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Shank, S. D.

Publications and source records attributed to Shank, S. D..

7 recordsLinked to original sources
bioRxiv2026

Within- and between-host dynamics of highly pathogenic avian influenza in domestic birds from Pennsylvania farms and live bird markets

Since late 2021, highly pathogenic avian influenza viruses (HPAI) of the H5 subtype clade 2.3.4.4b have spread across the Americas, devastating wildlife, agricultural animals, and resulting in dozens of human spillovers. National surveillance strategies generally provide only a single representative sequence per poultry outbreak, precluding fine-scale geographic transmission inference or studies of within-outbreak evolution. We produced high-quality deep sequence data from 46 infected Galliformes and Anseriformes sampled from commercial farm and live bird market (LBM) outbreaks in Pennsylvania from 2023-2025. We found that H5N1 viruses were introduced into Pennsylvania at least 68 independent times. We recover independent origins of live bird market outbreaks within the same county 3 weeks apart, and transmission between Pennsylvania LBM and New York commercial birds, suggesting high transmission risk within the Northeast live bird market distribution system. Analyses of within-farm variant populations show frequent variant sharing between samples from the same outbreak, suggesting that variants are propagated among epidemiologically linked infections. We identified 9 known adaptive mutations in these samples, including one instance of PB2 D701N in a LBM chicken sample, suggesting that while rare, concerning mammalian adaptive mutations can be present within these domestic outbreaks. Our data suggest that domestic bird outbreaks support high circulating diversity and wide transmission bottlenecks, increasing the risk of minority variants arising and propagating between infections. These data can help inform targeted biosecurity measures and better quantify the risk of viral adaptation during agricultural outbreaks.

genomics↗
bioRxiv2022

High-throughput single-cell sequencing for retroviral reservoir characterization

During the course of infection, human immunodeficiency virus (HIV) maintains a stably integrated reservoir of replication-competent viruses within the host genome that are unaffected by antiretroviral therapy. Curative advancements rely heavily on targeting the anatomical reservoirs, though determinants of their evolutionary origins through phyloanatomic inference remain ill-supported through current sequencing and sequence analysis strategies. The vast replication-defective genomic landscape that comprises the HIV DNA population is often discarded in these evolutionary endeavors, despite key information regarding competent ancestry that can be gained from captured genomic regions outside the historically used viral envelope gene. Here, we describe the application of small-amplicon, single-cell DNA sequencing to blood and lymph node samples from a treatment-interrupted S[imian]IV-infected animal model and evaluate the contribution of genome coverage and inclusion on phylogenetic resolution and phyloanatomic inference. Findings from this study point to incomplete genomes as a significant source of phylogenetic information on movement of virus between tissue reservoirs during therapy.

genomics↗
bioRxiv2022

Selection analysis identifies unusual clustered mutational changes in Omicron lineage BA.1 that likely impact Spike function

Among the 30 non-synonymous nucleotide substitutions in the Omicron S-gene are 13 that have only rarely been seen in other SARS-CoV-2 sequences. These mutations cluster within three functionally important regions of the S-gene at sites that will likely impact (i) interactions between subunits of the Spike trimer and the predisposition of subunits to shift from down to up configurations, (ii) interactions of Spike with ACE2 receptors, and (iii) the priming of Spike for membrane fusion. We show here that, based on both the rarity of these 13 mutations in intrapatient sequencing reads and patterns of selection at the codon sites where the mutations occur in SARS-CoV-2 and related sarbecoviruses, prior to the emergence of Omicron the mutations would have been predicted to decrease the fitness of any genomes within which they occurred. We further propose that the mutations in each of the three clusters therefore cooperatively interact to both mitigate their individual fitness costs, and adaptively alter the function of Spike. Given the evident epidemic growth advantages of Omicron over all previously known SARS-CoV-2 lineages, it is crucial to determine both how such complex and highly adaptive mutation constellations were assembled within the Omicron S-gene, and why, despite unprecedented global genomic surveillance efforts, the early stages of this assembly process went completely undetected.

