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.

Introduction. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been one of the most significant pandemics of the modern era. This coronavirus has a high mutation rate, resulting in variants with changes in the spike protein, which hinder containment efforts. Genomic surveillance is crucial for public health and vaccination strategies, especially in lowand middle-income countries, where the impact has been considerable. Objective. To identify viral variants and their clinical presentations in a prospective cohort of hospitalized patients with SARS-CoV-2 infection between October 2021 and February 2023. Materials and methods. We collected patients’ demographic data, medical histories, vaccination status, and clinical progression. Viral genome sequencing was performed on nasopharyngeal swab samples confirmed by real-time reverse transcription polymerase chain reaction to classify strains and detect variants. Results. The predominant variant in the 63 SARS-CoV-2-positive samples was omicron (84%), followed by delta (14%). A higher proportion of critical illness was observed in delta cases (100%) compared to omicron (30%). Mutations in the spike protein were identified and classified into four categories (A-D), along with specific mutations in the S gene. Conclusion. The mutational patterns observed in this study are consistent with global reports, with delta cases presenting greater clinical severity. We identified spike protein mutations that may confer distinctive properties to the virus. These findings underscore the need for ongoing genomic surveillance to better understand viral dynamics and guide public health strategies.

Introduction:To comply with biosafety regulations for the transport of wild-caught common vampire bats (Desmodus rotundus) by land from San Luis Potosí, Mexico to Madison, Wisconsin, USA, we designed a unique container that allowed for feeding (with bovine blood) while maintaining a sealed environment and preventing escape of animals or potential sources of infectious materials (e.g., spills, aerosols). Methods:The container was designed by modifying a commercially available mouse transport container and installing a tube/syringe system that allowed delivering and retrieving the blood during the feeding session and cleaning afterward. We transported 93 vampire bats in ten transport containers with no more than ten individuals per container. Conclusion:During transit, the vampire bats acclimated well to the novel environment and were able to access blood during feeding. Although one bat was found dead on arrival, the remaining 92 were transported without complications and deposited at a biosafety level 3 facility once in the U.S.

Yellow fever virus (YFV) is an arbovirus that causes acute febrile illness (AFI), in tropical areas of South America and Africa. Through a 2020-2023 AFI study in Leticia, Colombia, leveraging metagenomic next-generation sequencing (mNGS), we identified and isolated YFV (LET1450). Phylogenetic analysis showed this strain belongs to South American genotype II (SamII), linked to Peruvian and Bolivian sequences emerging around 1989. Phylodynamic analysis indicates these strains, with a unique genetic makeup, could have reduced vaccine susceptibility, and due to positive Darwinian selection have an enhanced adaptive capacity. Antigenic analysis identified additional immune-evasive traits and this strain's potential for wider Latin American spread. Phylogeographic reconstruction demonstrated the persistence of YFV in Colombia is not due to repeated external introductions, but results from continuous, cryptic internal circulation. This study highlights the crucial role of mNGS in monitoring emerging strains and underscores the need for genomic surveillance of YFV and other arboviral infections.

Objectives Surveillance of acute respiratory infection (ARI) informs vaccination, preventive, and management decisions. In many countries, immunofluorescence is the cornerstone for ARI surveillance. We aimed to determine the effect of adding multiplex polymerase chain reaction (mPCR) to conventional surveillance in ARI.Methods Respiratory samples from patients with influenza-like illness (ILI) and severe acute respiratory infection (SARI) were tested by a conventional approach [direct immunofluorescence (DIF) and SARS-CoV-2 PCR, and a subset of samples underwent routine testing]. Negative specimens were tested by multiplex PCR (mPCR), and remain negative samples were sequenced. Descriptive, multivariable regression analyses were conducted.Results Between March and June 2022, 299 patients were enrolled. Pathogens were detected in 43.8% of samples (131/299) tested by the conventional approach. Of the 168 negatives after the conventional approach, 157 (93.4%) were positive by mPCR, increasing the detection rate to 96.3% (288/299). With the conventional approach, the most frequent pathogen was respiratory syncytial virus (50.3%, 66/131), whereas with mPCR it was Haemophilus influenzae (37.5%, 63/168). mPCR significantly improved pathogen detection in ARI surveillance (Adjusted Incidence Rate Ratios 4.22 95% IC 4.22-5.85).Conclusion Adding mPCR to respiratory surveillance conventionally based on DIF significantly enhanced virus and bacteria detection. mPCR should be considered for routine ARI surveillance.

