Trustees Of The University Of Pennsylvania, The

AWARD OF THE BASE TO UPENN FOR CEIRR CONTRACT 75N93021C00015. THIS CONTRACT WILL SUPPORT THE NIAID CENTERS OF EXCELLENCE FOR INFLUENZA RESEARCH AND RESPONSE (CEIRR)

SEVER AND PROTECT: SEPARATE ENVIRONMENT FOR VULNERABILITY ELIMINATION AND REDUCTION AND POLICY RULES ORGANIZED TO ENFORCE COMPARTMENT TRANSITIONS

AFFILIATE RADIATION ONCOLOGY SERVICES

SUBJECT INCENTIVES WILL BE PROVIDED AT THE ENROLLMENT, ILLNESS VISIT, AND BLOOD DRAW VISITS. THE SPECIFIC BREAKDOWN OF INCENTIVE COSTS IS AS FOLLOWS:  ENROLLMENT AND ANNUAL RE-ENGAGEMENT VISITS FOR INDIVIDUALS CONTRIBUTING SPECIMENS TO PROPOSED ANALYSES. ESTIMATED INCENTIVE IS $10 PER INDIVIDUAL FOR 1,400 INDIVIDUALS EACH YEAR FOR A TOTAL COST OF $14,000 ANNUALLY.  STUDY SITE ILLNESS VISITS FOR SPECIMEN COLLECTION TO SUPPORT LABORATORY CONFIRMATION OF INFLUENZA ILLNESS. ESTIMATED INCENTIVE IS $15 PER VISIT FOR 1,200 ILLNESS VISITS EACH YEAR FOR A TOTAL COST OF $18,000 ANNUALLY.  BLOOD COLLECTION VISITS ARE ANTICIPATED FOR THE FOLLOWING: 550 PARTICIPANTS 2 TIMES PER YEAR (1100 TOTAL) AND A 7-DAY POST-VACCINATION COLLECTION IN 250 VACCINATED INDIVIDUALS, FOR A TOTAL OF 1,350 COLLECTIONS. ESTIMATED INCENTIVE IS $20 PER VISIT FOR A TOTAL COST OF $27,000 ANNUALLY. INCENTIVE PAYMENT AMOUNTS ARE BASED UPON AMOUNTS PROVIDED IN PAST SUCCESSFUL STUDIES.

