Background: The emergence of highly transmissible SARS-CoV-2 variants has led to surges in cases and the need for global genomic surveillance. While some variants rapidly spread worldwide, other variants only persist nationally. There is a need for more fine-scale analysis to understand transmission dynamics at a country scale. For instance, the Mu variant of interest, also known as lineage B.1.621, was first detected in Colombia and was responsible for a large local wave but only a few sporadic cases elsewhere.Methods: To better understand the epidemiology of SARS-Cov-2 variants in Colombia, we used 14,049 complete SARS-CoV-2 genomes from the 32 states of Colombia. We performed Bayesian phylodynamic analyses to estimate the time of variants’ introduction, their respective effective reproductive number, and effective population size, and the impact of disease control measures.Results: Here, we detect a total of 188 SARS-CoV-2 Pango lineages circulating in Colombia since the pandemic’s start. We show that the effective reproduction number oscillated drastically throughout the first two years of the pandemic, with Mu showing the highest transmissibility (Re and growth rate estimation).Conclusions: Our results reinforce that genomic surveillance programs are essential for countries to make evidence-driven interventions toward the emergence and circulation of novel SARS-CoV-2 variants.

Dengue fever, a major mosquito-borne viral disease, is transmitted by Aedes mosquitoes and poses a significant global health burden. Despite extensive research, the spatiotemporal dynamics of dengue virus (DENV) lineages in Colombia remain understudied. Here, we analyze 11,443 complete genome sequences from Colombia and the Americas to map the genomic epidemiology of DENV-2 and DENV-3. Phylogeographic reconstruction revealed multiple independent introductions and exportations of the DENV-2 II and III lineages, as well as the DENV-3 lineage III_C.2, underscoring Colombia's critical role as both a source and a sink of viral traffic within the Americas. Antigenic profiling demonstrated distinct clustering of emergent lineages in antigenic space, consistent with immune-escape-driven turnover. These results highlight the necessity of sustained, high-resolution genomic surveillance to guide targeted public health interventions and mitigate dengue transmission across the region.

El objetivo de este trabajo fue determinar la prevalencia de parásitos intestinales y de hongos dermatofitos en primates en cautiverio (Aoutus sp, Alouatta seniculus y Cebus albifrons) llevados al Centro de Atención y Valoración de Fauna y Flora Silvestre – CAVFFS (Valledupar, Colombia). Se realizaron exámenes de materia fecal y examen directo micológico en muestras de piel y pelo a 17 primates que ingresaron al CAVFFS entre enero y mayo de 2018. Se encontró Entamoeba histolytica (41%), Entamoeba coli (29%), Endolimax nana (24%), Strongyloides sp (18%), Enterobius vermicularis (18%), Ascaris lumbricoides (12%) y Balantidium sp (12%) en las muestras de heces, así como hongos de los géneros Aspergillus, Rhizopus, Candida y Fusarium en las muestras de piel o pelo.

SUMMARY: Dengue fever, a major mosquito-borne viral disease, is transmitted by Aedes mosquitoes and poses a significant global health burden. Despite extensive research, the spatiotemporal dynamics of dengue virus (DENV) lineages in Colombia remain understudied. Here we analyze 11,443 complete genome sequences from Colombia and the Americas to map the genomic epidemiology of DENV-2 and DENV-3. Phylogeographic reconstruction revealed multiple independent introductions and exportations of the DENV-2 II and III lineages, as well as the DENV-3 lineage III C.2, underscoring Colombia’s critical role both as a source and a sink of viral traffic within the Americas. Antigenic profiling demonstrated distinct clustering of emergent lineages in antigenic space, consistent with immune-escape–driven turnover. These results highlight the necessity of sustained, high-resolution genomic surveillance to guide targeted public-health interventions and mitigate dengue transmission across the region.

Since the appearance of the Severe Acute Respiratory Syndrome (SARS) virus, there has been increased interest in understanding the role of bats in the maintenance and circulation of coronaviruses. This study aimed to describe the phylogenetic and evolutionary relationships and antigenic architecture of a new coronavirus detected in bats in the Department of Córdoba. In a surveillance study of pathogens of interest to public health, a bat Phyllostomus hastatus was captured. Rectal swabs samples were collected from the bats, and RNA was extracted and sequenced using NGS with MGI-G50 equipment. The results were analyzed using bioinformatics software. A contig of 28,619 nucleotides associated with the Coronaviridae family was obtained. Phylogenetic and molecular clock analyses of the ORF1ab gene revealed a novel divergent Alphacoronavirus that originated directly from an ancestral node. The analysis of the spike (S) protein and receptor-binding domain (RBD) is similar to that of humans (HCoV-229E) and porcine coronaviruses. In silico analysis suggests potential RBD interaction sites with human and pig cellular receptor aminopeptidase N. There is a possible risk of interspecies jumping of the new AlphaCoV/P. hastatus in humans and pigs. This is the first study to perform phylogenetic, evolutionary, and antigenic characterization of bat coronaviruses in Colombia.

El objetivo del estudio fue determinar la distribución de microorganismos a nivel sanguíneo en gatos y perros ingresados a una clínica veterinaria de la ciudad de Valledupar, Colombia durante el periodo 2016-2018. Se analizaron 957 historias médicas con antecedentes de infecciones hemoparasitarias o bacterianas (847 en perros y 110 en gatos). En perros, se encontró una seroprevalencia de A. platys, Ehrlichia sp, Hepatozoon sp, Babesia sp, Trypanosoma sp y D. immitis de 51.5, 30.9, 22.3, 6.7 y 0.1%, respectivamente. Asimismo, una coinfección en 4.8% en perros. En gatos, M. haemofelis estuvo presente en todos los casos. La diversidad de microorganismos encontrados manifiesta el posible riesgo zoonótico, principalmente por Anaplasma sp, Ehrlichia sp, Hepatozoon sp, Babesia sp y Trypanosoma sp, al que están expuestos los dueños y el personal veterinario en la ciudad de Valledupar.