Abstract Background Adenovirus (HAdV) is a common cause of acute respiratory infection (ARI). In healthy people, infections are usually mild and self-limiting. However, during the second half of 2022, an HAdV severe acute respiratory infection (SARI) outbreak occurred in Colombia. Although HAdV epidemiological data in South America is scarce, SARS-CoV-2 pre-pandemic studies reported HAdV-B3 as the main cause of respiratory adenoviral infections. Our study investigated the circulating HAdV genotype before, during, and after this outbreak along with clinical data associated.Figure 1. Tracking of HAdV Severe Acute Respiratory Infection in Antioquia, February 2022 to April 2023 The quarterly distribution of various human adenovirus genotypes in Antioquia-Colombia starting from the first quarter of 2022 to the second quarter of 2023. Areas represent the percentage prevalence of strains obtained in each quarter: HAdV-C89 (red), HAdV-C1 (green), HAdV-B78 (yellow), HAdV-C5 (purple), HAdV-B3 (blue), HAdV-B7 (orange), and all HAdV SARI cases enrolled (grey). Methods During February 2022 and April 2023, children with HAdV SARI were enrolled after medical attention. Inclusion criteria were respiratory symptoms onset within 15 days and HAdV PCR positive test result. After written informed consent, a nasopharyngeal aspirate was collected. Respiratory Pathogen ID/AMR Enrichment Panel Kit was used to sequence samples collected before the outbreak while those collected during and after the outbreak were sequenced using hexon gene-specific primers. Descriptive analysis of study data and phylogenetic analysis of the sequences were done.Table 1.Clinical Characteristics of Children with HAdV Acute Respiratory Infection in Antioquia in the Pre-Outbreak, Outbreak and After-Outbreak Results A total of 133 patients were enrolled, from whom 54 samples were sequenced. The outbreak started in the second week of July, reached its peak between August and September, and concluded by the end of December. The median age was 2 years old (IQR 1-4). During the outbreak, 63/88 patients had comorbidities, 25/88 developed pneumonia, and 17/88 required critical care attention. Pre-outbreak period, most sequences (71.4%, 10/14) were phylogenetically classified as the novel genotype HAdV-C89, while during and after the outbreak the majority (85.0%, 34/40) were HAdV-B3 genotype.Figure 2. Serotype and Genotype Phylogenetic Relationships of HAdV Maximum Likelihood trees were constructed using the IQ-Tree V 2.3.3 program with ultrafast bootstrapping (UFBoot) and 1,000 replicates. ModelFinder was calculated as the best-fit substitutional model according to Bayesian information criteria. Strains from this study were categorized by symbols corresponding to their respective batches: pentagons, stars, and circles representing strains from pre-outbreak, outbreak, and post-outbreak respectively. Red stars correspond to co-detection B3/C1. Each tree was constructed as follows: A) Phylogenetic tree of partial hexon sequence from A – G HAdV serotypes. B) B Genotypes phylogenetic tree of hexon partial sequence. C) C Genotypes phylogenetic tree of hexon partial sequence. D) C2 and C89 Genotypes phylogenetic tree of full penton sequence. Bootstrap values greater than 80 are shown in the branches. Conclusion Our result indicated that the novel HAdV-C89 genotype was causing SARI in Antioquia (Colombia) during the first half of 2022, after it was displaced by the re-emergence of HAdV-B3, causing an increase of HAdV SARI. Once discontinuing the pandemic measures, commonly known respiratory pathogens can re-emerge, therefore monitoring of those should be intensified.Table 2.Comparison of Demographic, Clinical Features, and Outcomes between Children with HAdV-C89 and B3 Respiratory Infection Disclosures Maria Angelica Maya, MD, Abbott: Grant/Research Support Francisco Averhoff, MD, MPH, Abbott Laboratories: Employee Michael G. Berg, PhD, Abbott Laboratories: employee|Abbott Laboratories: Stocks/Bonds (Public Company)

Dengue fever is a mosquito-borne viral disease rapidly creating a significant global public health burden, particularly in urban areas of tropical and sub-tropical countries. Hydroclimatic variables, particularly local temperature, precipitation, relative humidity, and large-scale climate teleconnections, can influence the prevalence of dengue by impacting vector population development, viral replication, and human-mosquito interactions. Leveraging predictions of these variables at lead times of weeks to months can facilitate early warning system preparatory actions such as allocating funding, acquisition and preparation of medical supplies, or implementation of vector control strategies. We develop hydroclimate-based statistical forecast models for dengue virus (DENV) at 1-, 3-, and 6- month lead times for four cities across Colombia (Cali, Cúcuta, Medellín, and Leticia) and compare with standard autoregressive models conditioned on dengue case counts. Our results indicate that (a) hydroclimate-based models are particularly skillful at 3- and 6- month lead times when autoregressive models often fail, (b) sea surface temperatures are the most skillful predictor at 3- and 6- month leads and (c) application of hydroclimate models are most beneficial when average DENV incidence is low, autoregressive relationships are weak, but outbreaks may still occur.