STATEMENT OF WORK – PROJECT 3 OBJECTIVES. WE WILL TARGET HUMAN-SWINE INTERFACES IN MAJOR SWINE PRODUCTION REGIONS IN THE US, EUROPE, AND ASIA. COORDINATED SURVEILLANCE WITH SWINE AND HUMAN SAMPLE COLLECTION THAT LEVERAGES EXISTING SURVEILLANCE [E.G., US DEPARTMENT OF AGRICULTURE (USDA) NATIONAL IAV IN SWINE (IAV-S) SURVEILLANCE SYSTEM AND VETERINARY DIAGNOSTIC LABS] WILL ALLOW US TO QUANTIFY DRIVERS OF IAV EVOLUTION IN THE SWINE HOST. OUR OVERALL OBJECTIVE IS TO DEVELOP A RISK FRAMEWORK THAT ARTICULATES HOW ANTIGENIC DIVERSITY AND OTHER PHENOTYPIC PROPERTIES OF CIRCULATING SWINE IAVS AFFECT HUMAN PANDEMIC POTENTIAL AND INTERSPECIES TRANSMISSION. WE WILL DETERMINE THE PUBLIC HEALTH RISK OF CIRCULATING AND EMERGING IAVS IN GLOBAL SWINE POPULATIONS BY A COORDINATED AND SYSTEMATIC PIPELINE OF IN SILICO, IN VITRO, AND IN VIVO TESTING AND ANALYSES. SWINE IAV ISOLATES IDENTIFIED AS UNIQUE THROUGH SURVEILLANCE AND IN VIVO ANALYSES WILL BE CHARACTERIZED BY A IN VIVO AND IN VITRO PANDEMIC POTENTIAL PIPELINE AMONG CEIRR INVESTIGATORS. APPROACH. THIS OBJECTIVE WILL BE ACCOMPLISHED WITH 4 STREAMS OF SWINE VIROLOGIC DATA: 1) ACTIVE SURVEILLANCE IN CAMBODIA; 2) ACTIVE AND PASSIVE SURVEILLANCE IN THE UK; 3) ACTIVE AND PASSIVE SURVEILLANCE IN THE USA; AND 4) LEVERAGING THE USDA SURVEILLANCE SYSTEM AND ESTABLISHED SWINE INFLUENZA NETWORKS. HUMAN SAMPLING WILL OCCUR AT THE SWINE INTERFACE IN CAMBODIA AND THE USA. SEROLOGIC SPECIMENS WILL BE USED FROM OCCUPATIONALLY EXPOSED HUMAN COHORTS TO EVALUATE ANTIBODY RESPONSES TO SWINE IAV AND COMPARE TO URBAN HUMAN COHORTS. SEQUENCE ANALYSIS OF IAV-S WILL BE SUPPORTED BY DEDICATED SWINE COMPUTATIONAL EXPERTISE AND ANTIGENIC AND PHENOTYPIC CHARACTERIZATION OF SWINE IAV FOR ASSESSMENT OF RISK TO HUMANS CONDUCTED IN AND IN VIVO AND IN VITRO PANDEMIC POTENTIAL PIPELINE. EACH OF THESE COMPONENTS WILL CONTRIBUTE TO DEVELOPMENT OF A RISK RANKING METHOD FOR SWINE IAV. METHODS. AIM 1. INVESTIGATE DYNAMICS OF IAV AT HUMAN-SWINE INTERFACES THROUGH: A) LONGITUDINAL SURVEILLANCE FROM RELEVANT SWINE POPULATIONS AND HUMAN-SWINE INTERFACES TO INCLUDE CHARACTERIZATION OF IAV GENETIC DIVERSITY; AND B) COLLECTION OF OCCUPATIONALLY EXPOSED HUMAN COHORT SERA AND VIROLOGIC ASSESSMENT OF INTERSPECIES TRANSMISSION. AIM 2. DEVELOP PHYLOGENETIC ALGORITHMS THAT RAPIDLY IDENTIFY NOVEL REASSORTED VIRUSES, QUANTIFY VIRAL DIVERSITY BETWEEN SWINE AND HUMAN IAV, AND IDENTIFY SWINE IAV STRAINS TO TEST FOR ANTIGENIC ADVANCE OR INCREASED REPLICATION AND TRANSMISSION IN SWINE. AIM 3. ANTIGENIC AND PHENOTYPIC CHARACTERIZATION OF SWINE IAV FOR RISK TO HUMANS BY CHARACTERIZING VIRAL PROPERTIES IN THE SWINE HOST, SWINE-TO-FERRET TRANSMISSION, KEY PREDICTORS OF THE PANDEMIC RISK OF SWINE IAV, AND OTHER DOWNSTREAM MEDIATORS VIA COLLABORATION WITH CEIRR INVESTIGATORS. SCHEDULE. EACH OF THE INVESTIGATORS AND SITE LEADERS IN THIS PROJECT HAVE ESTABLISHED PROGRAMS TO QUICKLY IMPLEMENT SAMPLE FLOW FOR OUR CEIRR PROJECT. CLINICAL SAMPLES FROM LONGITUDINALLY SAMPLED SWINE WILL BE EVALUATED PERIODICALLY THROUGHOUT EACH YEAR, WHEREAS PASSIVE SURVEILLANCE BASED ON ROUTINE SUBMISSIONS TO THE VETERINARY DIAGNOSTIC LABORATORIES PARTICIPATING IN THIS PROPOSAL WILL IMMEDIATELY BEGIN TO ENTER THE PROJECT. VIRAL EVOLUTION AT THE GENETIC AND ANTIGENIC LEVELS WILL BE ASSESSED AT LEAST BI-ANNUALLY TO SELECT STRAINS FOR FURTHER CHARACTERIZATION. AUTOMATED SEQUENCE AND DATA ANALYSIS ALGORITHMS WILL BE DEVELOPED AND IMPLEMENTED TO ASSIST IN THE SELECTION PROCESS. EACH YEAR, SWINE AND FERRET SERA WILL BE RAISED FOR ANTIGENIC CHARACTERIZATION OF UP TO 6 UNIQUE SWINE IAV AND TO TEST AGAINST HUMAN POPULATION SERA, UP TO 3 STRAINS WILL BE ASSESSED FOR PHENOTYPING IN THE SWINE HOST, AND UP TO 2 STRAINS WILL BE ASSESSED FOR AEROSOL TRANSMISSION BETWEEN SWINE AND FERRETS. SWINE IAV RANKED AS HIGHER RISK FOR HUMANS WILL BE SHARED AMONG CEIRR INVESTIGATORS FOR DOWNSTREAM RISK ASSESSMENT STUDIES AND POTENTIAL PUBLIC HEALTH ACTION.

