Sickle cell anemia is a genetic disease with high prevalence in people of African descent. There are five typical haplotypes associated with this disease and the haplotypes associated with the beta-globin gene cluster have been used to establish the origin of African-descendant people in America. In this work, we determined the frequency and the origin of haplotypes associated with hemoglobin S in a sample of individuals with sickle cell anemia (HbSS) and sickle cell hemoglobin trait (HbAS) in coastal regions of Colombia. Blood samples from 71 HbAS and 79 HbSS individuals were obtained. Haplotypes were determined based on the presence of variable restriction sites within the β-globin gene cluster. On the Pacific coast of Colombia the most frequent haplotype was Benin, while on the Atlantic coast Bantu was marginally higher than Benin. Eight atypical haplotypes were observed on both coasts, being more diverse in the Atlantic than in the Pacific region. These results suggest a differential settlement of the coasts, dependent on where slaves were brought from, either from the Gulf of Guinea or from Angola, where the haplotype distributions are similar. Atypical haplotypes probably originated from point mutations that lost or gained a restriction site and/or by recombination events.

Over the last decades, the use of phylogenetic methods in the study of emerging infectious diseases has gained considerable traction in public health. Particularly, the integration of phylogenetic analyses with the understanding of the pathogen dynamics at the population level has provided powerful tools for epidemiological surveillance systems. In the same way, the development of statistical methods and theory, as well as improvement of computational efficiency for evolutionary analysis, has expanded the use of these tools for vaccine and antiviral development. Today with the Coronavirus Disease 2019 (COVID-19), this seems to be critical. In this article, we discuss how the application of phylodynamic analysis can improve the understanding of current pandemic dynamics as well as the design, selection, and evaluation of vaccine candidates and antivirals.

Standard molecular detection of many pathogens, in particular RNA viruses, requires appropriate handling in the field for preserving the quality of the sample until processing. This could be challenging in remote tropical areas. Dengue virus (DENV), chikungunya virus (CHIKV), and Zika virus (ZIKV) are RNA viruses, prominent among the causes of fever in the tropics. We aimed to test the stability of arboviral RNA in contrived dried blood spots prepared on Whatman 903 Protein saver cards as a means of sample collection and storage. We were able to detect DENV, CHIKV, and ZIKV by real-time RT-PCR up to 180 days after card inoculation with stable Ct values across the study period. Our study supports dried blood spots (DBS) on protein saver cards as a platform for stable detection of arboviral RNA of sufficient quality to be used in diagnostic RT-PCR assays and next generation sequencing.

Background: SARS-CoV-2 revealed important gaps in infectious disease surveillance. Molecular epidemiology can help monitor and adapting traditional surveillance to surpass those limitations. This work aims to contrast data-driven from traditional surveillance with parameters inferred from molecular epidemiology in Latin America (LATAM) Methods: We obtained epidemiological data up to 4th June 2020. We estimated Effective Reproductive Number (Re) and epidemic curves using maximum likelihood (ML). SARS-CoV-2 genomes were obtained from GISAID up to June 4th 2020. We aligned sequences and generated ML phylogenetic tree, and ran a coalescent model Birth Death SIR. The phylodynamic analysis was performed for inferring Re, the number of infections and the date of introduction. Findings: A total of 1,144,077 cases were reported up to 4th June 2020. Countries with the largest cumulative cases were Chile, Peru and Panama. We found at least 18 different lineages circulating, with a predominance of B.1 and B.1.1. We inferred an underestimation of the daily incident cases. When contrasting observed and inferred Re, we did not find statistically significant differences except for Chile and Mexico. Temporal analysis of the introduction of SARS-CoV-2 suggested a detection lag of at least 21 days. Interpretation: Our results support that epidemiological and genomic surveillance are two complementary approaches. Even with a low number of genomes, proper estimations of Re could be performed. We suggest that countries, especially developing countries, should consider adding genomic surveillance to their systems for monitoring and adapting epidemiological control of SARS-CoV-2. Funding: None.

Background Age has been a major risk factor for death and complication due to dengue infection (DENV). Although antibody-dependent enhancement (ADE) has been proposed as an explanation, other variables could shape disease outcomes. We aimed to analyze the role of age as a risk factor for disease severity across departments (first administrative level), and epidemic years in Colombia considering poverty and inequity indexes. Methods We conducted a retrospective study analyzing DENV epidemiological data from Colombia between 2012 to 2017, and monetary poverty, extreme poverty, and GINI indexes. Total cases, incidence, incidence of severe DENV, mortality, case- fatality rates (CFR), and complication rates (CR) were calculated for each department and year. The effect of age, department, year of infection, monetary poverty, extreme poverty, and GINI on CR and CFR was evaluated by using a generalized additive model. Results After adjustment, age (p< 0.001), GINI (p< 0.001), monetary poverty (p< 0.001), and extreme poverty(p< 0.001) indexes were significantly associated with the CR, but age was the only variable significantly associated with CFR (p< 0.001). Our results revealed a first peak of CR in patients younger than 5 years old, the second peak in patients between 27 to 34 years old, and a third peak after 45 years old. Conclusion Our work has important implications for future designing of human cohorts analyzing the risk of complications in adults and provides evidence for improving clinical DENV risk assessment. Our findings are consistent with similar observations linking ADE with severe DENV in childhood and suggest protective antibody decay during adulthood. The interplay of biological and socioeconomic factors shaping clinical outcomes in DENV is complex and should be further analyzed Disclosures All Authors: No reported disclosures.