CRESSENT Schematic
Worried your ssDNA virus genomes aren't getting enough love? Now they can, thanks to CRESSENT, a new software package from Ricardo Pavan, @sullivan-lab.bsky.social, and I! 🧬💻🧪
Out now: doi.org/10.1099/mgen...
05.02.2026 23:06 — 👍 2 🔁 1 💬 1 📌 0
🚨 New paper in Eurosurveillance - @karatasmustafa.bsky.social
We used shotgun metagenomics on indoor air in a Belgian daycare to track respiratory, enteric & skin viruses.
👉 40/42 samples contained human viruses—even when kids seemed healthy!
📄 Read here: pubmed.ncbi.nlm.nih.gov/41000028/
30.09.2025 07:43 — 👍 3 🔁 3 💬 0 📌 0
Shotgun metagenomics on indoor air for surveillance of respiratory, enteric, and skin viruses in a Belgian daycare setting, January to December 2022
BACKGROUND Hospital-based communicable disease surveillance may be costly during large outbreaks and often misses mild or asymptomatic infections. It can be enhanced by environmental surveillance, which monitors circulating pathogens, even from asymptomatic carriers. AIM We investigated if tracking viruses in indoor air could be used for their surveillance in a community setting. We also tested the value of untargeted metagenomics to identify viruses in air samples. METHODS Weekly indoor air samples were collected with active air samplers from January until December 2022 from a daycare centre in Leuven, Belgium. Samples were analysed using respiratory and enteric quantitative (q)PCR panels, as well as with untargeted metagenomics, enabling both targeted and agnostic viral detections. RESULTS Human-associated viruses were detected in 40 of 42 samples across the study period, with MW polyomavirus being most prevalent (33 samples). Respiratory agents such as rhinoviruses and RSV-B and enteric viruses including rotavirus A, astrovirus, and adenovirus appeared at epidemiologically expected times. Skin-associated viruses were also observed, notably Merkel cell polyomavirus and STL polyomavirus. Metagenomics enabled reconstructing multiple complete genomes, distinguishing viral subtypes and detecting copresence of closely related variants. Additionally, several animal, insect, fungal, and plant viruses were found, reflecting both indoor and outdoor environmental exposure. CONCLUSION Indoor air monitoring, combined with untargeted metagenomics, demonstrates a potential to support virus surveillance. This approach can allow monitoring circulation of viruses in community settings, including those causing asymptomatic or mild infections. By enabling to reconstruct complete viral genomes, it allows detailed variant tracking, facilitating adapted public health responses.
www.eurosurveillance.org/content/10.2...
26.09.2025 13:18 — 👍 2 🔁 2 💬 0 📌 0
Figure 3. (A–N) Sequencing coverage plots of genetic sequences of viruses detected in indoor air samples of a daycare and phylogenetic analyses of sequences of (O) two human bocaviruses and (P) one RSV identified in some samples, Belgium, January–December 2022
New paper out!
We sampled indoor air for a year in a Belgian daycare and used shotgun metagenomics to track viruses. We recovered many viral genomes of interest.
What would you sample next?
Read at @eurosurveillance.org
@emmanuel-microb.bsky.social, @jellematthijnssens.bsky.social
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26.09.2025 13:18 — 👍 9 🔁 5 💬 2 📌 0
An innovative outbreak detection program that tracks viruses in #wastewater identified the #measles virus in #Houston in early January 2025, before cases were reported. #TailorLabs #saracregeen @miketisza.bsky.social @bcmhouston.bsky.social #TEPHITexas #RiceU @apha.org www.bcm.edu/news/measles...
13.05.2025 15:46 — 👍 4 🔁 3 💬 0 📌 0
Another example of how wastewater sequencing is going to positively impact Public Health. TEPHI's Outbreak Detection program shows once more the sensitivity and specificity of agnostic sequencing .... ajph.aphapublications.org/doi/abs/10.2...
09.05.2025 00:12 — 👍 2 🔁 2 💬 0 📌 0
Check out our latest paper on how #wastewater can be used to track animal and #zoonotic #viruses in urban settings!
pubmed.ncbi.nlm.nih.gov/40318358/
Great work by @karatasmustafa.bsky.social in collaboration with @marcvanranst.bsky.social @wollants.bsky.social @stevenvangucht.bsky.social
05.05.2025 19:18 — 👍 6 🔁 1 💬 0 📌 0
and what we found is probably just the beginning. There’s a whole world of viruses out there in the sewers!
You can check out all the details here, at Environment International:
doi.org/10.1016/j.en...
@jellematthijnssens.bsky.social
@wollants.bsky.social @vanranstmarc.bsky.social
29.04.2025 18:30 — 👍 0 🔁 0 💬 0 📌 0
that animal viruses are part of the urban environment too. And just like us, they leave their mark in the wastewater!
In our latest study, we used a hybrid-capture metagenomics approach on wastewater to detect not only human viruses but also a wide range of animal viruses —
29.04.2025 18:30 — 👍 0 🔁 0 💬 1 📌 0
🎉🎉 Happy to share our new paper! 🎉🎉
Have you ever wondered about the animal viruses living right alongside us in our cities?