STATEMENT OF WORK – FRED HUTCHINSON CANCER RESEARCH CENTER BLOOM LAB THE BLOOM LAB WILL PERFORM EXPERIMENTAL AND COMPUTATIONAL WORK TO CHARACTERIZE INFLUENZA VIRUS EVOLUTION. IN PROJECT 3, THEY WILL USE MUTATIONAL ANTIGENIC PROFILING TO EXPERIMENTALLY MAP THE EFFECTS OF VIRAL MUTATIONS ON IMMUNE RECOGNITION. IN THE COMPUTATIONAL CORE, THEY WILL DEVELOP TOOL TO ANALYZE AND VISUALIZE THE EFFECTS OF VIRAL MUTATIONS. BEDFORD LAB THE BEDFORD LAB AT THE FRED HUTCH WILL BE RESPONSIBLE FOR IMPLEMENTATION OF PROJECT 3, AIM 2 (PREDICT AND VISUALIZE WHICH CIRCULATING CLADES OF INFLUENZA WILL DOMINATE USING PHYLOGENETIC ANALYSES, AGE-STRUCTURED SEROLOGY, MUTATIONAL ANTIGENIC PROFILING, AND VACCINATION COVERAGE). FOR THIS, THE BEDFORD LAB WILL DEVELOP AND IMPLEMENT A PREDICTIVE MODEL THAT INCORPORATES DATA GENERATED BY THE BLOOM LAB FOR PROJECT 3, AIM 1 AS WELL AS OTHER SEROLOGICAL DATA GENERATED BY THE CENTER. THE BEDFORD LAB WILL INTEGRATE THIS SEROLOGICAL DATA WITH PUBLICLY AVAILABLE INFLUENZA GENETIC SEQUENCE DATA. THIS MODEL WILL ESTIMATE THE EVOLUTIONARY TRAJECTORY OF THE INFLUENZA VIRUS POPULATION. THE BEDFORD LAB WILL ALSO BE RESPONSIBLE FOR CONTRIBUTING KEY COMPONENTS TO THE MODELING AND COMPUTATIONAL CORE. THIS PRIMARILY CONSISTS OF USING THE EXISTING NEXTSTRAIN FRAMEWORK TO SUPPORT ANALYSIS AND SHARING OF DATA GENERATED BY THE CENTER. THE BEDFORD LAB ALREADY WORKS CLOSELY WITH WHO COLLABORATING CENTERS TO INTEGRATE AND ANALYZE INFLUENZA SEROLOGICAL AND SEQUENCE DATA. THE INTERACTION WITH THE CENTER SHOULD BE SIMILAR. THE BEDFORD LAB WILL DEVELOP A COMPUTATIONAL PREDICTIVE MODEL TO (1) ESTIMATE THE HUMAN POPULATION IMMUNE LANDSCAPE AGAINST DIFFERENT STRAINS OF SEASONAL INFLUENZA AND (2) PREDICT UPCOMING STRAIN DYNAMICS FOR THE INFLUENZA VIRUS POPULATION. DATA TO INFORM (1) WILL BE INTEGRATED FROM THE DEEP MUTATIONAL SCANNING (DMS) EXPERIMENTS CONDUCTED BY THE BLOOM LAB ALONGSIDE OTHER SEROLOGICAL DATA GENERATED BY OTHER STUDIES IN THE CENTER. WITH AN ESTIMATE OF POPULATION IMMUNITY IN HAND, WE WILL INFER FITNESS VALUES FOR CIRCULATING VIRUSES AND USE THESE FITNESS VALUES TO PREDICT WHETHER STRAINS INCREASE IN FREQUENCY OR DECLINE. THIS MODEL WILL BE IMPLEMENTED IN AN OPEN SOURCE PYTHON FRAMEWORK FOLLOWING OUR EXISTING STRAIN FORECASTING CODEBASE. THE PRIMARY ADDITIONS FOR THE CURRENT PROJECT ARE TO: (1) INTEGRATE HUMAN POPULATION IMMUNITY THROUGH DMS AND SEROLOGICAL DATA AND (2) INCORPORATE A GEOGRAPHICALLY STRUCTURED VIRUS POPULATION. THIS MODEL WILL BE RUN CONTINUALLY AS NEW DATA BECOMES AVAILABLE AND UP-TO-DATE FORECASTS PROVIDED FROM THE NEXTSTRAIN.ORG WEBSITE. THE BEDFORD LAB WILL EXTEND THE NEXTSTRAIN PLATFORM TO INTEGRATE AND SHARE DATA GENERATED BY THE CENTER. THE BEDFORD LAB WILL CREATE A NEW CEIRR NEXTSTRAIN GROUP THAT WILL HOUSE ALL THE CEIRR ANALYSES. THIS GROUP ALLOWS FOR BOTH PUBLIC DATASETS AND FOR PRIVATE DATASETS, BOTH OF WHICH SHOULD BE USEFUL FOR THESE PURPOSES. THE BEDFORD LAB WILL ALSO HOUSE A DATABASE OF SEROLOGICAL AND SEQUENCE DATA FOR CENTER PROJECTS CORRESPONDING TO THE WAY THE BEDFORD LAB CURRENTLY HOUSES WHO COLLABORATING CENTER DATA.

