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Real-time tracking of virus evolution for vaccine strain selection and epidemiological investigation

Award Number: R35GM119774
ORGANIZATION: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES
OPDIV: NIH
AWARD CLASS: DISCRETIONARY
AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)
PERIOD OF PERFORMANCE START DATE: 08/23/2016
PERIOD OF PERFORMANCE END DATE: 05/31/2026

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Real-time tracking of virus evolution for vaccine strain selection and epidemiological investigation - Project Summary Viral pathogens are an enduring threat to global public health. This project aims to use viral genomic data to improve understanding of ongoing virus evolution and to make actionable inferences to reduce the global burden of viral infectious disease. In order to be relevant for public health interventions, analyses of viral sequence data need to be incredibly rapid, both in terms of computation and in terms of dissemination. To accomplish these goals, this project will create novel methodological tools to analyze evolutionary dynamics from inﬂuenza genetic sequence data and to analyze transmission patterns from outbreak sequence data. Over the current project period (2016-2021), we developed a real-time analysis platform called Nextstrain, which provides up-to-date analyses for a variety of pathogens including inﬂuenza virus, Ebola virus, Zika virus, dengue virus, mumps virus, tuberculosis and SARS-CoV-2. Bioinformatic pipelines developed through Nextstrain are reusable by academic groups and public health labs and resulting analyses are shareable via the website nextstrain.org. In the upcoming project period (2021-2026), we will reﬁne methods for forecasting strain dynamics of inﬂuenza virus. Monitoring and forecasting evolution of viral strains is of paramount importance. New antigenic variants of inﬂuenza that partially escape from prior human immunity emerge and rapidly sweep through the viral population. Such strains are less susceptible to vaccine-derived immunity and so antigenic evolution results in the need to frequently update the seasonal inﬂuenza vaccine. This project aims to reﬁne methods to forecast strain dynamics and predict the makeup of the future inﬂuenza population. This forecasting is especially relevant to inﬂuenza vaccine strain selection, as a vaccine strain is chosen for the Northern Hemisphere in February for deployment the following winter. Accurate projections will aid in vaccine match for seasonal inﬂuenza viruses and result in improved vaccine efﬁcacy. Technical innovations focus on extending models to work across different viruses, different gene segments and to incorporate spatial dynamics. In an outbreak scenario such as the West African Ebola epidemic, the American Zika epidemic or the SARS- CoV-2 pandemic, the focus of public health interventions focus on early diagnosis, contact tracing, isolation and treatment. Epidemiological understanding of transmission dynamics is of paramount importance to outbreak response. Viral genomic data can reveal otherwise hidden transmission patterns and aid in efﬁcient contact tracing. Geographic spread is especially amenable to genomic inferences. This project will develop tools to make epidemiological inferences from outbreak sequence data. These methods will continue to be deployed via the Nextstrain platform, allowing epidemiologists throughout the world to analyze their own datasets. Genomic epidemiology has the potential to truly inform outbreak response. Nextstrain has been instrumental to SARS-CoV-2 genomic epidemiology in the United States and world. Improvements to the accuracy and capabilities of the platform would be well placed.


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: 2025 ( Subtotal = $418,074 )
2025	2025	FRED HUTCHINSON CANCER CENTER	1100 FAIRVIEW AVE N	SEATTLE	WA	98109	KING	USA	Biomedical Research and Research Training	001	11	5/26/2025	NON-COMPETING CONTINUATION	$418,074
2025	2024	FRED HUTCHINSON CANCER CENTER	1100 FAIRVIEW AVE N	SEATTLE	WA	98109	KING	USA	Biomedical Research and Research Training	000	10	11/5/2024	NON-COMPETING CONTINUATION	$0
														Subtotal = $418,074

Issue Date FY: 2024 ( Subtotal = $418,074 )
2024	2024	FRED HUTCHINSON CANCER CENTER	1100 FAIRVIEW AVE N	SEATTLE	WA	98109	KING	USA	Biomedical Research and Research Training	000	10	5/9/2024	NON-COMPETING CONTINUATION	$418,074
														Subtotal = $418,074

Issue Date FY: 2023 ( Subtotal = $418,074 )
2023	2023	FRED HUTCHINSON CANCER CENTER	1100 FAIRVIEW AVE N	SEATTLE	WA	98109	KING	USA	Biomedical Research and Research Training	002	9	6/7/2023	NON-COMPETING CONTINUATION	$418,074
2023	2021	FRED HUTCHINSON CANCER RESEARCH CENTER	1100 FAIRVIEW AVE N J6-300	SEATTLE	WA	98109	KING	USA	Biomedical Research and Research Training	000	6	11/8/2022	COMPETING CONTINUATION	-$224,825
2023	2021	FRED HUTCHINSON CANCER CENTER	1100 FAIRVIEW AVE N	SEATTLE	WA	98109	KING	USA	Biomedical Research and Research Training	001	7	11/8/2022	CHANGE OF GRANTEE / TRAINING INSTITUTION / AWARDING INSTITUTION	$224,825
														Subtotal = $418,074

