https://tinyurl.com/artic-live | ARTIC table-top genomic epidemiology by ARTIC-admin https://padlet.com/articnetwork/livefeed Grand Challenges, Brussels, 25th October 2022 en-us 2022-10-21 11:04:01 UTC 2023-03-12 12:54:52 UTC hello@padlet.com https://padlet-uploads.storage.googleapis.com/1770010710/6fcc870daa3ac0bbbd88e1f43cf5c14a/logo_no_text.png Good morning! articadmin https://padlet.com/articnetwork/livefeed/wish/2350492285 Disclaimer: The events depicted in this workshop are entirely fictional. Any resemblance to actual persons, living or dead, actual events or outbreaks before or afterwards is purely coincidental. ]]> 2022-10-21 10:24:36 UTC https://padlet.com/articnetwork/livefeed/wish/2350492285 ACDC alert - undiagnosed febrile illness articadmin https://padlet.com/articnetwork/livefeed/wish/2350493178 2022-09-12: A 30 year old male in Southern California presented to the emergency department complaining of fever, tiredness, aches. On examination he has a temperature of 38.3C and is jaundiced. His ALP is 220U/ml with platelets of 10. Over the course of the day he becomes progressively more unwell and begins bleeding profusely. Viral screen including hepatitis A-E is negative. ]]> 2022-10-21 10:25:29 UTC https://padlet.com/articnetwork/livefeed/wish/2350493178 Metagenomic Sequencing of Index Case articadmin https://padlet.com/articnetwork/livefeed/wish/2351920821 Total DNA and RNA extracted from blood of the primary case was sequenced using Illumina technology with paired 150bp reads at a willing academic laboratory that routinely sequences microbial genomes and metagenomes. The sequencing generated around 1M reads in total. There was no target enrichment for specific pathogens. Bioinformatics analysis was performed with Kraken2 of reads searched against Ben Langmead’s “Standard” microbial taxonomic database.]]> 2022-10-22 20:56:36 UTC https://padlet.com/articnetwork/livefeed/wish/2351920821 articadmin https://padlet.com/articnetwork/livefeed/wish/2353627485 2022-10-24 13:47:25 UTC https://padlet.com/articnetwork/livefeed/wish/2353627485 Enhanced epidemiology investigation articadmin https://padlet.com/articnetwork/livefeed/wish/2353636754 2022-10-24 13:51:48 UTC https://padlet.com/articnetwork/livefeed/wish/2353636754 Pet Shop Environmental Sequencing sajwilkinson https://padlet.com/articnetwork/livefeed/wish/2353715779 https://artic-network.github.io/artic-live/gc/pet_shop_env_title.html]]> 2022-10-24 14:28:00 UTC https://padlet.com/articnetwork/livefeed/wish/2353715779 Heavy metal-associated controls: Metalgenomics sajwilkinson https://padlet.com/articnetwork/livefeed/wish/2353718412 https://artic-network.github.io/artic-live/gc/control_1_title.html

https://artic-network.github.io/artic-live/gc/control_2_title.html

https://artic-network.github.io/artic-live/gc/control_3_title.html]]> 2022-10-24 14:29:18 UTC https://padlet.com/articnetwork/livefeed/wish/2353718412 Heavy metal-associated cases: Metalgenomics sajwilkinson https://padlet.com/articnetwork/livefeed/wish/2353726362 https://artic-network.github.io/artic-live/gc/case_2_title.html

https://artic-network.github.io/artic-live/gc/case_3_title.html

https://artic-network.github.io/artic-live/gc/case_4_title.html]]> 2022-10-24 14:33:21 UTC https://padlet.com/articnetwork/livefeed/wish/2353726362 Course of action: articadmin https://padlet.com/articnetwork/livefeed/wish/2353737787 http://tinyurl.com/biom25-slido]]> 2022-10-24 14:39:11 UTC https://padlet.com/articnetwork/livefeed/wish/2353737787 Wastewater Sequencing sajwilkinson https://padlet.com/articnetwork/livefeed/wish/2353749419 https://artic-network.github.io/artic-live/gc/wastewater_seq_title.html]]> 2022-10-24 14:44:50 UTC https://padlet.com/articnetwork/livefeed/wish/2353749419 What plausible pathogenic agents did you find? articadmin https://padlet.com/articnetwork/livefeed/wish/2353773259 http://tinyurl.com/biom25-slido]]> 2022-10-24 14:57:25 UTC https://padlet.com/articnetwork/livefeed/wish/2353773259 What do we sequence next? articadmin https://padlet.com/articnetwork/livefeed/wish/2353778548 http://tinyurl.com/biom25-slido]]> 2022-10-24 15:00:17 UTC https://padlet.com/articnetwork/livefeed/wish/2353778548 What pathogens are you ruling out and why? articadmin https://padlet.com/articnetwork/livefeed/wish/2353785638 http://tinyurl.com/biom25-slido

