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No more business as usual: responding to the COVID-19 pandemic through open data genome and evolutionary analytics.

Award Number: R01AI134384
ORGANIZATION: NATIONAL INSTITUTE OF ALLERGY & INFECTIOUS DISEASES
OPDIV: NIH
AWARD CLASS: DISCRETIONARY
AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)

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The rapid worldwide spread and severe regional outbreaks of COVID-19 following its emergence in Wuhan in November 2019 has created a sense of urgency and alarm. There are many more cases (>100,000) and deaths (~5,000) than in other recent viral outbreaks/epidemics (SARS, MERS, Ebola and Zika viruses); but in many other respects the epidemic is “typical” – zoonotic introduction from a (yet undetermined) animal reservoir, followed by a period of undetected transmission among humans (with possible adaptation to the new host), and then generalized transmission. The same types of questions arise during each of these emerging outbreaks: Where did the pathogen come from? Is it evolving in the human population? How is it spreading? How to develop reliable diagnostics? What are promising vaccine targets? Many, if not all, of these questions depend on rapid and reliable genomic analysis of diverse viral sample sequences by multiple laboratories. Yet, time and time again, including COVID-19, we encounter the same avoidable shortcomings early in the viral investigation: lack of reproducibility, rigor, and data/analytic sharing. The initial publications describing genomic features of COVID-19 [1–4] used Illumina and Oxford nanopore data to elucidate the sequence composition of patient specimens (although only Wu et al. [3] explicitly provided the accession numbers for their raw short read sequencing data). However, their approaches to processing, assembly, and analysis of raw data differed widely and ranged from transparent [3] to entirely opaque [4]. Such lack of analytical transparency sets a dangerous precedent. Infectious disease outbreaks often occur in locations where infrastructure necessary for data analysis may be inaccessible or unbiased interpretation of results may be politically untenable. Essential questions such as the extent of intra-host genomic variability (indicative of adaptation or multiple infection), viral evolution (selection, recombination), transmission (phylogentic and phylogeographic) cannot be answered reliably if researchers cannot trust/replicate the source data and analytical approaches. The key goals/deliverables of this supplement will be the open analytic workflows that can be used to curate and standardize genomic data, and high quality annotated variation data for SARS-CoV-2 and potential future outbreaks. These workflows will be distributed through proven, fully open, and highly used infrastructure provided by the Galaxy (http://covid19.galaxyproject.org) and HyPhy/Datamonkey (http://covid19.datamonkey.org/) projects.


Issue Date FY	Funding FY	Legal Entity Name	Legal Entity Address	Legal Entity City	Legal Entity State	Legal Entity Zip Code	Legal Entity COUNTY	Legal Entity COUNTRY	Assistance Listing	Award Code	Budget Year	Action Date	Action Type	Action Amount

Issue Date FY: 2024 ( Subtotal = $0 )
2024	2021	THE PENNSYLVANIA STATE UNIVERSITY	201 OLD MAIN	UNIVERSITY PARK	PA	16802	CENTRE	USA	Allergy and Infectious Diseases Research	001	5	12/8/2023	SUPPLEMENT FOR EXPANSION	$0
2024	2021	THE PENNSYLVANIA STATE UNIVERSITY	201 OLD MAIN	UNIVERSITY PARK	PA	16802	CENTRE	USA	Allergy and Infectious Diseases Research	000	5	12/8/2023	NON-COMPETING CONTINUATION	$0
														Subtotal = $0

Issue Date FY: 2021 ( Subtotal = $1,059,624 )
2021	2021	PENNSYLVANIA STATE UNIVERSITY, THE	201 OLD MAIN	UNIVERSITY PARK	PA	16802	CENTRE	USA	Allergy and Infectious Diseases Research	000	5	5/14/2021	NON-COMPETING CONTINUATION	$691,343
2021	2021	PENNSYLVANIA STATE UNIVERSITY, THE	201 OLD MAIN	UNIVERSITY PARK	PA	16802	CENTRE	USA	Allergy and Infectious Diseases Research	001	5	5/18/2021	SUPPLEMENT FOR EXPANSION	$368,281
														Subtotal = $1,059,624

Issue Date FY: 2020 ( Subtotal = $1,066,080 )
2020	2020	PENNSYLVANIA STATE UNIVERSITY, THE	201 OLD MAIN	UNIVERSITY PARK	PA	16802	CENTRE	USA	Allergy and Infectious Diseases Research	002	4	7/9/2020	SUPPLEMENT FOR EXPANSION	$374,737
2020	2020	PENNSYLVANIA STATE UNIVERSITY, THE	201 OLD MAIN	UNIVERSITY PARK	PA	16802	CENTRE	USA	Allergy and Infectious Diseases Research	001	4	6/30/2020	NON-COMPETING CONTINUATION	$0
2020	2020	PENNSYLVANIA STATE UNIVERSITY, THE	201 OLD MAIN	UNIVERSITY PARK	PA	16802	CENTRE	USA	Allergy and Infectious Diseases Research	000	4	5/22/2020	NON-COMPETING CONTINUATION	$691,343
														Subtotal = $1,066,080

Issue Date FY: 2019 ( Subtotal = $691,343 )
2019	2019	PENNSYLVANIA STATE UNIVERSITY, THE	201 OLD MAIN	UNIVERSITY PARK	PA	16802	CENTRE	USA	Allergy and Infectious Diseases Research	000	3	6/3/2019	NON-COMPETING CONTINUATION	$691,343
														Subtotal = $691,343

Issue Date FY: 2018 ( Subtotal = $691,316 )
2018	2018	PENNSYLVANIA STATE UNIVERSITY, THE	201 OLD MAIN	UNIVERSITY PARK	PA	16802	CENTRE	USA	Allergy and Infectious Diseases Research	000	2	4/27/2018	NON-COMPETING CONTINUATION	$691,316
														Subtotal = $691,316

Issue Date FY: 2017 ( Subtotal = $716,247 )
2017	2017	PENNSYLVANIA STATE UNIVERSITY, THE	201 OLD MAIN	UNIVERSITY PARK	PA	16802	CENTRE	USA	Allergy and Infectious Diseases Research	000	1	6/19/2017	NEW	$716,247
														Subtotal = $716,247

Grand Total All Awards = $4,224,610

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No more business as usual: responding to the COVID-19 pandemic through open data genome and evolutionary analytics.

Award Number: R01AI134384

ORGANIZATION: NATIONAL INSTITUTE OF ALLERGY & INFECTIOUS DISEASES

OPDIV: NIH

AWARD CLASS: DISCRETIONARY

AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)

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