About

Christopher B. Brooke is an Associate Professor of Microbiology at the School of Molecular & Cellular Biology, Illinois College of Liberal Arts & Sciences. His research focuses on understanding viral replication, pathogenesis, and evolution, with a particular emphasis on influenza virus. His laboratory investigates how heterogeneity and collective interactions within virus populations influence viral evolution and infection outcomes. Brooke's work explores the mechanisms that govern influenza virus transmission, immune escape, and antigenic evolution, employing approaches spanning molecular virology, cell biology, evolutionary biology, bioinformatics, and mathematical modeling. He aims to improve strategies for universal vaccination by dissecting the genetic and population dynamics of influenza viruses and their interactions with host immune responses.

Research topics

• Virology
• Medicine
• Biology
• Immunology
• Internal medicine
• Pathology
• Biochemistry
• Political Science
• Computational biology
• Computer Science
• Microbiology
• Pharmacology
• Environmental health
• Telecommunications
• Genetics
• Nursing

Selected publications

• Stratification of viral shedding patterns in saliva of COVID-19 patients

  eLife · 2026-01-07

  articleOpen access

  Living with COVID-19 requires continued vigilance against the spread and emergence of variants of concern (VOCs). Rapid and accurate saliva diagnostic testing, alongside basic public health responses, is a viable option contributing to effective transmission control. Nevertheless, our knowledge regarding the dynamics of SARS-CoV-2 infection in saliva is not as advanced as our understanding of the respiratory tract. Here, we analyzed longitudinal viral load data of SARS-CoV-2 in saliva samples from 144 patients with mild COVID-19 (a combination of our collected data and published data). Using a mathematical model, we quantified individual-level viral dynamics and stratified them into three groups using a clustering approach. Notably, the three groups exhibited distinct differences in viral RNA detection durations: 11.5 days (95% CI: 10.6–12.4), 17.4 days (16.6–18.2), and 30.0 days (28.1–31.8), respectively. Surprisingly, this stratified grouping remained unexplained despite our analysis of 47 types of clinical data, including basic demographic information, clinical symptoms, results of blood tests, and vital signs. Additionally, we quantified the expression levels of 92 micro-RNAs in a subset of saliva samples, but these also failed to explain the observed stratification, although the mir-1846 level may have been weakly correlated with peak viral load. Our study provides insights into SARS-CoV-2 infection dynamics in saliva, highlighting the challenges in predicting the duration of viral RNA detection without indicators that directly reflect an individual’s immune response, such as antibody induction. Given the significant individual heterogeneity in the kinetics of saliva viral shedding, identifying biomarker(s) for viral shedding patterns will be crucial for improving public health interventions in the era of living with COVID-19.

  PublisherDOI

• TRIM21 is a molecular rheostat for influenza A virus replication

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-03-17

  articleOpen access

  TRIM21 is a multifunctional E3 ubiquitin ligase and intracellular antibody receptor, yet its role during viral infection remains unclear, with reports describing both antiviral and proviral activities. Here, we show that TRIM21 regulates influenza infection in an expression-dependent manner by functioning as a molecular rheostat rather than a binary restriction factor. This graded activity of TRIM21, which leads to both suppression and promotion of influenza replication, couples linkage-specific ubiquitination of viral nucleoprotein with modulation of innate immune signaling. Additionally, loss of TRIM21 unmasks a compensatory antiviral program centered on PRKDC, which is a ubiquitination target of TRIM21. This positions PRKDC as a latent restriction factor selectively engaged when primary TRIM21 control is lost. Together, these findings reveal a hierarchical and plastic antiviral network in which TRIM21 sets an adjustable threshold for host defense while restraining secondary restriction pathways. This framework highlights the sophisticated layers of regulation of the host ubiquitin-mediated antiviral immunity.

