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Thanks to the organizers for making this possible! Follow the link to watch me, Matthew Hall, Xavier Didelot , @gerrythill, @Chjulian, Colin Worby, Thibaut Jombart present the current field of inferring pathogen direction of transmission.

OpenABM-COVID19, the model which has been a key tool in many aspects of international epidemic responses, now peer-reviewed and published in PLOS Comp Biol doi.org/10.1371/journa…

New paper with ISARIC (non-genomic) on variations in the hospital journey of COVID-19 patients during last year. Main cautionary point - using e.g. death or ICU admission as an outcome variable is inadvisable during a rapidly-changing situation. elifesciences.org/articles/70970

Me taking a COVID test in 2020: sanitising entire room, triple washing hands, following instructions page by page. Me taking one now: In one smooth movement wipe crumbs off nearest surface, open the shot of buffer solution with my teeth and start violating my nostril.

Work with ISARIC on the change in hospital journey for COVID-19 over the first year of the pandemic now published at eLife - the journal elifesciences.org/articles/70970

We discovered a highly virulent variant of HIV in the Netherlands, now published in Science. Levels of virus 3.5-5.5x higher, immune cell decline 2x faster, increased transmissibility. Striking eg of evolution. W Christophe Fraser Group @HIVMonitoringNL & partners science.org/doi/10.1126/sc…

New work by Valentin Druelle on mutations that make the HIV-1 genome closer to the global HIV consensus: - These mutations are positively selected within host. - At the population level, these mutations result in spuriously low rate estimates. 1/ biorxiv.org/content/10.110…

Summer internship, aimed at 2nd/3rd year undergrads or Masters students, at Big Data Institute with Katrina Lythgoe and myself on SARS-CoV-2 coinfections bdi.ox.ac.uk/study/bdi-summ…

Blaming an organisation that doesnt exist anymore seems convenient. SAGE had no expert on care homes or nursing on it. The sector was modelled as a closed system (which anyone with real world knowledge would have know was a false assumption) #COVID19 #carehomes

Hey #rstats, delighted to bring you another issue of R Weekly (R Weekly) 🔗: rweekly.org/2022-W30.html Highlights 🌟: 1⃣ {nplyr}: Nested data manipulation - Mark Rieke 2⃣ {rtweet}: ✅ consistent output - Lluís Revilla Sancho 3⃣ {ggarchery}: Flexible ↕️ geoms for #ggplot2 - M. Hall

My little package ggarchery github.com/mdhall272/ggar… makes R Weekly #rstats

When can phylogenetic methods alone predict the direction of transmission? We (@Chjulian, Katrina Lythgoe, Matthew Hall, @BaxtrJames et al.) help to quantify this in our new PNASNews study out today! doi.org/10.1073/pnas.2…

Super happy about our new paper in PNAS Nexus! It is a collaborative approach that combines phylogeny, network theory and epidemic modelling to estimate the pandemic potential of emergent variants from limited/noisy data doi.org/10.1093/pnasne… a 🧵

New research article Demographics of sources of #HIV-1 transmission in #Zambia: a molecular epidemiology analysis in the HPTN 071 #PopART study thelancet.com/journals/lanmi… #InfectiousDiseases

👏Congratulations to Matthew Hall and team on their publication in the Lancet. The study showed that men 25-40 years account for a disproportionate fraction of #HIV transmission. thelancet.com/journals/lanmi… Christophe Fraser Group Tanya Golubchik Mohammed Limbada Dr. Musonda Simwinga @helen_ayles

Something we noticed when analysing HIV sequences with the classic Gamma rate heterogeneity model biorxiv.org/content/10.110…