Indigenous populations advocate for collaborative research principles that they help define. Ethical engagement with these communities improves health outcomes while creating beneficial partnerships between researchers and Indigenous peoples. This article outlines key principles for ethical health research with Indigenous Peoples and Ethnic Groups in Colombia, emphasizing bilateral communication, respect for cultural values and traditional knowledge, responsible biodiversity use, community participation, and autonomy. These principles provide a framework for conducting respectful, beneficial, culturally relevant, and ethical research. Based on experience and consultation, the article offers good practices to guide researchers and train health professionals, promoting equitable research relationships with Indigenous communities.

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. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement This research was supported by the Global Health Institute of the University of Wisconsin-Madison, the National University of Colombia-Medellin, and the virus discovery research program of the Abbott Pandemic Defense Coalition (APDC). ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: The protocol for this study was approved by the ethics committee of the Corporacion de Investigaciones Biologicas (SC-6230-1) in Colombia I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes All data produced in the present work are contained in the manuscript

Dengue virus (DENV) is a significant public health concern in Colombia, with increased transmission of DENV type 1 (DENV-1) in the departments of Risaralda and Valle del Cauca in the Central-West region of the country following a large outbreak in 2019. However, little is known about the source, genetic diversity, and evolution of circulating viruses. We obtained serum samples from individuals with acute DENV infection and analysed DENV-1 genetic diversity, phylodynamics, and phylogeography. We found that most viruses belonged to DENV-1 genotype V, and phylogenetic analysis revealed three distinct clades, each of which was most closely related to viruses from neighbouring departments of Colombia sampled over the last 5-10 years. Thus, the 2019 outbreak and subsequent DENV-1 circulation was not due to the introduction of a new lineage to the country but rather reflected local DENV-1 V dispersion and evolution. We identified amino acid positions under positive selection in structural proteins and NS1, which may have a role in immune evasion and pathogenesis. Overall, our analysis of DENV-1 V diversity, evolution, and spread within Colombia highlights the important role of genomic surveillance in understanding virus dynamics during endemic circulation and outbreaks.

[This corrects the article DOI: 10.1371/journal.pntd.0011642.].

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.

Upon the pandemic transitioning into a new phase, research into the immune pathophysiology of severe and critical coronavirus disease 2019 has become increasingly crucial. Such studies are pivotal in shaping advanced treatment strategies and driving the development of innovative therapeutics, including more effective vaccines targeting the virus. High-risk comorbidities and pre-existing immunocompromised states have been identified as significant factors contributing to increased susceptibility to severe coronavirus disease 2019. Moreover, cases of severe infections, particularly those characterized by relapses or viral persistence, provide invaluable insights into the evolving behavior and dynamics of this pathogen. We report three cases involving mixed-race Colombian female patients aged 58, 35, and 63 years who experienced multiple episodes of coronavirus disease 2019 infection, with the most recent episode progressing to critical illness. These cases were characterized by relapses or persistent infections, and genomic analyses consistently identified the Omicron severe acute respiratory syndrome coronavirus 2 lineage as the causative variant. Notably, individuals with underlying immunosuppressive conditions developed severe acute respiratory syndrome coronavirus 2 infections that were more severe, leading to fatal outcomes that included acute respiratory distress syndrome, multiorgan dysfunction, and death. In contrast, one vaccinated patient with significant comorbidities exhibited persistent critical coronavirus disease 2019 but responded positively to treatment with tocilizumab. The key takeaway is the critical need for continued investigation into coronavirus disease 2019 among individuals with high-risk comorbidities and those undergoing immunosuppressive therapy. Recurrent episodes of infection, including cases marked by relapses or persistent viral presence in these populations, create conditions conducive to viral replication and adaptation. Such environments may potentially act as breeding grounds for the emergence of significant new viral mutations.

