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Article ; Online: Genotyping of dengue virus from infected tissue samples embedded in paraffin.

Rivera, Jorge Alonso / Rengifo, Aura Caterine / Rosales-Munar, Alicia / Díaz-Herrera, Taylor H / Ciro, José Usme / Parra, Edgar / Alvarez-Díaz, Diego A / Laiton-Donato, Katherine / Caldas, María Leonor

Virology journal

2023 Volume 20, Issue 1, Page(s) 100

Abstract: Dengue has become one of the vector-borne diseases that affect humans worldwide. In Latin American countries, Colombia is historically one of the most affected by epidemics of this flavivirus. The underreporting of signs and symptoms of probable cases of ...

Abstract	Dengue has become one of the vector-borne diseases that affect humans worldwide. In Latin American countries, Colombia is historically one of the most affected by epidemics of this flavivirus. The underreporting of signs and symptoms of probable cases of dengue, the lack of characterization of the serotypes of the infection, and the few detailed studies of postmortem necropsies of patients are among other conditions that have delayed progress in the knowledge of the pathogenesis of the disease. This study presents the results of fragment sequencing assays on paraffin-embedded tissue samples from fatal DENV cases during the 2010 epidemic in Colombia. We found that the predominant serotype was DENV-2, with the Asian/American genotype of lineages 1 and 2. This work is one of the few reports of the circulating genotypes of dengue during the 2010 epidemic in Colombia, one of the most lethal dates in the country's history.
MeSH term(s)	Humans ; Dengue Virus/genetics ; Dengue/epidemiology ; Paraffin ; Genotype ; Phylogeny ; Serogroup
Chemical Substances	Paraffin (8002-74-2)
Language	English
Publishing date	2023-05-25
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2160640-7
ISSN	1743-422X ; 1743-422X
ISSN (online)	1743-422X
ISSN	1743-422X
DOI	10.1186/s12985-023-02072-5
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Histopathology of COVID-19: An illustration of the findings from fatal cases.

Rivera, Jorge / Corchuelo, Sheryll / Naizaque, Julián / Parra, Édgar / Meek, Eugenio Aladino / Álvarez-Díaz, Diego / Mercado, María / Torres-Fernández, Orlando

Biomedica : revista del Instituto Nacional de Salud

2023 Volume 43, Issue 1, Page(s) 8–21

Title translation	Histopatología de la COVID-19: una ilustración de los hallazgos en casos fatales
MeSH term(s)	Humans ; COVID-19 ; SARS-CoV-2
Language	Spanish
Publishing date	2023-03-30
Publishing country	Colombia
Document type	Journal Article
ZDB-ID	2059952-3
ISSN	2590-7379 ; 2590-7379
ISSN (online)	2590-7379
ISSN	2590-7379
DOI	10.7705/biomedica.6737
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Article ; Online: Morphological and Molecular Changes in the Cortex and Cerebellum of Immunocompetent Mice Infected with Zika Virus.

Rengifo, Aura Caterine / Rivera, Jorge / Álvarez-Díaz, Diego Alejandro / Naizaque, Julián / Santamaria, Gerardo / Corchuelo, Sheryll / Gómez, Claudia Yadira / Torres-Fernández, Orlando

Viruses

2023 Volume 15, Issue 8

Abstract: Zika virus (ZIKV) disease continues to be a threat to public health, and it is estimated that millions of people have been infected and that there have been more cases of serious complications than those already reported. Despite many studies on the ... ...

