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McCaffrey, K.

Publications and source records attributed to McCaffrey, K..

3 recordsLinked to original sources

Molecular basis for protection and cross-protection by human antibodies targeting the parainfluenza virus hemagglutinin-neuraminidase protein

Human parainfluenza viruses (PIVs) are a leading cause of respiratory illness, particularly in vulnerable populations where infection can lead to severe disease. Despite their clinical impact, there are currently no licensed vaccines or effective antiviral treatments available. PIVs have two large surface proteins, the fusion and hemagglutinin-neuraminidase (HN) proteins, both of which are targets of neutralizing antibodies. In this study, we identified and characterized two human monoclonal antibodies (mAbs), 5217-2 and 5217-9, which bind recombinant PIV3 HN protein, bind PIV3-infected cells, and are neutralizing in vitro. We determined the binding epitopes of the PIV3 HN-specific mAbs via biolayer interferometry and found mAb 5217-9 targets a previously defined neutralizing epitope while mAb 5217-2 binds a unique epitope, enabling a more complete understanding of the antigenic landscape. To further understand the newly defined epitope, we determined a cryo-electron microscopy (cryo-EM) structure of mAb 5217-2, which revealed an epitope adjacent to the PIV3 HN protein active site. We also determined the structure of the previously discovered anti-PIV3 HN mAb PIV3HN-09, which was previously shown to be partially protective in vivo. In a hamster challenge model of PIV3, mAb 5217-2 was determined to significantly reduce lung viral titers, demonstrating its protective capacity. Furthermore, as the site 2-directed mAb PIV3HN-05 was previously shown to cross-neutralize PIV1, we evaluated its protective efficacy in an animal challenge model with PIV1, which demonstrated a reduction in lung viral titers. Overall, these findings provide new insights into the antigenic epitopes on the PIV3 HN protein to support structure-based vaccine design efforts and demonstrate new protective mAbs for both PIV3 and PIV1.

immunology↗

The complete genome of a songbird

Bird genomes are the smallest among amniotes, but remain challenging to assemble due to their structural complexity. This study presents the first fully phased, diploid, telomere-to-telomere (T2T) reference genome for the zebra finch (Taeniopygia guttata), a model organism for neuroscience and evolutionary genomics. Combining multiple sequencing strategies resulted in closing nearly all gaps, adding [~]90 Mbp of previously missing sequence (7.8%). This includes T2T assemblies for all microchromosomes, including dot chromosomes, and the previously almost entirely missing chr16. The T2T genome is comprehensively annotated for genes, repeats, structural variants, and long-read methylation calls. Complete centromeric structures were assembled and annotated along with kinetochore binding sites. Relative to the previous high-quality reference of the Vertebrate Genomes Project, 2,778 (8.51%) previously unassembled or unannotated genes were identified, of which 9% overlap with segmental duplications. This first complete genome of a songbird, now the new public reference, illuminates avian genome architecture and function.

genomics↗

Evaluation of sequencing reads at scale using rdeval

MotivationLarge sequencing data sets are produced and deposited into public archives at unprecedented rates. The availability of tools that can reliably and efficiently generate and store sequencing read summary statistics has become critical. ResultsAs part of the effort by the Vertebrate Genomes Project (VGP) to generate high-quality reference genomes at scale, we sought to address the community need for efficient sequencing data evaluation by developing rdeval, a standalone tool to quickly compute and dynamically display sequencing read metrics. Rdeval can either run on the fly or store key sequence data metrics in read sketches, with dramatic compression gains. Statistics can then be efficiently recalled from sketches for additional processing. Rdeval can convert fa*[.gz] files to and from other popular formats including BAM and CRAM for better compression. Overall, while CRAM achieves the best compression, the gain is marginal, and BAM achieves the best compromise between data compression and accessing speed. Rdeval also generates a detailed visual report with multiple data analytics that can be exported in various formats. We showcase rdevals functionalities using human and VGP read data from different sequencing platforms and species. For PacBio long-read sequencing, our analysis shows dramatic improvements both in read length and quality over time, and a benefit of additional coverage for genome assembly. Availability and implementationRdeval is implemented in C++ for data processivity and in R for data visualization. Precompiled releases (Linux, MacOS, Windows) and commented source code for rdeval are available under MIT license at https://github.com/vgl-hub/rdeval. Documentation is available using ReadTheDocs (https://rdeval-documentation.readthedocs.io). Rdeval is also available in Bioconda and in Galaxy (https://usegalaxy.org). An automated test workflow ensures the consistency of software updates. Supplementary informationSupplementary data are available at Bioinformatics online.

bioinformatics↗