@guybaele.bsky.social
@sdellicour.bsky.social
@emmanuel-microb.bsky.social

A novel methodology for assessing contact tracing precision: Phylogenetic validation of a contact tracing program for COVID-19 in Belgium During the COVID-19 pandemic, contact tracing was widely used to limit virus propagation and implement targeted disease control measures. It can howev…

In the COVID-19 Omicron surge, #KULeuven combined contact tracing with sequencing.

Only 1/3 of contacts shared the same strain 🤯, so most people misperceived where they got infected.

@thibaut-jonathan.bsky.social and team show how to assess contact tracing accuracy in the future!

#IDSky #EpiSky

🚨 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/

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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New study on reaching people with undiagnosed tuberculosis in Rwanda: “… our results suggest that analyzing satellite imagery may allow the identification of urban areas where inhabitants are at higher risk of tuberculosis.”

One of my favorite #ESCMIDGlobal sessions is "Year in #PublicHealth".
Yi Lang Hsu summarizes outbreaks that occurred in the last year: Mpox, Avian Influenza, Marburg, Oropouche!
#PublicHealthSky #IDsky #ESCMIDGlobal2025

Silence=Death Redux: Infectious Diseases, Public Health, and the Imperative to Resist The second Trump administration has released a torrent of executive policies hostile to public health, science, and marginalized populations. We outline th

Our patients persecuted; colleagues and public health institutions under attack. Our field needs to rise up & fight back

Silence=Death Redux: Infectious Diseases, Public Health, and the Imperative to Resist

Viewpoint by @ericmeyerowitz.bsky.social & me

OpenAccess: academic.oup.com/cid/advance-...

Interpretation of indoor air surveillance for respiratory infections: a prospective longitudinal observational study in a childcare setting Our results suggest that air sampling could provide sensitive, responsive epidemiological indicators for the surveillance of respiratory pathogens. Using air CO2 concentrations to normalise such signa...

New #kuleuven study: indoor air sampling to monitor respiratory infections in childcare settings. 🧒🏽🏫 Key findings: 🔬 Sensitive pathogen detection 🌬️ Correlation with CO2 & infection rates 📈 Early outbreak warnings
👇 www.thelancet.com/journals/ebi...
#PublicHealth #Epidemiology #RespiratoryInfections

Mapping of regions with low tuberculosis notification and estimation of diagnostic gaps in Cameroon, evidence from OpenStreetMap and WorldPop data Scientific Reports - Mapping of regions with low tuberculosis notification and estimation of diagnostic gaps in Cameroon, evidence from OpenStreetMap and WorldPop data

New publication by Christelle Jouego & cols. maps TB hotspots in Cameroon using OpenStreetMap & WorldPop data. Reveals up to 53% of TB cases go undiagnosed in some regions 🧐. Urgent need to reallocate diagnostic tools where they're needed most. #GlobalHealth #TB www.nature.com/articles/s41...

Centralised Air Sampling From a Ventilation System for the Surveillance of Respiratory Pathogens Background: The COVID-19 pandemic has triggered a renewed interest in indoor air sampling for infectious disease surveillance. However, scalability is currently limited, as samples are usually collec...

3️⃣ Scaling up:
A single air sample from a central ventilation shaft could capture infections of many people in a building.
(Michiel Happaerts et al, Indoor Air)

In the future, maybe a small number of busy sentinel sites could be enough to help anticipate and monitor epidemics…

Untargeted viral metagenomics of indoor air as a novel surveillance tool for respiratory, enteric and skin viruses Conventional hospital-based infectious disease surveillance struggles to detect mild or asymptomatic infections and incurs high costs for large-scale testing during outbreaks. In contrast, environment...

2️⃣ Metagenomics can find unexpected viruses in air. Also viruses associated with skin infections or gastroenteritis.

More in this preprint with the Rega Institute’s Viral Metagenomics Lab:
@karatasmustafa.bsky.social , @jellematthijnssens.bsky.social

www.medrxiv.org/content/10.1...

Indoor air surveillance and factors associated with respiratory pathogen detection in community settings in Belgium - Nature Communications Surveillance of respiratory pathogens in air may improve understanding of indoor transmission risks but impacts of context-specific factors on pathogen abundance are not well understood. Here, the aut...

This builds on previous work at our Clinical Microbiology Lab:

1️⃣ In one study, we found on average 3.9 pathogens in 341 air samples from 21 locations, from bars to care homes.

