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Launching HBV with RNA to assess antiviral resistance and explore fundamental aspects of virus-host biology

Award Number: R01AI150275
ORGANIZATION: NATIONAL INSTITUTE OF ALLERGY & INFECTIOUS DISEASES
OPDIV: NIH
AWARD CLASS: DISCRETIONARY
AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)
PERIOD OF PERFORMANCE START DATE: 02/10/2020
PERIOD OF PERFORMANCE END DATE: 01/31/2025

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Launching HBV with RNA to assess antiviral resistance and explore fundamental aspects of virus-host biology - Project Summary More than 250 million people are chronically infected with hepatitis B virus (HBV), living at increased risk of liver failure, cancer, and early death. Though there is a vaccine to prevent HBV infection, it does not prevent vertical transfer, nor does it help the millions of people already infected. While there are therapies (e.g. nucleoside analogs) to suppress virus replication, treatment is life-long and rarely leads to cure. Achieving a functional cure for chronic HBV infection therefore represents a major global unmet medical need. Fortunately, new classes of HBV inhibitors are being developed and some have already entered clinical trials, but many fundamental (and clinically-relevant) aspects of HBV biology remain unanswered. The broad long-term objectives of this project are to address knowledge gaps in the field using a new cell culture-based method we developed to initiate HBV replication with RNA. Specifically, we capitalize on the most unique features of this technology to (i) address a practical problem of drug development—antiviral resistance, (ii) to fill gaps in our fundamental knowledge of HBV protein translation and genome replication, and (iii) as a discovery tool to identify host factors that restrict or promote the HBV lifecycle. There is currently no way to assess antiviral resistance with existing HBV cell culture-based systems. With our RNA approach, we take advantage of the fact that phage polymerases (e.g. T7) commonly used to in vitro-transcribe RNA are error-prone. As such, initiating HBV replication with RNA rather than DNA (like most systems) allows a diverse population of viral variants to be sampled. As we show with compelling preliminary data, this sequence diversity coupled with deep sequencing technology makes it possible to select for and detect rare HBV drug-resistant viral variants. Aim 1 of this proposal is to further develop this technology. Initiating HBV replication with RNA largely eliminates the background signal that contaminates HBV qPCR reactions, and since not all viral RNAs are required to initiate replication, some viral proteins are made only if the viral lifecycle progresses and the viral DNA template—covalently closed circular DNA (cccDNA)—is established. We capitalize on this in Aim 2 to study fundamental aspects of HBV protein translation and genome replication, and in Aim 3 to discover virus-host interactions. Specifically we use the method in Aim 2 to study mutations that frequently arise in chronically infected individuals and differences in HBV genotypes. We use the method in Aim 3 as the basis for a genome-wide CRISPR knockout screen to identify HBV host factors. Until we have a solution for eliminating chronic HBV, continuing and new fundamental studies of HBV biology are needed to identify new strategies that can be explored for therapeutic intervention. The new RNA- based system we developed to study HBV biology and assess antiviral resistance align well with the NIH's strategic plan to cure chronic HBV and the work we propose will contribute significantly to this ongoing effort.


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 = $738,557 )
2025	2025	ROCKEFELLER UNIVERSITY	1230 YORK AVE	NEW YORK	NY	10065	NEW YORK	USA	Allergy and Infectious Diseases Research	000	5	5/12/2025	NON-COMPETING CONTINUATION	$738,557
2025	2024	ROCKEFELLER UNIVERSITY	1230 YORK AVE	NEW YORK	NY	10065	NEW YORK	USA	Allergy and Infectious Diseases Research	001	5	5/12/2025	NON-COMPETING CONTINUATION	$0
2025	2024	ROCKEFELLER UNIVERSITY	1230 YORK AVE	NEW YORK	NY	10065	NEW YORK	USA	Allergy and Infectious Diseases Research	000	5	5/12/2025	NON-COMPETING CONTINUATION	$0
														Subtotal = $738,557

Issue Date FY: 2024 ( Subtotal = $611,076 )
2024	2024	ROCKEFELLER UNIVERSITY	1230 YORK AVE	NEW YORK	NY	10065	NEW YORK	USA	Allergy and Infectious Diseases Research	001	5	5/23/2024	NON-COMPETING CONTINUATION	$61,108
2024	2024	ROCKEFELLER UNIVERSITY	1230 YORK AVE	NEW YORK	NY	10065	NEW YORK	USA	Allergy and Infectious Diseases Research	000	5	1/16/2024	NON-COMPETING CONTINUATION	$549,968
														Subtotal = $611,076

Issue Date FY: 2023 ( Subtotal = $611,076 )
2023	2023	ROCKEFELLER UNIVERSITY	1230 YORK AVE	NEW YORK	NY	10065	NEW YORK	USA	Allergy and Infectious Diseases Research	001	4	4/12/2023	NON-COMPETING CONTINUATION	$0
2023	2023	ROCKEFELLER UNIVERSITY	1230 YORK AVE	NEW YORK	NY	10065	NEW YORK	USA	Allergy and Infectious Diseases Research	000	4	1/13/2023	NON-COMPETING CONTINUATION	$611,076
														Subtotal = $611,076

Issue Date FY: 2022 ( Subtotal = $630,683 )
2022	2022	ROCKEFELLER UNIVERSITY, THE	1230 YORK AVE	NEW YORK	NY	10065	NEW YORK	USA	Allergy and Infectious Diseases Research	000	3	1/25/2022	NON-COMPETING CONTINUATION	$630,683
														Subtotal = $630,683

Issue Date FY: 2021 ( Subtotal = $565,164 )
2021	2021	ROCKEFELLER UNIVERSITY, THE	1230 YORK AVE	NEW YORK	NY	10065	NEW YORK	USA	Allergy and Infectious Diseases Research	000	2	1/29/2021	NON-COMPETING CONTINUATION	$565,164
														Subtotal = $565,164

Issue Date FY: 2020 ( Subtotal = $560,079 )
2020	2020	ROCKEFELLER UNIVERSITY, THE	1230 YORK AVE	NEW YORK	NY	10065	NEW YORK	USA	Allergy and Infectious Diseases Research	000	1	2/10/2020	NEW	$560,079
														Subtotal = $560,079

Grand Total All Awards = $3,716,635

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Launching HBV with RNA to assess antiviral resistance and explore fundamental aspects of virus-host biology

Award Number: R01AI150275

ORGANIZATION: NATIONAL INSTITUTE OF ALLERGY & INFECTIOUS DISEASES

OPDIV: NIH

AWARD CLASS: DISCRETIONARY

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

PERIOD OF PERFORMANCE START DATE: 02/10/2020

PERIOD OF PERFORMANCE END DATE: 01/31/2025

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