Rabies vaccination of vampire bats ( Desmodus rotundus ) has been proposed as a superior control method to culling but has yet to be implemented. Success of rabies vaccination depends on a topical vehicle that spreads through a bat colony via allogrooming while additionally preserving vaccine immunogenicity. This work describes the in vitro and in vivo optimization of a new orotopical gel for rabies vaccine delivery to vampire bats. Autonomous transferability of our carboxymethyl cellulose (CMC) gel vaccine delivery formulation was tested in a microchipped vampire bat colony in rural Jalisco, Mexico. Intra-colony gel uptake was traced using the fluorescent biomarker rhodamine B. Importantly, application of topical treatment of ∼20% of the bat colony resulted in estimated uptake by over 85% of the colony. The in vitro stability of our raccoon poxviral-vectored rabies vaccine candidate within CMC was measured at time points up to 3 months at 40 °C, 23 °C, and 4 °C. Extended storage at 4 °C and short exposure at higher temperatures of potential vampire bat environments preserved vaccine titers within CMC. Furthermore, physical properties of our CMC formulation were compared to the previously used glycerin jelly at 40 °C, 20 °C, and 0 °C using rheological tests. These tests indicate that CMC exhibits optimal properties for topical application to bats even at extreme temperatures possible during field vaccination. This study advances our rabies vaccination strategy for vampire bats by providing a topical vehicle suitable for field application that may additionally be employed for other significant bat diseases. ### Competing Interest Statement The authors have declared no competing interest. NSF/BBSRC Ecology and Evolution of Infectious Diseases Program, DEB 2011069, BB/V003798/1 NSF, DMR-1121288, 0079983, 0520057, 0832760, and 0425880 Wellcome Trust, https://ror.org/029chgv08, 217221/Z/19/Z Virus Cross Species Transmission Programme, MC\_UU\_00034/3 University of Wisconsin Madison Comparative Biomedical Sciences Student Travel Award

ABSTRACT To effectively curb coronavirus disease 2019 (COVID‐19), it is essential to understand the risk factors for breakthrough acute infections of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS‐CoV‐2) despite vaccination. We conducted a case‐control study to assess risk factors for acute SARS‐CoV‐2 infections requiring hospitalization in vaccinated individuals. The study included 50 vaccinated patients who experienced breakthrough infections requiring hospitalization (inpatient cohort) and 250 control participants from the outpatient cohort of the “Genomic Surveillance and Immune Response Monitoring for COVID‐19 in the Metropolitan Area of the Aburrá Valley, Medellín‐Colombia”. Demographic characteristics, vaccination status, and immune responses were compared between cases and controls using multivariate logistic regression. Advanced age (≥ 65 years), male sex, high‐risk comorbidities, and immunosuppression were associated with an increased risk of breakthrough SARS‐CoV‐2 infections despite prior vaccination. In contrast, receipt of a booster dose and the presence of neutralizing antibodies were linked to a reduced risk of such infections. This study identifies key risk and protective factors associated with breakthrough SARS‐CoV‐2 infections. Derived from a high–middle‐income setting, these real‐world findings provide valuable insights to guide targeted vaccination strategies for vulnerable populations.

Before Zika virus (ZIKV) infections were observed in the Americas, an association between ZIKV and microcephaly or other congenital malformations was not well documented. Initial reports suggested strong associations between ZIKV and congenital malformations, but plausible estimates of causal effects from prospective studies with adequate sample size and covariate data were few. From 2016–2018, the Zika in Infants and Pregnancy (ZIP) study enrolled pregnant people before 18 weeks gestation or with confirmed symptomatic ZIKV in a prospective cohort across 10 sites in South and Central America, and in Puerto Rico. Pregnancies were followed monthly through delivery and 6 weeks postpartum. Infants were followed quarterly to age 12 months. Prespecified co-primary analyses evaluated the associations between a composite endpoint of adverse fetal, neonatal, and infant outcomes with intrauterine ZIKV exposure overall and with symptomatic intrauterine ZIKV exposure. Secondary analyses separately evaluated the association of intrauterine ZIKV exposure with individual components of the primary endpoint. Six thousand one hundred pregnant participants were included in the primary analysis, including 61 with ZIKV infection during pregnancy confirmed by a ZIKV-specific RNA test. For the primary analyses, the relative risk (RR) for the composite endpoint associated with any ZIKV exposure was 1.64 (95

IntroductionMayaro Fever (MF) is a tropical disease caused by the Mayaro virus (MAYV), with outbreaks documented in Latin America.MethodsA hospital-based fever surveillance in Leticia, Colombian Amazon, collected sera from 1,460 patients aged 5-89 between December 2020 and April 2023.ResultsDengue and malaria were the main diagnoses (19.4 and 5.8%, respectively), leaving 71.4% of cases unidentified after testing. Metagenomic sequencing and real-time RT-qPCR testing identified MAYV in two patients (25-year-old male and an 80-year-old female) exhibiting typical symptoms, of MF including rash, joint pain, and fever. Phylogenetics analysis of these two viruses revealed a close relationship to Peruvian strains within the MAYV D genotype.DiscussionThe study of AFI in Leticia, Colombia, identified dengue as prevalent, with malaria, COVID-19, Influenza, and Zika viruses also detected. Despite extensive testing, most cases remained unexplained until metagenomic sequencing revealed MAYV, previously unseen in Colombia but known in neighboring countries.ConclusionThis study presents the first near full-length genomes of MAYV in Colombia, highlighting the need for further seroprevalence studies and enhanced surveillance to understand and control the spread of the virus in the region.