NEWS:
1.5.24
Its been a busy, uhh looks like 9 months since the last update here. Lots of exciting stuff has happened INCLUDING:
Joel authored a news and views on IAV modulation of host transcription at Nature Microbiology here.
Mireille’s paper on within-host evolution and compartmentalization of SARS-CoV-2 in humans came out in Journal of Virology, with the bonus “Editor’s pick” distinction.
We received a new R01 to study the constraints that limit IAV evolutionary potential, a CEIRR contract to study epistasis between the HA and NA genes, and another CEIRR contract to set up a clinical study to capture frequent longitudinal virus and blood samples from people infected with flu or other common respiratory viruses.
Steven Eichinger passed his prelim exam, congrats!
Kyle Heimburger and Gabi Shipman joined the lab as PhD student and Lorenzo D’Alessio joined as a technician. Excited to have them on board!!
We also, amongst other things, went on another lab paintball outing and attended ASV in force:
4.5.23
Wow, almost a year since the last update, going to have to get better about that. Anyways here are some highlights form the past several months…
Tony’s paper on the influence of NA over HA evolution was published at Cell Host & Microbe
Mireille authored commentaries on SARS-CoV-2 transmission (@mSphere) and influenza virus superinfection exclusion (@Nature)
Tony won third place talk at the School of MCB retreat; and Joel and Mireille won first and second place poster awards respectively at the departmental retreat. Our lab (with floormates from the Blanke lab) also won the overall multi-event microbiology olympics competition at our departmental retreat:
The lab held its second ever paintball outing:
4.29.22
We’ve got a bunch of updates from the last few months:
Fadi had his paper on the packaging of influenza virus defective interferring particle (DIP)-associated genome segments (DelVGs) published at mBio
Meghan had a paper on how substitutions in NP can selectively modulate NA segment expression published in Journal of Virology
Two papers on variation in the longitudinal dynamics of virus shedding during acute infection of naive or vaccinated individuals captured through the COVIDdetect study were published at Nature Microbiology and Open Forum Infectious Diseases
Steven Eichinger joined the lab as a graduate student, screening for novel cis- and trans-acting elements in the influenza virus genome. Kevin Scardina joined as a lab manager and to work on developing new diagnostic test methods for influenza virus.
February lab get-together:
9.3.21 - 6 years in…
Lots of news over the past several months:
We have had a few papers come out based on our longitudinal study of SARS-CoV-2 infection in humans. Lots of cool findings on test sensitivity over time, heterogeneity in infectious virus shedding between people, variants, vaccine breakthrough, etc. Check them out on the publications page!
Fadi has a new preprint out showing that defective interferring particle (DIP)-associated genome segments are inefficiently packaged compared to their wild-type counterparts. This goes against the dogma surrounding DIPs and raises some interesting questions about how DIPs are able to replicate to high frequency.
Both Joel and Tony passed their prelims! Congrats to them!! Liz and Mireille also did well on their first year advisories.
Chris got tenure, so the lab won’t be shutting down any time soon.
Chris and Fadi won actual medals for their work developing the covidSHIELD saliva test:
12.28.20 - December update
This year has sucked in a lot of ways but at least there have been some positive developments in the lab:
Brigitte’s paper on the phenotypic consequences of cellular co-infection, a close collaboration with Katia Koelle’s group, has been published in PLOS Pathogens here.
Chris is leading an NIH-funded clinical study aimed at comparing different CoV testing methods (rapid antigen, nasal qPCR, saliva qPCR) with live virus shedding longitudinally over the course of SARS-CoV-2 infection. The COVID detect study is a collaboration with the UMass Clinical Studies Core and Johns Hopkins, and builds upon the SHIELD surveillance program on the UIUC campus (based on the saliva RTqPCR test developed in our lab).
We are part of a new NSF BII run by Rachel Whitaker called “GEMS: Genomic and Eco-evolution of Multi-scale Symbioses”. Our part will be developing new tools and approaches to study honeybee evolution and host-interactions in collaboration with Adam Dolezal.
Two new students joined the lab in Dec.: Mireille Farjo and Liz Thayer! Mireille will be studying influenza virus superinfection and SARS-CoV-2 evolutionary dynamics while Liz will be studying the factors that govern cellular decision making during viral infection.
Izabella Lach graduated with a degree in Integrative Biology with distinction after doing her thesis on mutations that evolve during long-term co-evolution between wild-type viruses and defective interfering particles.
Finally, Jiayi defended his thesis, making him the first Ph.D. graduate from the Brooke lab!! Jiayi is staying on briefly as a postdoc until he is able to start his “real” postdoc in Patrick Wilson’s lab.
7.16.20 - Lab reopened
Well, this year took a pretty awful turn. Luckily everyone in the lab is healthy, and case numbers in the area have been low. We shut everything down in mid-March and were finally able to open back up (with restrictions of course) in early June.
While things were shut down, Fadi and Chris helped develop a direct saliva-to-RTqPCR diagnostic test for COVID-19 with the goal of being able to run >10K tests per day on campus once students return. That method is available in a pre-print here.