Abstract	Zika virus (ZIKV) disease continues to be a threat to public health, and it is estimated that millions of people have been infected and that there have been more cases of serious complications than those already reported. Despite many studies on the pathogenesis of ZIKV, several of the genes involved in the malformations associated with viral infection are still unknown. In this work, the morphological and molecular changes in the cortex and cerebellum of mice infected with ZIKV were evaluated. Neonatal BALB/c mice were inoculated with ZIKV intraperitoneally, and the respective controls were inoculated with a solution devoid of the virus. At day 10 postinoculation, the mice were euthanized to measure the expression of the markers involved in cortical and cerebellar neurodevelopment. The infected mice presented morphological changes accompanied by calcifications, as well as a decrease in most of the markers evaluated in the cortex and cerebellum. The modifications found could be predictive of astrocytosis, dendritic pathology, alterations in the regulation systems of neuronal excitation and inhibition, and premature maturation, conditions previously described in other models of ZIKV infection and microcephaly.
MeSH term(s)	Animals ; Mice ; Zika Virus ; Zika Virus Infection ; Cerebellum ; Gliosis ; Mice, Inbred BALB C
Language	English
Publishing date	2023-07-27
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2516098-9
ISSN	1999-4915 ; 1999-4915
ISSN (online)	1999-4915
ISSN	1999-4915
DOI	10.3390/v15081632
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Article ; Online: SARS-CoV-2 sequencing: The technological initiative to strengthen early warning systems for public health emergencies in Latin America and the Caribbean

Álvarez-Díaz, Diego A / Laiton-Donato, Katherine / Franco-Muñoz, Carlos / Mercado-Reyes, Marcela

Biomedica : revista del Instituto Nacional de Salud

2020 Volume 40, Issue Supl. 2, Page(s) 188–197

Abstract: The COVID-19 pandemic caused by SARS-CoV-2 is a public health problem on a scale unprecedented in the last 100 years, as has been the response focused on the rapid genomic characterization of SARS-CoV-2 in virtually all regions of the planet. This ... ...

Title translation	[Secuenciación del SARS-CoV-2: la iniciativa tecnológica para fortalecer los sistemas de alerta temprana ante emergencias de salud pública en Latinoamérica y el Caribe].
Abstract	The COVID-19 pandemic caused by SARS-CoV-2 is a public health problem on a scale unprecedented in the last 100 years, as has been the response focused on the rapid genomic characterization of SARS-CoV-2 in virtually all regions of the planet. This pandemic emerged during the era of genomic epidemiology, a science fueled by continued advances in next-generation sequencing. Since its recent appearance, genomic epidemiology included the precise identification of new lineages or species of pathogens and the reconstruction of their genetic variability in real time, evidenced in past outbreaks of influenza H1N1, MERS, and SARS. However, the global and uncontrolled scale of this pandemic created a scenario where genomic epidemiology was put into practice en masse, from the rapid identification of SARS-CoV-2 to the registration of new lineages and their active surveillance throughout the world. Prior to the COVID-19 pandemic, the availability of genomic data on circulating pathogens in several Latin America and the Caribbean countries was scarce or nil. With the arrival of SARS-CoV-2, this scenario changed significantly, although the amount of available information remains scarce and, in countries such as Colombia, Brazil, Argentina, and Chile, the genomic information of SARS-CoV-2 was obtained mainly by research groups in genomic epidemiology rather than the product of a public health surveillance policy or program. This indicates the need to establish public health policies aimed at implementing genomic epidemiology as a tool to strengthen surveillance and early warning systems against threats to public health in the region.
MeSH term(s)	Base Sequence ; Betacoronavirus/genetics ; COVID-19 ; Caribbean Region ; Communicable Diseases, Emerging ; Coronavirus Infections/epidemiology ; Coronavirus Infections/prevention & control ; Coronavirus Infections/virology ; Disaster Planning ; Disease Outbreaks ; Genome, Viral ; Humans ; Information Dissemination ; Latin America/epidemiology ; Molecular Epidemiology/methods ; Molecular Epidemiology/trends ; Pandemics/prevention & control ; Pneumonia, Viral/epidemiology ; Pneumonia, Viral/prevention & control ; Pneumonia, Viral/virology ; Population Surveillance ; Procedures and Techniques Utilization ; Public Health ; RNA, Viral/genetics ; RNA-Seq ; SARS-CoV-2 ; Sequence Analysis, RNA ; Sustainable Development ; Virus Diseases/epidemiology
Chemical Substances	RNA, Viral
Keywords	covid19
Language	Spanish
Publishing date	2020-10-30
Publishing country	Colombia
Document type	Journal Article
ZDB-ID	2059952-3
ISSN	2590-7379 ; 2590-7379
ISSN (online)	2590-7379
ISSN	2590-7379
DOI	10.7705/biomedica.5841
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Article ; Online: Multisystem Failure in Fatal Dengue: Associations between the Infectious Viral Serotype and Clinical and Histopathological Findings.