Takeaways:
- Poor ventilation = more pathogens in air
- Air samples can mirror epidemiology

(Raymenants et al, Nat Comms)

New questions and avenues for research regarding interpretation of the significance of respiratory viruses adrift in the air Respiratory infections are the leading reason for hospitalisations worldwide.1 While numerous human respiratory viruses have been identified, the manner by which they are transmitted person-to-person ...

“The results highlight the differing shedding patterns between pathogens, while supporting the use of air pathogen counts and CO2 concentrations to estimate population-level prevalence.”

The relevance of this study and avenues for future research are highlighted in a comment by John Lednicky:

Interpretation of indoor air surveillance for respiratory infections: a prospective longitudinal observational study in a childcare setting Our results suggest that air sampling could provide sensitive, responsive epidemiological indicators for the surveillance of respiratory pathogens. Using air CO2 concentrations to normalise such signa...

What we tested:
- Air samples from a childcare centre over 5 months
- Used paper tissues from the same children
- Tested for 29 respiratory pathogens

Most infections were detectable in air, sometimes a week before we saw an outbreak!

lancet.com/journals/ebiom/article/PIIS2352-3964(24)00548-6

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 🛟

🚨 #PhDPosition Opportunity Alert 🚨
Join the Matthijnssens-lab @KU_Leuven to explore the early-life #virome dynamics and their impact on immunity in infants from Ghana & Zambia! 🌍🧬
📅 Start: June 2025
🔗 kuleuven.be/personeel/jobs…
#microbiome #bioinformatics #phage #NGS

In severe bird flu cases, the virus can mutate as it lingers in the body As the seasonal flu picks up, there are even more opportunities for the bird flu to acquire mutations as the different influenza viruses mix.

It's not so much mutations spontaneously emerging in individuals that is most concerning, but the fact that flu season is ramping up, giving H5N1 more opportunities to mix with human influenza strains, @angierasmussen.bsky.social told me. www.nbcnews.com/health/healt...

#IDEpi

IDEpi: a dedicated Bluesky feed for Infectious Disease Epidemiology.

This feed collects posts tagged with #IDEpi or keyword combinations like #IDSky + #EpiSky.
Comments and suggestions welcome!

Access here: bsky.app/profile/did:...

Unravelling the effect of New Year’s Eve celebrations on SARS-CoV-2 transmission - Scientific Reports Scientific Reports - Unravelling the effect of New Year’s Eve celebrations on SARS-CoV-2 transmission

4️⃣ Not large super-spreading events, but many small gatherings caused a surge in COVID-19 transmission on New Year’s Eve (2022).
(Sci Rep)

Of course, the virus was a bigger concern back then. Wishing everyone a happy, festive start to 2025!

Stay tuned as we work to prepare for future pandemics.

Risk factors for SARS-CoV-2 transmission in student residences: a case-ascertained study - Archives of Public Health Background We aimed to investigate the overall secondary attack rates (SAR) of COVID-19 in student residences and to identify risk factors for higher transmission. Methods We retrospectively analysed ...

3️⃣ Shared showers/toilets increased COVID-19 transmission risk in student residences.

(Vanbesien et al; Arch Pub Health)
archpublichealth.biomedcentral.com/articles/10.1186/s13690-022-00966-4

Individual level analysis of digital proximity tracing for COVID-19 in Belgium highlights major bottlenecks - Nature Communications Digital proximity tracing apps were widely used during the COVID-19 pandemic but have not been thoroughly evaluated. Here, the authors use data from students in Leuven, Belgium and estimate that apps ...

2️⃣ Despite high uptake, the Belgian digital contact tracing app (based on the Google-Apple framework) was much less effective than conventional contact tracing.

(Geenen, Raymenants, et al; Nat Comms)
www.nature.com/articles/s41467-023-42518-6

Empirical evidence on the efficiency of backward contact tracing in COVID-19 - Nature Communications Backward contact tracing aims to identify individuals who were infected by the same person as infected an index case, and has been shown to be effective in modelling studies of SARS-COV-2. Here, the a...

Hello Bluesky! A quick overview of what we learned doing contact tracing for COVID-19 at KU Leuven.

#IDEpi #PublicHealth #EpiSky #IDSky @Emmanuel_microb

1️⃣ Tracing sources of infections (backward contact tracing) could efficiently slow COVID-19 spread.
(Raymenants, Geenen, et al; Nat Comms)

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