Arbovirus infections are frequent causes of acute febrile illness (AFI) in tropical countries. We conducted health facility based AFI surveillance at four sites in Colombia (Cucuta, Cali, Villavicencio, Leticia) during 2019-2022. Demographic, clinical and risk factor data were collected from persons with AFI that consented to participate in the study (n=2,967). Serologic specimens were obtained and tested for multiple pathogens by RT-PCR and rapid test (Antigen/IgM), with 20.7% identified as dengue positive from combined testing. Oropouche virus (OROV) was initially detected in serum by metagenomic next generation sequencing (mNGS) and virus target capture in a patient from Cúcuta. Three additional infections from Leticia were confirmed by conventional PCR, sequenced, and isolated in tissue culture. Phylogenetic analysis determined there have been at least two independent OROV introductions into Colombia. To assess OROV spread, a RT-qPCR dual-target assay was developed which identified 87/791 (10.9%) viremic cases in AFI specimens from Cali (3/53), Cucuta (3/19), Villavicencio (38/566), and Leticia (43/153). In parallel, an automated anti-nucleocapsid antibody assay detected IgM in 27/503 (5.4%) and IgG in 92/568 (16.2%) patients screened, for which 24/68 (35.3%) of PCR positives had antibodies. Dengue was found primarily in people aged <18 years and linked to several clinical manifestations (weakness, skin rash and petechiae), whereas Oropouche cases were associated with the location, climate phase, and odynophagia symptom. Our results confirm OROV as an emerging pathogen and recommend increased surveillance to determine its burden as a cause of AFI in Colombia. GRAPHICAL ABSTRACT

: 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.

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.

Background: Despite hybrid and vaccine-induced immunity, SARS-CoV-2 continues to cause disease. The characterization of humoral and cellular immune responses is essential for guiding prevention strategies and booster dose policies; Methods: A prospective cohort study was conducted with 131 hospitalized patients with confirmed COVID-19 in the Aburrá Metropolitan Valley, Colombia. Clinical and immunological data were evaluated on days 1–3, days 5–7, days 8–12, and 4–5 months after diagnosis. Humoral immunity was assessed by enzyme-linked immunosorbent assay (ELISA), chemiluminescent microparticle immunoassay (CMIA), and neutralization testing, and cellular immunity by CD4⁺/CD8 T-cell responses. Results: vaccinated patients had higher baseline levels of IgG and neutralizing antibody positivity than unvaccinated patients (ELISA 89.1% vs. 60.0%; CMIA 86.4% vs. 50.0%; neutralizing antibodies 88.2% vs. 65.0%), but cases of severe disease occurred in both groups. Adults aged ≥65 years had higher antibody positivity, but severe disease persisted. Mortality at 28 days was 7.6%, mainly among critically ill patients with comorbidities. Antibodies persisted at 4–5 months but were lower in those with severe acute disease. Those who received the booster dose showed stronger CD4⁺/CD8⁺ activation (notably against the Omicron variant) than unvaccinated/partially vaccinated patients. Conclusions: Vaccination improved humoral and cellular responses, but severe breakthrough infections still occurred, particularly in high-risk patients.

Oropouche virus (OROV), an arthropod-borne virus, has reemerged in the Americas. In 2023-2024, the largest quantitative reverse-transcription PCR (RT-qPCR)-confirmed outbreak of OROV was reported and was associated with severe clinical outcomes for the first time. Moreover, a dramatic increase in cases is unfolding in early 2025. Here, we provide a protocol for detecting OROV from human serum. We describe steps for viral isolation, titration, and an in-house RT-qPCR validated in the field. We then detail procedures for measurement of anti-OROV-neutralizing antibodies. For complete details on the use and execution of this protocol, please refer to Ciuoderis et al.¹ and Usuga et al.².