  PublisherOA PDFDOI

• Identifying the optimal rapid antigen test for screening and determining the end of isolation: A modeling study

  PLoS Computational Biology · 2026-04-02

  articleOpen access

  During the COVID-19 pandemic, rapid antigen tests (RATs) were used to detect infections, improving the effectiveness of targeted non-pharmaceutical interventions (NPIs). However, RATs based on either nasal swab or saliva samples were used, raising the question as to which type of RAT is most effective at detecting viral infections. Here, we develop a model-driven computational framework to assess different RATs and identify the most suitable test for a specified purpose, such as infection screening or determining the end of isolation, for various viral infections. Using symptomatic COVID-19 cases as a case study, we found that saliva-based RATs reduced transmission risk on average by 6.2% (95% CI: 6.1 - 6.3) compared to nasal-based RATs in the pre-symptomatic period. In addition, by ending isolation of infected individuals who have developed symptoms when consecutive RATs return negative results, the mean risk of transmission was reduced by 5.9% (95% CI: 5.7 - 6.1) using a saliva-based RAT compared to using a nasal-based RAT. These findings suggest that saliva RATs may be a useful option for mitigating SARS-CoV-2 transmission effectively. However, real-world variability in test sensitivity and sample collection should be carefully considered when evaluating the practical use of each RAT type. Our novel approach can be applied to other viruses and types of tests, enabling its use to inform public health policy decisions about which types of RAT to prioritize in future infectious disease epidemics.

  PublisherDOI

• Author response: Stratification of viral shedding patterns in saliva of COVID-19 patients

  2026-01-16

  peer-reviewOpen access
  PublisherDOI

• The fitness consequences of coinfection and reassortment for segmented viruses depend upon viral genetic structure

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-07-26

  preprintOpen accessSenior authorCorresponding

  Cellular coinfection between multiple virions is a common feature of viral infections. The collective virus-virus interactions enabled by these coinfections can influence the fitness of viral populations and give rise to novel infection phenotypes. Multi-strain coinfections allow viral resources to be shared between multiple individuals, and enable genetic combination and recombination between genotypes, potentially giving rise to hybrid progeny with enhanced fitness. However, coinfection can also impose fitness costs in certain situations. For example, resource sharing among viruses can lead to the persistence of low-fitness genotypes, and reassortment between different strains can lead to negative inter-segment epistasis when genes are poorly matched to one another. Thus, the fitness implications of cellular coinfection are poorly defined and likely context dependent. To investigate the specific conditions that lead to positive or negative fitness consequences for multi-strain coinfections, we formulated a model in which different genotypes of a three-segment virus replicate under varying degrees of inter-strain mixing. We observed that increased mixing had negative fitness consequences under a variety of scenarios, and that this effect was exacerbated with increasing genetic divergence between strains. Inter-strain mixing only enhanced viral fitness (a) when positive genetic dominance interactions were at play, and (b) under very specific conditions of selective pressure. We also observed that reassortment arising from mixing could generate hybrid genotypes with higher fitness than either parental virus, but that these outcomes were relatively rare. Overall, using a model segmented virus, we found that the heterologous coinfection was deleterious under most conditions, suggesting that it may be beneficial for many viruses to limit the extent of cellular coinfection.

  PublisherOA PDFDOI

• Probing the functional constraints of influenza A virus NEP by deep mutational scanning

  Cell Reports · 2025-01-01 · 5 citations

  articleOpen access

  The influenza A virus nuclear export protein (NEP) is a multifunctional protein that is essential for the viral life cycle and has very high sequence conservation. However, since the open reading frame of NEP largely overlaps with that of another influenza viral protein, non-structural protein 1, it is difficult to infer the functional constraints of NEP based on sequence conservation analysis. In addition, the N-terminal of NEP is structurally disordered, which further complicates the understanding of its function. Here, we systematically measure the replication fitness effects of >1,800 mutations of NEP. Our results show that the N-terminal domain has high mutational tolerance. Additional experiments show that N-terminal domain mutations affect viral transcription and replication dynamics, host cellular responses, and mammalian adaptation of avian influenza virus. Overall, our study not only advances the functional understanding of NEP but also provides insights into its evolutionary constraints.