Issue Date FY: 2022 ( Subtotal = $418,074 )
2022	2022	FRED HUTCHINSON CANCER CENTER	1100 FAIRVIEW AVE N	SEATTLE	WA	98109	KING	USA	Biomedical Research and Research Training	004	8	8/22/2022	NON-COMPETING CONTINUATION	$418,074
2022	2021	FRED HUTCHINSON CANCER RESEARCH CENTER	1100 FAIRVIEW AVE N J6-300	SEATTLE	WA	98109	KING	USA	Biomedical Research and Research Training	001	6	11/6/2021	COMPETING CONTINUATION	$238,357
2022	2021	FRED HUTCHINSON CANCER CENTER	1100 FAIRVIEW AVE N	SEATTLE	WA	98109	KING	USA	Biomedical Research and Research Training	003	7	6/16/2022	CHANGE OF GRANTEE / TRAINING INSTITUTION / AWARDING INSTITUTION	$214,463
2022	2021	FRED HUTCHINSON CANCER RESEARCH CENTER	1100 FAIRVIEW AVE N J6-300	SEATTLE	WA	98109	KING	USA	Biomedical Research and Research Training	002	6	6/15/2022	COMPETING CONTINUATION	-$214,463
2022	2020	FRED HUTCHINSON CANCER RESEARCH CENTER	1100 FAIRVIEW AVE N J6-300	SEATTLE	WA	98109	KING	USA	Biomedical Research and Research Training	000	5	11/6/2021	NON-COMPETING CONTINUATION	-$238,357
														Subtotal = $418,074

Issue Date FY: 2021 ( Subtotal = $418,074 )
2021	2021	FRED HUTCHINSON CANCER RESEARCH CENTER	1100 FAIRVIEW AVE N J6-300	SEATTLE	WA	98109	KING	USA	Biomedical Research and Research Training	000	6	4/23/2021	COMPETING CONTINUATION	$418,074
														Subtotal = $418,074

Issue Date FY: 2020 ( Subtotal = $401,525 )
2020	2020	FRED HUTCHINSON CANCER RESEARCH CENTER	1100 FAIRVIEW AVE N J6-300	SEATTLE	WA	98109	KING	USA	Biomedical Research and Research Training	000	5	5/12/2020	NON-COMPETING CONTINUATION	$401,525
														Subtotal = $401,525

Issue Date FY: 2019 ( Subtotal = $403,857 )
2019	2019	FRED HUTCHINSON CANCER RESEARCH CENTER	1100 FAIRVIEW AVE N J6-300	SEATTLE	WA	98109	KING	USA	Biomedical Research and Research Training	000	4	5/20/2019	NON-COMPETING CONTINUATION	$403,857
														Subtotal = $403,857

Issue Date FY: 2018 ( Subtotal = $406,123 )
2018	2018	FRED HUTCHINSON CANCER RESEARCH CENTER	1100 FAIRVIEW AVE N J6-300	SEATTLE	WA	98109	KING	USA	Biomedical Research and Research Training	000	3	5/29/2018	NON-COMPETING CONTINUATION	$406,123
														Subtotal = $406,123

Issue Date FY: 2017 ( Subtotal = $408,327 )
2017	2017	FRED HUTCHINSON CANCER RESEARCH CENTER	1100 FAIRVIEW AVE N J6-300	SEATTLE	WA	98109	KING	USA	Biomedical Research and Research Training	000	2	5/31/2017	NON-COMPETING CONTINUATION	$408,327
														Subtotal = $408,327

Issue Date FY: 2016 ( Subtotal = $410,473 )
2016	2016	FRED HUTCHINSON CANCER RESEARCH CENTER	1100 FAIRVIEW AVE NO J6-330	SEATTLE	WA	98109	KING	USA	Biomedical Research and Research Training	000	1	8/23/2016	NEW	$410,473
														Subtotal = $410,473

Grand Total All Awards = $4,120,675

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Real-time tracking of virus evolution for vaccine strain selection and epidemiological investigation

Award Number: R35GM119774

ORGANIZATION: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES

OPDIV: NIH

AWARD CLASS: DISCRETIONARY

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

PERIOD OF PERFORMANCE START DATE: 08/23/2016

PERIOD OF PERFORMANCE END DATE: 05/31/2026

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