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Alexander Bartel

@ndevln.biostats.dev

Alexander Bartel @ndevln.biostats.dev · 5mo ago

Our new rapid communication in @eurosurveillance.org: We currently observe mpox clade Ib transmission among MSM in Berlin. 35 cases mostly reported local exposure. Sequencing showed high genomic relatedness, suggesting a larger transmission network. Vaccination remains key. 🔗 doi.org/10.2807/1560...

Epidemiological curve showing the number of reported mpox cases in Berlin by reporting week, from week 45 of 2025 through week 10 of 2026. Case counts are low with up to three cases from weeks 45–49 of 2025, with primarily clade IIb and some unknown cases. The first clade Ib case is observed in week 50 with five cases overall in this week. Starting around week 1 of 2026, clade Ib cases begin appearing alongside clade IIb cases, while cases increase to up to five per week. From week 6 onward, there is an increase in reported mpox cases dominated by clade Ib, with nine cases in week 9.

Phylogenetic tree of MPXV sequences. The tree is rooted with clade Ia sequences at the base, followed by a clearly labeled clade Ib branch that includes the majority of sequences shown. Within clade Ib sequences a tightly clustered group is shown. This cluster includes all Berlin and Germany MSM-associated sequences and a small number of sequences from Netherlands, Brazil and Belgium. Travel or household associated sequences from Germany interspersed throughout the clade Ib branch, which also includes sequences from the USA, DRC, Kenya, Uganda, India, Thailand, France, Pakistan, Sweden and Canada. Clade Ia sequences appear at the base of the tree as an outgroup.

Nils Gubela @nillegu.bsky.social · 7mo ago

In our latest publication, we analyzed how transient reductions in contacts influenced the 2022 mpox outbreak. Read it here: www.nature.com/articles/s43...

Client Challenge

nature.com

Alexander Bartel @ndevln.biostats.dev · last yr.

📦 My R package {ggsurveillance} now supports nested date scales. All thanks to the fantastic {legendry} package by @teunbrand.bsky.social 🔗 ggsurveillance.biostats.dev/ 🔗 teunbrand.github.io/legendry/ ggplot rules supreme #rstats #ggplot #DataViz

Nested Date scales in ggplot2:
> scale_x_datetime(date_breaks = "2 month", date_labels = "%b-%Y",
> guide = ggsurveillance::guide_axis_nested_date())

Nested Date Scale example. Measles Cases per Month as an epicurve.

John Green @johngreensbluesky.bsky.social · 2y ago

Just received this photo from a friend of a warehouse in Kinshasa. These are tuberculosis medications--ALREADY PAID FOR--that aren't being distributed due to the Trump Administration's stop work order. TB treatment is being interrupted in SO many patients around the world. What does that mean? (1/2)

Photograph of a warehouse in Kinshasa where unboxed tuberculosis medications are going undistributed due to the stop work order by the Trump Administration.

CRAN Package Updates Bot @cranberriesfeed.bsky.social · 2y ago

New CRAN package ggsurveillance with initial version 0.1.1 #rstats https://cran.r-project.org/package=ggsurveillance

CRAN: Package ggsurveillance

Create epicurves or epigantt charts in 'ggplot2'. Prepare data for visualisation or other reporting for infectious disease surveillance and outbreak investigation. Includes functions to solve date based transformations for common reporting tasks, like (A) seasonal date alignment for respiratory disease surveillance, (B) date-based case binning based on specified time intervals like isoweek, epiweek, month and more, (C) automated detection and marking of the new year based on the date/datetime axis of the 'ggplot2'. An introduction on how to use epicurves can be found on the US CDC website (2012, <<a href="https://www.cdc.gov/training/quicklearns/epimode/index.html" target="_top">https://www.cdc.gov/training/quicklearns/epimode/index.html</a>>).

cran.r-project.org

Emanuel Wyler @ewyler.bsky.social · 2y ago

Looking for ways to improve detection of viral RNAs from wastewater? Check out our technical paper by Berliner Wasserbetriebe, Lageso Berlin, Amedes and @mdc-berlin.bsky.social on the use of inhibitor removal columns for better sensitivity: www.mdpi.com/2076-2607/12...

Effective Inhibitor Removal from Wastewater Samples Increases Sensitivity of RT-dPCR and Sequencing Analyses and Enhances the Stability of Wastewater-Based Surveillance

Wastewater-based surveillance (WBS) is a proven tool for monitoring population-level infection events. Wastewater contains high concentrations of inhibitors, which contaminate the total nucleic acids ...

mdpi.com