]]> 2022-10-24 15:04:05 UTC https://padlet.com/articnetwork/livefeed/wish/2353785638 articadmin https://padlet.com/articnetwork/livefeed/wish/2353795060 2022-10-24 15:09:09 UTC https://padlet.com/articnetwork/livefeed/wish/2353795060 What is the likely causative agent? articadmin https://padlet.com/articnetwork/livefeed/wish/2353796569 http://tinyurl.com/biom25-slido]]> 2022-10-24 15:09:57 UTC https://padlet.com/articnetwork/livefeed/wish/2353796569 What interventions are appropriate? articadmin https://padlet.com/articnetwork/livefeed/wish/2353796992 http://tinyurl.com/biom25-slido]]> 2022-10-24 15:10:13 UTC https://padlet.com/articnetwork/livefeed/wish/2353796992 articadmin https://padlet.com/articnetwork/livefeed/wish/2354373052 2022-10-24 21:28:32 UTC https://padlet.com/articnetwork/livefeed/wish/2354373052 articadmin https://padlet.com/articnetwork/livefeed/wish/2354390751 2022-10-24 21:52:34 UTC https://padlet.com/articnetwork/livefeed/wish/2354390751 articadmin https://padlet.com/articnetwork/livefeed/wish/2354392200 2022-10-24 21:54:36 UTC https://padlet.com/articnetwork/livefeed/wish/2354392200 Welcome to Day 2 articadmin https://padlet.com/articnetwork/livefeed/wish/2355203355 Disclaimer: The events depicted in this workshop are entirely fictional. Any resemblance to actual persons, living or dead, actual events or outbreaks before or afterwards is purely coincidental. ]]> 2022-10-25 10:28:41 UTC https://padlet.com/articnetwork/livefeed/wish/2355203355 Evolutionary History Virus Phylogeny sajwilkinson https://padlet.com/articnetwork/livefeed/wish/2355230713 Segment L: https://nextstrain.org/community/emmahodcroft/GC/arenavirus/L
Segment S: https://nextstrain.org/community/emmahodcroft/GC/arenavirus/S]]> 2022-10-25 10:54:22 UTC https://padlet.com/articnetwork/livefeed/wish/2355230713 Assembled Genome Segments sajwilkinson https://padlet.com/articnetwork/livefeed/wish/2355260766 Segment S - https://artic-network.github.io/artic-live/gc/segment_S.fasta.txt