Rivera, Jorge / Rengifo, Aura Caterine / Alvarez-Díaz, Diego / Parra, Edgar / Usme-Ciro, José / Castellanos, Jaime / Velandia, Myriam / Laiton-Donato, Katherine / Rico, Angélica / Pardo, Lisseth / Caldas, María Leonor

The American journal of tropical medicine and hygiene

2023 Volume 109, Issue 4, Page(s) 908–916

Abstract: Dengue is the most important arthropod-borne viral infection of humans. However, its viral pathogenesis is still unknown. The information collected from dengue fatal cases is crucial for understanding the complex interactions between virulence and host ... ...

Abstract	Dengue is the most important arthropod-borne viral infection of humans. However, its viral pathogenesis is still unknown. The information collected from dengue fatal cases is crucial for understanding the complex interactions between virulence and host factors. This study aimed to establish possible associations between the clinical characteristics, histopathological changes, replication, and tissue location of viral serotypes in dengue fatal cases. Clinical and histopathological characterizations, antigen localization in tissue, and detection of the infecting serotype and replication using real-time polymerase chain reaction were all performed on the dengue fatal cases. The majority of the cases involved people under the age of 20. Bleeding (48.3%), abdominal pain (44.8%), myalgia (52.9%), and headache (48.3%) were the most common clinical manifestations in the cases. There was multiorgan pathology, with histopathological changes primarily in the liver, spleen, and lung. Similarly, the viral antigen was found primarily in these organs; however, there were no associations between tissue changes, viral location, infecting serotypes, and replication processes. Dengue infection should be considered a multiorgan disease, the outcome of which is possibly not associated with the infecting viral serotype.
Language	English
Publishing date	2023-08-21
Publishing country	United States
Document type	Journal Article
ZDB-ID	2942-7
ISSN	1476-1645 ; 0002-9637
ISSN (online)	1476-1645
ISSN	0002-9637
DOI	10.4269/ajtmh.22-0587
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Article ; Online: Neuroetica del trasplante de cuerpo.

Alvarez-Diaz, J A

Revista de neurologia

2018 Volume 67, Issue 12, Page(s) 505–512

Abstract: ... on the methodology of Diego Gracia on ethics and bioethics and an analysis of facts, values and duties. Furthermore ...

Title translation	Neuroethics of body transplantation.
Abstract	Introduction: Recent contributions to the specialised literature address the topic of body transplantation, mostly produced by Sergio Canavero and a group of researchers from China. For several years they have been announcing that they will carry out the procedure, but it has still not been performed. Aims: The aim of this study is to perform a neuroethical analysis of body transplantation, based on the methodology of Diego Gracia on ethics and bioethics and an analysis of facts, values and duties. Furthermore, we also propose that, with the knowledge available today, body transplantation must be addressed from the perspective of research ethics. Development: As regards the facts, it can be said that, although the history of attempts to perform a body transplant dates back almost a century, there are many limitations preventing it from being performed with our current knowledge. This is due to the fact that no serious and rigorous preclinical research has been conducted (at most some anecdotal data can be found). With the data that is available, it does not even seem possible to think of designing a protocol to include human beings for body transplantation. In terms of values, according to the model developed by Emanuel, who proposes eight requirements that must be met to comply with the ethics of clinical research, it is not even possible to comply with one of them. Regarding duties, it would be wise to recommend that such a procedure should not be carried out on humans. Conclusions: Considering the scientific knowledge currently available and the values of research ethics, a body transplantation should not be performed in human beings either as clinical research or as clinical practice.
MeSH term(s)	Bioethical Issues ; Biomedical Research/ethics ; Head/surgery ; Humans ; Neurology/ethics ; Transplantation/ethics
Language	Spanish
Publishing date	2018-12-07
Publishing country	Spain
Document type	Journal Article ; Review
ZDB-ID	1468278-3
ISSN	1576-6578 ; 0210-0010
ISSN (online)	1576-6578
ISSN	0210-0010
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Article ; Online: Monkeypox virus genome sequence from an imported human case in Colombia.