LE SAGE SCOPE OF WORK FOR PENN-CEIRR OPTION 18.L THIS CEIRR CONCEPT PROPOSAL HAS TWO DISTINCT AIMS THAT WILL ENABLE CHARACTERIZATION OF H5N1 HIGHLY PATHOGENIC AVIAN INFLUENZA (HPAI) VIRUS IN TERMS OF HOST AND ENVIRONMENTAL FACTORS THAT AFFECT TRANSMISSIBILITY. H5N1 HPAI STRAINS THAT ARE IMPORTANT TO THE DAIRY CATTLE OUTBREAK WILL BE ASSESS IN THE FOLLOWING AIMS. THERE ARE MANY IN VITRO CHARACTERISTICS THAT HAVE AN IMPACT ON EFFICIENT TRANSMISSION OF INFLUENZA VIRUS. IN AIM 1, I WILL CHARACTERIZE H5N1 HPAI STRAINS TO BETTER UNDERSTAND HOST TROPISM AND ENVIRONMENTAL STABILITY. THE FOLLOWING TASKS WILL BE ACCOMPLISHED: 1. EXAMINE REPLICATION KINETICS OF H5N1 HPAI IN PRIMARY HUMAN AIRWAY EPITHELIAL CELLS AND COMPARE IT TO A SEASONAL INFLUENZA VIRUS. 2. PERFORM SINGLE CELL RNA SEQUENCING ON THE INFECTED PRIMARY HUMAN AIRWAY EPITHELIAL CELLS TO COMPARE HOST TROPISM BETWEEN H5N1 HPAI AND SEASONAL INFLUENZA VIRUS. 3. COMPARE THE SECRETED CYTOKINES AND CHEMOKINES FROM H5N1 HPAI OR SEASONAL INFLUENZA VIRUS INFECTED PRIMARY HUMAN AIRWAY EPITHELIAL CELLS USING LUMINEX ASSAY. 4. DETERMINE THE ENVIRONMENTAL STABILITY UNDER A RANGE OF RELATIVE HUMIDITIES IN STATIONARY DROPLETS THAT CONTAIN MUCUS, COLLECTED FROM PRIMARY HUMAN AIRWAY EPITHELIAL CELLS. PRE-EXISTING IMMUNITY IS AN IMPORTANT BARRIER TO INFLUENZA VIRUS TRANSMISSION. IN AIM 2, I WILL ASSESS THE IMPACT OF SEASONAL VACCINATION IN FERRETS PRIOR TO CHALLENGE WITH H5N1 HPAI. THE FOLLOWING TASKS WILL BE ACCOMPLISHED: 1. PERFORM FERRET PATHOGENESIS AND SURVIVAL STUDIES IN FERRETS THAT HAVE BEEN VACCINATED WITH A SEASONAL INFLUENZA VIRUS THREE MONTHS PRIOR TO INTRANASAL CHALLENGE. 2. AS AIRBORNE TRANSMISSION IS NOT EFFICIENT FOR HPAI STRAINS, I WILL LEVERAGE THE AEROBIOLOGY CORE AT THE UNIVERSITY OF PITTSBURGH TO COMPARE THE SUSCEPTIBILITY OF VACCINATED FERRETS TO AEROSOL CHALLENGE OF H5N1 HPAI CHALLENGE. 3. PERFORM SEROLOGICAL ASSAYS TO DETERMINE THE LEVELS OF CROSS-REACTIVE HA AND NA ANTIBODIES GENERATED BY THESE VACCINATED FERRETS BEFORE AND AFTER CHALLENGE.