evolutionary biology↗
bioRxiv2022

RASCL: Rapid Assessment Of SARS-CoV-2 Clades Through Molecular Sequence Analysis

An important component of efforts to manage the ongoing COVID19 pandemic is the Rapid Assessment of how natural selection contributes to the emergence and proliferation of potentially dangerous SARS-CoV-2 lineages and CLades (RASCL). The RASCL pipeline enables continuous comparative phylogenetics-based selection analyses of rapidly growing clade-focused genome surveillance datasets, such as those produced following the initial detection of potentially dangerous variants. From such datasets RASCL automatically generates down-sampled codon alignments of individual genes/ORFs containing contextualizing background reference sequences, analyzes these with a battery of selection tests, and outputs results as both machine readable JSON files, and interactive notebook-based visualizations. AvailabilityRASCL is available from a dedicated repository at https://github.com/veg/RASCL and as a Galaxy workflow https://usegalaxy.eu/u/hyphy/w/rascl. Existing clade/variant analysis results are available here: https://observablehq.com/@aglucaci/rascl. ContactDr. Sergei L Kosakovsky Pond (spond@temple.edu). Supplementary informationN/A

bioinformatics↗
bioRxiv2020

Extra base hits: widespread empirical support for instantaneous multiple-nucleotide changes

Despite many attempts to introduce evolutionary models that permit substitutions that instantly alter more than one nucleotide in a codon, the prevailing wisdom remains that such changes are rare and generally negligible (or are reflective of non-biological artifacts, such as alignment errors), and codon models continue to posit that only single nucleotide change have non-zero rates. We develop and test a simple hierarchy of codon-substitution models with non-zero evolutionary rates for only one-nucleotide (1H), one- and two-nucleotide (2H), or any (3H) codon substitutions. Using 35,000 empirical alignments, we find widespread statistical support for multiple hits: 58% of alignments prefer models with 2H allowed, and 22% - with 3H allowed. Analyses of simulated data suggest that these results are not likely to be due to simple artifacts such as model misclassification or alignment errors. Further modeling revealed that synonymous codon island jumping among codons encoding serine, especially along short branches, contributes significantly to this 3H signal. While serine codons were prominently involved in multiple-hit substitutions, there were other common exchanges contributing to better model fit. It appears that a small subset of sites in most alignments have unusual evolutionary dynamics not well explained by existing model formalisms, and that commonly estimated quantities, such as dN/dS ratios may be biased by model misspecification. Our findings highlight the need for continued evaluation of assumptions underlying workhorse evolutionary models and subsequent evolutionary inference techniques. We provide a software implementation for evolutionary biologists to assess the potential impact of extra base hits in their data in the HyPhy package.

bioinformatics↗
bioRxiv2018

Monocyte Infection Dynamics Shape HIV-1 Phyloanatomy in the Peripheral Blood

Human immunodeficiency virus (HIV) RNA and DNA have been isolated from patient monocytes, an immune cell population that is quite different in several aspects from the canonical T-cell viral target. Because monocytes are migratory and resilient to both natural and synthetic antiviral defenses, knowledge of the contribution of monocyte infection to ongoing viral evolution and spread in vivo is of significant interest for drug development and treatment strategies. Using single viral genome sequencing from different peripheral blood compartments and phyloanatomic statistical inference, we demonstrate that productively infected monocytes follow an evolutionary trajectory that is distinct from peripheral T cells during multiple stages of disease progression. Gene flow and selection analysis reveal plasticity in the source of monocyte infection and in the region of the HIV envelope glycoprotein that experiences selection pressure across individuals. The findings, thus, point to a potential reservoir showing a range of infection and transmission dynamics, for which the current universal, T cell-targeted treatment strategies would be inadequate.\n\nAuthor summaryHuman immunodeficiency virus is a rapidly evolving virus, allowing its genetic material to act as a fingerprint for epidemiological processes among, as well as within, individual infected hosts. In this study, sampling of viral RNA from plasma and differing infected immune cell populations from the peripheral blood was undertaken for three separate individuals in order to infer such processes. The results revealed a productively infected monocyte cell population, for which distinct selection pressures were linked to differing spatiotemporal origins of infection. In light of previous evidence of the migratory nature of these cells and resilience to both natural and synthetic antiviral defenses, this study underscores the importance of further investigation into the role of monocytes, and monocyte-rich tissues, as viral reservoirs during treatment of HIV with antiretroviral therapy.

evolutionary biology↗