Laiton-Donato, Katherine / Álvarez-Díaz, Diego A / Franco-Muñoz, Carlos / Ruiz-Moreno, Héctor A / Rojas-Estévez, Paola / Prada, Andrés / Rosales, Alicia / Ospina, Martha Lucía / Mercado-Reyes, Marcela

Biomedica : revista del Instituto Nacional de Salud

2022 Volume 42, Issue 3, Page(s) 541–545

Abstract: Introduction: Monkeypox virus (MPXV) is an enveloped double-stranded DNA virus with a genome of approximately 197.209 bp. The current classification divides MPXV into three clades: Clade I (Central African or Congo Basin clade) and clades IIa and IIb ( ... ...

Title translation	Secuencia genómica del virus de la viruela símica de un caso importado en Colombia
Abstract	Introduction: Monkeypox virus (MPXV) is an enveloped double-stranded DNA virus with a genome of approximately 197.209 bp. The current classification divides MPXV into three clades: Clade I (Central African or Congo Basin clade) and clades IIa and IIb (West African clades). Objective: To report the complete genome and phylogenetic analysis of a human monkeypox case detected in Colombia. Materials and methods: Exudate from vesicular lesions was obtained from a male patient with recent travel history to Spain. A direct genomic approach was implemented in which total DNA from the sample was purified through a column-based method, followed by sequencing on the Nanopore GridION. Reads were aligned against the MPXV reference genome using minimap2 v.2.24 and phylogenetic inference was performed using maximum likelihood estimation. Results: A total of 11.951 reads mapped directly to a reference genome with 96.8% of coverage (190.898 bp). Conclusion: Phylogenetic analysis of the MPXV circulating in Colombia demonstrated its close relationship to clade IIb responsible for the multi-country outbreak in 2022.
MeSH term(s)	Colombia ; Humans ; Male ; Mpox (monkeypox)/diagnosis ; Mpox (monkeypox)/epidemiology ; Mpox (monkeypox)/pathology ; Monkeypox virus/genetics ; Phylogeny ; Sequence Analysis, DNA
Language	Spanish
Publishing date	2022-09-02
Publishing country	Colombia
Document type	Journal Article
ZDB-ID	2059952-3
ISSN	2590-7379 ; 2590-7379
ISSN (online)	2590-7379
ISSN	2590-7379
DOI	10.7705/biomedica.6647
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Article: Reduced levels of convalescent neutralizing antibodies against SARS-CoV-2 B.1+L249S+E484K lineage

Álvarez-Díaz, Diego A. / Laiton-Donato, Katherine / Torres-García, Orlando Alfredo / Ruiz-Moreno, Hector Alejandro / Franco-Muñoz, Carlos / Beltran, Maria Angie / Mercado-Reyes, Marcela / Rueda, Miguel Germán / Muñoz, Ana Luisa

Virus research. 2022 Jan. 15, v. 308

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 ... ...

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.
Keywords	Severe acute respiratory syndrome coronavirus 2 ; humoral immunity ; monitoring ; mutation ; neutralization ; public health ; research ; risk ; vaccination ; viruses
Language	English
Dates of publication	2022-0115
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	605780-9
ISSN	1872-7492 ; 0168-1702
ISSN (online)	1872-7492
ISSN	0168-1702
DOI	10.1016/j.virusres.2021.198629
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Secuenciación del SARS-CoV-2

Diego A. Álvarez-Díaz / Katherine Laiton-Donato / Carlos Franco-Muñoz / Marcela Mercado-Reyes

Biomédica: revista del Instituto Nacional de Salud, Vol 40, Iss Supl. 2, Pp 188-

la iniciativa tecnológica para fortalecer los sistemas de alerta temprana ante emergencias de salud pública en Latinoamérica y el Caribe

2020 Volume 197

Abstract: ... una situación que obligó a utilizar de forma masiva herramientas de la epidemiología genómica como la rápida ...