UNIVERSITY OF PENNSYLVANIA-STAND ALONE-ITEM LEVEL-R AND D

STATEMENT OF WORK MLP€„¢S DIGITAL TOOLS PROVIDE ACCESS TO MONTHLY DATA TRACKING 20 EVENTS BEARING ON CIVIC SPACE, INCLUDING CENSORSHIP, CORRUPTION, AND LEGAL CHANGES, AND 22 EVENTS INDICATIVE OF FOREIGN INFLUENCE BY GEOPOLITICAL COMPETITORS, RANGING FROM SECURITY ENGAGEMENTS TO DOMESTIC INTERFERENCE. IMPORTANTLY, THESE DATA ARE UPDATED EVERY 90 DAYS, ENSURING THEIR TIMELINESS FOR ANALYZING CURRENT EVENTS IN ADDITION TO LONGER-TERM TRENDS. MLP DATA AND ANALYTICS ARE MADE PUBLICLY AVAILABLE THROUGH FIVE INTERACTIVE DATA DASHBOARDS PUBLICLY AVAILABLE AT MLPEACE.ORG. THE REMAINDER OF THIS SECTION OUTLINES HOW THE FULL TARDIS PROJECT WILL SUPPORT THE CONTINUATION AND EXPANSION OF THE MLP PLATFORM. FOR EACH TASK IN THE TASKING REQUEST, WE DESCRIBE THE ASSOCIATED ACTIVITIES AND DELIVERABLES. DELIVERABLES TASK 2 DELIVERABLES: —Ͽ½ CONTINUATION OF CORE MLP ACTIVITIES O QUARTERLY FORECASTING REPORTS FOR ALL CURRENT MLP COUNTRIES. O CONTINUED UPDATING OF DATA DASHBOARDS ON MLPEACE.ORG —Ͽ½ IMPROVEMENTS TO MLP€„¢S FORECAST MODELS O INTRODUCTION OF NEW FORECASTING DATA DASHBOARD WITH RESULTS FROM MORE SOPHISTICATED MODELS THAT USE TEMPORAL CROSS-VALIDATION AND MORE COMPLEX NON-LINEAR MODELING —Ͽ½ VIRTUAL PRESENTATION TO CORE STAKEHOLDERS TASK 3 DELIVERABLES: —Ͽ½ CO-DEVELOPED LIST OF NEW COUNTRIES TO BE ADDED TO MLP —Ͽ½ QUARTERLY FORECASTING REPORTS FOR ALL NEW COUNTRIES TASK 4 DELIVERABLES: —Ͽ½ PILOT REPORT ON ANTI-US FOREIGN ASSISTANCE MEDIA NARRATIVES IN PILOT COUNTRIES —Ͽ½ FINAL REPORT ON THE PRESENCE OF ANTI-US FOREIGN ASSISTANCE MEDIA NARRATIVES TASK 5 DELIVERABLES: —Ͽ½ MACHINE READABLE DATA ON MONTHLY INCIDENTS OF AUTHORITARIAN INFLUENCE DATA FOR PEPID DASHBOARD SITE TASK 6 DELIVERABLES: —Ͽ½ FOUR CUSTOMIZED RESEARCH REPORTS TO INFORM THE DEMOCRATIC OPENING TEAM AND PDD€„¢S ANNUAL WORK PLANNING PROCESSES.