medicine at Mount Sinai, New York, USA
| | - Juan David Ramírez
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia.
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19
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Novoa W, Miller H, Mattar S, Faccini-Martínez ÁA, Rivero R, Serrano-Coll H. A first probable case of SARS-CoV-2 reinfection in Colombia. Ann Clin Microbiol Antimicrob 2021; 20:7. [PMID: 33435982 PMCID: PMC7802059 DOI: 10.1186/s12941-020-00413-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 12/17/2020] [Indexed: 02/06/2023] Open
Affiliation(s)
| | | | - Salim Mattar
- Universidad de Cordoba, Instituto de Investigaciones Biologicas del Tropico, Monteria, Colombia.
| | | | - Ricardo Rivero
- Universidad de Cordoba, Instituto de Investigaciones Biologicas del Tropico, Monteria, Colombia
| | - Hector Serrano-Coll
- Universidad de Cordoba, Instituto de Investigaciones Biologicas del Tropico, Monteria, Colombia
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20
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Fiorentini S, Messali S, Zani A, Caccuri F, Giovanetti M, Ciccozzi M, Caruso A. First detection of SARS-CoV-2 spike protein N501 mutation in Italy in August, 2020. THE LANCET. INFECTIOUS DISEASES 2021; 21:e147. [PMID: 33450180 PMCID: PMC7836831 DOI: 10.1016/s1473-3099(21)00007-4] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 01/06/2021] [Indexed: 11/29/2022]
Affiliation(s)
- Simona Fiorentini
- Section of Microbiology, Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy
| | - Serena Messali
- Section of Microbiology, Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy
| | - Alberto Zani
- Section of Microbiology, Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy
| | - Francesca Caccuri
- Section of Microbiology, Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy
| | - Marta Giovanetti
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil; Laboratório de Genética Celular e Molecular, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Massimo Ciccozzi
- Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, Rome, Italy
| | - Arnaldo Caruso
- Section of Microbiology, Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy.
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21
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Gutierrez B, Márquez S, Prado-Vivar B, Becerra-Wong M, Guadalupe JJ, Candido DDS, Fernandez-Cadena JC, Morey-Leon G, Armas-Gonzalez R, Andrade-Molina DM, Bruno A, De Mora D, Olmedo M, Portugal D, Gonzalez M, Orlando A, Drexler JF, Moreira-Soto A, Sander AL, Brünink S, Kühne A, Patiño L, Carrazco-Montalvo A, Mestanza O, Zurita J, Sevillano G, Du Plessis L, McCrone JT, Coloma J, Trueba G, Barragán V, Rojas-Silva P, Grunauer M, Kraemer MUG, Faria NR, Escalera-Zamudio M, Pybus OG, Cárdenas P. Genomic epidemiology of SARS-CoV-2 transmission lineages in Ecuador. Virus Evol 2021; 7:veab051. [PMID: 34527281 PMCID: PMC8244811 DOI: 10.1093/ve/veab051] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 05/12/2021] [Accepted: 06/03/2021] [Indexed: 12/23/2022] Open
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.
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Affiliation(s)
- Bernardo Gutierrez
- Department of Zoology, University of Oxford, Oxford, Oxfordshire OX1 3SY, UK
| | - Sully Márquez
- Instituto de Microbiología, Universidad San Francisco de Quito, Quito 170901, Ecuador
| | - Belén Prado-Vivar
- Instituto de Microbiología, Universidad San Francisco de Quito, Quito 170901, Ecuador
| | - Mónica Becerra-Wong
- Instituto de Microbiología, Universidad San Francisco de Quito, Quito 170901, Ecuador
| | - Juan José Guadalupe
- Laboratorio de Biotecnología Vegetal, Universidad San Francisco de Quito, Quito 170901, Ecuador
| | | | - Juan Carlos Fernandez-Cadena
- Omics Sciences Laboratory, Faculty of Medical Sciences, Universidad de Especialidades Espíritu Santo, Samborondón 092301, Ecuador
| | - Gabriel Morey-Leon
- Faculty of Medical Sciences, Universidad de Guayaquil, Guayaquil 090613, Ecuador
| | - Rubén Armas-Gonzalez
- Faculty of Sciences, Escuela Superior Politécnica del Litoral, Guayaquil 090112, Ecuador
| | - Derly Madeleiny Andrade-Molina
- Omics Sciences Laboratory, Faculty of Medical Sciences, Universidad de Especialidades Espíritu Santo, Samborondón 092301, Ecuador
| | - Alfredo Bruno
- Instituto Nacional de Investigación en Salud Pública, Guayaquil 3961, Ecuador
| | - Domenica De Mora
- Instituto Nacional de Investigación en Salud Pública, Guayaquil 3961, Ecuador
| | - Maritza Olmedo
- Instituto Nacional de Investigación en Salud Pública, Guayaquil 3961, Ecuador
| | - Denisse Portugal
- Instituto Nacional de Investigación en Salud Pública, Guayaquil 3961, Ecuador
| | - Manuel Gonzalez
- Instituto Nacional de Investigación en Salud Pública, Guayaquil 3961, Ecuador
| | - Alberto Orlando
- Instituto Nacional de Investigación en Salud Pública, Guayaquil 3961, Ecuador
| | - Jan Felix Drexler
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin 10117, Germany
| | - Andres Moreira-Soto
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin 10117, Germany
| | - Anna-Lena Sander
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin 10117, Germany
| | - Sebastian Brünink
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin 10117, Germany
| | - Arne Kühne
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin 10117, Germany
| | - Leandro Patiño
- Instituto Nacional de Investigación en Salud Pública, Guayaquil 3961, Ecuador
| | | | - Orson Mestanza
- Servicio de Genética, Instituto Nacional de Salud del Niño San Borja, Lima 15037, Perú
| | - Jeannete Zurita
- Facultad de Medicina, Pontificia Universidad Católica del Ecuador, Quito 170143, Ecuador
| | - Gabriela Sevillano
- Unidad de Investigaciones en Biomedicina, Zurita & Zurita Laboratorios, Quito 170104, Ecuador
| | - Louis Du Plessis
- Department of Zoology, University of Oxford, Oxford, Oxfordshire OX1 3SY, UK
| | - John T McCrone
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3JW, UK
| | - Josefina Coloma
- School of Public Health, University of California, Berkeley CA 94704, USA
| | - Gabriel Trueba
- Instituto de Microbiología, Universidad San Francisco de Quito, Quito 170901, Ecuador
| | - Verónica Barragán
- Instituto de Microbiología, Universidad San Francisco de Quito, Quito 170901, Ecuador
| | - Patricio Rojas-Silva
- Instituto de Microbiología, Universidad San Francisco de Quito, Quito 170901, Ecuador
| | - Michelle Grunauer
- Escuela de Medicina, Universidad San Francisco de Quito, Quito 170901, Ecuador
| | - Moritz U G Kraemer
- Department of Zoology, University of Oxford, Oxford, Oxfordshire OX1 3SY, UK
| | - Nuno R Faria
- Department of Zoology, University of Oxford, Oxford, Oxfordshire OX1 3SY, UK
| | | | - Oliver G Pybus
- Department of Zoology, University of Oxford, Oxford, Oxfordshire OX1 3SY, UK
| | - Paúl Cárdenas
- Instituto de Microbiología, Universidad San Francisco de Quito, Quito 170901, Ecuador
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