Some bacteria can rapidly change their surface proteins to undergo antigenic variation – what is the diversity of these proteins and how do they evolve? We delved into this question in Neisseria gonorrhoeae, the cause of the sexually transmitted infection gonorrhea: journals.plos.org/plospathogen...

Diversity and evolution of a phase-variable multi-locus antigen in Neisseria gonorrhoeae

Author summary The rising levels of antibiotic resistance in Neisseria gonorrhoeae make controlling the spread of this sexually transmitted pathogen a public health priority. N. gonorrhoeae rapidly va...

journals.plos.org

Exciting new method to directly infer pathogen transmission rates using sequencing data. Amazing work led by Takashi Okada and @ohallats.bsky.social. Check out @ohallats.bsky.social's great summary thread below.

Oskar Hallatschek@ohallats.bsky.social · 2y ago

After a long and winding odyssey, excited to finally drop anchor in open-access waters. This preprint shows how neutral allele frequency time series can illuminate disease transmission rates between communities— key for epidemic fore- & backcasting. medrxiv.org/content/10.1... 🧵

Very proud to share my very first book written together with Alli Black! It covers the principles & considerations of genomic epidemiology as well as real-world examples. We hope it'll prove a useful teaching resource for the field. Psst... the free version lives here: alliblk.github.io/genepi-book/

How do you track an ongoing epidemic, especially without large-scale testing? We explored the use of routinely collected RT-qPCR cycle threshold values in our new preprint out now! doi.org/10.1101/2024... 1/

Nowcasting epidemic trends using hospital- and community-based virologic test data

Epidemiological surveillance typically relies on reported incidence of cases or hospitalizations, which can suffer significant reporting lags, biases and under-ascertainment. Here, we evaluated the po...

doi.org