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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.

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tinyurl.com/cadde-workshop

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ACDC alert - undiagnosed febrile illness

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ACDC alert - undiagnosed febrile illness

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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.

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http://tinyurl.com/biom25-slido

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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.

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http://tinyurl.com/biom25-slido

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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

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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

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

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

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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

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Paste your sequence in the Query Sequence box

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align two sequences using blast (bl2seq)

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Nucleotide BLAST: Search nucleotide databases using a nucleotide query

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An official website of the United States government

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Segment L: https://nextstrain.org/community/emmahodcroft/GC/arenavirus/L
Segment S: https://nextstrain.org/community/emmahodcroft/GC/arenavirus/S

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https://nextstrain.org/community/emmahodcroft/GC/HMFV/FC