Katherine Siddle

🚨 It's still time to apply to the Pasteur-Paris University International Doctoral Program Deadline 📆 oct. 31 Apply now ➡️ ppu.pasteur.fr/ppu_etud_accue… #PhDProgram #EmergingInfectiousDiseases #AMR

@RhysHParry Hi Rhys, Thanks for reading our paper. Detecting contamination is something we think a lot about, but concluded unlikely as would require >=2 independent events from related but novel viruses at high levels. Would welcome any thoughts you have about it, always happy to discuss.

Metagenomic surveillance from febrile cases in Nigeria uncovers more human blood-associated dicistroviruses. Given their position, extraordinary proof is needed to prove these are not contaminants. 🎵Come with me and you'll see a world of run contamination nature.com/articles/s4146…

Over the last month, #RSV has surged early and hard, placing immense pressure on hospitals and clinics. Despite this, genomic insights have been limited. Check out our Virological post describing an initial look into the #RSV surge in MA 🦠🧬 virological.org/t/preliminary-… 1/12

@dndiaye23 @SyMOUHAMAD1 @CCigass Thank you for welcoming us! It was wonderful to be back & congratulations on the new CIGASS center.

Très heureux d'avoir reçu mes collaborateurs Américains de l’Institut BROAD de MIT aux États Unis au CIGASS dans le cadre d’une visite de travail. #cigass @CCigass

An absolute pleasure to work on this study alongside many partners including @sabeti_lab @broadinstitute @MassDPH @BCHDCapeCod @HumanServicesBC @PIH's CTC @HarvardChanSPH. Many thanks also to @patternvizlab for the beautiful graphical abstract.

Our new! preprint! Learning from COVID-19 outbreak in Provincetown this July⬇ medrxiv.org/content/10.110… Ptown outbreak: - 99% Delta - 74% vaccinated, 79% w symptoms Takeaways: - SARS-CoV-2 spread from+btwn fully vaxxed - Contained, likely thx to vaccine+public health response 1/

Members of the Broad Institute of MIT and Harvard and Endicott College are conducting research about perceptions of the COVID-19 pandemic. If you were involved in COVID-19 response, please consider sharing your insights: harvard.az1.qualtrics.com/jfe/form/SV_41….

@NathanGrubaugh @YaleEMD @GISAID Thanks! We'll take a look for them.

There are now over 50 SARS-CoV-2 genomes of the P.1 Variant of Concern lineage from Massachusetts, largely detected in the Cape Cod area over the past month (tinyurl.com/y322v8). A few observations (from me & @dannyjpark @bronwynmacinnis @glipsnort @sabeti_lab). [1/10]

Analyses above made possible by data contributors to @GISAID. Some new MA genomes are currently in submission and will be released by @CDC_AMD on @GISAID soon. Meanwhile, we have made a P.1-focused @nextstrain build available at auspice.broadinstitute.org/sars-cov-2/ma-… [10/10]

The extent of community transmission of P.1 in MA is not yet established. The data are suggestive of additional undetected P.1 cases, though more extensive epidemiological and genomic surveillance is needed. [9/10]

Explore this data in more detail in a @nextstrain narrative (auspice.broadinstitute.org/narratives/sar…) and public terra workspace (#workspaces/pathogen-genomic-surveillance/COVID-19_Broad_Viral_NGS" target="_blank" rel="nofollow noopener">app.terra.bio/#workspaces/pa…). We’ll post more genomes as we generate them and are working hard to make our dataset more comprehensive and representative. 7/7

These 772 genomes were obtained from NP swabs from individuals with confirmed SARS-CoV-2 infection, primarily from the Boston area collected by @MGH_ID, @MassDPH between March 3 and May 9, 2020 and sequenced @broadinstitute by an amazing lab team broadinstitute.org/blog/inside-br… 6/7

Pleased to share our latest pre-print using 772 SARS-CoV-2 genomes to investigate the introduction and spread in the Boston area. A huge team effort and great partnership between @sabeti_lab, @MGH_ID, @MassDPH and others; medrxiv.org/content/10.110… 1/7