Segment L - https://artic-network.github.io/artic-live/gc/segment_L.fasta.txt

]]> 2022-10-25 11:23:11 UTC https://padlet.com/articnetwork/livefeed/wish/2355260766 Phylogenetic analysis of rock concert cases sajwilkinson https://padlet.com/articnetwork/livefeed/wish/2355275985 https://nextstrain.org/community/emmahodcroft/GC/HMFV/FC?p=grid]]> 2022-10-25 11:37:55 UTC https://padlet.com/articnetwork/livefeed/wish/2355275985 Phylogenetic update 2 sajwilkinson https://padlet.com/articnetwork/livefeed/wish/2355278976 2022-10-25 11:40:05 UTC https://padlet.com/articnetwork/livefeed/wish/2355278976 NCBI Blast sajwilkinson https://padlet.com/articnetwork/livefeed/wish/2355361093 Paste your sequence in the Query Sequence box]]> 2022-10-25 12:41:58 UTC https://padlet.com/articnetwork/livefeed/wish/2355361093 What is this virus? sajwilkinson https://padlet.com/articnetwork/livefeed/wish/2355493125 http://tinyurl.com/biom25-slido]]> 2022-10-25 13:55:33 UTC https://padlet.com/articnetwork/livefeed/wish/2355493125 What do you want to do next? sajwilkinson https://padlet.com/articnetwork/livefeed/wish/2355495651 http://tinyurl.com/biom25-slido]]> 2022-10-25 13:56:48 UTC https://padlet.com/articnetwork/livefeed/wish/2355495651 otoolea2 https://padlet.com/articnetwork/livefeed/wish/2355569133 2022-10-25 14:35:48 UTC https://padlet.com/articnetwork/livefeed/wish/2355569133 Tanglegram of Segment S/L Phylogenies sajwilkinson https://padlet.com/articnetwork/livefeed/wish/2355758332 https://nextstrain.org/community/emmahodcroft/GC/arenavirus/S:community/emmahodcroft/GC/arenavirus/L]]> 2022-10-25 16:18:21 UTC https://padlet.com/articnetwork/livefeed/wish/2355758332 Segment S BLAST results articadmin https://padlet.com/articnetwork/livefeed/wish/2355772962 2022-10-25 16:26:37 UTC https://padlet.com/articnetwork/livefeed/wish/2355772962 Segment L BLAST results articadmin https://padlet.com/articnetwork/livefeed/wish/2355786603 2022-10-25 16:33:41 UTC https://padlet.com/articnetwork/livefeed/wish/2355786603 otoolea2 https://padlet.com/articnetwork/livefeed/wish/2355789157 2022-10-25 16:35:10 UTC https://padlet.com/articnetwork/livefeed/wish/2355789157 What should the virus be named? articadmin https://padlet.com/articnetwork/livefeed/wish/2355812676 http://tinyurl.com/biom25-slido]]> 2022-10-25 16:49:12 UTC https://padlet.com/articnetwork/livefeed/wish/2355812676 articadmin https://padlet.com/articnetwork/livefeed/wish/2355820757 2022-10-25 16:53:51 UTC https://padlet.com/articnetwork/livefeed/wish/2355820757 articadmin https://padlet.com/articnetwork/livefeed/wish/2355822980 2022-10-25 16:55:06 UTC https://padlet.com/articnetwork/livefeed/wish/2355822980 otoolea2 https://padlet.com/articnetwork/livefeed/wish/2355830188 2022-10-25 16:59:29 UTC https://padlet.com/articnetwork/livefeed/wish/2355830188 BEAST phylodynamic report articadmin https://padlet.com/articnetwork/livefeed/wish/2356642754 2022-10-26 04:40:25 UTC https://padlet.com/articnetwork/livefeed/wish/2356642754 Advise policymakers on what this can tell us about the novel virus articadmin https://padlet.com/articnetwork/livefeed/wish/2356700498 http://tinyurl.com/biom25-slido]]> 2022-10-26 05:39:36 UTC https://padlet.com/articnetwork/livefeed/wish/2356700498 If you selected "Other" yesterday, how do you self identify? sajwilkinson https://padlet.com/articnetwork/livefeed/wish/2356703653 http://tinyurl.com/biom25-slido]]> 2022-10-26 05:42:41 UTC https://padlet.com/articnetwork/livefeed/wish/2356703653 Final Nextstrain Phylogeny sajwilkinson https://padlet.com/articnetwork/livefeed/wish/2356709261 2022-10-26 05:48:39 UTC https://padlet.com/articnetwork/livefeed/wish/2356709261 Does this change what we think about the outbreak? sajwilkinson https://padlet.com/articnetwork/livefeed/wish/2356713250 http://tinyurl.com/biom25-slido]]> 2022-10-26 05:52:38 UTC https://padlet.com/articnetwork/livefeed/wish/2356713250 How do we stop this outbreak becoming a pandemic? sajwilkinson https://padlet.com/articnetwork/livefeed/wish/2356714308 http://tinyurl.com/biom25-slido]]> 2022-10-26 05:53:27 UTC https://padlet.com/articnetwork/livefeed/wish/2356714308 What can this tell us about the outbreak and when it may have started? sajwilkinson https://padlet.com/articnetwork/livefeed/wish/2356746188 http://tinyurl.com/biom25-slido]]> 2022-10-26 06:24:04 UTC https://padlet.com/articnetwork/livefeed/wish/2356746188 Metal cluster sequencing otoolea2 https://padlet.com/articnetwork/livefeed/wish/2356989600 https://nextstrain.org/community/emmahodcroft/GC/HMFV/FC]]> 2022-10-26 09:44:15 UTC https://padlet.com/articnetwork/livefeed/wish/2356989600 Lets try out Slido sajwilkinson https://padlet.com/articnetwork/livefeed/wish/2496420050 tinyurl.com/cadde-workshop]]> 2023-02-27 14:16:04 UTC https://padlet.com/articnetwork/livefeed/wish/2496420050 What is your differential diagnosis? sajwilkinson https://padlet.com/articnetwork/livefeed/wish/2496420848 http://tinyurl.com/biom25-slido]]> 2023-02-27 14:16:35 UTC https://padlet.com/articnetwork/livefeed/wish/2496420848