Abstract	La pandemia de COVID-19 causada por el SARS-CoV-2 es un problema de salud pública sin precedentes en los últimos 100 años, así como la respuesta centrada en la caracterización genómica del SARS-CoV-2 prácticamente en todas las regiones del planeta. Esta pandemia surgió durante la era de la epidemiología genómica impulsada por los continuos avances en la secuenciación de próxima generación. Desde su reciente aparición, la epidemiología genómica permitió la identificación precisa de nuevos linajes o especies de agentes patógenos y la reconstrucción de su variabilidad genética en tiempo real, lo que se hizo evidente en los brotes de influenza H1N1, MERS y SARS. Sin embargo, la escala global y descontrolada de esta pandemia ha generado una situación que obligó a utilizar de forma masiva herramientas de la epidemiología genómica como la rápida identificación del SARS-CoV-2 y el registro de nuevos linajes y su vigilancia activa en todo el mundo. Antes de la pandemia de COVID-19 la disponibilidad e datos genómicos de agentes patógenos circulantes en varios países de Latinoamérica y el Caribe era escasa o nula. Con la llegada del SARS-CoV-2 dicha situación cambió significativamente, aunque la cantidad de información disponible sigue siendo escasa y, en países como Colombia, Brasil, Argentina y Chile, la información genómica del SARS-CoV-2 provino principalmente de grupos de investigación en epidemiología genómica más que como producto de una política o programa de vigilancia en salud pública.
Keywords	infecciones por coronavirus ; síndrome respiratorio agudo grave ; virus del sras ; secuenciación de nucleótidos de alto rendimiento ; vigilancia epidemiológica ; políticas en salud pública ; Medicine ; R ; Arctic medicine. Tropical medicine ; RC955-962
Language	English
Publishing date	2020-10-01T00:00:00Z
Publisher	Instituto Nacional de Salud
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Low Neutralizing Antibody Titers against the Mu Variant of SARS-CoV-2 in 31 BNT162b2 Vaccinated Individuals in Colombia.

Álvarez-Díaz, Diego A / Muñoz, Ana Luisa / Tavera-Rodríguez, Pilar / Herrera-Sepúlveda, María T / Ruiz-Moreno, Hector Alejandro / Laiton-Donato, Katherine / Franco-Muñoz, Carlos / Pelaez-Carvajal, Dioselina / Cuellar, Diego / Muñoz-Suarez, Alejandra M / Galindo, Marisol / Arias-Ramírez, Edgar J / Mercado-Reyes, Marcela

Vaccines

2022 Volume 10, Issue 2

Abstract: Global surveillance programs for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are showing the emergence of variants with mutations in the spike protein. Genomic and laboratory surveillance are important to determine if these variants may ... ...

Abstract	Global surveillance programs for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are showing the emergence of variants with mutations in the spike protein. Genomic and laboratory surveillance are important to determine if these variants may be more infectious or less susceptible to antiviral treatments and vaccine-induced antibodies. Three of the most predominant SARS-CoV-2 variants in Colombia during the epidemiological peaks of 2021 were isolated: Mu, a variant of interest; Gamma, a variant of concern; B.1.111, which lacks genetic markers associated with greater virulence. Microneutralization assays were performed by incubating 120 mean tissue culture infectious doses (TCID50) of each SARS-CoV-2 isolate with five two-fold serial dilutions of sera from 31 BNT162b2-vaccinated volunteers. The mean neutralization titer (MN50) was calculated by the Reed-Muench method. At the end of August, Mu represented 49% of coronavirus disease 2019 (COVID-19) cases in Colombia, followed by 25% of Gamma. In contrast, B.1.111 became almost undetectable. The evaluation of neutralizing antibodies suggests that patients vaccinated with BNT162b2 generate neutralizing antibody titers against the Mu variant at significantly lower concentrations relative to B.1.111 and Gamma. This study shows the importance of continuing surveillance programs of emerging variants, as well as the need to evaluate the neutralizing antibody response induced by other vaccines.
Language	English
Publishing date	2022-01-24
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2703319-3
ISSN	2076-393X
ISSN	2076-393X
DOI	10.3390/vaccines10020180
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