  PublisherDOI

• Stratification of viral shedding patterns in saliva of COVID-19 patients

  eLife · 2025-11-17

  articleOpen access

  Living with COVID-19 requires continued vigilance against the spread and emergence of variants of concern (VOCs). Rapid and accurate saliva diagnostic testing, alongside basic public health responses, is a viable option contributing to effective transmission control. Nevertheless, our knowledge regarding the dynamics of SARS-CoV-2 infection in saliva is not as advanced as our understanding of the respiratory tract. Here we analyzed longitudinal viral load data of SARS-CoV-2 in saliva samples from 144 patients with mild COVID-19 (a combination of our collected data and published data). Using a mathematical model, we quantified individual-level viral dynamics and stratified them into three groups using a clustering approach. Notably, the three groups exhibited distinct differences viral RNA detection durations: 11.5 days (95% CI: 10.6 to 12.4), 17.4 days (16.6 to 18.2), and 30.0 days (28.1 to 31.8), respectively. Surprisingly, this stratified grouping remained unexplained despite our analysis of 47 types of clinical data, including basic demographic information, clinical symptoms, results of blood tests, and vital signs. Additionally, we quantified the expression levels of 92 micro-RNAs in a subset of saliva samples, but these also failed to explain the observed stratification, although the mir-1846 level may have been weakly correlated with peak viral load. Our study provides insights into SARS-CoV-2 infection dynamics in saliva, highlighting the challenges in predicting the duration of viral RNA detection without indicators that directly reflect an individual’s immune response, such as antibody induction. Given the significant individual heterogeneity in the kinetics of saliva viral shedding, identifying biomarker(s) for viral shedding patterns will be crucial for improving public health interventions in the era of living with COVID-19.

  PublisherDOI

• Longitudinal analysis of influenza A virus deletion-containing viral genomes reveals key determinants of co-evolutionary dynamics and interference

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-11-03 · 2 citations

  preprintOpen accessSenior authorCorresponding

  The substantial genetic diversity generated during influenza A virus replication facilitates both evasion of pre-existing host immunity and cross-species emergence. A major contributor to this diversity is the ubiquitous production of deletion-containing viral genomes (DelVGs) - viral RNAs with large internal deletions that arise during replication. DelVGs directly compete with wild-type (WT) genomes, and their accumulation has been implicated in modulating disease severity. However, the specific functional and genetic interactions between DelVGs and WT genomes remain poorly understood. To examine how DelVGs and WT genomes may co-evolve in mixed populations, we serially passaged influenza A virus under sustained high multiplicity-of-infection (MOI) conditions and used next-generation sequencing to build a longitudinal profile of DelVG emergence and dynamics. Early passages yielded a highly diverse repertoire of DelVGs across multiple segments, followed by a sharp contraction in overall diversity and the rise of one to two PB2-derived DelVGs that persisted at sustained high frequency. We identified a single-nucleotide substitution within PB2-derived DelVGs that significantly enhanced their replication and interference, whereas the same mutation proved lethal in the WT background. Collectively, these findings indicate that DelVGs are not mere byproducts of replication but dynamic genomic elements shaped by selection; their capacity to acquire adaptive mutations and outcompete WT genomes underscores their active role in shaping within-population viral dynamics.

  PublisherOA PDFDOI

• Single-cell heterogeneity in interferon induction potential is heritable and governed by variation in cell state

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-12-12 · 2 citations

  articleOpen accessSenior authorCorresponding

  SUMMARY Type I and III interferons (IFNs) are among the first lines of defense against viral infection, yet they are generally only produced by a tiny fraction of infected cells. Here, we show that cellular heterogeneity in IFN induction potential upon treatment with immunostimulatory RNA is not due to variability in sensing of stimuli but instead is shaped by heterogeneity in tonic cell signaling state. Using complementary single-cell approaches, we found that baseline variation in the c-Jun N-terminal kinase (JNK) and activator protein (AP)-1 transcription factor families correlated with IFNL1 expression predisposition. We further show that drug-based inhibition of JNK signaling virtually eliminates the innate antiviral response to immunostimulatory RNA. Finally, we show that single cell heterogeneity in IFN induction potential is heritable and stably maintained over numerous generations. Together, our study emphasizes the influence of intrinsic variability in cell state on innate immune regulation and IFN induction heterogeneity.

  PublisherDOI

• :<i>The Oxford Handbook of Early Modern Women’s Writing in English, 1540–1700</i>

  Early Modern Women An Interdisciplinary Journal · 2025-03-01

  article1st authorCorresponding
  PublisherDOI

Recent grants

• Defining novel mechanisms of influenza virus gene regulation

  NIH · $268k · 2016–2019

• The effects of influenza virus genomic heterogeneity on replication dynamics and the host response

  NIH · $1.9M · 2018–2024

Frequent coauthors

• Janet Burton

  100 shared

• Chris Webb

  Vanderbilt University Medical Center

  100 shared

• Richard H. Helmholz

  Bridge University

  100 shared

• Philippa Hoskin

  100 shared

• Brian Kemp

  100 shared

• Julia Barrow

  University of Leeds

  100 shared

• Alison K. McHardy

  100 shared

• F. Donald Logan

  Emmanuel College - Massachusetts

  100 shared

Labs

• BROOKE LABPI