Biology subjects

Vogels, C. B.

Publications and source records attributed to Vogels, C. B..

3 recordsLinked to original sources

bioRxiv2025

TICKHUNTER: A Targeted Hybridization-Capture Sequencing Approach for the Detection and Characterization of Tick-borne Pathogens and Blood Meals

As weather systems quickly change, vector communities and their pathogens evolve faster than assay panels can be redesigned. Additionally, PCRs narrow target range makes it structurally unable to catch divergent or reassorted agents. We developed a hybrid capture next-generation sequencing enrichment platform that provides comprehensive detection and characterization of tick-borne agents alongside ecological vertebrate host identification with low-pass sequencing. Analytical validation demonstrated performance comparable to qPCR with superior variant tolerance and multiplexing capacity. Field deployment in subtropical, metropolitan New York detected Anaplasma phagocytophilum strains (n=3) linked to human granulocytic anaplasmosis and a Babesia microti-like species in urban raccoon (Procyon lotor) populations. Tick vector screening revealed a putatively novel chimeric Flavi-like virus in invasive Haemaphysalis longicornis ticks combining segmented and unsegmented genomic features, with codon adaptation analysis indicating strong human compatibility. Serology revealed high Flavivirus seropositivity in NYC raccoons, suggesting an unrecognized urban reservoir role. Blood meal analysis simultaneously revealed complex ecological pathogen transmission networks spanning multiple vertebrate hosts. This integrated surveillance system enables comprehensive pathogen discovery, real-time evolutionary monitoring, and ecological risk assessment, transforming our capacity to detect emerging tick-borne threats in rapidly changing environments and prevent spillovers.

microbiology↗

bioRxiv2020

Detection of long SARS-CoV-2 nucleocapsid sequences in peripheral blood monocytes collected soon after hospital admission

Many viruses infect circulating mononuclear cells thereby facilitating infection of diverse organs. Blood monocytes (PBMC) are being intensively studied as immunologic and pathologic responders to the new SARS-CoV-2 virus (CoV19) but direct evidence showing CoV19 in monocytes is lacking. Circulating myeloid cells that take up residence in various organs can harbor viral genomes for many years in lymphatic tissues and brain, and act as a source for re-infection and/or post-viral organ pathology. Because nucleocapsid (NC) proteins protect the viral genome we tested PBMC from acutely ill patients for the diagnostic 72bp NC RNA plus adjacent longer (301bp) transcripts. In 2/11 patient PBMC, but no uninfected controls, long NCs were positive as early as 2-6 days after hospital admission as validated by sequencing. Pathogenic viral fragments, or the infectious virus, are probably disseminated by rare myeloid migratory cells that incorporate CoV19 by several pathways. Predictably, these cells carried CoV19 to heart and brain educing the late post-viral pathologies now evident.

microbiology↗

bioRxiv2018

International travelers and genomics uncover a ‘hidden’ Zika outbreak

The ongoing Zika epidemic in the Americas has challenged public health surveillance, response, and control systems. Even as the epidemic appears to be near its end in the Americas, it is unclear whether substantial Zika virus transmission may still be ongoing. This issue is exacerbated by large discrepancies in local case reporting and significant delays in detecting outbreaks due to surveillance gaps. To uncover locations with lingering outbreaks in the Americas, we investigated travel-associated Zika cases diagnosed in the United States and Europe to identify signatures of transmission dynamics that were not captured by local reporting. We found that a large and unreported Zika outbreak occurred in Cuba during 2017, a year after peak transmission in neighboring countries, with cases still appearing in 2018. By sequencing Zika virus from infected travelers, we show that the 2017 outbreak in Cuba was sparked by long-lived lineages of Zika virus introduced from multiple places in the Americas a year prior. Our data suggest that while aggressive mosquito control in Cuba may initially have been effective at mitigating Zika virus transmission, in the absence of vaccines, herd immunity, or strong international coordination, such control measures may need to be maintained to be effective. Our study highlights how Zika virus may still be silently spreading in the Americas and provides a framework for more accurately understanding outbreak dynamics.

epidemiology↗