Meghan, Joel, and Tony spent part of the shutdown making viral transport media (VTM) to help expand statewide testing capacity. Details on that here.
Finally, we’ve had a couple papers come out: Fadi had a mini-review on defective interfering particles in PLOS Pathogens, and Jiayi and Cris had their paper on single cell heterogeneity in the host innate response to influenza virus infection also come out in PLOS Pathogens. The latter was featured in a research highlight in Nature Reviews Microbiology here.
1.2.20 - Diving into 2020
A preprint of our work using single cell RNAseq to understand how viral population heterogeneity influences the host response to infection is online here. This work was jointly led by Cris Vera on the computational side and Jiayi Sun at the bench, and was greatly enhanced through a collaboration with Ruian Ke at LANL. The single cell RNAseq analysis pipeline we developed is available via the ‘Software’ tab. Hopefully it might be useful for people interested at looking at interplay between viral and host genes in scRNAseq datasets.
Cris has also left the lab to work for a biotech startup in California. His loss is offset by the exciting arrival of two new Ph.D. students who have joined the lab: Joel Rivera and Tongyu (Tony) Liu. Joel will be studying how DIPs and other incomplete particles influence the host response and Tony will be exploring how interactions between viral genome segments influence antigenic evolution.
8.30.19 - New preprint
We have a new preprint out with Brigitte Martin as the lead author, defining the phenotypic consequences of cellular co-infection by influenza viruses. This work came out of a great collaboration with the Koelle group at Emory. See it here.
7.24.19 - ASV2019
The lab just got back from ASV in Minneapolis where Meghan, Jiayi, Brigitte, and Fadi gave awesome presentations and then apparently reassorted with the Mehle lab, giving rise to a new lab genotype with enhanced pandemic emergence potential:
Thanks to ASV for travel awards for both Fadi and Jiayi!
5.15.19 - Fadi’s paper is cover article in Journal of Virology
Check out the recent JVI cover based on Fadi’s paper, featuring animal illustrations by Allegra Raff:
4.22.19 - Lots of stuff
A lot has happened over the past few months:
- Fadi has a new paper using next-gen sequencing to map defective interfering particle-associated deletions across influenza A and B viruses, check it out here.
- Our DARPA contract has been renewed for another two years. Details on the INTERCEPT program here, and on our specific project here.
- A bunch of people in the lab won awards. Jiayi won a Carl DeBoer fellowship and an ASV travel award, Fadi won an ASV travel award, Morgan won a Helen Alford Hays Microbiology scholarship, and Izabella won an Oliver Bell scholarship.
10.30.18 - Jiayi’s paper out in mBio
Jiayi’s paper revealing a role for genomic heterogeneity within viral populations in regulating influenza virus superinfection potential is out in mBio. You can find it here.
10.13.18 - Lab paintball outing
Everyone survived! Check out the before and after shots:
9.21.18 - New NIH R01 grant
We just received an R01 from NIH to study how influenza virus genomic heterogeneity influences superinfection dynamics and the host response to infection.
8.8.18 - New review article by Meghan and Jiayi
Meghan Diefenbacher and Jiayi Sun have published a review on semi-infectious particles in Current Opinion in Virology as part of a special issue on multi-component virus systems. Check it out here
7.10.18 - Check us out at ASV2018
Multiple lab members will be presenting at ASV this year, come check them out:
Fadi Alnaji - W7-8: Longitudinal deep sequencing analysis of defective interfering particles during long-term influenza A virus passage
Meghan Diefenbacher - P24-9: Epistatic regulation of influenza A virus glycoprotein expression by nucleoprotein
Brigitte Martin - W26-10: In-depth analysis of the effects of MOI on influenza A virus replication dynamics
Jiayi Sun - W35-6: Influenza A virus superinfection potential is regulated by viral genomic heterogeneity
4.10.18 - ASV travel award
Congrats to Meghan Diefenbacher for winning an ASV travel award!! She will be presenting her work on epistatic regulation of glycoprotein gene expression. Be sure to check it out.
10.2.17 - New group member
We welcome Cris Vera to the lab as a bioinformatics analyst. Cris will take point on the development and improvement of analysis pipelines for multiple projects in the lab.
9.5.17 - New review article in Journal of Virology
Chris has a new review out on influenza virus population diversity in Journal of Virology. Check it out here.
8.24.17 - Press on our recent DARPA contract
The Institute for Genomic Biology and the School of Molecular and Cellular Biology here at Illinois have both done write-ups on our recent DARPA contract:
https://www.igb.illinois.edu/article/combating-antiviral-drug-resistance-dynamic-therapeutics
https://mcb.illinois.edu/news/highlight/436/
7.28.17 - A lot has happened over the past few months...
Meghan and Jiayi both passed their prelims. Also we have welcomed two new postdocs, Fadi Alnaji and Brigitte Martin, as well as a new research specialist, Kelsie Green, to the lab.
Awesome!