Biology subjects

Ramirez, J. D.

Publications and source records attributed to Ramirez, J. D..

4 recordsLinked to original sources

bioRxiv2025

Genomic Characterization of a Locally Transmitted Leishmania mexicana Isolate from Texas

Cutaneous leishmaniasis (CL) is caused by Leishmania species transmitted by sand flies. Although considered a neglected tropical disease, growing evidence indicates that local transmission can occur in subtropical, higher-resource regions where sand fly vectors are present, including the southern United States. Here, we report the first whole-genome sequence of Leishmania mexicana from an autochthonous U.S. case--a 3-year-old boy from Ellis County, Texas, with no travel history. Genomic DNA was extracted from a skin biopsy specimen and sequenced using Illumina technology. Phylogenomic analysis based on nuclear and mitochondrial SNPs confirmed the isolate as L. mexicana, clustering with other members of the L. mexicana complex. The parasite exhibited a predominantly disomic karyotype, with chromosome 30 displaying trisomy. We identified 172 genes with significant copy number variations, including genes involved in ubiquitination, nucleic acid metabolism, and protein translation. Additionally, 53,964 SNPs were detected, over 22,000 of which were predicted to have moderate or high functional impact, affecting genes linked to host-pathogen interactions, metabolic pathways, and signal transduction. This study provides the first genomic characterization of a locally acquired L. mexicana strain in the U.S. and underscores the value of molecular surveillance and increased clinical awareness of leishmaniasis in subtropical regions where competent vectors are present.

microbiology↗

bioRxiv2024

Bats from the Colombian Caribbean Reveal a new subtype of Influenza A (H18N12)

Influenza viruses have an excellent capacity for mutation and adaptation in mammalian hosts, which makes them viruses of medical and veterinary importance. Influenzaviruses have been studied mainly in birds but minor in bats. It is unknown whether Chiroptera are reservoirs of influenza viruses. However, circulation in bats showed molecular divergence from H17N10 (Guatemala) and H18N11 (Peru), and they were designated as new subtypes. The study aimed to characterize the influenza A virus detected in the fishing bat Noctilio albiventris. A surveillance study of pathogens of public health interest was carried out; rectal samples were taken from four fishing bats (N. albiventris) captured in Talaigua Nuevo, Bolivar, Colombia. The samples were sequenced by NGS using DNBseq (MGI-G50(R)) and analyzed with bioinformatics tools. Eight viral contigs associated with the Orthomyxoviridae family were obtained. The identified segments showed around 90% similarity with H18N11, except for the neuraminidase (N). The phylogenetic analysis of the N protein showed the appearance of a basal branch to the N11 subtype, and the molecular clock indicates that it does not share a recent common ancestor. 3D modeling indicates that the N protein of N. albiventris presents three mutations (K363R, T242K, and I139V) near the hypothetical active site of the protein. These mutations potentially increase the interaction with the HLA-DR of bats, which could have significant implications for the viruss behavior. The phylogenetic, evolutionary, and antigenic divergence of the N protein of N. albiventris suggests a new subtype called H18N12. Its role as a pathogen must be studied.

bioinformatics↗

bioRxiv2018

Genomic epidemiology supports multiple introductions and cryptic transmission of Zika virus in Colombia

BackgroundColombia was the second most affected country during the American Zika virus (ZIKV) epidemic, with over 109,000 reported cases. Despite the scale of the outbreak, limited genomic sequence data were available from Colombia. We sought to sequence additional samples and use genomic epidemiology to describe ZIKV dynamics in Colombia.\n\nMethodsWe sequenced ZIKV genomes directly from clinical diagnostic specimens and infected Aedes ae-gypti samples selected to cover the temporal and geographic breadth of the Colombian outbreak. We performed phylogeographic analysis of these genomes, along with other publicly-available ZIKV genomes from the Americas, to estimate the frequency and timing of ZIKV introductions to Colombia.\n\nResultsWe attempted PCR amplification on 184 samples; 19 samples amplified sufficiently to perform sequencing. Of these, 8 samples yielded sequences with at least 50% coverage. Our phylogeo-graphic reconstruction indicates two separate introductions of ZIKV to Colombia, one of which was previously unrecognized. We find that ZIKV was first introduced to Colombia in February 2015 (95%CI: Jan 2015 - Apr 2015), corresponding to 5 to 8 months of cryptic ZIKV transmission prior to confirmation in September 2015. Despite the presence of multiple introductions, we find that the majority of Colombian ZIKV diversity descends from a single introduction. We find evidence for movement of ZIKV from Colombia into bordering countries, including Peru, Ecuador, Panama, and Venezuela.\n\nConclusionsSimilarly to genomic epidemiologic studies of ZIKV dynamics in other countries, we find that ZIKV circulated cryptically in Colombia. This more accurate dating of when ZIKV was circulating refines our definition of the population at risk. Additionally, our finding that the majority of ZIKV transmission within Colombia was attributable to transmission between individuals, rather than repeated travel-related importations, indicates that improved detection and control might have succeeded in limiting the scale of the outbreak within Colombia.

genomics↗

bioRxiv2018

Repeat-driven generation of antigenic diversity in a major human pathogen, Trypanosoma cruzi

Trypanosoma cruzi, a zoonotic kinetoplastid protozoan with a complex genome, is the causative agent of American trypanosomiasis (Chagas disease). The parasite uses a highly diverse repertoire of surface molecules, with roles in cell invasion, immune evasion and pathogenesis. Thus far, the genomic regions containing these genes have been impossible to resolve and it has been impossible to study the structure and function of the several thousand repetitive genes encoding the surface molecules of the parasite. We here present an improved genome assembly of a T. cruzi clade I (TcI) strain using high coverage PacBio single molecule sequencing, together with Illumina sequencing of 34 T. cruzi TcI isolates and clones from different geographic locations, sample sources and clinical outcomes. Resolution of the surface molecule gene structure reveals an unusual duality in the organisation of the parasite genome, a core genomic region syntenous with related protozoa flanked by unique and highly plastic subtelomeric regions encoding surface antigens. The presence of abundant interspersed retrotransposons in the subtelomeres suggests that these elements are involved in a recombination mechanism for the generation of antigenic variation and evasion of the host immune response. The comparative genomic analysis of the cohort of TcI strains revealed multiple cases of such recombination events involving surface molecule genes and has provided new insights into T. cruzi population structure.

genomics↗