Between our pets at home, rats in the sewers, pigeons on the streets, insects everywhere, and even farm animals nearby, it’s no surprise +++
29.04.2025 18:30 — 👍 2 🔁 1 💬 1 📌 0
To answer their study question on the influence of the COVID-19 pandemic on rotavirus infections in Belgium, @karatasmustafa.bsky.social et al. used data collected 10 years before, 2 years during, and 2 years after the pandemic
#IDsky #EpiSky 🦠
👇🏽
27.03.2025 17:25 — 👍 7 🔁 5 💬 0 📌 1
• A new equine-like G3P[8] rotavirus variant has become dominant, especially post-pandemic. While vaccines prevent severe disease, they may be less effective against this genotype.
• Continuous genomic surveillance is crucial!
Feel free to read more in our article!
@jellematthijnssens.bsky.social
27.03.2025 18:43 — 👍 2 🔁 1 💬 0 📌 0
• COVID-19 measures reduced rotavirus circulation, but easing restrictions led to a resurgence, especially among children between 2 and 5 years old.
• Seasonality was disrupted and was linked to measures.
• We may be overlooking rotavirus cases in older populations due to testing practices.
27.03.2025 18:43 — 👍 1 🔁 1 💬 1 📌 0
📢 Excited to share the first paper of my PhD: 14 years of rotavirus epidemiology in Belgium!
Read the full story on Eurosurveillance: @eurosurveillance.org
👉 www.eurosurveillance.org/content/10.2...
#Rotavirus #Virology #PublicHealth #Epidemiology #EpiSky #IDsky
Key messages -->
27.03.2025 18:43 — 👍 7 🔁 5 💬 2 📌 0
Heatmap chart showing the detection of various pathogens over different sampling weeks (W9 to W30). Pathogens are listed on the y-axis, including viruses and bacteria such as Streptococcus pneumoniae, human coronaviruses, influenza viruses, and others. The x-axis represents the sampling weeks. Black dots indicate detection of the pathogen in the air. The colour gradient, ranging from white to dark red, represents the proportion of positive paper tissue samples, with darker shades indicating higher proportions. This alt text was generated by ChatGPT.
A chart showing the relative detection of pathogens in air versus paper tissues, with pathogens listed on the y-axis (e.g., Pneumocystis jirovecii, herpes simplex virus type 1, SARS-CoV-2). The x-axis represents ∆Ct values, where negative values indicate higher detection in air and positive values indicate higher detection in paper tissues. Red dots represent the mean ∆Ct for each pathogen, and horizontal red error bars represent the 95% confidence intervals. Individual grey dots indicate data points for each sample. Pathogens are arranged by their relative prevalence in air and paper tissues. This alt text was generated by ChatGPT.
New study: analysing indoor air to detect outbreaks.
“… Air sampling could provide sensitive, responsive #epidemiology indicators for surveillance of respiratory pathogens…”
See thread for details and previous air sampling work with @emmanuel-microb.bsky.social…
#IDEpi #IDsky #PedsID #KULeuven 🛟
30.01.2025 10:55 — 👍 8 🔁 2 💬 2 📌 0
🦠Human-associated viruses were detected in 95% of samples (pathogenic and non-pathogenic!)
📈Results correlated with epidemiological patterns
🧬Genome reconstructions allowed discrimination of viral subtypes
Thanks to my supervisors
@jellematthijnssens.bsky.social & Emmanuel André
#metagenomics
24.12.2024 15:29 — 👍 0 🔁 0 💬 0 📌 0
Happy to share my first post here!
Feel free to look at our preprint, which is currently under review (with constructive and encouraging comments from reviewers!).
We performed viral metagenomics to track viruses in the indoor air of a daycare center:
Our findings... (see the next post!)-->
24.12.2024 15:29 — 👍 1 🔁 0 💬 1 📌 0
Assist. Prof | Leiden University | Mucosal Immunology | Human Disease | Single-Cell | Organoids | former postdoc Mark Davis & Calvin Kuo Lab at Stanford🌈 vanunenlab.org 🌐
Senior Scientist of Coastal and Marine Ecology Division at GUIDE. Oceanography and Marine biologist.
By nature I'm curious. MD., PhD.
Computational virologist. Currently working with enteric viruses and organoids. #Metagenomics #Bioinformatics #Virome. Women in STEM. PostDoc @ BCM Houston
A journal from @natureportfolio.bsky.social launched in January 2023 and publishing cutting-edge research on all aspects of the relationship between water and society
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Ph.D. Health Sciences; Bioinformatics; Postdoctoral fellow at FIOCRUZ-BA
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CDO at Bluesquare. Developing data systems for epidemic surveillance. Generally interested in Global Health, Data, African and Latino American affairs. Brussels based European.
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Evolutionary & population biology of vector-borne viral disease systems. 🦟 genetics PhD student in NC.
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Postdoc @ RCSI Converge 🇮🇪, PhD from Western University 🇨🇦 in Epidemiology and Biostatistics. Research interests in diabetes, chronic illness, global surgery, causal inference, Bayesian stats, evidence synthesis & research methods
