: Dengue virus (DENV) is the etiological agent of dengue fever (DF), which is among the most prevalent vector-borne diseases in the tropics. In 2022, the Colombian health surveillance system reported more than 69,000 cases of DF. As part of a hospital-based fever surveillance study, acute-phase sera were collected from 4,545 patients with suspected dengue between 2020 and 2023 in three municipalities of Colombia. Combined reverse transcription–polymerase chain reaction and antigen rapid testing confirmed that 376 patients (8.3%) had DF. The virus was isolated in cell culture from 166 of these patients (44.1%), and genome sequencing was performed successfully on 122 (73.5%). Three DENV serotypes (1, 2, and 3) were identified. Phylogenetic analyses of the DENV-2 sequences revealed that 42 of 50 of the isolates (84%) belonged to the DENV-2 cosmopolitan genotype lineage, clustering with sequences from Asia, Peru, and Brazil. We report the detection, isolation, and whole-genome sequencing (11 Kb) of the DENV-2 cosmopolitan genotype and its recent introduction to Colombia.

Equine influenza is a viral disease caused by the equine influenza virus (EIV), and according to the WOAH, it is mandatory to report these infections. In Latin America and Colombia, EIV risk factors have not been analyzed. The objective of this research is to perform an epidemiological and molecular analysis of the EIV in horses with respiratory symptoms from 2020 to 2023 in Colombia. Molecular EIV detection was performed using RT–qPCR and nanopore sequencing. A risk analysis was also performed via the GEE method. A total of 188 equines with EIV respiratory symptoms were recruited. The positivity rate was 33.5%. The descriptive analysis showed that only 12.8% of the horses were vaccinated, and measures such as the quarantine and isolation of symptomatic animals accounted for 91.5% and 88.8%, respectively. The variables associated with the EIV were the non-isolation of positive individuals (OR = 8.16, 95% CI (1.52–43.67), p = 0.014) and sharing space with poultry (OR = 2.16, 95% CI (1.09–4.26), p = 0.027). In conclusion, this is the first EIV investigation in symptomatic horses in Colombia, highlighting the presence of the virus in the country and the need to improve preventive and control measures.

Influenza A viruses (IAV) impose significant respiratory disease burdens in both swine and humans worldwide, with frequent human-to-swine transmission driving viral evolution in pigs and highlighting the risk at the animal-human interface. Therefore, a comprehensive One Health approach (interconnection among human, animal, and environmental health) is needed for IAV prevention, control, and response. Animal influenza genomic surveillance remains limited in many Latin American countries, including Colombia. To address this gap, we genetically characterized 170 swine specimens from Colombia (2011-2017). Whole genome sequencing revealed a predominance of pandemic-like H1N1 lineage, with a minority belonging to H3N2 and H1N2 human seasonal-like lineage and H1N1 early classical swine lineages. Significantly, we have identified reassortant and recombinant viruses (H3N2, H1N1) not previously reported in Colombia. This suggests a broad genotypic viral diversity, likely resulting from reassortment between classical endemic viruses and new introductions established in Colombia's swine population (e.g. the 2009 H1N1 pandemic). Our study highlights the importance of a One Health approach in disease control, particularly in an ecosystem where humans are a main source of IAV to swine populations, and emphasizes the need for continued surveillance and enhanced biosecurity measures. The co-circulation of multiple subtypes in regions with high swine density facilitates viral exchange, underscoring the importance of monitoring viral evolution to inform vaccine selection and public health policies locally and globally.

Background: Human Adenovirus (HAdV) is a common cause of acute respiratory infections, typically mild in healthy individuals. However, in late 2022, an outbreak of severe acute respiratory infection caused by HAdV emerged among children in Colombia and other countries. Methods: We described an HAdV outbreak between February 2022 and April 2023. Children with severe acute respiratory infection and HAdV infection confirmed by polymerase chain reaction were included in 4 institutions in Antioquia, Colombia. Our study investigated the clinical manifestations and circulating HAdV genotypes before, during and after this HAdV outbreak. Results: A total of 133 HAdV cases were analyzed, 37 (27.8%) cases were classified as the preoutbreak group, 88 (66.1%) as the outbreak and 8 (6.0%) as the postoutbreak group. Predominant symptoms were fever (87.0%), rhinorrhea (57.1%) and dyspnea (36.8%). The need for intensive care unit admission and supplemental oxygen increased during the outbreak and peaked in the postoutbreak period. Phylogenetic analysis revealed that 71.4% (10/14) of preoutbreak sequences belonged to genotype HAdV-C89, while during the outbreak, 75.6% (28/37) were HAdV-B3. Clinical symptoms did not significantly differ between HAdV-C89 and HAdV-B3 infections, but children infected with HAdV-B3 were significantly older. Conclusions: This study highlights the shifting dynamics of HAdV genotypes in children and their epidemiologic impact. The emergence of HAdV-B3 in the post-COVID-19 period contributed to a severe acute respiratory infection outbreak, emphasizing the need for ongoing surveillance.

Introducción. El coronavirus del SARS-CoV-2 ha sido una de las pandemias más significativas de la era moderna. Es un coronavirus con alta tasa de mutación, lo que genera variantes con cambios en la proteína espícula (spike), que dificulta su contención. La vigilancia genómica es crucial para adaptar estrategias de salud pública y vacunación, especialmente en los países de ingresos bajos y medios, donde el impacto ha sido considerable.Objetivo. Identificar variantes virales y sus presentaciones clínicas en una cohorte prospectiva de pacientes hospitalizados con infección por SARS-CoV-2 entre octubre de 2021 y febrero de 2023.Materiales y métodos. Se recopilaron datos demográficos, historial médico, estado de vacunación y progresión clínica. Se hizo secuenciación del genoma viral en muestras de hisopados nasales confirmadas con la prueba de reacción en cadena de la polimerasa en tiempo real con transcripción inversa para clasificar las cepas y detectar variantes.Resultados. De 63 muestras positivas para SARS-CoV-2, la variante predominante fue ómicron (84 %), seguida de la delta (14 %). La variante delta presentó la mayor proporción de enfermedad grave (100 % casos críticos) comparada con ómicron (30 % casos críticos). Se identificaron mutaciones en la proteína espícula en cuatro categorías (A-D), junto con mutaciones específicas del gen S.Conclusión. Los patrones de mutación observados coinciden con los reportes globales, con mayor seriedad clínica en la variante delta. Se identificaron mutaciones en la proteína espiga que confieren propiedades distintivas al virus. Estos hallazgos resaltan la necesidad de la vigilancia genómica continua para comprender la dinámica de la infección y orientar las estrategias de salud pública.

In early 2024, explosive outbreaks of Oropouche virus (OROV) linked to a novel viral lineage were documented in the Brazilian Amazon. Here, we report the introduction of this emerging orthobunyavirus into Colombia and its co-circulation with another OROV lineage. This investigation highlights the complex arbovirus dynamics in South America.